Rapid experimental measurements of physicochemical properties to inform models and testing.

PubMed

Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

2018-05-02

The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data. Published by Elsevier B.V.

The Elusive Nature of Adaptive Mitochondrial DNA Evolution of an Arctic Lineage Prone to Frequent Introgression

PubMed Central

Melo-Ferreira, José; Vilela, Joana; Fonseca, Miguel M.; da Fonseca, Rute R.; Boursot, Pierre; Alves, Paulo C.

2014-01-01

Mitochondria play a fundamental role in cellular metabolism, being responsible for most of the energy production of the cell in the oxidative phosphorylation (OXPHOS) pathway. Mitochondrial DNA (mtDNA) encodes for key components of this process, but its direct role in adaptation remains far from understood. Hares (Lepus spp.) are privileged models to study the impact of natural selection on mitogenomic evolution because 1) species are adapted to contrasting environments, including arctic, with different metabolic pressures, and 2) mtDNA introgression from arctic into temperate species is widespread. Here, we analyzed the sequences of 11 complete mitogenomes (ten newly obtained) of hares of temperate and arctic origins (including two of arctic origin introgressed into temperate species). The analysis of patterns of codon substitutions along the reconstructed phylogeny showed evidence for positive selection in several codons in genes of the OXPHOS complexes, most notably affecting the arctic lineage. However, using theoretical models, no predictable effect of these differences was found on the structure and physicochemical properties of the encoded proteins, suggesting that the focus of selection may lie on complex interactions with nuclear encoded peptides. Also, a cloverleaf structure was detected in the control region only from the arctic mtDNA lineage, which may influence mtDNA replication and transcription. These results suggest that adaptation impacted the evolution of hare mtDNA and may have influenced the occurrence and consequences of the many reported cases of massive mtDNA introgression. However, the origin of adaptation remains elusive. PMID:24696399

Automatic classification of protein structures using physicochemical parameters.

PubMed

Mohan, Abhilash; Rao, M Divya; Sunderrajan, Shruthi; Pennathur, Gautam

2014-09-01

Protein classification is the first step to functional annotation; SCOP and Pfam databases are currently the most relevant protein classification schemes. However, the disproportion in the number of three dimensional (3D) protein structures generated versus their classification into relevant superfamilies/families emphasizes the need for automated classification schemes. Predicting function of novel proteins based on sequence information alone has proven to be a major challenge. The present study focuses on the use of physicochemical parameters in conjunction with machine learning algorithms (Naive Bayes, Decision Trees, Random Forest and Support Vector Machines) to classify proteins into their respective SCOP superfamily/Pfam family, using sequence derived information. Spectrophores™, a 1D descriptor of the 3D molecular field surrounding a structure was used as a benchmark to compare the performance of the physicochemical parameters. The machine learning algorithms were modified to select features based on information gain for each SCOP superfamily/Pfam family. The effect of combining physicochemical parameters and spectrophores on classification accuracy (CA) was studied. Machine learning algorithms trained with the physicochemical parameters consistently classified SCOP superfamilies and Pfam families with a classification accuracy above 90%, while spectrophores performed with a CA of around 85%. Feature selection improved classification accuracy for both physicochemical parameters and spectrophores based machine learning algorithms. Combining both attributes resulted in a marginal loss of performance. Physicochemical parameters were able to classify proteins from both schemes with classification accuracy ranging from 90-96%. These results suggest the usefulness of this method in classifying proteins from amino acid sequences.

Structural and physico-chemical properties of insoluble rice bran fiber: effect of acid–base induced modifications

USDA-ARS?s Scientific Manuscript database

The structural modifications of insoluble rice bran fiber (IRBF) by sequential regimes of sulphuric acid (H2SO4) and their effects on the physicochemical attributes were studied. The increment of H2SO4 concentration resulted in decreased water holding capacity that ultimately enhanced the oil bindin...

Physico-chemical properties and cytotoxic effects of sugar-based surfactants: Impact of structural variations.

PubMed

Lu, Biao; Vayssade, Muriel; Miao, Yong; Chagnault, Vincent; Grand, Eric; Wadouachi, Anne; Postel, Denis; Drelich, Audrey; Egles, Christophe; Pezron, Isabelle

2016-09-01

Surfactants derived from the biorefinery process can present interesting surface-active properties, low cytotoxicity, high biocompatibility and biodegradability. They are therefore considered as potential sustainable substitutes to currently used petroleum-based surfactants. To better understand and anticipate their performances, structure-property relationships need to be carefully investigated. For this reason, we applied a multidisciplinary approach to systematically explore the effect of subtle structural variations on both physico-chemical properties and biological effects. Four sugar-based surfactants, each with an eight carbon alkyl chain bound to a glucose or maltose head group by an amide linkage, were synthesized and evaluated together along with two commercially available standard surfactants. Physico-chemical properties including solubility, Krafft point, surface-tension lowering and critical micellar concentration (CMC) in water and biological medium were explored. Cytotoxicity evaluation by measuring proliferation index and metabolic activity against dermal fibroblasts showed that all surfactants studied may induce cell death at low concentrations (below their CMC). Results revealed significant differences in both physico-chemical properties and cytotoxic effects depending on molecule structural features, such as the position of the linkage on the sugar head-group, or the orientation of the amide linkage. Furthermore, the cytotoxic response increased with the reduction of surfactant CMC. This study underscores the relevance of a methodical and multidisciplinary approach that enables the consideration of surfactant solution properties when applied to biological materials. Overall, our results will contribute to a better understanding of the concomitant impact of surfactant structure at physico-chemical and biological levels. Copyright © 2016 Elsevier B.V. All rights reserved.

Computational and Statistical Analyses of Amino Acid Usage and Physico-Chemical Properties of the Twelve Late Embryogenesis Abundant Protein Classes

PubMed Central

Jaspard, Emmanuel; Macherel, David; Hunault, Gilles

2012-01-01

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs. PMID:22615859

Some pungent arguments against the physico-chemical theories of the origin of the genetic code and corroborating the coevolution theory.

PubMed

Di Giulio, Massimo

2017-02-07

Whereas it is extremely easy to prove that "if the biosynthetic relationships between amino acids were fundamental in the structuring of the genetic code, then their physico-chemical properties might also be revealed in the genetic code table"; it is, on the contrary, impossible to prove that "if the physico-chemical properties of amino acids were fundamental in the structuring of the genetic code, then the presence of the biosynthetic relationships between amino acids should not be revealed in the genetic code". And, given that in the genetic code table are mirrored both the biosynthetic relationships between amino acids and their physico-chemical properties, all this would be a test that would falsify the physico-chemical theories of the origin of the genetic code. That is to say, if the physico-chemical properties of amino acids had a fundamental role in organizing the genetic code, then we would not have duly revealed the presence - in the genetic code - of the biosynthetic relationships between amino acids, and on the contrary this has been observed. Therefore, this falsifies the physico-chemical theories of genetic code origin. Whereas, the coevolution theory of the origin of the genetic code would be corroborated by this analysis, because it would be able to give a description of evolution of the genetic code more coherent with the indisputable empirical observations that link both the biosynthetic relationships of amino acids and their physico-chemical properties to the evolutionary organization of the genetic code. Copyright © 2016 Elsevier Ltd. All rights reserved.

Chemical structures and characteristics of animal manures and composts during composting and assessment of maturity indices

PubMed Central

Huang, Jieying; Yu, Zixuan; Gao, Hongjian; Yan, Xiaoming; Chang, Jiang; Wang, Chengming; Hu, Jingwei

2017-01-01

Changes in physicochemical characteristics, chemical structures and maturity of swine, cattle and chicken manures and composts during 70-day composting without addition of bulking agents were investigated. Physicochemical characteristics were measured by routine analyses and chemical structures by solid-state 13C NMR and FT-IR. Three manures were of distinct properties. Their changes in physicochemical characteristics, chemical structures, and maturity were different not only from each other but also from those with addition of bulking agents during composting. Aromaticity in chicken manure composts decreased at first, and then increased whereas that in cattle and swine manure composts increased. Enhanced ammonia volatilization occurred without addition of bulking agents. NMR structural information indicated that cattle and chicken composts were relatively stable at day 36 and 56, respectively, but swine manure composts were not mature up to day 70. Finally, the days required for three manures to reach the threshold values of different maturity indices were different. PMID:28604783

Docking-based classification models for exploratory toxicology ...

EPA Pesticide Factsheets

Background: Exploratory toxicology is a new emerging research area whose ultimate mission is that of protecting human health and environment from risks posed by chemicals. In this regard, the ethical and practical limitation of animal testing has encouraged the promotion of computational methods for the fast screening of huge collections of chemicals available on the market. Results: We derived 24 reliable docking-based classification models able to predict the estrogenic potential of a large collection of chemicals having high quality experimental data, kindly provided by the U.S. Environmental Protection Agency (EPA). The predictive power of our docking-based models was supported by values of AUC, EF1% (EFmax = 7.1), -LR (at SE = 0.75) and +LR (at SE = 0.25) ranging from 0.63 to 0.72, from 2.5 to 6.2, from 0.35 to 0.67 and from 2.05 to 9.84, respectively. In addition, external predictions were successfully made on some representative known estrogenic chemicals. Conclusion: We show how structure-based methods, widely applied to drug discovery programs, can be adapted to meet the conditions of the regulatory context. Importantly, these methods enable one to employ the physicochemical information contained in the X-ray solved biological target and to screen structurally-unrelated chemicals. Shows how structure-based methods, widely applied to drug discovery programs, can be adapted to meet the conditions of the regulatory context. Evaluation of 24 reliable dockin

Structural Prediction and In Silico Physicochemical Characterization for Mouse Caltrin I and Bovine Caltrin Proteins

PubMed Central

Grasso, Ernesto J.; Sottile, Adolfo E.; Coronel, Carlos E.

2016-01-01

It is known that caltrin (calcium transport inhibitor) protein binds to sperm cells during ejaculation and inhibits extracellular Ca2+ uptake. Although the sequence and some biological features of mouse caltrin I and bovine caltrin are known, their physicochemical properties and tertiary structure are mainly unknown. We predicted the 3D structures of mouse caltrin I and bovine caltrin by molecular homology modeling and threading. Surface electrostatic potentials and electric fields were calculated using the Poisson–Boltzmann equation. Several different bioinformatics tools and available web servers were used to thoroughly analyze the physicochemical characteristics of both proteins, such as their Kyte and Doolittle hydropathy scores and helical wheel projections. The results presented in this work significantly aid further understanding of the molecular mechanisms of caltrin proteins modulating physiological processes associated with fertilization. PMID:27812283

Composition, structure, physicochemical properties, and modifications of cassava starch.

PubMed

Zhu, Fan

2015-05-20

Cassava is highly tolerant to harsh climatic conditions and has great productivity on marginal lands. The supply of cassava starch, the major component of the root, is thus sustainable and cheap. This review summarizes the current knowledge of the composition, physical and chemical structures, physicochemical properties, nutritional quality, and modifications of cassava starch. Research opportunities to better understand this starch are provided. Copyright © 2014 Elsevier Ltd. All rights reserved.

Insights into the sequence parameters for halophilic adaptation.

PubMed

Nath, Abhigyan

2016-03-01

The sequence parameters for halophilic adaptation are still not fully understood. To understand the molecular basis of protein hypersaline adaptation, a detailed analysis is carried out, and investigated the likely association of protein sequence attributes to halophilic adaptation. A two-stage strategy is implemented, where in the first stage a supervised machine learning classifier is build, giving an overall accuracy of 86 % on stratified tenfold cross validation and 90 % on blind testing set, which are better than the previously reported results. The second stage consists of statistical analysis of sequence features and possible extraction of halophilic molecular signatures. The results of this study showed that, halophilic proteins are characterized by lower average charge, lower K content, and lower S content. A statistically significant preference/avoidance list of sequence parameters is also reported giving insights into the molecular basis of halophilic adaptation. D, Q, E, H, P, T, V are significantly preferred while N, C, I, K, M, F, S are significantly avoided. Among amino acid physicochemical groups, small, polar, charged, acidic and hydrophilic groups are preferred over other groups. The halophilic proteins also showed a preference for higher average flexibility, higher average polarity and avoidance for higher average positive charge, average bulkiness and average hydrophobicity. Some interesting trends observed in dipeptide counts are also reported. Further a systematic statistical comparison is undertaken for gaining insights into the sequence feature distribution in different residue structural states. The current analysis may facilitate the understanding of the mechanism of halophilic adaptation clearer, which can be further used for rational design of halophilic proteins.

An FPGA Implementation to Detect Selective Cationic Antibacterial Peptides

PubMed Central

Polanco González, Carlos; Nuño Maganda, Marco Aurelio; Arias-Estrada, Miguel; del Rio, Gabriel

2011-01-01

Exhaustive prediction of physicochemical properties of peptide sequences is used in different areas of biological research. One example is the identification of selective cationic antibacterial peptides (SCAPs), which may be used in the treatment of different diseases. Due to the discrete nature of peptide sequences, the physicochemical properties calculation is considered a high-performance computing problem. A competitive solution for this class of problems is to embed algorithms into dedicated hardware. In the present work we present the adaptation, design and implementation of an algorithm for SCAPs prediction into a Field Programmable Gate Array (FPGA) platform. Four physicochemical properties codes useful in the identification of peptide sequences with potential selective antibacterial activity were implemented into an FPGA board. The speed-up gained in a single-copy implementation was up to 108 times compared with a single Intel processor cycle for cycle. The inherent scalability of our design allows for replication of this code into multiple FPGA cards and consequently improvements in speed are possible. Our results show the first embedded SCAPs prediction solution described and constitutes the grounds to efficiently perform the exhaustive analysis of the sequence-physicochemical properties relationship of peptides. PMID:21738652

Physicochemical conditions in affecting the distribution of spring phytoplankton community

NASA Astrophysics Data System (ADS)

Wei, Yuqiu; Liu, Haijiao; Zhang, Xiaodong; Xue, Bing; Munir, Sonia; Sun, Jun

2017-11-01

To better understand the physicochemical conditions in affecting regional distribution of phytoplankton community, one research cruise was carried out in the Bohai Sea and Yellow Sea during 3rd and 23th May, 2010. The phytoplankton community, including Bacillariophyta (105 taxa), Pyrrophyta (54 taxa), Chrysophyta (1 taxon) and Chlorophyta (2 taxa), had been identified and clearly described from six ecological provinces. And, the six ecological provinces were partitioned based on the top twenty dominant species related with notable physicochemical parameters. In general, the regional distributions of phytoplankton ecological provinces were predominantly influenced by the physicochemical properties induced by the variable water masses and circulations. The predominant diatoms in most of water samples showed well adaptability in turbulent and eutrophic conditions. However, several species of dinoflagellates e.g., Protoperidinium conicum, Protoperidinium triestinum, Protoperidinium sp. and Gymnodinium lohmanni preferred warmer, saltier and nutrient-poor environment. Moreover, the dinoflagellates with high frequency in the Yellow Sea might be transported from the Yellow Sea Warm Current. The horizontal distribution of phytoplankton was depicted by diatoms and controlled by phosphate concentration, while the vertical distribution was mainly supported by light and nutrients availability in the subsurface and bottom layers, respectively.

Effect of high hydrostatic pressure and retrogradation treatments on structural and physicochemical properties of waxy wheat starch.

PubMed

Hu, Xiao-Pei; Zhang, Bao; Jin, Zheng-Yu; Xu, Xue-Ming; Chen, Han-Qing

2017-10-01

In this study, the effects of high hydrostatic pressure and retrogradation (HHPR) treatments on in vitro digestibility, structural and physicochemical properties of waxy wheat starch were investigated. The waxy wheat starch slurries (10%, w/v) were treated with high hydrostatic pressures of 300, 400, 500, 600MPa at 20°C for 30min, respectively, and then retrograded at 4°C for 4d. The results indicated that the content of slowly digestible starch (SDS) in HHPR-treated starch samples increased with increasing pressure level, and it reached the maximum (31.12%) at 600MPa. HHPR treatment decreased the gelatinization temperatures, the gelatinization enthalpy, the relative crystallinity and the peak viscosity of the starch samples. Moreover, HHPR treatment destroyed the surface and interior structures of starch granules. These results suggest that the in vitro digestibility, physicochemical, and structural properties of waxy wheat starch are effectively modified by HHPR. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structure Property Relationships of Carboxylic Acid Isosteres.

PubMed

Lassalas, Pierrik; Gay, Bryant; Lasfargeas, Caroline; James, Michael J; Tran, Van; Vijayendran, Krishna G; Brunden, Kurt R; Kozlowski, Marisa C; Thomas, Craig J; Smith, Amos B; Huryn, Donna M; Ballatore, Carlo

2016-04-14

The replacement of a carboxylic acid with a surrogate structure, or (bio)-isostere, is a classical strategy in medicinal chemistry. The general underlying principle is that by maintaining the features of the carboxylic acid critical for biological activity, but appropriately modifying the physicochemical properties, improved analogs may result. In this context, a systematic assessment of the physicochemical properties of carboxylic acid isosteres would be desirable to enable more informed decisions of potential replacements to be used for analog design. Herein we report the structure-property relationships (SPR) of 35 phenylpropionic acid derivatives, in which the carboxylic acid moiety is replaced with a series of known isosteres. The data set generated provides an assessment of the relative impact on the physicochemical properties that these replacements may have compared to the carboxylic acid analog. As such, this study presents a framework for how to rationally apply isosteric replacements of the carboxylic acid functional group.

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites

PubMed Central

Toneatti, Diego M.; Albarracín, Virginia H.; Flores, Maria R.; Polerecky, Lubos; Farías, María E.

2017-01-01

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H2S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth. PMID:28446906

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites.

PubMed

Toneatti, Diego M; Albarracín, Virginia H; Flores, Maria R; Polerecky, Lubos; Farías, María E

2017-01-01

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H 2 S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5-7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.

Beneficial reuse of fly ashes in geotechnical engineering with physicochemical and electron microscopic methods.

DOT National Transportation Integrated Search

2013-06-01

The sedimentation behavior of fine grained soil is largely dependent on its pore fluid chemistry. Physicochemical properties of the : pore fluid, such as ionic strength and pH, could greatly influence the micro structure of kaolinite which in turn in...

20180318 - Rapid collection of experimental physicochemical property data to inform various models and testing methods (ACS Spring)

EPA Science Inventory

In order to determine the potential toxicological effects, toxicokinetics, and route(s) of exposure for chemicals, their structures and corresponding physicochemical properties are required. With this data, the risk for thousands of environmental chemicals can be prioritized. How...

Use of microalgae to remove pollutants from power plant discharges

DOEpatents

Wilde, Edward W.; Benemann, John R.; Weissman, Joseph C.; Tillett, David M.

1991-01-01

A method and system for removing pollutants dissolved in the aqueous discharge of a plant, such as a power plant, from a body of water having known hydraulogy and physicochemical characteristics, the method comprising (a) modifying the hydraulic system of the body of water including use of physical barriers to define a zone in a portion of the body of water which zone includes the discharge point and where the water has a range of physicochemical characteristics; (b) selecting a large and preferably filamentous, planktonically growing strain of algae adapted to absorb the particular pollutants and genetically dominating algae at the physicochemical characteristics of the zone; (c) establishing a colony of the selected algal strain in the zone; (d) harvesting a portion of the colony; and (e) reinnoculating the zone near the discharge point with a fraction of the harvested portion. The fraction used for reinnoculation can be adjusted to balance the rate of pollutant removal to the rate of pollutant discharge.

Use of microalgae to remove pollutants from power plant discharges

DOEpatents

Wilde, E.W.; Benemann, J.R.; Weissman, J.C.; Tillett, D.M.

1991-04-30

A method and system are described for removing pollutants dissolved in the aqueous discharge of a plant, such as a power plant, from a body of water having known hydraulic and physicochemical characteristics, the method comprising (a) modifying the hydraulic system of the body of water including use of physical barriers to define a zone in a portion of the body of water which zone includes the discharge point and where the water has a range of physicochemical characteristics; (b) selecting a large and preferably filamentous, planktonically growing strain of algae adapted to absorb the particular pollutants and genetically dominating algae at the physicochemical characteristics of the zone; (c) establishing a colony of the selected algal strain in the zone; (d) harvesting a portion of the colony; and (e) reinoculating the zone near the discharge point with a fraction of the harvested portion. The fraction used for reinoculation can be adjusted to balance the rate of pollutant removal to the rate of pollutant discharge. 4 figures.

Impact of diverse cultivars on molecular and crystalline structures of rice starch for food processing.

PubMed

Lee, Seul; Lee, Ju Hun; Chung, Hyun-Jung

2017-08-01

The objective of this study was to determine the molecular and crystalline structures of starches from diverse rice cultivars for three major food processing in Korea (cooked rice, brewing and rice cake). Rice starches were isolated from 10 different rice varieties grown in Korea. Apparent amylose contents of rice starches from cooked rice, brewing and rice cake varieties were 21.1-22.4%, 22.9-24.6%, and 20.1-22.0%, respectively. Rice starches from rice cake varieties showed higher peak viscosity but lower pasting temperature than those from cooked rice and brewing varieties. Swelling factor at 80°C of rice starches from cooked rice, brewing and rice cake varieties was 16.6-19.0, 17.8-19.3, and 17.8-19.2, respectively. Based on structure and physicochemical properties of rice starches extracted from different rice varieties, principal component analysis (PCA) results showed that these rice varieties could be clearly classified according to processing adaptability for cooked rice and rice cake. Copyright © 2017 Elsevier Ltd. All rights reserved.

Computing the Ediz eccentric connectivity index of discrete dynamic structures

NASA Astrophysics Data System (ADS)

Wu, Hualong; Kamran Siddiqui, Muhammad; Zhao, Bo; Gan, Jianhou; Gao, Wei

2017-06-01

From the earlier studies in physical and chemical sciences, it is found that the physico-chemical characteristics of chemical compounds are internally connected with their molecular structures. As a theoretical basis, it provides a new way of thinking by analyzing the molecular structure of the compounds to understand their physical and chemical properties. In our article, we study the physico-chemical properties of certain molecular structures via computing the Ediz eccentric connectivity index from mathematical standpoint. The results we yielded mainly apply to the techniques of distance and degree computation of mathematical derivation, and the conclusions have guiding significance in physical engineering.

Habitat Fragmentation can Modulate Drought Effects on the Plant-soil-microbial System in Mediterranean Holm Oak (Quercus ilex) Forests.

PubMed

Flores-Rentería, Dulce; Curiel Yuste, Jorge; Rincón, Ana; Brearley, Francis Q; García-Gil, Juan Carlos; Valladares, Fernando

2015-05-01

Ecological transformations derived from habitat fragmentation have led to increased threats to above-ground biodiversity. However, the impacts of forest fragmentation on soils and their microbial communities are not well understood. We examined the effects of contrasting fragment sizes on the structure and functioning of soil microbial communities from holm oak forest patches in two bioclimatically different regions of Spain. We used a microcosm approach to simulate the annual summer drought cycle and first autumn rainfall (rewetting), evaluating the functional response of a plant-soil-microbial system. Forest fragment size had a significant effect on physicochemical characteristics and microbial functioning of soils, although the diversity and structure of microbial communities were not affected. The response of our plant-soil-microbial systems to drought was strongly modulated by the bioclimatic conditions and the fragment size from where the soils were obtained. Decreasing fragment size modulated the effects of drought by improving local environmental conditions with higher water and nutrient availability. However, this modulation was stronger for plant-soil-microbial systems built with soils from the northern region (colder and wetter) than for those built with soils from the southern region (warmer and drier) suggesting that the responsiveness of the soil-plant-microbial system to habitat fragmentation was strongly dependent on both the physicochemical characteristics of soils and the historical adaptation of soil microbial communities to specific bioclimatic conditions. This interaction challenges our understanding of future global change scenarios in Mediterranean ecosystems involving drier conditions and increased frequency of forest fragmentation.

Recent progress in cellulose nanocrystals: sources and production.

PubMed

Trache, Djalal; Hussin, M Hazwan; Haafiz, M K Mohamad; Thakur, Vijay Kumar

2017-02-02

Cellulose nanocrystals, a class of fascinating bio-based nanoscale materials, have received a tremendous amount of interest both in industry and academia owing to its unique structural features and impressive physicochemical properties such as biocompatibility, biodegradability, renewability, low density, adaptable surface chemistry, optical transparency, and improved mechanical properties. This nanomaterial is a promising candidate for applications in fields such as biomedical, pharmaceuticals, electronics, barrier films, nanocomposites, membranes, supercapacitors, etc. New resources, new extraction procedures, and new treatments are currently under development to satisfy the increasing demand of manufacturing new types of cellulose nanocrystals-based materials on an industrial scale. Therefore, this review addresses the recent progress in the production methodologies of cellulose nanocrystals, covering principal cellulose resources and the main processes used for its isolation. A critical and analytical examination of the shortcomings of various approaches employed so far is made. Additionally, structural organization of cellulose and nomenclature of cellulose nanomaterials have also been discussed for beginners in this field.

Niche specialization of terrestrial archaeal ammonia oxidizers.

PubMed

Gubry-Rangin, Cécile; Hai, Brigitte; Quince, Christopher; Engel, Marion; Thomson, Bruce C; James, Phillip; Schloter, Michael; Griffiths, Robert I; Prosser, James I; Nicol, Graeme W

2011-12-27

Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5 ≤ pH <7), or alkalinophilic (pH ≥ 7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5-8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5-7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling.

Physicochemical properties of precursors of Al2O3-ZrO2 oxide ceramics prepared by electrochemical method

NASA Astrophysics Data System (ADS)

Petrova, E. V.; Dresvyannikov, A. F.; Ahmadi Daryakenari, M.; Khairullina, A. I.

2016-05-01

Scanning electron microscopy, X-ray, and thermal analysis are used to examine the structure and properties of dispersive systems based on aluminum and zirconium oxides prepared electrochemically. The effect the conditions of synthesis have on the structure and morphology of Al2O3-ZrO2 particles is studied. It is shown that the effect of an electric field on the reaction medium allows us to adjust the physicochemical properties and morphology.

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure

PubMed Central

Neshich, Goran; Rocchia, Walter; Mancini, Adauto L.; Yamagishi, Michel E. B.; Kuser, Paula R.; Fileto, Renato; Baudet, Christian; Pinto, Ivan P.; Montagner, Arnaldo J.; Palandrani, Juliana F.; Krauchenco, Joao N.; Torres, Renato C.; Souza, Savio; Togawa, Roberto C.; Higa, Roberto H.

2004-01-01

JavaProtein Dossier (JPD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data grouping allows us to generate different parameters with the potential to provide new insights into the sequence–structure–function relationship. In JPD, residue selection can be performed according to multiple criteria. JPD can simultaneously display and analyze all the physicochemical parameters of any pair of structures, using precalculated structural alignments, allowing direct parameter comparison at corresponding amino acid positions among homologous structures. In order to focus on the physicochemical (and consequently pharmacological) profile of proteins, visualization tools (showing the structure and structural parameters) also had to be optimized. Our response to this challenge was the use of Java technology with its exceptional level of interactivity. JPD is freely accessible (within the Gold Sting Suite) at http://sms.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS, http://trantor.bioc.columbia.edu/SMS and http://www.es.embnet.org/SMS/ (Option: JavaProtein Dossier). PMID:15215458

Effect of heat-moisture treatment on the structural, physicochemical, and rheological characteristics of arrowroot starch.

PubMed

Pepe, Larissa S; Moraes, Jaqueline; Albano, Kivia M; Telis, Vânia R N; Franco, Célia M L

2016-04-01

The effect of heat-moisture treatment on structural, physicochemical, and rheological characteristics of arrowroot starch was investigated. Heat-moisture treatment was performed with starch samples conditioned to 28% moisture at 100 ℃ for 2, 4, 8, and 16 h. Structural and physicochemical characterization of native and modified starches, as well as rheological assays with gels of native and 4 h modified starches subjected to acid and sterilization stresses were performed. Arrowroot starch had 23.1% of amylose and a CA-type crystalline pattern that changed over the treatment time to A-type. Modified starches had higher pasting temperature and lower peak viscosity while breakdown viscosity practically disappeared, independently of the treatment time. Gelatinization temperature and crystallinity increased, while enthalpy, swelling power, and solubility decreased with the treatment. Gels from modified starches, independently of the stress conditions, were found to have more stable apparent viscosities and higher G' and G″ than gels from native starch. Heat-moisture treatment caused a reorganization of starch chains that increased molecular interactions. This increase resulted in higher paste stability and strengthened gels that showed higher resistance to shearing and heat, even after acid or sterilization conditions. A treatment time of 4 h was enough to deeply changing the physicochemical properties of starch. © The Author(s) 2015.

A combined approach of physicochemical and biological methods for the characterization of petroleum hydrocarbon-contaminated soil.

PubMed

Masakorala, Kanaji; Yao, Jun; Chandankere, Radhika; Liu, Haijun; Liu, Wenjuan; Cai, Minmin; Choi, Martin M F

2014-01-01

Main physicochemical and microbiological parameters of collected petroleum-contaminated soils with different degrees of contamination from DaGang oil field (southeast of Tianjin, northeast China) were comparatively analyzed in order to assess the influence of petroleum contaminants on the physicochemical and microbiological properties of soil. An integration of microcalorimetric technique with urease enzyme analysis was used with the aim to assess a general status of soil metabolism and the potential availability of nitrogen nutrient in soils stressed by petroleum-derived contaminants. The total petroleum hydrocarbon (TPH) content of contaminated soils varied from 752.3 to 29,114 mg kg(−1). Although the studied physicochemical and biological parameters showed variations dependent on TPH content, the correlation matrix showed also highly significant correlation coefficients among parameters, suggesting their utility in describing a complex matrix such as soil even in the presence of a high level of contaminants. The microcalorimetric measures gave evidence of microbial adaptation under highest TPH concentration; this would help in assessing the potential of a polluted soil to promote self-degradation of oil-derived hydrocarbon under natural or assisted remediation. The results highlighted the importance of the application of combined approach in the study of those parameters driving the soil amelioration and bioremediation.

Effects of spent mushroom compost application on the physicochemical properties of a degraded soil

NASA Astrophysics Data System (ADS)

Gümüş, İlknur; Şeker, Cevdet

2017-11-01

Under field and laboratory conditions, the application of organic amendments has generally shown an improvement in soil physicochemical properties. Here, spent mushroom compost (SMC) is proposed as a suitable organic amendment for soil structure restoration. Our study assessed the impact of SMC on the physicochemical properties of a weak-structured and physically degraded soil. The approach involved the establishment of a pot experiment with SMC applications into soil (control, 0.5, 1, 2, 4 and 8 %). Soils were incubated at field capacity (-33 kPa) for 21, 42, and 62 days under laboratory conditions. SMC applications into the soil significantly increased the aggregate stability (AS) and decreased the modulus of rupture. The application of SMC at rates of 1, 2, 4, and 8 % significantly increased the total nitrogen and soil organic carbon contents of the degraded soil at all incubation periods (p < 0.05). The results obtained in this study indicate that the application of SMC can improve soil physicochemical properties, which may benefit farmers, land managers, and mushroom growers.

Importance of asparagine on the conformational stability and chemical reactivity of selected anti-inflammatory peptides

NASA Astrophysics Data System (ADS)

Soriano-Correa, Catalina; Barrientos-Salcedo, Carolina; Campos-Fernández, Linda; Alvarado-Salazar, Andres; Esquivel, Rodolfo O.

2015-08-01

Inflammatory response events are initiated by a complex series of molecular reactions that generate chemical intermediaries. The structure and properties of peptides and proteins are determined by the charge distribution of their side chains, which play an essential role in its electronic structure and physicochemical properties, hence on its biological functionality. The aim of this study was to analyze the effect of changing one central amino acid, such as substituting asparagine for aspartic acid, from Cys-Asn-Ser in aqueous solution, by assessing the conformational stability, physicochemical properties, chemical reactivity and their relationship with anti-inflammatory activity; employing quantum-chemical descriptors at the M06-2X/6-311+G(d,p) level. Our results suggest that asparagine plays a more critical role than aspartic acid in the structural stability, physicochemical features, and chemical reactivity of these tripeptides. Substituent groups in the side chain cause significant changes on the conformational stability and chemical reactivity, and consequently on their anti-inflammatory activity.

The first report of the physicochemical structure of chitin isolated from Hermetia illucens.

PubMed

Waśko, Adam; Bulak, Piotr; Polak-Berecka, Magdalena; Nowak, Katarzyna; Polakowski, Cezary; Bieganowski, Andrzej

2016-11-01

This is the first report on the physicochemical properties of chitin obtained from larvae and imagoes of black soldier flies (Hermetia illucens). Scanning electron microscopy revealed differences in surface morphologies of the two types of chitin. The crystalline index values of chitins from adult flies and larvae were 24.9% and 35%, respectively. This is a trait that differentiates these biopolymers from chitins extracted from other sources described so far. X-ray diffraction patterns and IR spectroscopy revealed that both types of samples of chitin were in an α crystalline form. Also, the results of elemental analysis, thermal stabilities and FTIR spectroscopy of the chitins from larvae and adults of H. illucens were similar, which points to a general similarity in their physicochemical structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Correlation between soil physicochemical properties and vegetation parameters in secondary tropical forest in Sabal, Sarawak, Malaysia

NASA Astrophysics Data System (ADS)

Karyati, K.; Ipor, I. B.; Jusoh, I.; Wasli, M. E.

2018-04-01

The tree growth is influenced by soil morphological and physicochemical properties in the site. The purpose of this study was to describe correlation between soil properties under various stage secondary forests and vegetation parameters, such as floristic structure parameters and floristic diversity indices. The vegetation surveys were conducted in 5, 10, and 20 years old at secondary tropical forests in Sarawak, Malaysia. Nine sub plots sized 20 m × 20 m were established within each study site. The Pearson analysis showed that soil physicochemical properties were significantly correlated to floristic structure parameters and floristic diversity indices. The result of PCA clarified the correlation among most important soil properties, floristic structure parameters, and floristic diversity indices. The PC1 represented cation retention capacity and soil texture which were little affected by the fallow age and its also were correlated by floristic structure and diversity. The PC2 was linked to the levels of soil acidity. This property reflected the remnant effects of ash addition and fallow duration, and the significant correlation were showed among pH (H2O), floristic structure and diversity. The PC3 represented the soil compactness. The soil hardness could be influenced by fallow period and it was also correlated by floristic structure.

The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.

PubMed

Ponce de Leon, Miguel; de Miranda, Antonio Basilio; Alvarez-Valin, Fernando; Carels, Nicolas

2014-01-01

For this report, we analyzed protein secondary structures in relation to the statistics of three nucleotide codon positions. The purpose of this investigation was to find which properties of the ribosome, tRNA or protein level, could explain the purine bias (Rrr) as it is observed in coding DNA. We found that the Rrr pattern is the consequence of a regularity (the codon structure) resulting from physicochemical constraints on proteins and thermodynamic constraints on ribosomal machinery. The physicochemical constraints on proteins mainly come from the hydropathy and molecular weight (MW) of secondary structures as well as the energy cost of amino acid synthesis. These constraints appear through a network of statistical correlations, such as (i) the cost of amino acid synthesis, which is in favor of a higher level of guanine in the first codon position, (ii) the constructive contribution of hydropathy alternation in proteins, (iii) the spatial organization of secondary structure in proteins according to solvent accessibility, (iv) the spatial organization of secondary structure according to amino acid hydropathy, (v) the statistical correlation of MW with protein secondary structures and their overall hydropathy, (vi) the statistical correlation of thymine in the second codon position with hydropathy and the energy cost of amino acid synthesis, and (vii) the statistical correlation of adenine in the second codon position with amino acid complexity and the MW of secondary protein structures. Amino acid physicochemical properties and functional constraints on proteins constitute a code that is translated into a purine bias within the coding DNA via tRNAs. In that sense, the Rrr pattern within coding DNA is the effect of information transfer on nucleotide composition from protein to DNA by selection according to the codon positions. Thus, coding DNA structure and ribosomal machinery co-evolved to minimize the energy cost of protein coding given the functional constraints on proteins.

Atomic substitutions in synthetic apatite; Insights from solid-state NMR spectroscopy

NASA Astrophysics Data System (ADS)

Vaughn, John S.

Apatite, Ca5(PO4)3X (where X = F, Cl, or OH), is a unique mineral group capable of atomic substitutions for cations and anions of varied size and charge. Accommodation of differing substituents requires some kind of structural adaptation, e.g. new atomic positions, vacancies, or coupled substitutions. These structural adaptations often give rise to important physicochemical properties relevant to a range of scientific disciplines. Examples include volatile trapping during apatite crystallization, substitution for large radionuclides for long-term storage of nuclear fission waste, substitution for fluoride to improve acid resistivity in dental enamel composed dominantly of hydroxylapatite, and the development of novel biomaterials with enhanced biocompatibility. Despite the importance and ubiquity of atomic substitutions in apatite materials, many of the mechanisms by which these reactions occur are poorly understood. Presence of substituents at dilute concentration and occupancy of disordered atomic positions hinder detection by bulk characterization methods such as X-ray diffraction (XRD) and infrared (IR) spectroscopy. Solid-state nuclear magnetic resonance (NMR) spectroscopy is an isotope-specific structural characterization technique that does not require ordered atomic arrangements, and is therefore well suited to investigate atomic substitutions and structural adaptations in apatite. In the present work, solid-state NMR is utilized to investigate structural adaptations in three different types of apatite materials; a series of near-binary F, Cl apatite, carbonate-hydroxylapatite compositions prepared under various synthesis conditions, and a heat-treated hydroxylapatite enriched in 17O. The results indicate that hydroxyl groups in low-H, near binary F,Cl apatite facilitate solid-solution between F and Cl via column reversals, which result in average hexagonal symmetry despite very dilute OH concentration ( 2 mol percent). In addition, 19F NMR spectra indicate that fluorine occupies a complex distribution of atomic positions, which give rise to complex 19F peak shapes owing to varied F-Ca distance. 13C NMR analysis of carbonate-hydroxylapatite indicates that AB-type carbonate hydroxylapatite can be prepared without the presence of sodium or heat treatment. Isotopic 17O enrichment of hydroxylapatite and 17O NMR analysis reveals distinct signals corresponding to phosphate and hydroxyl oxygens, and heat treatment under vacuum results in loss of hydroxyl signal due to decomposition to tricalcium phosphate, which was observed by powder X-Ray diffraction (PXRD).

Discovery of Antibiotics-derived Polymers for Gene Delivery using Combinatorial Synthesis and Cheminformatics Modeling

PubMed Central

Potta, Thrimoorthy; Zhen, Zhuo; Grandhi, Taraka Sai Pavan; Christensen, Matthew D.; Ramos, James; Breneman, Curt M.; Rege, Kaushal

2014-01-01

We describe the combinatorial synthesis and cheminformatics modeling of aminoglycoside antibiotics-derived polymers for transgene delivery and expression. Fifty-six polymers were synthesized by polymerizing aminoglycosides with diglycidyl ether cross-linkers. Parallel screening resulted in identification of several lead polymers that resulted in high transgene expression levels in cells. The role of polymer physicochemical properties in determining efficacy of transgene expression was investigated using Quantitative Structure-Activity Relationship (QSAR) cheminformatics models based on Support Vector Regression (SVR) and ‘building block’ polymer structures. The QSAR model exhibited high predictive ability, and investigation of descriptors in the model, using molecular visualization and correlation plots, indicated that physicochemical attributes related to both, aminoglycosides and diglycidyl ethers facilitated transgene expression. This work synergistically combines combinatorial synthesis and parallel screening with cheminformatics-based QSAR models for discovery and physicochemical elucidation of effective antibiotics-derived polymers for transgene delivery in medicine and biotechnology. PMID:24331709

Application of Spectroscopic Methods for Structural Analysis of Chitin and Chitosan

PubMed Central

Kumirska, Jolanta; Czerwicka, Małgorzata; Kaczyński, Zbigniew; Bychowska, Anna; Brzozowski, Krzysztof; Thöming, Jorg; Stepnowski, Piotr

2010-01-01

Chitin, the second most important natural polymer in the world, and its N-deacetylated derivative chitosan, have been identified as versatile biopolymers for a broad range of applications in medicine, agriculture and the food industry. Two of the main reasons for this are firstly the unique chemical, physicochemical and biological properties of chitin and chitosan, and secondly the unlimited supply of raw materials for their production. These polymers exhibit widely differing physicochemical properties depending on the chitin source and the conditions of chitosan production. The presence of reactive functional groups as well as the polysaccharide nature of these biopolymers enables them to undergo diverse chemical modifications. A complete chemical and physicochemical characterization of chitin, chitosan and their derivatives is not possible without using spectroscopic techniques. This review focuses on the application of spectroscopic methods for the structural analysis of these compounds. PMID:20559489

EVALUATION OF THE SYNTHESIS AND STRUCTURE OF NEW AZETIDIN-2-ONES OF FERULIC ACID.

PubMed

Stan, Cătălina Daniela; Drăgan, Maria; Pânzariu, Andreea; Profire, Lenuţa

2016-01-01

To synthesize some new azetidin-2-ones of ferulic acid and to evaluate them from physicochemical and spectral point of view. The synthesis was carried out in several steps: (i) obtaining the ferulic acid chloride; (ii) obtaining the ferulic acid hydrazide with hydrazine hydrate (98%); (iii) condensation of ferulic acid hydrazide with different benzaldehydes (2-hydroxy-/2-nitro-/4-chloro-/4- fluoro-/4-bromo-benzaldehyde) in order to obtain the corresponding hydrazones; (iv) cy- clization of ferulic acid hydrazones with chloroacethyl chloride in freshly distilled toluene medium and in the presence of triethylamine, resulting in the corresponding azetidin-2-ones. Six new azetidin-2-ones of ferulic acid were synthesized. They were characterized in terms of their physicochemical properties and their structure was confirmed by IR and 1H-NMR spectroscopy. Six new azetidin-2-ones of ferulic acid were synthesized, physicochemically characterized and validated spectrally. A

Unique battery with a multi-functional, physicochemically active membrane separator/electrolyte-electrode monolith and a method making the same

DOEpatents

Gerald, II, Rex E; Ruscic, Katarina J; Sears, Devin N; Smith, Luis J; Klinger, Robert J; Rathke, Jerome W

2013-11-26

The invention relates to a unique battery having a physicochemically active membrane separator/electrolyte-electrode monolith and method of making the same. The Applicant's invented battery employs a physicochemically active membrane separator/electrolyte-electrode that acts as a separator, electrolyte, and electrode, within the same monolithic structure. The chemical composition, physical arrangement of molecules, and physical geometry of the pores play a role in the sequestration and conduction of ions. In one preferred embodiment, ions are transported via the ion-hoping mechanism where the oxygens of the Al.sub.2O.sub.3 wall are available for positive ion coordination (i.e. Li.sup.+). This active membrane-electrode composite can be adjusted to a desired level of ion conductivity by manipulating the chemical composition and structure of the pore wall to either increase or decrease ion conduction.

Unique battery with a multi-functional, physicochemically active membrane separator/electrolyte-electrode monolith and a method making the same

DOEpatents

Gerald II, Rex E.; Ruscic, Katarina J.; Sears, Devin N.; Smith, Luis J.; Klingler, Robert J.; Rathke, Jerome W.

2012-07-24

The invention relates to a unique battery having a physicochemically active membrane separator/electrolyte-electrode monolith and method of making the same. The Applicant's invented battery employs a physicochemically active membrane separator/electrolyte-electrode that acts as a separator, electrolyte, and electrode, within the same monolithic structure. The chemical composition, physical arrangement of molecules, and physical geometry of the pores play a role in the sequestration and conduction of ions. In one preferred embodiment, ions are transported via the ion-hoping mechanism where the oxygens of the Al₂O₃ wall are available for positive ion coordination (i.e. Li⁺). This active membrane-electrode composite can be adjusted to a desired level of ion conductivity by manipulating the chemical composition and structure of the pore wall to either increase or decrease ion conduction.

Associations between soil bacterial community structure and nutrient cycling functions in long-term organic farm soils following cover crop and organic fertilizer amendment.

PubMed

Fernandez, Adria L; Sheaffer, Craig C; Wyse, Donald L; Staley, Christopher; Gould, Trevor J; Sadowsky, Michael J

2016-10-01

Agricultural management practices can produce changes in soil microbial populations whose functions are crucial to crop production and may be detectable using high-throughput sequencing of bacterial 16S rRNA. To apply sequencing-derived bacterial community structure data to on-farm decision-making will require a better understanding of the complex associations between soil microbial community structure and soil function. Here 16S rRNA sequencing was used to profile soil bacterial communities following application of cover crops and organic fertilizer treatments in certified organic field cropping systems. Amendment treatments were hairy vetch (Vicia villosa), winter rye (Secale cereale), oilseed radish (Raphanus sativus), buckwheat (Fagopyrum esculentum), beef manure, pelleted poultry manure, Sustane(®) 8-2-4, and a no-amendment control. Enzyme activities, net N mineralization, soil respiration, and soil physicochemical properties including nutrient levels, organic matter (OM) and pH were measured. Relationships between these functional and physicochemical parameters and soil bacterial community structure were assessed using multivariate methods including redundancy analysis, discriminant analysis, and Bayesian inference. Several cover crops and fertilizers affected soil functions including N-acetyl-β-d-glucosaminidase and β-glucosidase activity. Effects, however, were not consistent across locations and sampling timepoints. Correlations were observed among functional parameters and relative abundances of individual bacterial families and phyla. Bayesian analysis inferred no directional relationships between functional activities, bacterial families, and physicochemical parameters. Soil functional profiles were more strongly predicted by location than by treatment, and differences were largely explained by soil physicochemical parameters. Composition of soil bacterial communities was predictive of soil functional profiles. Differences in soil function were better explained using both soil physicochemical test values and bacterial community structure data than using soil tests alone. Pursuing a better understanding of bacterial community composition and how it is affected by farming practices is a promising avenue for increasing our ability to predict the impact of management practices on important soil functions. Copyright © 2016. Published by Elsevier B.V.

Niche specialization of terrestrial archaeal ammonia oxidizers

PubMed Central

Gubry-Rangin, Cécile; Hai, Brigitte; Quince, Christopher; Engel, Marion; Thomson, Bruce C.; James, Phillip; Schloter, Michael; Griffiths, Robert I.; Prosser, James I.; Nicol, Graeme W.

2011-01-01

Soil pH is a major determinant of microbial ecosystem processes and potentially a major driver of evolution, adaptation, and diversity of ammonia oxidizers, which control soil nitrification. Archaea are major components of soil microbial communities and contribute significantly to ammonia oxidation in some soils. To determine whether pH drives evolutionary adaptation and community structure of soil archaeal ammonia oxidizers, sequences of amoA, a key functional gene of ammonia oxidation, were examined in soils at global, regional, and local scales. Globally distributed database sequences clustered into 18 well-supported phylogenetic lineages that dominated specific soil pH ranges classified as acidic (pH <5), acido-neutral (5≤ pH <7), or alkalinophilic (pH ≥7). To determine whether patterns were reproduced at regional and local scales, amoA gene fragments were amplified from DNA extracted from 47 soils in the United Kingdom (pH 3.5–8.7), including a pH-gradient formed by seven soils at a single site (pH 4.5–7.5). High-throughput sequencing and analysis of amoA gene fragments identified an additional, previously undiscovered phylogenetic lineage and revealed similar pH-associated distribution patterns at global, regional, and local scales, which were most evident for the five most abundant clusters. Archaeal amoA abundance and diversity increased with soil pH, which was the only physicochemical characteristic measured that significantly influenced community structure. These results suggest evolution based on specific adaptations to soil pH and niche specialization, resulting in a global distribution of archaeal lineages that have important consequences for soil ecosystem function and nitrogen cycling. PMID:22158986

Calibration model maintenance in melamine resin production: Integrating drift detection, smart sample selection and model adaptation.

PubMed

Nikzad-Langerodi, Ramin; Lughofer, Edwin; Cernuda, Carlos; Reischer, Thomas; Kantner, Wolfgang; Pawliczek, Marcin; Brandstetter, Markus

2018-07-12

The physico-chemical properties of Melamine Formaldehyde (MF) based thermosets are largely influenced by the degree of polymerization (DP) in the underlying resin. On-line supervision of the turbidity point by means of vibrational spectroscopy has recently emerged as a promising technique to monitor the DP of MF resins. However, spectroscopic determination of the DP relies on chemometric models, which are usually sensitive to drifts caused by instrumental and/or sample-associated changes occurring over time. In order to detect the time point when drifts start causing prediction bias, we here explore a universal drift detector based on a faded version of the Page-Hinkley (PH) statistic, which we test in three data streams from an industrial MF resin production process. We employ committee disagreement (CD), computed as the variance of model predictions from an ensemble of partial least squares (PLS) models, as a measure for sample-wise prediction uncertainty and use the PH statistic to detect changes in this quantity. We further explore supervised and unsupervised strategies for (semi-)automatic model adaptation upon detection of a drift. For the former, manual reference measurements are requested whenever statistical thresholds on Hotelling's T 2 and/or Q-Residuals are violated. Models are subsequently re-calibrated using weighted partial least squares in order to increase the influence of newer samples, which increases the flexibility when adapting to new (drifted) states. Unsupervised model adaptation is carried out exploiting the dual antecedent-consequent structure of a recently developed fuzzy systems variant of PLS termed FLEXFIS-PLS. In particular, antecedent parts are updated while maintaining the internal structure of the local linear predictors (i.e. the consequents). We found improved drift detection capability of the CD compared to Hotelling's T 2 and Q-Residuals when used in combination with the proposed PH test. Furthermore, we found that active selection of samples by active learning (AL) used for subsequent model adaptation is advantageous compared to passive (random) selection in case that a drift leads to persistent prediction bias allowing more rapid adaptation at lower reference measurement rates. Fully unsupervised adaptation using FLEXFIS-PLS could improve predictive accuracy significantly for light drifts but was not able to fully compensate for prediction bias in case of significant lack of fit w.r.t. the latent variable space. Copyright © 2018 Elsevier B.V. All rights reserved.

Physico-chemical characteristics and antimicrobial studies of silver doped hydroxyapatite

NASA Astrophysics Data System (ADS)

Predoi, D.; Predoi, M. V.; Kettani, Moncef Ech Cherif El; Leduc, Damien; Iconaru, S. L.; Ciobanu, C. S.; Buton, N.; Petre, C. C.; Prodan, A. M.

2018-02-01

The present research is focused on the synthesis, structural and morphological characterization and antimicrobial evaluation of silver doped hydroxyapatite (AgHAp) in water. The preliminary ultrasonic characterizations of the AgHAp in water synthesized by an adapted co-precipitation method are also presented. X-ray diffraction result showed that silver ions were substituted in the hydroxyapatite structure. The lattice parameters increased when the silver substitution increased. The morphology of AgHAp were evaluated by Scanning Electron Microscopy (SEM). By EDX analysis the constituents elements of hydroxyapatite were detected in all analyzed samples. The silver was also found in the samples with xAg = 0.5 and 0.2. The colloidal properties of the resulted AgHAp (xAg = 0.0, 0.05 and 0.2) in water were analyzed by Dynamic Light Scattering (DLS) and zeta potential. On the other hand, the novelty of our research consists of preliminary ultrasonic measurements (US) conducted on AgHAp in water. Furthermore, the antimicrobial activity of AgHAp was evaluated and a decrease in the number of surviving cells was established.

Selecting criteria for the right prosthesis in defect of the abdominal wall surgery.

PubMed

Mohamed, H; Ion, D; Serban, M B; Ciurea, M

2009-01-01

The article is debating a theme of great interest for the defect of the abdominal wall surgery--the use of biocompatible prosthesis. The surgeon is often confused by the avalanche of offers made by the mesh producers, making it mandatory for him to know very well the behavior of these alloplastic structures in the tissue environment. From this point of view, we have discussed both the physicochemical properties and the histological reaction brought by the most common type of meshes: polypropylene, polyethylene - tereftalat, polytetrafluorideethylene. This presentation brings out the minimal but mandatory criteria for any mesh to be accepted, but also the criteria that need to be taken into consideration when we try to improve the qualities of the mesh closer to the desideratum of the "ideal mesh". The main conclusion of this review is that we have to change the myth of the "ideal mesh" with "the right chosen mesh", that based on its chemical, physical, structural and biological qualities will adapt perfectly first to the patient's needs and second to the surgeon's needs.

Unique battery with an active membrane separator having uniform physico-chemically functionalized ion channels and a method making the same

DOEpatents

Gerald, II, Rex E.; Ruscic, Katarina J [Chicago, IL; Sears, Devin N [Spruce Grove, CA; Smith, Luis J [Natick, MA; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL

2012-02-21

The invention relates to a unique battery having an active, porous membrane and method of making the same. More specifically the invention relates to a sealed battery system having a porous, metal oxide membrane with uniform, physicochemically functionalized ion channels capable of adjustable ionic interaction. The physicochemically-active porous membrane purports dual functions: an electronic insulator (separator) and a unidirectional ion-transporter (electrolyte). The electrochemical cell membrane is activated for the transport of ions by contiguous ion coordination sites on the interior two-dimensional surfaces of the trans-membrane unidirectional pores. The membrane material is designed to have physicochemical interaction with ions. Control of the extent of the interactions between the ions and the interior pore walls of the membrane and other materials, chemicals, or structures contained within the pores provides adjustability of the ionic conductivity of the membrane.

THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

EPA Science Inventory

Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions.

PubMed

Townsend, Catherine L; Laffy, Julie M J; Wu, Yu-Chang Bryan; Silva O'Hare, Joselli; Martin, Victoria; Kipling, David; Fraternali, Franca; Dunn-Walters, Deborah K

2016-01-01

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response.

Significant Differences in Physicochemical Properties of Human Immunoglobulin Kappa and Lambda CDR3 Regions

PubMed Central

Townsend, Catherine L.; Laffy, Julie M. J.; Wu, Yu-Chang Bryan; Silva O’Hare, Joselli; Martin, Victoria; Kipling, David; Fraternali, Franca; Dunn-Walters, Deborah K.

2016-01-01

Antibody variable regions are composed of a heavy and a light chain, and in humans, there are two light chain isotypes: kappa and lambda. Despite their importance in receptor editing, the light chain is often overlooked in the antibody literature, with the focus being on the heavy chain complementarity-determining region (CDR)-H3 region. In this paper, we set out to investigate the physicochemical and structural differences between human kappa and lambda light chain CDR regions. We constructed a dataset containing over 29,000 light chain variable region sequences from IgM-transcribing, newly formed B cells isolated from human bone marrow and peripheral blood. We also used a published human naïve dataset to investigate the CDR-H3 properties of heavy chains paired with kappa and lambda light chains and probed the Protein Data Bank to investigate the structural differences between kappa and lambda antibody CDR regions. We found that kappa and lambda light chains have very different CDR physicochemical and structural properties, whereas the heavy chains with which they are paired do not differ significantly. We also observed that the mean CDR3 N nucleotide addition in the kappa, lambda, and heavy chain gene rearrangements are correlated within donors but can differ between donors. This indicates that terminal deoxynucleotidyl transferase may work with differing efficiencies between different people but the same efficiency in the different classes of immunoglobulin chain within one person. We have observed large differences in the physicochemical and structural properties of kappa and lambda light chain CDR regions. This may reflect different roles in the humoral immune response. PMID:27729912

Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity.

PubMed

Korkuć, Paula; Walther, Dirk

2015-01-01

To better understand and ultimately predict both the metabolic activities as well as the signaling functions of metabolites, a detailed understanding of the physical interactions of metabolites with proteins is highly desirable. Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. Promiscuously binding metabolites and drugs are characterized by low molecular weight and high structural flexibility. Unlike reported for drug compounds, low rather than high hydrophobicity appears associated, albeit weakly, with promiscuous binding for the metabolite set investigated in this study. Across several physicochemical properties, drug compounds exhibit characteristic binding propensities that are distinguishable from those associated with metabolites. Prediction of target diversity and compound promiscuity using physicochemical properties was possible at modest accuracy levels only, but was consistently better for drugs than for metabolites. Compound properties capturing structural flexibility and hydrogen-bond formation descriptors proved most informative in PLS-based prediction models. With regard to diversity of enzymatic activities of the respective metabolite target enzymes, the metabolites benzylsuccinate, hypoxanthine, trimethylamine N-oxide, oleoylglycerol, and resorcinol showed very narrow process involvement, while glycine, imidazole, tryptophan, succinate, and glutathione were identified to possess broad enzymatic reaction scopes. Promiscuous metabolites were found to mainly serve as general energy currency compounds, but were identified to also be involved in signaling processes and to appear in diverse organismal systems (digestive and nervous system) suggesting specific molecular and physiological roles of promiscuous metabolites.

Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity

PubMed Central

Korkuć, Paula; Walther, Dirk

2015-01-01

To better understand and ultimately predict both the metabolic activities as well as the signaling functions of metabolites, a detailed understanding of the physical interactions of metabolites with proteins is highly desirable. Focusing in particular on protein binding specificity vs. promiscuity, we performed a comprehensive analysis of the physicochemical properties of compound-protein binding events as reported in the Protein Data Bank (PDB). We compared the molecular and structural characteristics obtained for metabolites to those of the well-studied interactions of drug compounds with proteins. Promiscuously binding metabolites and drugs are characterized by low molecular weight and high structural flexibility. Unlike reported for drug compounds, low rather than high hydrophobicity appears associated, albeit weakly, with promiscuous binding for the metabolite set investigated in this study. Across several physicochemical properties, drug compounds exhibit characteristic binding propensities that are distinguishable from those associated with metabolites. Prediction of target diversity and compound promiscuity using physicochemical properties was possible at modest accuracy levels only, but was consistently better for drugs than for metabolites. Compound properties capturing structural flexibility and hydrogen-bond formation descriptors proved most informative in PLS-based prediction models. With regard to diversity of enzymatic activities of the respective metabolite target enzymes, the metabolites benzylsuccinate, hypoxanthine, trimethylamine N-oxide, oleoylglycerol, and resorcinol showed very narrow process involvement, while glycine, imidazole, tryptophan, succinate, and glutathione were identified to possess broad enzymatic reaction scopes. Promiscuous metabolites were found to mainly serve as general energy currency compounds, but were identified to also be involved in signaling processes and to appear in diverse organismal systems (digestive and nervous system) suggesting specific molecular and physiological roles of promiscuous metabolites. PMID:26442281

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

PubMed Central

Fusco, Diana; Barnum, Timothy J.; Bruno, Andrew E.; Luft, Joseph R.; Snell, Edward H.; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis. PMID:24988076

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

PubMed

Fusco, Diana; Barnum, Timothy J; Bruno, Andrew E; Luft, Joseph R; Snell, Edward H; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system.

PubMed

Sainudiin, Raazesh; Wong, Wendy Shuk Wan; Yogeeswaran, Krithika; Nasrallah, June B; Yang, Ziheng; Nielsen, Rasmus

2005-03-01

Models of codon substitution are developed that incorporate physicochemical properties of amino acids. When amino acid sites are inferred to be under positive selection, these models suggest the nature and extent of the physicochemical properties under selection. This is accomplished by first partitioning the codons on the basis of some property of the encoded amino acids. This partition is used to parametrize the rates of property-conserving and property-altering base substitutions at the codon level by means of finite mixtures of Markov models that also account for codon and transition:transversion biases. Here, we apply this method to two positively selected receptors involved in ligand-recognition: the class I alleles of the human major histocompatibility complex (MHC) of known structure and the S-locus receptor kinase (SRK) of the sporophytic self-incompatibility system (SSI) in cruciferous plants (Brassicaceae), whose structure is unknown. Through likelihood ratio tests we demonstrate that at some sites, the positively selected MHC and SRK proteins are under physicochemical selective pressures to alter polarity, volume, polarity and/or volume, and charge to various extents. An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins.

Physicochemical properties/descriptors governing the solubility and partitioning of chemicals in water-solvent-gas systems. Part 2. Solubility in 1-octanol.

PubMed

Raevsky, O A; Perlovich, G L; Schaper, K-J

2007-01-01

On the basis of octanol solubility data (log S(o)) for 218 structurally diverse solid chemicals it was shown that the exclusive consideration of melting points did not provide satisfactory results in the quantitative prediction of this parameter (s = 0.92). The application of HYBOT physicochemical descriptors separately (s = 0.94) and together with melting points (s = 0.70) in the framework of a common regression model also was not successful, although contributions of volume-related and H-bond terms to solubility in octanol were identified. It was proposed that the main reason for such behaviour was the different crystal lattice interaction of different classes of chemicals. Successful calculations of the solubility in octanol of chemicals of interest were performed on the basis of the experimental solubility of structurally/physicochemically/numerically similar nearest neighbours with consideration of their difference in physicochemical parameters (molecular polarisability, H-bond acceptor and donor factors (s = 0.66)) and of these descriptors together with melting point differences (s = 0.38). Good results were obtained for all compounds having nearest neighbours with sufficient similarity, expressed by Tanimoto indexes, and by distances in the scaled 3D descriptor space. Obviously the success of this approach depends on the size of the database.

Physicochemical Drivers of Microbial Community Structure in Sediments of Lake Hazen, Nunavut, Canada.

PubMed

Ruuskanen, Matti O; St Pierre, Kyra A; St Louis, Vincent L; Aris-Brosou, Stéphane; Poulain, Alexandre J

2018-01-01

The Arctic is undergoing rapid environmental change, potentially affecting the physicochemical constraints of microbial communities that play a large role in both carbon and nutrient cycling in lacustrine environments. However, the microbial communities in such Arctic environments have seldom been studied, and the drivers of their composition are poorly characterized. To address these gaps, we surveyed the biologically active surface sediments in Lake Hazen, the largest lake by volume north of the Arctic Circle, and a small lake and shoreline pond in its watershed. High-throughput amplicon sequencing of the 16S rRNA gene uncovered a community dominated by Proteobacteria, Bacteroidetes, and Chloroflexi, similar to those found in other cold and oligotrophic lake sediments. We also show that the microbial community structure in this Arctic polar desert is shaped by pH and redox gradients. This study lays the groundwork for predicting how sediment microbial communities in the Arctic could respond as climate change proceeds to alter their physicochemical constraints.

[The influence of N-, S-containing chinasolone derivatives (NC-224) on the biochemical and physicochemical parameters of membrane endoplasmatic reticulum and nuclear chromatine fractions of rats liver cells in conditions of its injury by tetrachloromethane].

PubMed

Gubs'kyî, Iu I; Goriushko, G G; Belenichev, I F; Kovalenko, S I; Litvinova, N V; Marchenko, O M; Kurapova, T M; Babenko, L P; Velychko, O M

2010-01-01

Using biochemical and physicochemical methods of investigation in vivo, the effect of the substance NC-224, N-, S-chinasolone-derivative, on the lipoperoxidation activity in rat liver endoplasmatic reticulum membranes and nuclear chromatin fractions under tetrachloromethane intoxication have been studied. It was shown that NC-224 has pronounced antioxidant activity which is the biochemical basis of the substance membrane- and genome-protective effects and its ability to restore physicochemical properties of the surface and hydrophobic zones of hepatocyte membranes and structural parameter nuclear chromatin fractions in the conditions of chemical liver injury.

Molecular modeling of polymers 16. Gaseous diffusion in polymers: a quantitative structure-property relationship (QSPR) analysis.

PubMed

Patel, H C; Tokarski, J S; Hopfinger, A J

1997-10-01

The purpose of this study was to identify the key physicochemical molecular properties of polymeric materials responsible for gaseous diffusion in the polymers. Quantitative structure-property relationships, QSPRs were constructed using a genetic algorithm on a training set of 16 polymers for which CO2, N2, O2 diffusion constants were measured. Nine physicochemical properties of each of the polymers were used in the trial basis set for QSPR model construction. The linear cross-correlation matrices were constructed and investigated for colinearity among the members of the training sets. Common water diffusion measures for a limited training set of six polymers was used to construct a "semi-QSPR" model. The bulk modulus of the polymer was overwhelmingly found to be the dominant physicochemical polymer property that governs CO2, N2 and O2 diffusion. Some secondary physicochemical properties controlling diffusion, including conformational entropy, were also identified as correlation descriptors. Very significant QSPR diffusion models were constructed for all three gases. Cohesive energy was identified as the main correlation physicochemical property with aqueous diffusion measures. The dominant role of polymer bulk modulus on gaseous diffusion makes it difficult to develop criteria for selective transport of gases through polymers. Moreover, high bulk moduli are predicted to be necessary for effective gas barrier materials. This property requirement may limit the processing and packaging features of the material. Aqueous diffusion in polymers may occur by a different mechanism than gaseous diffusion since bulk modulus does not correlate with aqueous diffusion, but rather cohesive energy of the polymer.

Obscure phenomena in statistical analysis of quantitative structure-activity relationships. Part 1: Multicollinearity of physicochemical descriptors.

PubMed

Mager, P P; Rothe, H

1990-10-01

Multicollinearity of physicochemical descriptors leads to serious consequences in quantitative structure-activity relationship (QSAR) analysis, such as incorrect estimators and test statistics of regression coefficients of the ordinary least-squares (OLS) model applied usually to QSARs. Beside the diagnosis of the known simple collinearity, principal component regression analysis (PCRA) also allows the diagnosis of various types of multicollinearity. Only if the absolute values of PCRA estimators are order statistics that decrease monotonically, the effects of multicollinearity can be circumvented. Otherwise, obscure phenomena may be observed, such as good data recognition but low predictive model power of a QSAR model.

Inclusion compound of vitamin B6 in β-CD. Physico-chemical and structural investigations

NASA Astrophysics Data System (ADS)

Borodi, Gheorghe; Kacso, Irina; Farcaş, Sorin I.; Bratu, Ioan

2009-08-01

Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with β-cyclodextrin (β-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, 1H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the 1H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the β-CD-vitamin B6 inclusion complex.

[Resistant starches. Part II. Physico-chemical and technological aspects solution medico-biological problems].

PubMed

Iur'ev, V P; Gapparov, M M; Vasserman, L A; Genkina, N K

2006-01-01

This paper is a review of the recent literature data related to structure, composition and physico-chemical properties of starches as well as the special methods of processing of the starch containing raw sources producing the food products with increasing content of resistant starches. The prognosis is made about usefulness of such resistant starches for control of some metabolic disorder in human organism and for prophylactic aims.

OH-PRED: prediction of protein hydroxylation sites by incorporating adapted normal distribution bi-profile Bayes feature extraction and physicochemical properties of amino acids.

PubMed

Jia, Cang-Zhi; He, Wen-Ying; Yao, Yu-Hua

2017-03-01

Hydroxylation of proline or lysine residues in proteins is a common post-translational modification event, and such modifications are found in many physiological and pathological processes. Nonetheless, the exact molecular mechanism of hydroxylation remains under investigation. Because experimental identification of hydroxylation is time-consuming and expensive, bioinformatics tools with high accuracy represent desirable alternatives for large-scale rapid identification of protein hydroxylation sites. In view of this, we developed a supporter vector machine-based tool, OH-PRED, for the prediction of protein hydroxylation sites using the adapted normal distribution bi-profile Bayes feature extraction in combination with the physicochemical property indexes of the amino acids. In a jackknife cross validation, OH-PRED yields an accuracy of 91.88% and a Matthew's correlation coefficient (MCC) of 0.838 for the prediction of hydroxyproline sites, and yields an accuracy of 97.42% and a MCC of 0.949 for the prediction of hydroxylysine sites. These results demonstrate that OH-PRED increased significantly the prediction accuracy of hydroxyproline and hydroxylysine sites by 7.37 and 14.09%, respectively, when compared with the latest predictor PredHydroxy. In independent tests, OH-PRED also outperforms previously published methods.

Magnetic ionic liquids in analytical chemistry: A review.

PubMed

Clark, Kevin D; Nacham, Omprakash; Purslow, Jeffrey A; Pierson, Stephen A; Anderson, Jared L

2016-08-31

Magnetic ionic liquids (MILs) have recently generated a cascade of innovative applications in numerous areas of analytical chemistry. By incorporating a paramagnetic component within the cation or anion, MILs exhibit a strong response toward external magnetic fields. Careful design of the MIL structure has yielded magnetoactive compounds with unique physicochemical properties including high magnetic moments, enhanced hydrophobicity, and the ability to solvate a broad range of molecules. The structural tunability and paramagnetic properties of MILs have enabled magnet-based technologies that can easily be added to the analytical method workflow, complement needed extraction requirements, or target specific analytes. This review highlights the application of MILs in analytical chemistry and examines the important structural features of MILs that largely influence their physicochemical and magnetic properties. Copyright © 2016 Elsevier B.V. All rights reserved.

Directional Darwinian Selection in proteins.

PubMed

McClellan, David A

2013-01-01

Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

Periodontal Ligament Entheses and their Adaptive Role in the Context of Dentoalveolar Joint Function

PubMed Central

Lin, Jeremy D.; Jang, Andrew T.; Kurylo, Michael P.; Hurng, Jonathan; Yang, Feifei; Yang, Lynn; Pal, Arvin; Chen, Ling; Ho, Sunita P.

2017-01-01

Objectives The dynamic bone-periodontal ligament (PDL)-tooth fibrous joint consists of two adaptive functionally graded interfaces (FGI), the PDL-bone and PDL-cementum that respond to mechanical strain transmitted during mastication. In general, from a materials and mechanics perspective, FGI prevent catastrophic failure during prolonged cyclic loading. This review is a discourse of results gathered from literature to illustrate the dynamic adaptive nature of the fibrous joint in response to physiologic and pathologic simulated functions, and experimental tooth movement. Methods Historically, studies have investigated soft to hard tissue transitions through analytical techniques that provided insights into structural, biochemical, and mechanical characterization methods. Experimental approaches included two dimensional to three dimensional advanced in situ imaging and analytical techniques. These techniques allowed mapping and correlation of deformations to physicochemical and mechanobiological changes within volumes of the complex subjected to concentric and eccentric loading regimes respectively. Results Tooth movement is facilitated by mechanobiological activity at the interfaces of the fibrous joint and generates elastic discontinuities at these interfaces in response to eccentric loading. Both concentric and eccentric loads mediated cellular responses to strains, and prompted self-regulating mineral forming and resorbing zones that in turn altered the functional space of the joint. Significance A multiscale biomechanics and mechanobiology approach is important for correlating joint function to tissue-level strain-adaptive properties with overall effects on joint form as related to physiologic and pathologic functions. Elucidating the shift in localization of biomolecules specifically at interfaces during development, function, and therapeutic loading of the joint is critical for developing “functional regeneration and adaptation” strategies with an emphasis on restoring physiologic joint function. PMID:28476202

Xanthine oxidase inhibitors beyond allopurinol and febuxostat; an overview and selection of potential leads based on in silico calculated physico-chemical properties, predicted pharmacokinetics and toxicity.

PubMed

Šmelcerović, Andrija; Tomović, Katarina; Šmelcerović, Žaklina; Petronijević, Živomir; Kocić, Gordana; Tomašič, Tihomir; Jakopin, Žiga; Anderluh, Marko

2017-07-28

Xanthine oxidase (XO), a versatile metalloflavoprotein enzyme, catalyzes the oxidative hydroxylation of hypoxanthine and xanthine to uric acid in purine catabolism while simultaneously producing reactive oxygen species. Both lead to the gout-causing hyperuricemia and oxidative damage of the tissues where overactivity of XO is present. Over the past years, significant progress and efforts towards the discovery and development of new XO inhibitors have been made and we believe that not only experts in the field, but also general readership would benefit from a review that addresses this topic. Accordingly, the aim of this article was to overview and select the most potent recently reported XO inhibitors and to compare their structures, mechanisms of action, potency and effectiveness of their inhibitory activity, in silico calculated physico-chemical properties as well as predicted pharmacokinetics and toxicity. Derivatives of imidazole, 1,3-thiazole and pyrimidine proved to be more potent than febuxostat while also displaying/possessing favorable predicted physico-chemical, pharmacokinetic and toxicological properties. Although being structurally similar to febuxostat, these optimized inhibitors bear some structural freshness and could be adopted as hits for hit-to-lead development and further evaluation by in vivo studies towards novel drug candidates, and represent valuable model structures for design of novel XO inhibitors. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Understanding physicochemical properties changes from multi-scale structures of starch/CNT nanocomposite films.

PubMed

Liu, Siyuan; Li, Xiaoxi; Chen, Ling; Li, Lin; Li, Bing; Zhu, Jie

2017-11-01

From the view of multi-scale structures of hydroxypropyl starch (HPS)/carbon nanotube (CNT) nanocomposite films, the film physicochemical properties were affected by comprehensive factors including molecular interaction, short range molecular conformation, crystalline structure and aggregated structure. The less original HPS hydrogen bonding that was broken, less decreased order of HPS short range molecular conformation, lower film crystallinity and larger size of micro-ordered regions contributed to higher tensile strength and Young's modulus of the film with CNT content of 0.5% (g/g, CNT in HPS). The higher film overall crystallinity and larger size of micro-ordered regions of the film with CNT content of 0.05%-0.3% compared with those of control contributed to better film barrier property. The addition of CNT with the content of 0.05%-0.5% broke the original HPS hydrogen bonding and decreased the order of starch short range molecular conformation, which counteracted the positive effect of CNT on the thermal stability of the material, thus thermal degradation temperature of these nanocomposite films did not increase. But the sharp increase of film crystallinity increased film thermal degradation temperature. This study provided a better understanding of film physicochemical properties changes which guides to rational design of starch-based nanocomposite films for packaging and coating application. Copyright © 2017. Published by Elsevier B.V.

Detection and Physicochemical Characterization of Membrane Vesicles (MVs) of Lactobacillus reuteri DSM 17938

PubMed Central

Grande, Rossella; Celia, Christian; Mincione, Gabriella; Stringaro, Annarita; Di Marzio, Luisa; Colone, Marisa; Di Marcantonio, Maria C.; Savino, Luca; Puca, Valentina; Santoliquido, Roberto; Locatelli, Marcello; Muraro, Raffaella; Hall-Stoodley, Luanne; Stoodley, Paul

2017-01-01

Membrane vesicles (MVs) are bilayer structures which bleb from bacteria, and are important in trafficking biomolecules to other bacteria or host cells. There are few data about MVs produced by the Gram-positive commensal-derived probiotic Lactobacillus reuteri; however, MVs from this species may have potential therapeutic benefit. The aim of this study was to detect and characterize MVs produced from biofilm (bMVs), and planktonic (pMVs) phenotypes of L. reuteri DSM 17938. MVs were analyzed for structure and physicochemical characterization by Scanning Electron Microscope (SEM) and Dynamic Light Scattering (DLS). Their composition was interrogated using various digestive enzyme treatments and subsequent Transmission Electron Microscopy (TEM) analysis. eDNA (extracellular DNA) was detected and quantified using PicoGreen. We found that planktonic and biofilm of L. reuteri cultures generated MVs with a broad size distribution. Our data also showed that eDNA was associated with pMVs and bMVs (eMVsDNA). DNase I treatment demonstrated no modifications of MVs, suggesting that an eDNA-MVs complex protected the eMVsDNA. Proteinase K and Phospholipase C treatments modified the structure of MVs, showing that lipids and proteins are important structural components of L. reuteri MVs. The biological composition and the physicochemical characterization of MVs generated by the probiotic L. reuteri may represent a starting point for future applications in the development of vesicles-based therapeutic systems. PMID:28659878

MOLE 2.0: advanced approach for analysis of biomacromolecular channels

PubMed Central

2013-01-01

Background Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. Results We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. Conclusion Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz. PMID:23953065

Physicochemical parameters optimization, and purification of phycobiliproteins from the isolated Nostoc sp.

PubMed

Johnson, Eldin M; Kumar, Kanhaiya; Das, Debabrata

2014-08-01

The present study investigated the effects of several physicochemical parameters on the improvement of phycobiliproteins (especially phycocyanin) synthesis in a newly isolated species of Nostoc sp. Standard BG11₀ medium was modified to enhance the biomass productivity in different photobioreactors. The initial pH of 8, light intensity of 40 μmol m(-2)s(-1), temperature of 35 °C, diurnal cycle of 16:8 h (light:dark regime), 75.48 μM Na₂CO₃ and 17.65 mM NaNO₃ were found most suitable for the phycobiliproteins synthesis. Cyanobacteria exhibited chromatic adaptation, causing overexpression of phycocyanin in red and phycoerythrin in green light. The maximum phycobiliproteins yield of 0.13 gg(-1) dry cell weight was obtained in green light. Phycocyanin was further purified using thin layer chromatography (TLC), anion exchange chromatography and SDS-PAGE (denaturing gel) electrophoresis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage

PubMed Central

Bozek, Katarzyna; Lengauer, Thomas; Sierra, Saleta; Kaiser, Rolf; Domingues, Francisco S.

2013-01-01

The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%). We additionally assessed the predictive power of the new method on clinically derived ‘bulk’ sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/. PMID:23555214

Application of ultra high pressure (UHP) in starch chemistry.

PubMed

Kim, Hyun-Seok; Kim, Byung-Yong; Baik, Moo-Yeol

2012-01-01

Ultra high pressure (UHP) processing is an attractive non-thermal technique for food treatment and preservation at room temperature, with the potential to achieve interesting functional effects. The majority of UHP process applications in food systems have focused on shelf-life extension associated with non-thermal sterilization and a reduction or increase in enzymatic activity. Only a few studies have investigated modifications of structural characteristics and/or protein functionalities. Despite the rapid expansion of UHP applications in food systems, limited information is available on the effects of UHP on the structural and physicochemical properties of starch and/or its chemical derivatives included in most processed foods as major ingredients or minor additives. Starch and its chemical derivatives are responsible for textural and physical properties of food systems, impacting their end-use quality and/or shelf-life. This article reviews UHP processes for native (unmodified) starch granules and their effects on the physicochemical properties of UHP-treated starch. Furthermore, functional roles of UHP in acid-hydrolysis, hydroxypropylation, acetylation, and cross-linking reactions of starch granules, as well as the physicochemical properties of UHP-assisted starch chemical derivatives, are discussed.

Physicochemical characterization of ultrasmall superparamagnetic iron oxide particles (USPIO) for biomedical application as MRI contrast agents

PubMed Central

Di Marco, Mariagrazia; Sadun, Claudia; Port, Marc; Guilbert, Irene; Couvreur, Patrick; Dubernet, Catherine

2007-01-01

Ultrasmall superparamagnetic iron oxide (USPIO) particles are maghemite or magnetite nanoparticles currently used as contrast agent in magnetic resonance imaging. The coatings surrounding the USPIO inorganic core play a major role in both the in vitro stability and, over all, USPIO’s in vivo fate. Different physicochemical properties such as final size, surface charge and coating density are key factors in this respect. Up to now no precise structure – activity relationship has been described to predict entirely the USPIOs stability, as well as their pharmacokinetics and their safety. This review is focused on both the classical and the latest available techniques allowing a better insight in the magnetic core structure and the organic surface of these particles. Concurrently, this work clearly shows the difficulty to obtain a complete physicochemical characterization of USPIOs particles owing to their small dimensions, reaching the analytical resolution limits of many commercial instruments. An extended characterization is therefore necessary to improve the understanding of the properties of USPIOs when dispersed in an aqueous environment and to set the specifications and limits for their conception. PMID:18203428

Estimation of Melting Points of Organics.

PubMed

Yalkowsky, Samuel H; Alantary, Doaa

2018-05-01

Unified physicochemical property estimation relationships is a system of empirical and theoretical relationships that relate 20 physicochemical properties of organic molecules to each other and to chemical structure. Melting point is a key parameter in the unified physicochemical property estimation relationships scheme because it is a determinant of several other properties including vapor pressure, and solubility. This review describes the first-principals calculation of the melting points of organic compounds from structure. The calculation is based on the fact that the melting point, T m , is equal to the ratio of the heat of melting, ΔH m , to the entropy of melting, ΔS m . The heat of melting is shown to be an additive constitutive property. However, the entropy of melting is not entirely group additive. It is primarily dependent on molecular geometry, including parameters which reflect the degree of restriction of molecular motion in the crystal to that of the liquid. Symmetry, eccentricity, chirality, flexibility, and hydrogen bonding, each affect molecular freedom in different ways and thus make different contributions to the total entropy of fusion. The relationships of these entropy determining parameters to chemical structure are used to develop a reasonably accurate means of predicting the melting points over 2000 compounds. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

PRince: a web server for structural and physicochemical analysis of protein-RNA interface.

PubMed

Barik, Amita; Mishra, Abhishek; Bahadur, Ranjit Prasad

2012-07-01

We have developed a web server, PRince, which analyzes the structural features and physicochemical properties of the protein-RNA interface. Users need to submit a PDB file containing the atomic coordinates of both the protein and the RNA molecules in complex form (in '.pdb' format). They should also mention the chain identifiers of interacting protein and RNA molecules. The size of the protein-RNA interface is estimated by measuring the solvent accessible surface area buried in contact. For a given protein-RNA complex, PRince calculates structural, physicochemical and hydration properties of the interacting surfaces. All these parameters generated by the server are presented in a tabular format. The interacting surfaces can also be visualized with software plug-in like Jmol. In addition, the output files containing the list of the atomic coordinates of the interacting protein, RNA and interface water molecules can be downloaded. The parameters generated by PRince are novel, and users can correlate them with the experimentally determined biophysical and biochemical parameters for better understanding the specificity of the protein-RNA recognition process. This server will be continuously upgraded to include more parameters. PRince is publicly accessible and free for use. Available at http://www.facweb.iitkgp.ernet.in/~rbahadur/prince/home.html.

Type II Collagen and Gelatin from Silvertip Shark (Carcharhinus albimarginatus) Cartilage: Isolation, Purification, Physicochemical and Antioxidant Properties

PubMed Central

Jeevithan, Elango; Bao, Bin; Bu, Yongshi; Zhou, Yu; Zhao, Qingbo; Wu, Wenhui

2014-01-01

Type II acid soluble collagen (CIIA), pepsin soluble collagen (CIIP) and type II gelatin (GII) were isolated from silvertip shark (Carcharhinus albimarginatus) cartilage and examined for their physicochemical and antioxidant properties. GII had a higher hydroxyproline content (173 mg/g) than the collagens and cartilage. CIIA, CIIP and GII were composed of two identical α1 and β chains and were characterized as type II. Amino acid analysis of CIIA, CIIP and GII indicated imino acid contents of 150, 156 and 153 amino acid residues per 1000 residues, respectively. Differing Fourier transform infrared (FTIR) spectra of CIIA, CIIP and GII were observed, which suggested that the isolation process affected the secondary structure and molecular order of collagen, particularly the triple-helical structure. The denaturation temperature of GII (32.5 °C) was higher than that of CIIA and CIIP. The antioxidant activity against 1,1-diphenyl-2-picrylhydrazyl radicals and the reducing power of CIIP was greater than that of CIIA and GII. SEM microstructure of the collagens depicted a porous, fibrillary and multi-layered structure. Accordingly, the physicochemical and antioxidant properties of type II collagens (CIIA, CIIP) and GII isolated from shark cartilage were found to be suitable for biomedical applications. PMID:24979271

'Pro et contra' ionic liquid drugs - Challenges and opportunities for pharmaceutical translation.

PubMed

Balk, Anja; Holzgrabe, Ulrike; Meinel, Lorenz

2015-08-01

Ionic liquids (ILs) are organic salts with a melting point below 100°C. Active pharmaceutical ingredients (APIs) are transformed into ILs by combining them with typically large yet charged counterions. ILs hold promise to build a large design space for relevant pharmaceutical parameters, particularly for poorly water soluble drugs. It is for this wide design space that ILs may be the entry into the fascinating vision of modifying physico-chemical properties without the need to structurally modify the active pharmaceutical ingredient itself. This extremely intriguing pharmaceutical option is critically discussed including its potential and limitations. The review is starting off with an introduction to the metathesis and characterization of ILs, and leads over to examples for pharmaceutical application, including enhancement of dissolution rate and kinetic solubility and hygroscopicity adaptation, respectively. Tuning biopharmaceutics and toxicology by proper IL design is another focus. The review connects the interrelated chemical, physical, pharmaceutical, and toxicological outcome of API-ILs, serving as guidance for the formulation scientist who aims at expanding ones armamentarium for poorly water soluble APIs while avoiding structural modification, thereof. Copyright © 2015 Elsevier B.V. All rights reserved.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space.

PubMed

Lungu, Claudiu N; Diudea, Mircea V; Putz, Mihai V; Grudziński, Ireneusz P

2016-04-13

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose.

Linear and Branched PEIs (Polyethylenimines) and Their Property Space

PubMed Central

Lungu, Claudiu N.; Diudea, Mircea V.; Putz, Mihai V.; Grudziński, Ireneusz P.

2016-01-01

A chemical property space defines the adaptability of a molecule to changing conditions and its interaction with other molecular systems determining a pharmacological response. Within a congeneric molecular series (compounds with the same derivatization algorithm and thus the same brute formula) the chemical properties vary in a monotonic manner, i.e., congeneric compounds share the same chemical property space. The chemical property space is a key component in molecular design, where some building blocks are functionalized, i.e., derivatized, and eventually self-assembled in more complex systems, such as enzyme-ligand systems, of which (physico-chemical) properties/bioactivity may be predicted by QSPR/QSAR (quantitative structure-property/activity relationship) studies. The system structure is determined by the binding type (temporal/permanent; electrostatic/covalent) and is reflected in its local electronic (and/or magnetic) properties. Such nano-systems play the role of molecular devices, important in nano-medicine. In the present article, the behavior of polyethylenimine (PEI) macromolecules (linear LPEI and branched BPEI, respectively) with respect to the glucose oxidase enzyme GOx is described in terms of their (interacting) energy, geometry and topology, in an attempt to find the best shape and size of PEIs to be useful for a chosen (nanochemistry) purpose. PMID:27089324

Human health no-effect levels of TiO2 nanoparticles as a function of their primary size

NASA Astrophysics Data System (ADS)

Laurent, Alexis; Harkema, Jack R.; Andersen, Elisabeth W.; Owsianiak, Mikołaj; Vea, Eldbjørg B.; Jolliet, Olivier

2017-04-01

As engineered nanomaterials are increasingly introduced on the market into a broad range of commodities or nanoproducts, there is a need for operational, reliable tool, enabling to consistently assess the risks and impacts associated with the releases of nanoparticles. The lack of a developed metric that accurately represents their toxic effects while capturing the influence of the most relevant physicochemical properties is one of the major impediments. Here, we investigate the relationships between the toxic responses of nano-sized and micro-sized particles in in vivo toxicological studies and their physicochemical properties. Our results for TiO2 particles indicate statistically significant associations between the primary particle size and their toxicity responses for combined inhalation and ingestion exposure routes, although the numerical values should be considered with care due to the inability to encompass influences from other relevant physicochemical properties like surface coatings. These findings allow for expressing mass-based adverse effect levels as a continuous function of the primary size of particles. This meaningful, exploratory metric can thus be used for screening purposes and pave the way for reaching adaptive, robust risk assessments of nanomaterials, e.g. for setting up consistent threshold levels, as well as consistent life cycle assessments of nanoproducts. We provide examples of such applications.

Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials.

PubMed

Nguyen, Peter Q; Courchesne, Noémie-Manuelle Dorval; Duraj-Thatte, Anna; Praveschotinunt, Pichet; Joshi, Neel S

2018-05-01

Vast potential exists for the development of novel, engineered platforms that manipulate biology for the production of programmed advanced materials. Such systems would possess the autonomous, adaptive, and self-healing characteristics of living organisms, but would be engineered with the goal of assembling bulk materials with designer physicochemical or mechanical properties, across multiple length scales. Early efforts toward such engineered living materials (ELMs) are reviewed here, with an emphasis on engineered bacterial systems, living composite materials which integrate inorganic components, successful examples of large-scale implementation, and production methods. In addition, a conceptual exploration of the fundamental criteria of ELM technology and its future challenges is presented. Cradled within the rich intersection of synthetic biology and self-assembling materials, the development of ELM technologies allows the power of biology to be leveraged to grow complex structures and objects using a palette of bio-nanomaterials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Preparation and physicochemical properties of protein concentrate and isolate produced from Acacia tortilis (Forssk.) Hayne ssp. raddiana.

PubMed

Embaby, Hassan E; Swailam, Hesham M; Rayan, Ahmed M

2018-02-01

The composition and physicochemical properties of defatted acacia flour (DFAF), acacia protein concentrate (APC) and acacia protein isolate (API) were evaluated. The results indicated that API had lower, ash and fat content, than DFAF and APC. Also, significant difference in protein content was noticed among DFAF, APC and API (37.5, 63.7 and 91.8%, respectively). Acacia protein concentrate and isolates were good sources of essential amino acids except cystine and methionine. The physicochemical and functional properties of acacia protein improved with the processing of acacia into protein concentrate and protein isolate. The results of scanning electron micrographs showed that DFAF had a compact structure; protein concentrate were, flaky, and porous type, and protein isolate had intact flakes morphology.

Influence of food intrinsic complexity on Listeria monocytogenes growth in/on vacuum-packed model systems at suboptimal temperatures.

PubMed

Baka, Maria; Noriega, Estefanía; Van Langendonck, Kristof; Van Impe, Jan F

2016-10-17

Food intrinsic factors e.g., food (micro)structure, compositional and physicochemical aspects, which are mutually dependent, influence microbial growth. While the effect of composition and physicochemical properties on microbial growth has been thoroughly assessed and characterised, the role of food (micro)structure still remains unravelled. Most studies on food (micro)structure focus on comparing planktonic growth in liquid (microbiological) media with colonial growth in/on solid-like systems or on real food surfaces. However, foods are not only liquids or solids; they can also be emulsions or gelled emulsions and have complex compositions. In this study, Listeria monocytogenes growth was studied on the whole spectrum of (micro)structure, in terms of food (model) systems. The model systems varied not only in (micro)structure, which was the target of the study, but also in compositional and physicochemical characteristics, which was an inevitable consequence of the (micro)structural variability. The compositional and physicochemical differences were mainly due to the presence or absence of fat and gelling agents. The targeted (micro)structures were: i) liquids, ii) aqueous gels, iii) emulsions and iv) gelled emulsions. Furthermore, the microbial dynamics were studied and compared in/on all these model systems, as well as on a compositionally predefined canned meat, developed in order to have equal compositional level to the gelled emulsion model system and represent a real food system. Frankfurter sausages were the targeted real foods, selected as a case study, to which the canned meat had similar compositional characteristics. All systems were vacuum packed and incubated at 4, 8 and 12°C. The most appropriate protocol for the preparation of the model systems was developed. The pH, water activity and resistance to penetration of the model systems were characterised. Results indicated that low temperature contributes to growth variations among the model systems. Additionally, the firmer the solid system, the faster L. monocytogenes grew on it. Finally, it was found that L. monocytogenes grows faster on canned meat and real Frankfurters, as found in a previous study, followed by liquids, aqueous gels, emulsions and gelled emulsions. This observation indicates that all model systems, developed in this study, underestimated L. monocytogenes growth. Despite some limitations, model systems are overall advantageous and therefore, their validation is always recommended prior to further use. Copyright © 2016. Published by Elsevier B.V.

NATURAL AND HUMAN FACTORS STRUCTURING FISH ASSEMBLAGES IN WEST VIRGINIA WADEABLE STREAMS

EPA Science Inventory

We surveyed fishes and environmental variables in 119 stream basins to identify natural and anthropogenic factors structuring fish assemblages. We collected fishes and physico-chemical variables using standardized EPA methods and compiled basin characteristics (e.g., land cover)...

Physico-chemical properties and gasification reactivity of co-pyrolysis char from different rank of coal blended with lignocellulosic biomass: Effects of the cellulose.

PubMed

Wu, Zhiqiang; Wang, Shuzhong; Luo, Zhengyuan; Chen, Lin; Meng, Haiyu; Zhao, Jun

2017-07-01

In this paper, the influence of cellulose on the physicochemical properties and the gasification reactivity of co-pyrolysis char was investigated. A specific surface area analyzer and an X-ray diffraction system were used to characterize the pore structure and the micro-crystalline structure of char. Fractal theory and deconvolution method were applied to quantitatively investigate the influence of cellulose on the structure of co-pyrolysis char. The results indicate that the improvements in the pore structure due to the presence of cellulose are more pronounced in the case of anthracite char with respect to bituminous char. Cellulose promotes the ordering of micro-scale structure and the uniformity of both anthracite and bituminous char, while the negative synergetic effect was observed during gasification of co-pyrolysis char. The exponential relationships between fractal dimension and specific surface area were determined, along with the relations between the gasification reactivity index and the microcrystalline structure parameter. Copyright © 2017 Elsevier Ltd. All rights reserved.

Heterocyclic cationic gemini surfactants: a comparative overview of their synthesis, self-assembling, physicochemical, and biological properties.

PubMed

Sharma, Vishnu Dutt; Ilies, Marc A

2014-01-01

Gemini surfactants (GS) are presently receiving substantial attention due to their special self-assembling properties and unique interfacial activity. This comprehensive review is focused on positively charged heterocyclic GS, presenting their major synthetic access routes and examining the impact of structural elements on physicochemical and aggregation properties of this class of amphiphiles. Interaction of geminis surfactants with cells and their biological properties as novel transfection agents are emphasized through a detailed structure-activity relationship analysis. Throughout the review we have also presented the properties of selected ammonium GS, simple surfactants and lipid congeners, in order to emphasize the advantages conferred by using heterocyclic polar heads in GS design. © 2012 Wiley Periodicals, Inc.

Improving predictions of protein-protein interfaces by combining amino acid-specific classifiers based on structural and physicochemical descriptors with their weighted neighbor averages.

PubMed

de Moraes, Fábio R; Neshich, Izabella A P; Mazoni, Ivan; Yano, Inácio H; Pereira, José G C; Salim, José A; Jardine, José G; Neshich, Goran

2014-01-01

Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html).

Improving Predictions of Protein-Protein Interfaces by Combining Amino Acid-Specific Classifiers Based on Structural and Physicochemical Descriptors with Their Weighted Neighbor Averages

PubMed Central

de Moraes, Fábio R.; Neshich, Izabella A. P.; Mazoni, Ivan; Yano, Inácio H.; Pereira, José G. C.; Salim, José A.; Jardine, José G.; Neshich, Goran

2014-01-01

Protein-protein interactions are involved in nearly all regulatory processes in the cell and are considered one of the most important issues in molecular biology and pharmaceutical sciences but are still not fully understood. Structural and computational biology contributed greatly to the elucidation of the mechanism of protein interactions. In this paper, we present a collection of the physicochemical and structural characteristics that distinguish interface-forming residues (IFR) from free surface residues (FSR). We formulated a linear discriminative analysis (LDA) classifier to assess whether chosen descriptors from the BlueStar STING database (http://www.cbi.cnptia.embrapa.br/SMS/) are suitable for such a task. Receiver operating characteristic (ROC) analysis indicates that the particular physicochemical and structural descriptors used for building the linear classifier perform much better than a random classifier and in fact, successfully outperform some of the previously published procedures, whose performance indicators were recently compared by other research groups. The results presented here show that the selected set of descriptors can be utilized to predict IFRs, even when homologue proteins are missing (particularly important for orphan proteins where no homologue is available for comparative analysis/indication) or, when certain conformational changes accompany interface formation. The development of amino acid type specific classifiers is shown to increase IFR classification performance. Also, we found that the addition of an amino acid conservation attribute did not improve the classification prediction. This result indicates that the increase in predictive power associated with amino acid conservation is exhausted by adequate use of an extensive list of independent physicochemical and structural parameters that, by themselves, fully describe the nano-environment at protein-protein interfaces. The IFR classifier developed in this study is now integrated into the BlueStar STING suite of programs. Consequently, the prediction of protein-protein interfaces for all proteins available in the PDB is possible through STING_interfaces module, accessible at the following website: (http://www.cbi.cnptia.embrapa.br/SMS/predictions/index.html). PMID:24489849

Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties

PubMed Central

2011-01-01

Background Existing methods of predicting DNA-binding proteins used valuable features of physicochemical properties to design support vector machine (SVM) based classifiers. Generally, selection of physicochemical properties and determination of their corresponding feature vectors rely mainly on known properties of binding mechanism and experience of designers. However, there exists a troublesome problem for designers that some different physicochemical properties have similar vectors of representing 20 amino acids and some closely related physicochemical properties have dissimilar vectors. Results This study proposes a systematic approach (named Auto-IDPCPs) to automatically identify a set of physicochemical and biochemical properties in the AAindex database to design SVM-based classifiers for predicting and analyzing DNA-binding domains/proteins. Auto-IDPCPs consists of 1) clustering 531 amino acid indices in AAindex into 20 clusters using a fuzzy c-means algorithm, 2) utilizing an efficient genetic algorithm based optimization method IBCGA to select an informative feature set of size m to represent sequences, and 3) analyzing the selected features to identify related physicochemical properties which may affect the binding mechanism of DNA-binding domains/proteins. The proposed Auto-IDPCPs identified m=22 features of properties belonging to five clusters for predicting DNA-binding domains with a five-fold cross-validation accuracy of 87.12%, which is promising compared with the accuracy of 86.62% of the existing method PSSM-400. For predicting DNA-binding sequences, the accuracy of 75.50% was obtained using m=28 features, where PSSM-400 has an accuracy of 74.22%. Auto-IDPCPs and PSSM-400 have accuracies of 80.73% and 82.81%, respectively, applied to an independent test data set of DNA-binding domains. Some typical physicochemical properties discovered are hydrophobicity, secondary structure, charge, solvent accessibility, polarity, flexibility, normalized Van Der Waals volume, pK (pK-C, pK-N, pK-COOH and pK-a(RCOOH)), etc. Conclusions The proposed approach Auto-IDPCPs would help designers to investigate informative physicochemical and biochemical properties by considering both prediction accuracy and analysis of binding mechanism simultaneously. The approach Auto-IDPCPs can be also applicable to predict and analyze other protein functions from sequences. PMID:21342579

Influence of selected physicochemical parameters on microbiological activity of mucks.

NASA Astrophysics Data System (ADS)

Całka, A.; Sokołowska, Z.; Warchulska, P.; Dąbek-Szreniawska, M.

2009-04-01

One of the basic factor decided about soil fertility are microorganisms that together with flora, determine trend and character of biochemical processes as well totality of fundamental transformations connected with biogeochemistry and physicochemical properties of soil. Determination of general bacteria number, quantity of selected groups of microorganisms and investigation of respiration intensity let estimate microbiological activity of soil. Intensity of microbiological processes is directly connected with physicochemical soil parameters. In that case, such structural parameters as bulk density, porosity, surface or carbon content play significant role. Microbiological activity also changes within the bounds of mucks with different stage of humification and secondary transformation. Knowledge of relations between structural properties, microorganism activity and degree of transformation and humification can lead to better understanding microbiological processes as well enable to estimate microbiological activity at given physicochemical conditions and at progressing process of soil transformation. The study was carried out on two peaty-moorsh (muck) soils at different state of secondary transformation and humification degree. Soil samples were collected from Polesie Lubelskie (layer depth: 5 - 25 cm). Investigated mucks originated from soils formed from low peatbogs. Soil sample marked as I belonged to muck group weakly secondary transformed. Second sample (II) represented soil group with middle stage of secondary transformation. The main purpose of the research was to examine the relations between some physicochemical and surface properties and their biological activity. Total number and respiration activity of microorganisms were determined. The effectiveness of utilizing the carbon substances from the soil by the bacteria increased simultaneously with the transformation state of the peat-muck soils. Quantity of organic carbon decreased distinctly in the soil at the higher stage of secondary transformation and it influenced quantity and activity of soil microorganisms. Bulk density and surface increased with increasing secondary transformation degree. On the other hand, porosity decreased with increasing secondary transformation index. Process of secondary transformation influenced the soil environment for the microbes by changing the physicochemical properties. This way it influenced the number of microorganisms and caused changes of biological activity in the soils.

Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

PubMed

Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

2015-07-01

Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect.

Mass Transfer Behavior of Perfluorinated Chemicals in Saturated Clay-rich Sands: A Laboratory-based Study on Fate and Transport in Groundwater and Sediments

NASA Astrophysics Data System (ADS)

Greenberg, R. R.; Tick, G. R.; Abbott, J. B., III; Carroll, K. C.

2017-12-01

Perfluoroalkyl substances (PFAS) are a class of emerging contaminants that pose a threat to the human health and the quality of groundwater, surface water, and drinking water supplies. This study aims to elucidate the primary physicochemical factors controlling the fate and transport of the PFAS contaminants, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), in groundwater. Physicochemical processes of intercalation, adsorption, and desorption were investigated for the retention of PFAS at different initial aqueous-phase concentrations in modified-natural sediments composed of sand (40/50 accusand; foc = 0.04% unmodified) with low, medium, and high organic carbon contents (foc = 10, 20, and 50%) and various pre-conditioned clay-fractions. Diffusional mass-transfer limitations were evaluated based on initial PFAS concentration, specific clay structure, and resulting contaminant intercalation (d-spacing changes). A series of short- (48 hr), medium- (7 day) and long-term (30 day) batch and column experiments were conducted to determine physicochemical processes as a function of compound chemistry, sediment geochemistry, sorbent crystalline structure, and contaminant/sediment contact-time. Physicochemical parameters, PFAS concentrations, and sediment characterization were conducted using high performance liquid chromatography (HPLC), X-ray diffraction (XRD), and furnace combustion analytical techniques. The results of PFAS contaminant transport, under the different conditions tested, provide a scientific contribution with application to the development of improved risk assessments, predictions of fate and transport, and more effective remediation strategies for emerging perfluorinated contaminants in soil and groundwater.

How far are rheological parameters from amplitude sweep tests predictable using common physicochemical soil properties?

NASA Astrophysics Data System (ADS)

Stoppe, N.; Horn, R.

2017-01-01

A basic understanding of soil behavior on the mesoscale resp. macroscale (i.e. soil aggregates resp. bulk soil) requires knowledge of the processes at the microscale (i.e. particle scale), therefore rheological investigations of natural soils receive growing attention. In the present research homogenized and sieved (< 2 mm) samples from Marshland soils of the riparian zone of the River Elbe (North Germany) were analyzed with a modular compact rheometer MCR 300 (Anton Paar, Ostfildern, Germany) with a profiled parallel-plate measuring system. Amplitude sweep tests (AST) with controlled shear deformation were conducted to investigate the viscoelastic properties of the studied soils under oszillatory stress. The gradual depletion of microstructural stiffness during AST cannot only be characterized by the well-known rheological parameters G, G″ and tan δ but also by the dimensionless area parameter integral z, which quantifies the elasticity of microstructure. To discover the physicochemical parameters, which influences the microstructural stiffness, statistical tests were used taking the combined effects of these parameters into account. Although the influence of the individual factors varies depending on soil texture, the physicochemical features significantly affecting soil micro structure were identified. Based on the determined statistical relationships between rheological and physicochemical parameters, pedotransfer functions (PTF) have been developed, which allow a mathematical estimation of the rheological target value integral z. Thus, stabilizing factors are: soil organic matter, concentration of Ca2+, content of CaCO3 and pedogenic iron oxides; whereas the concentration of Na+ and water content represent structurally unfavorable factors.

The evolution of ecological tolerance in prokaryotes

NASA Technical Reports Server (NTRS)

Knoll, A. H.; Bauld, J.

1989-01-01

The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.

Effect of acidity on the physicochemical properties of α- and β-chitin nanofibers.

PubMed

Suenaga, Shin; Totani, Kazuhide; Nomura, Yoshihiro; Yamashita, Kazuhiko; Shimada, Iori; Fukunaga, Hiroshi; Takahashi, Nobuhide; Osada, Mitsumasa

2017-09-01

We have investigated whether acidity can be used to control the physicochemical properties of chitin nanofibers (ChNFs). In this study, we define acidity as the molar ratio of dissociated protons from the acid to the amino groups in the raw chitin powder. The effect of acidity on the physicochemical properties of α- and β-ChNFs was compared. The transmittance and viscosity of the β-ChNFs drastically and continuously increased with increasing acidity, while those of the α-ChNFs were not affected by acidity. These differences are because of the higher ability for cationization based on the more flexible crystal structure of β-chitin than α-chitin. In addition, the effect of the acid species on the transmittance of β-ChNFs was investigated. The transmittance of β-ChNFs can be expressed by the acidity regardless of the acid species, such as hydrochloric acid, phosphoric acid, and acetic acid. These results indicate that the acidity defined in this work is an effective parameter to define and control the physicochemical properties of ChNFs. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural and physicochemical characterization of thermoplastic corn starch films containing microalgae.

PubMed

Fabra, María José; Martínez-Sanz, Marta; Gómez-Mascaraque, L G; Gavara, Rafael; López-Rubio, Amparo

2018-04-15

This work provides an in-depth analysis on how the addition of different microalgae species (Nannochloropsis, Spirulina and Scenedesmus) affected the structural and physicochemical properties of thermoplastic corn starch biocomposites. Structural characterization was conducted by combined SAXS/WAXS experiments and it was correlated with mechanical and barrier properties of the biocomposites. A water vapour permeability drop of ca. 54% was observed upon addition of the different microalgae species. The oxygen permeability and the mechanical properties of biocomposites containing Spirulina or Scenedesmus were not improved since the presence of microalgae hindered the re-arrangement and packing of the lamellar structure of starch polymeric chains, according to the SAXS results. Nannochloropsis caused a great reduction of the matrix rigidity and, the oxygen permeability was also improved. Therefore, all of these features make the Nannochloropsis biocomposites an alternative to generate biodegradable food packaging materials with the additional advantage that they can be easily scaled-up. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physicochemical evolution during rice straw and coal co-pyrolysis and its effect on co-gasification reactivity.

PubMed

Wei, Juntao; Gong, Yan; Guo, Qinghua; Ding, Lu; Wang, Fuchen; Yu, Guangsuo

2017-03-01

Physicochemical evolution (i.e. pore structure variation, carbon structure change and active AAEM transformation) during rice straw (RS) and Shenfu bituminous coal (SF) co-pyrolysis was quantitatively determined in this work. Moreover, the corresponding char gasification was conducted using a thermogravimetric analyzer (TGA) and relative reactivity was proposed to quantify the co-pyrolysis impact on co-gasification reactivity. The results showed that the development of pore structure in co-pyrolyzed chars was first inhibited and then enhanced with the decrease of SF proportion. The promotion effect of co-pyrolysis on order degree of co-pyrolyzed chars gradually weakened with increasing RS proportion. Co-pyrolysis mainly enhanced active K transformation in co-pyrolyzed chars and the promotion effect was alleviated with increasing RS proportion. The inhibition effect of co-pyrolysis on co-gasification reactivity weakened with increasing RS proportion and gasification temperature, which was mainly attributed to the combination of carbon structure evolution and active AAEM transformation in co-pyrolysis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis and physicochemical characterizations and antimicrobial activity of ZnO nanoparticles

NASA Astrophysics Data System (ADS)

Sharma, Bhumika K.; Patel, Kinjal; Roy, Debesh R.

2018-05-01

Nanoparticles exhibit very interesting and useful physicochemical properties when they interact with substrates and goes through some physicochemical and/or biological processes. ZnO is known to be a highly demanding nanomaterial due to its discreet properties, shapes and sizes. A detail experimental study on the synthesis, characterization and antibacterial activity of ZnO nanoparticles (NPs) is performed. ZnO NPs are synthesized using chemical precipitation method. The understanding of crystal structure, morphology and elemental compositions are explained using Powder X-Ray Diffraction (XRD) and Field Emission Scanning Electron Microscope (FE-SEM) respectively. Fourier transform infrared spectroscopy (FTIR) is performed to achieve the information on the presence of various functional groups. The antibacterial activity of these ZnO NPs is investigated in terms of Zone of Inhibition (ZOI) against Escherichia coli (Gram negative) microorganisms.

Physico-chemical characteristics of ZnO nanoparticles-based discs and toxic effect on human cervical cancer HeLa cells

NASA Astrophysics Data System (ADS)

Sirelkhatim, Amna; Mahmud, Shahrom; Seeni, Azman; Kaus, Noor Haida Mohd.; Sendi, Rabab

2014-10-01

In this study, we investigated physico-chemical properties of zinc oxide nanoparticles (ZnO NPs)-based discs and their toxicity on human cervical cancer HeLa cell lines. ZnO NPs (80 nm) were produced by the conventional ceramic processing method. FESEM analysis indicated dominant structure of nanorods with dimensions 100-500 nm in length, and 20-100 nm in diameter. The high content of ZnO nanorods in the discs probably played significant role in toxicity towards HeLa cells. Structural defects (oxygen vacancies and zinc/oxygen interstitials) were revealed by PL spectra peaks at 370-376 nm and 519-533 nm for the ZnO discs. The structural, optical and electrical properties of prepared sample have influenced the toxicological effects of ZnO discs towards HeLa cell lines via the generation of reactive oxygen species (ROS), internalization, membrane damage, and eventually cell death. The larger surface to volume area of the ZnO nanorods, combined with defects, stimulated enhanced toxicity via ROS generation hydrogen peroxide, hydroxyl radicals, and superoxide anion. The preliminary results confirmed the ZnO-disc toxicity on HeLa cells was significantly associated with the unique physicochemical properties of ZnO NPs and to our knowledge, this is the first cellular study for treatment of HeLa cells with ZnO discs made from 80 nm ZnO particles.

Evaluation of the structural, physicochemical, and biological characteristics of SB4, a biosimilar of etanercept

PubMed Central

Cho, Ick Hyun; Lee, Nayoung; Song, Dami; Jung, Seong Young; Bou-Assaf, George; Sosic, Zoran; Zhang, Wei; Lyubarskaya, Yelena

2016-01-01

ABSTRACT A biosimilar is a biological medicinal product that is comparable to a reference medicinal product in terms of quality, safety, and efficacy. SB4 was developed as a biosimilar to Enbrel® (etanercept) and was approved as Benepali®, the first biosimilar of etanercept licensed in the European Union (EU). The quality assessment of SB4 was performed in accordance with the ICH comparability guideline and the biosimilar guidelines of the European Medicines Agency and Food and Drug Administration. Extensive structural, physicochemical, and biological testing was performed with state-of-the-art technologies during a side-by-side comparison of the products. Similarity of critical quality attributes (CQAs) was evaluated on the basis of tolerance intervals established from quality data obtained from more than 60 lots of EU-sourced and US-sourced etanercept. Additional quality assessment was focused on a detailed investigation of immunogenicity-related quality attributes, including hydrophobic variants, high-molecular-weight (HMW) species, N-glycolylneuraminic acid (NGNA), and α-1,3-galactose. This comprehensive characterization study demonstrated that SB4 is highly similar to the reference product, Enbrel®, in structural, physicochemical, and biological quality attributes. In addition, the levels of potential immunogenicity-related quality attributes of SB4 such as hydrophobic variants, HMW aggregates, and α-1,3-galactose were less than those of the reference product. PMID:27246928

Self-organized structures in a superorganism: do ants “behave” like molecules?

NASA Astrophysics Data System (ADS)

Detrain, Claire; Deneubourg, Jean-Louis

2006-09-01

While the striking structures (e.g. nest architecture, trail networks) of insect societies may seem familiar to many of us, the understanding of pattern formation still constitutes a challenging problem. Over the last two decades, self-organization has dramatically changed our view on how collective decision-making and structures may emerge out of a population of ant workers having each their own individuality as well as a limited access to information. A variety of collective behaviour spontaneously outcome from multiple interactions between nestmates, even when there is no directing influence imposed by an external template, a pacemaker or a leader. By focussing this review on foraging structures, we show that ant societies display some properties which are usually considered in physico-chemical systems, as typical signatures of self-organization. We detail the key role played by feed-back loops, fluctuations, number of interacting units and sensitivity to environmental factors in the emergence of a structured collective behaviour. Nonetheless, going beyond simple analogies with non-living self-organized patterns, we stress on the specificities of social structures made of complex living units of which the biological features have been selected throughout the evolution depending on their adaptive value. In particular, we consider the ability of each ant individual to process information about environmental and social parameters, to accordingly tune its interactions with nestmates and ultimately to determine the final pattern emerging at the collective level. We emphasize on the parsimony and simplicity of behavioural rules at the individual level which allow an efficient processing of information, energy and matter within the whole colony.

The influence of water on the physicochemical characteristics of 1-butyl-3-methylimidazolium bromide ionic liquid

NASA Astrophysics Data System (ADS)

Ramenskaya, L. M.; Grishina, E. P.; Pimenova, A. M.; Gruzdev, M. S.

2008-07-01

A modified synthesis of 1-butyl-3-methylimidazolium bromide (BMImBr) was suggested and performed, and some physicochemical properties of the product containing 0.64 13.6 wt % water were determined. Water increased the electrical conductivity and decreased the viscosity and melting point of the substance but weakly influenced its density. Water in amounts of 5 8 wt % (45 50 mol %) caused structural changes. The BMImBr · 0.5H2O crystal hydrate was found to be stable thermodynamically.

Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

PubMed Central

Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

2016-01-01

This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

Acoustic characterisation of liquid foams with an impedance tube.

PubMed

Pierre, Juliette; Guillermic, Reine-Marie; Elias, Florence; Drenckhan, Wiebke; Leroy, Valentin

2013-10-01

Acoustic measurements provide convenient non-invasive means for the characterisation of materials. We show here for the first time how a commercial impedance tube can be used to provide accurate measurements of the velocity and attenuation of acoustic waves in liquid foams, as well as their effective "acoustic" density, over the 0.5-6kHz frequency range. We demonstrate this using two types of liquid foams: a commercial shaving foam and "home-made" foams with well-controlled physico-chemical and structural properties. The sound velocity in the latter foams is found to be independent of the bubble size distribution and is very well described by Wood's law. This implies that the impedance technique may be a convenient way to measure in situ the density of liquid foams. Important questions remain concerning the acoustic attenuation, which is found to be influenced in a currently unpredictible manner by the physico-chemical composition and the bubble size distribution of the characterised foams. We confirm differences in sound velocities in the two types of foams (having the same structural properties) which suggests that the physico-chemical composition of liquid foams has a non-negligible effect on their acoustic properties.

Physicochemical and microbiological effects of long- and short-term winery wastewater application to soils.

PubMed

Mosse, K P M; Patti, A F; Smernik, R J; Christen, E W; Cavagnaro, T R

2012-01-30

Application of winery wastewaters to soils for irrigation of various crops or landscapes is a common practice in the wine industry. In this study, we sought to investigate the effects of this practice, by comparing the physicochemical and microbiological soil properties in paired sites that differed in having had a history of winery waste application or not. We also compared the effects of a single application of untreated winery wastewater, to application of treated winery wastewater (sequencing batch reactor) and pure water to eliminate the effects of wetting alone. Long-term application of winery wastes was found to have significant impacts on soil microbial community structure, as determined by phospholipid fatty acid analysis, as well as on many physicochemical properties including pH, EC, and cation concentrations. (13)C NMR revealed only slight differences in the nature of the carbon present at each of the paired sites. A single application of untreated winery wastewater was shown to have significant impacts upon soil respiration, nitrogen cycling and microbial community structure, but the treated wastewater application showed no significant differences to wetting alone. Results are discussed in the context of sustainable winery wastewater disposal. Copyright © 2011 Elsevier B.V. All rights reserved.

Methods for Estimating Physicochemical Properties of Inorganic Chemicals of Environmental Concern. Volume 1

DTIC Science & Technology

1987-03-01

available. Kincaid et al. (221 provide an overview of the geochemical code history (up to 1983) in which they group models into four major families...plant. The *Ixample is adapted from a study by Morel ,’t al. 1291 for Los Angeles County. It is prv.ented in four ;ections: I ’ Problem statement, ý2...presents environmentally important priperty dJata for several groups of elements or compcui’ds. The data include, for Pxrimpie, precal- culated

Pollutants degradation performance and microbial community structure of aerobic granular sludge systems using inoculums adapted at mild and low temperature.

PubMed

Muñoz-Palazon, Barbara; Pesciaroli, Chiara; Rodriguez-Sanchez, Alejandro; Gonzalez-Lopez, Jesús; Gonzalez-Martinez, Alejandro

2018-08-01

Three aerobic granular sequencing batch reactors were inoculated using different inocula from Finland, Spain and a mix of both in order to investigate the effect over the degradation performance and the microbial community structure. The Finnish inoculum achieved a faster granulation and a higher depollution performance within the first two month of operation. However, after 90 days of operation, similar physico-chemical values were observed. On the other hand, the Real-time PCR showed that Archaea diminished from inoculum to granular biomass, while Bacteria and Fungi numbers remained stable. All granular biomass massive parallel sequencing studies were similar regardless of the inocula from which they formed, as confirmed by singular value decomposition principal coordinates analysis, expected effect size of OTUs, and β-diversity analyses. Thermoproteaceae, Meganema and a Trischosporonaceae members were the dominant phylotypes for the three domains studied. The analysis of oligotype distribution demonstrated that a fungal oligotype was ubiquitous. The dominant OTUs of Bacteria were correlated with bioreactors performance. The results obtained determined that the microbial community structure of aerobic granular sludge was similar regardless of their inocula, showing that the granulation of biomass is related to several phylotypes. This will be of future importance for the implementation of aerobic granular sludge to full-scale systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physicochemical Parameters Affecting the Electrospray Ionization Efficiency of Amino Acids after Acylation

PubMed Central

2017-01-01

Electrospray ionization (ESI) is widely used in liquid chromatography coupled to mass spectrometry (LC–MS) for the analysis of biomolecules. However, the ESI process is still not completely understood, and it is often a matter of trial and error to enhance ESI efficiency and, hence, the response of a given set of compounds. In this work we performed a systematic study of the ESI response of 14 amino acids that were acylated with organic acid anhydrides of increasing chain length and with poly(ethylene glycol) (PEG) changing certain physicochemical properties in a predictable manner. By comparing the ESI response of 70 derivatives, we found that there was a strong correlation between the calculated molecular volume and the ESI response, while correlation with hydrophobicity (log P values), pKa, and the inverse calculated surface tension was significantly lower although still present, especially for individual derivatized amino acids with increasing acyl chain lengths. Acylation with PEG containing five ethylene glycol units led to the largest gain in ESI response. This response was maximal independent of the calculated physicochemical properties or the type of amino acid. Since no actual physicochemical data is available for most derivatized compounds, the responses were also used as input for a quantitative structure–property relationship (QSPR) model to find the best physicochemical descriptors relating to the ESI response from molecular structures using the amino acids and their derivatives as a reference set. A topological descriptor related to molecular size (SPAN) was isolated next to a descriptor related to the atomic composition and structural groups (BIC0). The validity of the model was checked with a test set of 43 additional compounds that were unrelated to amino acids. While prediction was generally good (R2 > 0.9), compounds containing halogen atoms or nitro groups gave a lower predicted ESI response. PMID:28737384

Structural diversity, physicochemical properties and application of imidazolium surfactants: Recent advances.

PubMed

Bhadani, Avinash; Misono, Takeshi; Singh, Sukhprit; Sakai, Kenichi; Sakai, Hideki; Abe, Masahiko

2016-05-01

The current review covers recent advances on development and investigation of cationic surfactants containing imidazolium headgroup, which are being extensively investigated for their self-aggregation properties and are currently being utilized in various conventional and non-conventional application areas. These surfactants are being used as: soft template for synthesis of mesoporous/microporous materials, drug and gene delivery agent, stabilizing agent for nanoparticles, dispersants for single/multi walled carbon nanotubes, antimicrobial and antifungal agent, viscosity modifiers, preparing nanocomposite materials, stabilizing microemulsions, corrosion inhibitors and catalyst for organic reactions. Recently several structural derivatives of these surfactants have been developed having many interesting physicochemical properties and they have demonstrated enormous potential in the area of nanotechnology, material science and biomedical science. Copyright © 2016 Elsevier B.V. All rights reserved.

Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates.

PubMed

Sun, J-T; Jin, P-Y; Hoffmann, A A; Duan, X-Z; Dai, J; Hu, G; Xue, X-F; Hong, X-Y

2018-05-24

There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitochondrial genome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species, which distribute across different climates. We sequenced 26 complete mitogenomes of T. truncatus which occurs in both warm and cold regions, and 9 complete mitogenomes of T. pueraricola which is only restricted in warm regions. Patterns of evolution in the two species mitogenomes were compared through a series of d N /d S methods and physicochemical profiles of amino acid replacements. We found that (1) the mitogenomes of both species were under widespread purifying selection. (2) Elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus. (3) The strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation. This article is protected by copyright. All rights reserved. © 2018 The Royal Entomological Society.

Climate change impacts on marine water quality: The case study of the Northern Adriatic sea.

PubMed

Rizzi, J; Torresan, S; Critto, A; Zabeo, A; Brigolin, D; Carniel, S; Pastres, R; Marcomini, A

2016-01-30

Climate change is posing additional pressures on coastal ecosystems due to variations in water biogeochemical and physico-chemical parameters (e.g., pH, salinity) leading to aquatic ecosystem degradation. With the main aim of analyzing the potential impacts of climate change on marine water quality, a Regional Risk Assessment methodology was developed and applied to coastal marine waters of the North Adriatic. It integrates the outputs of regional biogeochemical and physico-chemical models considering future climate change scenarios (i.e., years 2070 and 2100) with site-specific environmental and socio-economic indicators. Results showed that salinity and temperature will be the main drivers of changes, together with macronutrients, especially in the area of the Po' river delta. The final outputs are exposure, susceptibility and risk maps supporting the communication of the potential consequences of climate change on water quality to decision makers and stakeholders and provide a basis for the definition of adaptation and management strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Oil-structuring characterization of natural waxes in canola oil oleogels: Rheological, thermal, and oxidative properties

USDA-ARS?s Scientific Manuscript database

Natural waxes (candelilla wax, carnauba wax, and beeswax) were utilized as canola oil structurants to produce oleogels and their physicochemical properties were evaluated from rheological, thermal, and oxidative points of view. The oleogels with candelilla wax exhibited the highest hardness, followe...

Active membrane having uniform physico-chemically functionalized ion channels

DOEpatents

Gerald, II, Rex E; Ruscic, Katarina J; Sears, Devin N; Smith, Luis J; Klingler, Robert J; Rathke, Jerome W

2012-09-24

The present invention relates to a physicochemically-active porous membrane for electrochemical cells that purports dual functions: an electronic insulator (separator) and a unidirectional ion-transporter (electrolyte). The electrochemical cell membrane is activated for the transport of ions by contiguous ion coordination sites on the interior two-dimensional surfaces of the trans-membrane unidirectional pores. One dimension of the pore surface has a macroscopic length (1 nm-1000 .mu.m) and is directed parallel to the direction of an electric field, which is produced between the cathode and the anode electrodes of an electrochemical cell. The membrane material is designed to have physicochemical interaction with ions. Control of the extent of the interactions between the ions and the interior pore walls of the membrane and other materials, chemicals, or structures contained within the pores provides adjustability of the ionic conductivity of the membrane.

Effect of Microwave Irradiation on the Physicochemical and Digestive Properties of Lotus Seed Starch.

PubMed

Zeng, Shaoxiao; Chen, Bingyan; Zeng, Hongliang; Guo, Zebin; Lu, Xu; Zhang, Yi; Zheng, Baodong

2016-03-30

The objective of this study is to investigate the effect of microwave irradiation on the physicochemical and digestive properties of lotus seed starch. The physicochemical properties of lotus seed starch were characterized by light microscopy, (1)H NMR, FT-IR spectroscopy, and HPSEC-MALLS-RI. The starch-water interaction and crystalline region increased due to the changed water distribution of starch granules and the increase of the double-helix structure. The swelling power, amylose leaching, molecular properties, and radius of gyration reduced with the increasing microwave power, which further affected the sensitivity of lotus seed starch to enzymatic degradation. Furthermore, the resistant starch and slowly digestible starch increased with the increasing microwave irradiation, which further resulted in their decreasing hydrolysis index and glycemic index. The digestive properties of lotus seed starch were mainly influenced by the reduced branching degree of amylopectin and the strong amylose-amylose interaction.

Physicochemical characterization of mineral (iron/zinc) bound caseinate and their mineral uptake in Caco-2 cells.

PubMed

Shilpashree, B G; Arora, Sumit; Kapila, Suman; Sharma, Vivek

2018-08-15

Milk proteins (especially caseins) are widely accepted as good vehicle for the delivery of various bioactive compounds including minerals. Succinylation is one of the most acceptable chemical modification techniques to enhance the mineral binding ability of caseins. Addition of minerals to succinylated proteins may alter their physicochemical and biochemical properties. Physicochemical characteristics of succinylated sodium caseinate (S.NaCN)-mineral (iron/zinc) complexes were elucidated. Chromatographic behaviour and fluorescence intensity confirmed the structural modification of S.NaCN upon binding with minerals. The bound mineral from protein complexes showed significantly higher (P < 0.05) in vitro bioavailability (mineral uptake) than mineral salts in Caco-2 cells. Also, iron bound S.NaCN showed higher cellular ferritin formation than iron in its free form. These mineral bound protein complexes with improved bioavailability could safely replace inorganic fortificants in various functional food formulations. Copyright © 2018 Elsevier Ltd. All rights reserved.

Sorption and biodegradation of organic micropollutants during river bank filtration: a laboratory column study.

PubMed

Bertelkamp, C; Reungoat, J; Cornelissen, E R; Singhal, N; Reynisson, J; Cabo, A J; van der Hoek, J P; Verliefde, A R D

2014-04-01

This study investigated sorption and biodegradation behaviour of 14 organic micropollutants (OMP) in soil columns representative of the first metre (oxic conditions) of the river bank filtration (RBF) process. Breakthrough curves were modelled to differentiate between OMP sorption and biodegradation. The main objective of this study was to investigate if the OMP biodegradation rate could be related to the physico-chemical properties (charge, hydrophobicity and molecular weight) or functional groups of the OMPs. Although trends were observed between charge or hydrophobicity and the biodegradation rate for charged compounds, a statistically significant linear relationship for the complete OMP mixture could not be obtained using these physico-chemical properties. However, a statistically significant relationship was obtained between biological degradation rates and the OMP functional groups. The presence of ethers and carbonyl groups will increase biodegradability, while the presence of amines, ring structures, aliphatic ethers and sulphur will decrease biodegradability. This predictive model based on functional groups can be used by drinking water companies to make a first estimate whether a newly detected compound will be biodegraded during the first metre of RBF or that additional treatment is required. In addition, the influence of active and inactive biomass (biosorption), sand grains and the water matrix on OMP sorption was found to be negligible under the conditions investigated in this study. Retardation factors for most compounds were close to 1, indicating mobile behaviour of these compounds during soil passage. Adaptation of the biomass towards the dosed OMPs was not observed for a 6 month period, implying that new developed RBF sites might not be able to biodegrade compounds such as atrazine and sulfamethoxazole in the first few months of operation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bitter or not? BitterPredict, a tool for predicting taste from chemical structure.

PubMed

Dagan-Wiener, Ayana; Nissim, Ido; Ben Abu, Natalie; Borgonovo, Gigliola; Bassoli, Angela; Niv, Masha Y

2017-09-21

Bitter taste is an innately aversive taste modality that is considered to protect animals from consuming toxic compounds. Yet, bitterness is not always noxious and some bitter compounds have beneficial effects on health. Hundreds of bitter compounds were reported (and are accessible via the BitterDB http://bitterdb.agri.huji.ac.il/dbbitter.php ), but numerous additional bitter molecules are still unknown. The dramatic chemical diversity of bitterants makes bitterness prediction a difficult task. Here we present a machine learning classifier, BitterPredict, which predicts whether a compound is bitter or not, based on its chemical structure. BitterDB was used as the positive set, and non-bitter molecules were gathered from literature to create the negative set. Adaptive Boosting (AdaBoost), based on decision trees machine-learning algorithm was applied to molecules that were represented using physicochemical and ADME/Tox descriptors. BitterPredict correctly classifies over 80% of the compounds in the hold-out test set, and 70-90% of the compounds in three independent external sets and in sensory test validation, providing a quick and reliable tool for classifying large sets of compounds into bitter and non-bitter groups. BitterPredict suggests that about 40% of random molecules, and a large portion (66%) of clinical and experimental drugs, and of natural products (77%) are bitter.

Microbial examination of anaerobic sludge adaptation to animal slurry.

PubMed

Moset, V; Cerisuelo, A; Ferrer, P; Jimenez, A; Bertolini, E; Cambra-López, M

2014-01-01

The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

Multiple-step preparation and physicochemical characterization of crystalline α-germanium hydrogenphosphate

NASA Astrophysics Data System (ADS)

Romano, Ricardo; Ruiz, Ana I.; Alves, Oswaldo L.

2004-04-01

The reaction between germanium oxide and phosphoric acid has previously been described and led to impure germanium hydrogenphosphate samples with low crystallinity. A new multiple-step route involving the same reaction under refluxing and soft hydrothermal conditions is described for the preparation of pure and crystalline α-GeP. The physicochemical characterization of the samples allows accompaniment of the reaction evolution as well as determining short- and long-range structural organization. The phase purity of the α-GeP sample was confirmed by applying Rietveld's profile analysis, which also determined the cell parameters of its crystals.

A model for homeopathic remedy effects: low dose nanoparticles, allostatic cross-adaptation, and time-dependent sensitization in a complex adaptive system

PubMed Central

2012-01-01

Background This paper proposes a novel model for homeopathic remedy action on living systems. Research indicates that homeopathic remedies (a) contain measurable source and silica nanoparticles heterogeneously dispersed in colloidal solution; (b) act by modulating biological function of the allostatic stress response network (c) evoke biphasic actions on living systems via organism-dependent adaptive and endogenously amplified effects; (d) improve systemic resilience. Discussion The proposed active components of homeopathic remedies are nanoparticles of source substance in water-based colloidal solution, not bulk-form drugs. Nanoparticles have unique biological and physico-chemical properties, including increased catalytic reactivity, protein and DNA adsorption, bioavailability, dose-sparing, electromagnetic, and quantum effects different from bulk-form materials. Trituration and/or liquid succussions during classical remedy preparation create “top-down” nanostructures. Plants can biosynthesize remedy-templated silica nanostructures. Nanoparticles stimulate hormesis, a beneficial low-dose adaptive response. Homeopathic remedies prescribed in low doses spaced intermittently over time act as biological signals that stimulate the organism’s allostatic biological stress response network, evoking nonlinear modulatory, self-organizing change. Potential mechanisms include time-dependent sensitization (TDS), a type of adaptive plasticity/metaplasticity involving progressive amplification of host responses, which reverse direction and oscillate at physiological limits. To mobilize hormesis and TDS, the remedy must be appraised as a salient, but low level, novel threat, stressor, or homeostatic disruption for the whole organism. Silica nanoparticles adsorb remedy source and amplify effects. Properly-timed remedy dosing elicits disease-primed compensatory reversal in direction of maladaptive dynamics of the allostatic network, thus promoting resilience and recovery from disease. Summary Homeopathic remedies are proposed as source nanoparticles that mobilize hormesis and time-dependent sensitization via non-pharmacological effects on specific biological adaptive and amplification mechanisms. The nanoparticle nature of remedies would distinguish them from conventional bulk drugs in structure, morphology, and functional properties. Outcomes would depend upon the ability of the organism to respond to the remedy as a novel stressor or heterotypic biological threat, initiating reversals of cumulative, cross-adapted biological maladaptations underlying disease in the allostatic stress response network. Systemic resilience would improve. This model provides a foundation for theory-driven research on the role of nanomaterials in living systems, mechanisms of homeopathic remedy actions and translational uses in nanomedicine. PMID:23088629

A model for homeopathic remedy effects: low dose nanoparticles, allostatic cross-adaptation, and time-dependent sensitization in a complex adaptive system.

PubMed

Bell, Iris R; Koithan, Mary

2012-10-22

This paper proposes a novel model for homeopathic remedy action on living systems. Research indicates that homeopathic remedies (a) contain measurable source and silica nanoparticles heterogeneously dispersed in colloidal solution; (b) act by modulating biological function of the allostatic stress response network (c) evoke biphasic actions on living systems via organism-dependent adaptive and endogenously amplified effects; (d) improve systemic resilience. The proposed active components of homeopathic remedies are nanoparticles of source substance in water-based colloidal solution, not bulk-form drugs. Nanoparticles have unique biological and physico-chemical properties, including increased catalytic reactivity, protein and DNA adsorption, bioavailability, dose-sparing, electromagnetic, and quantum effects different from bulk-form materials. Trituration and/or liquid succussions during classical remedy preparation create "top-down" nanostructures. Plants can biosynthesize remedy-templated silica nanostructures. Nanoparticles stimulate hormesis, a beneficial low-dose adaptive response. Homeopathic remedies prescribed in low doses spaced intermittently over time act as biological signals that stimulate the organism's allostatic biological stress response network, evoking nonlinear modulatory, self-organizing change. Potential mechanisms include time-dependent sensitization (TDS), a type of adaptive plasticity/metaplasticity involving progressive amplification of host responses, which reverse direction and oscillate at physiological limits. To mobilize hormesis and TDS, the remedy must be appraised as a salient, but low level, novel threat, stressor, or homeostatic disruption for the whole organism. Silica nanoparticles adsorb remedy source and amplify effects. Properly-timed remedy dosing elicits disease-primed compensatory reversal in direction of maladaptive dynamics of the allostatic network, thus promoting resilience and recovery from disease. Homeopathic remedies are proposed as source nanoparticles that mobilize hormesis and time-dependent sensitization via non-pharmacological effects on specific biological adaptive and amplification mechanisms. The nanoparticle nature of remedies would distinguish them from conventional bulk drugs in structure, morphology, and functional properties. Outcomes would depend upon the ability of the organism to respond to the remedy as a novel stressor or heterotypic biological threat, initiating reversals of cumulative, cross-adapted biological maladaptations underlying disease in the allostatic stress response network. Systemic resilience would improve. This model provides a foundation for theory-driven research on the role of nanomaterials in living systems, mechanisms of homeopathic remedy actions and translational uses in nanomedicine.

A combination of feature extraction methods with an ensemble of different classifiers for protein structural class prediction problem.

PubMed

Dehzangi, Abdollah; Paliwal, Kuldip; Sharma, Alok; Dehzangi, Omid; Sattar, Abdul

2013-01-01

Better understanding of structural class of a given protein reveals important information about its overall folding type and its domain. It can also be directly used to provide critical information on general tertiary structure of a protein which has a profound impact on protein function determination and drug design. Despite tremendous enhancements made by pattern recognition-based approaches to solve this problem, it still remains as an unsolved issue for bioinformatics that demands more attention and exploration. In this study, we propose a novel feature extraction model that incorporates physicochemical and evolutionary-based information simultaneously. We also propose overlapped segmented distribution and autocorrelation-based feature extraction methods to provide more local and global discriminatory information. The proposed feature extraction methods are explored for 15 most promising attributes that are selected from a wide range of physicochemical-based attributes. Finally, by applying an ensemble of different classifiers namely, Adaboost.M1, LogitBoost, naive Bayes, multilayer perceptron (MLP), and support vector machine (SVM) we show enhancement of the protein structural class prediction accuracy for four popular benchmarks.

The physico-chemical properties and structural characteristics of artificial soil for cut slope restoration in Southwestern China

PubMed Central

Chen, Shunan; Ai, Xiaoyan; Dong, Tengyun; Li, Binbin; Luo, Ruihong; Ai, Yingwei; Chen, Zhaoqiong; Li, Chuanren

2016-01-01

Cut slopes are frequently generated by construction work in hilly areas, and artificial soil is often sprayed onto them to promote ecological rehabilitation. The artificial soil properties are very important for effective management of the slopes. This paper uses fractal and moment methods to characterize soil particle size distribution (PSD) and aggregates composition. The fractal dimension (D) showed linear relationships between clay, silt, and sand contents, with coefficients of determination from 0.843 to 0.875, suggesting that using of D to evaluate the PSD of artificial soils is reasonable. The bias (CS) and peak convex (CE) coefficients showed significant correlations with structure failure rate, moisture content, and total porosity, which validated the moment method to quantitatively describe soil structure. Railway slope (RS) soil has lower organic carbon and soil moisture, and higher pH than natural slope soil. Overall, RS exhibited poor soil structure and physicochemical properties, increasing the risk of soil erosion. Hence, more effective management measures should be adopted to promote the restoration of cut slopes. PMID:26883986

Silver-induced reconstruction of an adeninate-based metal–organic framework for encapsulation of luminescent adenine-stabilized silver clusters† †Electronic supplementary information (ESI) available: Experimental details and additional structural, physicochemical and optical characterisation. See DOI: 10.1039/c6tc00260a Click here for additional data file.

PubMed Central

Jonckheere, Dries; Coutino-Gonzalez, Eduardo; Baekelant, Wouter; Bueken, Bart; Reinsch, Helge; Stassen, Ivo; Fenwick, Oliver; Richard, Fanny; Samorì, Paolo; Ameloot, Rob; Hofkens, Johan

2016-01-01

Bright luminescent silver-adenine species were successfully stabilized in the pores of the MOF-69A (zinc biphenyldicarboxylate) metal–organic framework, starting from the intrinsically blue luminescent bio-MOF-1 (zinc adeninate 4,4′-biphenyldicarboxylate). Bio-MOF-1 is transformed to the MOF-69A framework by selectively leaching structural adenine linkers from the original framework using silver nitrate solutions in aqueous ethanol. Simultaneously, bright blue-green luminescent silver-adenine clusters are formed inside the pores of the recrystallized MOF-69A matrix in high local concentrations. The structural transition and concurrent changes in optical properties were characterized using a range of structural, physicochemical and spectroscopic techniques (steady-state and time-resolved luminescence, quantum yield determination, fluorescence microscopy). The presented results open new avenues for exploring the use of MOFs containing luminescent silver clusters for solid-state lighting and sensor applications. PMID:28496980

PHYSICOCHEMICAL PROPERTY CALCULATIONS

EPA Science Inventory

Computer models have been developed to estimate a wide range of physical-chemical properties from molecular structure. The SPARC modeling system approaches calculations as site specific reactions (pKa, hydrolysis, hydration) and `whole molecule' properties (vapor pressure, boilin...

Effect of High-Pressure Treatment on Catalytic and Physicochemical Properties of Pepsin.

PubMed

Wang, Jianan; Bai, Tenghui; Ma, Yaping; Ma, Hanjun

2017-10-11

For a long time, high-pressure treatment has been used to destroy the compact structures of natural proteins in order to promote subsequent enzymatic hydrolysis. However, there are few reports evaluating the feasibility of directly improving the catalytic capability of proteases by using high-pressure treatments. In this study, the effects of high-pressure treatment on the catalytic capacity and structure of pepsin were investigated, and the relationship between its catalytic properties and changes in its physicochemical properties was explored. It was found that high-pressure treatment could lead to changes of the sulfhydryl group/disulfide bond content, hydrophobicity, hydrodynamic radius, intrinsic viscosity, and subunit composition of pepsin, and the conformational change of pepsin resulted in improvement to its enzymatic activity and hydrolysis efficiency, which had an obvious relationship with the high-pressure treatment conditions.

Microwave Assisted Synthesis, Physicochemical, Photophysical, Single Crystal X-ray and DFT Studies of Novel Push-Pull Chromophores.

PubMed

Khan, Salman A; Asiri, Abdullah M; Basisi, Hadi Mussa; Arshad, Muhammad Nadeem; Sharma, Kamlesh

2015-11-01

Two push-pull chromophores were synthesized by knoevenagel condensation under microwave irradiation. The structure of synthesized chromophores were established by spectroscopic (FT-IR, (1)H NMR, (13)C NMR, EI-MS) and elemental analysis. Structure of the chromophores was further conformed by X-ray crystallographic. UV-Vis and fluorescence spectroscopy measurements provided that chromophores were good absorbent and fluorescent properties. Fluorescence polarity studies demonstrated that chromophores were sensitive to the polarity of the microenvironment provided by different solvents. Physicochemical parameters, including singlet absorption, extinction coefficient, stokes shift, oscillator strength, dipole moment and flurescence quantum yield were investigated in order to explore the analytical potential of the synthesized chromophores. In addition, the total energy, frontier molecular orbitals, hardness, electron affinity, ionization energy, electrostatic potential map were also studied computationally by using density functional theoretical method.

Physicochemical characterization of ezetimibe and its impurities

NASA Astrophysics Data System (ADS)

Filip, Katarzyna; Bańkowski, Krzysztof; Sidoryk, Katarzyna; Zagrodzka, Joanna; Łaszcz, Marta; Trzcińska, Kinga; Szyprowska, Anna; Cmoch, Piotr; Maruszak, Wioleta

2011-04-01

The physicochemical characterization of major degradation and process-related impurities associated with the synthesis of ezetimibe was performed. The possibility of forming the undesirable ( R, R, S) stereoisomer of ezetimibe has been mentioned in literature (Vinod KK, Suhail A, Bhupendra T, Nitin G US 2010/0010212 A1, Ind-Swift Laboratories Limited WO 2008/096372), but no study of its structure determination has been published yet. This paper discusses the structure elucidation of the ( R, R, S) stereoisomer as well as ezetimibe degradation product on the bases of NMR, IR and MS data. Other potential impurities of ezetimibe are also described. A selective and stability-indicating high-performance liquid chromatography method with dual UV detection was developed for the determination of chemical and stereochemical purity of ezetimibe. The characterization of particle size and shape for ezetimibe and its stereoisomer is also described.

The Arctic Soil Bacterial Communities in the Vicinity of a Little Auk Colony

PubMed Central

Zielińska, Sylwia; Kidawa, Dorota; Stempniewicz, Lech; Łoś, Marcin; Łoś, Joanna M.

2016-01-01

Due to deposition of birds' guano, eggshells or feathers, the vicinity of a large seabirds' breeding colony is expected to have a substantial impact on the soil's physicochemical features as well as on diversity of vegetation and the soil invertebrates. Consequently, due to changing physicochemical features the structure of bacterial communities might fluctuate in different soil environments. The aim of this study was to investigate the bacterial assemblages in the Arctic soil within the area of a birds' colony and in a control sample from a topographically similar location but situated away from the colony's impact area. A high number of OTUs found in both areas indicates a highly complex microbial populations structure. The most abundant phyla in both of the tested samples were: Proteobacteria, Acidobacteria, Actinobacteria, and Chloroflexi, with different proportions in the total share. Despite differences in the physicochemical soil characteristics, the soil microbial community structures at the phylum level were similar to some extent in the two samples. The only share that was significantly higher in the control area when compared to the sample obtained within the birds' colony, belonged to the Actinobacteria phylum. Moreover, when analyzing the class level for each phylum, several differences between the samples were observed. Furthermore, lower proportions of Proteobacteria and Acidobacteria were observed in the soil sample under the influence of the bird's colony, which most probably could be linked to higher nitrogen concentrations in that sample. PMID:27667982

In vitro digestibility and physicochemical properties of milled rice.

PubMed

Dhital, Sushil; Dabit, Laura; Zhang, Bin; Flanagan, Bernadine; Shrestha, Ashok K

2015-04-01

Rice is a staple diet as well as a major ingredient in many processed foods. The physicochemical and supra-molecular structure of eight rice varieties with amylose content from 9% to 19% were studied to elucidate the factors responsible for variation in enzymatic digestibility of raw and cooked rice. Parboiled rice had a digestion rate coefficient almost 4.5 times higher than the least digestible Low GI rice. The rate coefficient was found to be independent of helical structure and long range molecular order, possibly attributed to the effect of rice flour architecture. Strong swelling and pasting behaviour and lower gelatinisation temperature were linked with apparently higher in vitro digestibility but the relationship was statistically insignificant. It is concluded that the enzymatic susceptibility of rice flours are independent of supra-molecular structure and are most likely controlled by external factors not limited to particle size, presence of intact cell wall and other non-starch polymers. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of citric acid esterification on digestibility, structural and physicochemical properties of cassava starch.

PubMed

Mei, Ji-Qiang; Zhou, Da-Nian; Jin, Zheng-Yu; Xu, Xue-Ming; Chen, Han-Qing

2015-11-15

In this study, citric acid was used to react with cassava starch in order to compare the digestibility, structural and physicochemical properties of citrate starch samples. The results indicated that citric acid esterification treatment significantly increased the content of resistant starch (RS) in starch samples. The swelling power and solubility of citrate starch samples were lower than those of native starch. Compared with native starch, a new peak at 1724 cm(-1) was appeared in all citrate starch samples, and crystalline peaks of all starch citrates became much smaller or even disappeared. Differential scanning calorimetry results indicated that the endothermic peak of citrate starches gradually shrank or even disappeared. Moreover, the citrate starch gels exhibited better freeze-thaw stability. These results suggested that citric acid esterification induced structural changes in cassava starch significantly affected its digestibility and it could be a potential method for the preparation of RS with thermal stability. Copyright © 2015 Elsevier Ltd. All rights reserved.

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

DOE PAGES

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi; ...

2016-12-30

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Physicochemical structural changes of cellulosic substrates during enzymatic saccharification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Xianzhi; Yoo, Chang Geun; Li, Mi

Enzymatic hydrolysis represents one of the major steps and barriers in the commercialization process of converting cellulosic substrates into biofuels and other value added products. It is usually achieved by a synergistic action of enzyme mixture typically consisting of multiple enzymes such as glucanase, cellobiohydrolase and β-glucosidase with different mode of actions. Due to the innate biomass recalcitrance, enzymatic hydrolysis normally starts with an initial fast rate of hydrolysis followed by a rapid decrease of rate toward the end of hydrolysis. With majority of literature studies focusing on the effect of key substrate characteristics on the initial rate or finalmore » yield of enzymatic hydrolysis, information about physicochemical structural changes of cellulosic substrates during enzymatic hydrolysis is still quite limited. Consequently, what slows down the reaction rate toward the end of hydrolysis is not well understood. Lastly, this review highlights recent advances in understanding the structural changes of cellulosic substrates during the hydrolysis process, to better understand the fundamental mechanisms of enzymatic hydrolysis.« less

Impact of amylosucrase modification on the structural and physicochemical properties of native and acid-thinned waxy corn starch.

PubMed

Zhang, Hao; Zhou, Xing; He, Jian; Wang, Tao; Luo, Xiaohu; Wang, Li; Wang, Ren; Chen, Zhengxing

2017-04-01

Recombinant amylosucrase from Neisseria polysaccharea was utilized to modify native and acid-thinned starches. The molecular structures and physicochemical properties of modified starches were investigated. Acid-thinned starch displayed much lower viscosity after gelatinization than did the native starch. However, the enzyme exhibited similar catalytic efficiency for both forms of starch. The modified starches had higher proportions of long (DP>33) and intermediate chains (DP 13-33), and X-ray diffraction showed a B-type crystalline structure for all modified starches. With increasing reaction time, the relative crystallinity and endothermic enthalpy of the modified starches gradually decreased, whereas the melting peak temperatures and resistant starch contents increased. Slight differences were observed in thermal parameters, relative crystallinity, and branch chain length distribution between the modified native and acid-thinned starches. Moreover, the digestibility of the modified starches was not affected by acid hydrolysis pretreatment, but was affected by the percentage of intermediate and long chains. Copyright © 2016 Elsevier Ltd. All rights reserved.

Investigating Pharmacological Similarity by Charting Chemical Space.

PubMed

Buonfiglio, Rosa; Engkvist, Ola; Várkonyi, Péter; Henz, Astrid; Vikeved, Elisabet; Backlund, Anders; Kogej, Thierry

2015-11-23

In this study, biologically relevant areas of the chemical space were analyzed using ChemGPS-NP. This application enables comparing groups of ligands within a multidimensional space based on principle components derived from physicochemical descriptors. Also, 3D visualization of the ChemGPS-NP global map can be used to conveniently evaluate bioactive compound similarity and visually distinguish between different types or groups of compounds. To further establish ChemGPS-NP as a method to accurately represent the chemical space, a comparison with structure-based fingerprint has been performed. Interesting complementarities between the two descriptions of molecules were observed. It has been shown that the accuracy of describing molecules with physicochemical descriptors like in ChemGPS-NP is similar to the accuracy of structural fingerprints in retrieving bioactive molecules. Lastly, pharmacological similarity of structurally diverse compounds has been investigated in ChemGPS-NP space. These results further strengthen the case of using ChemGPS-NP as a tool to explore and visualize chemical space.

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts

PubMed Central

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart EG; Robinson, Christopher T

2013-01-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning. PMID:23842653

Bacterial structures and ecosystem functions in glaciated floodplains: contemporary states and potential future shifts.

PubMed

Freimann, Remo; Bürgmann, Helmut; Findlay, Stuart E G; Robinson, Christopher T

2013-12-01

Glaciated alpine floodplains are responding quickly to climate change through shrinking ice masses. Given the expected future changes in their physicochemical environment, we anticipated variable shifts in structure and ecosystem functioning of hyporheic microbial communities in proglacial alpine streams, depending on present community characteristics and landscape structures. We examined microbial structure and functioning during different hydrologic periods in glacial (kryal) streams and, as contrasting systems, groundwater-fed (krenal) streams. Three catchments were chosen to cover an array of landscape features, including interconnected lakes, differences in local geology and degree of deglaciation. Community structure was assessed by automated ribosomal intergenic spacer analysis and microbial function by potential enzyme activities. We found each catchment to contain a distinct bacterial community structure and different degrees of separation in structure and functioning that were linked to the physicochemical properties of the waters within each catchment. Bacterial communities showed high functional plasticity, although achieved by different strategies in each system. Typical kryal communities showed a strong linkage of structure and function that indicated a major prevalence of specialists, whereas krenal sediments were dominated by generalists. With the rapid retreat of glaciers and therefore altered ecohydrological characteristics, lotic microbial structure and functioning are likely to change substantially in proglacial floodplains in the future. The trajectory of these changes will vary depending on contemporary bacterial community characteristics and landscape structures that ultimately determine the sustainability of ecosystem functioning.

[Regression analysis to select native-like structures from decoys of antigen-antibody docking].

PubMed

Chen, Zhengshan; Chi, Xiangyang; Fan, Pengfei; Zhang, Guanying; Wang, Meirong; Yu, Changming; Chen, Wei

2018-06-25

Given the increasing exploitation of antibodies in different contexts such as molecular diagnostics and therapeutics, it would be beneficial to unravel properties of antigen-antibody interaction with modeling of computational protein-protein docking, especially, in the absence of a cocrystal structure. However, obtaining a native-like antigen-antibody structure remains challenging due in part to failing to reliably discriminate accurate from inaccurate structures among tens of thousands of decoys after computational docking with existing scoring function. We hypothesized that some important physicochemical and energetic features could be used to describe antigen-antibody interfaces and identify native-like antigen-antibody structure. We prepared a dataset, a subset of Protein-Protein Docking Benchmark Version 4.0, comprising 37 nonredundant 3D structures of antigen-antibody complexes, and used it to train and test multivariate logistic regression equation which took several important physicochemical and energetic features of decoys as dependent variables. Our results indicate that the ability to identify native-like structures of our method is superior to ZRANK and ZDOCK score for the subset of antigen-antibody complexes. And then, we use our method in workflow of predicting epitope of anti-Ebola glycoprotein monoclonal antibody-4G7 and identify three accurate residues in its epitope.

An Invitation to Open Innovation in Malaria Drug Discovery: 47 Quality Starting Points from the TCAMS.

PubMed

Calderón, Félix; Barros, David; Bueno, José María; Coterón, José Miguel; Fernández, Esther; Gamo, Francisco Javier; Lavandera, José Luís; León, María Luisa; Macdonald, Simon J F; Mallo, Araceli; Manzano, Pilar; Porras, Esther; Fiandor, José María; Castro, Julia

2011-10-13

In 2010, GlaxoSmithKline published the structures of 13533 chemical starting points for antimalarial lead identification. By using an agglomerative structural clustering technique followed by computational filters such as antimalarial activity, physicochemical properties, and dissimilarity to known antimalarial structures, we have identified 47 starting points for lead optimization. Their structures are provided. We invite potential collaborators to work with us to discover new clinical candidates.

Predicting Cell Association of Surface-Modified Nanoparticles Using Protein Corona Structure - Activity Relationships (PCSAR).

PubMed

Kamath, Padmaja; Fernandez, Alberto; Giralt, Francesc; Rallo, Robert

2015-01-01

Nanoparticles are likely to interact in real-case application scenarios with mixtures of proteins and biomolecules that will absorb onto their surface forming the so-called protein corona. Information related to the composition of the protein corona and net cell association was collected from literature for a library of surface-modified gold and silver nanoparticles. For each protein in the corona, sequence information was extracted and used to calculate physicochemical properties and statistical descriptors. Data cleaning and preprocessing techniques including statistical analysis and feature selection methods were applied to remove highly correlated, redundant and non-significant features. A weighting technique was applied to construct specific signatures that represent the corona composition for each nanoparticle. Using this basic set of protein descriptors, a new Protein Corona Structure-Activity Relationship (PCSAR) that relates net cell association with the physicochemical descriptors of the proteins that form the corona was developed and validated. The features that resulted from the feature selection were in line with already published literature, and the computational model constructed on these features had a good accuracy (R(2)LOO=0.76 and R(2)LMO(25%)=0.72) and stability, with the advantage that the fingerprints based on physicochemical descriptors were independent of the specific proteins that form the corona.

Complexation of rice starch/flour and maize oil through heat moisture treatment: Structural, in vitro digestion and physicochemical properties.

PubMed

Chen, Xu; He, Xiaowei; Fu, Xiong; Zhang, Bin; Huang, Qiang

2017-05-01

This study investigated structural, in vitro digestion and physicochemical properties of normal rice starch (NRS)/flour (NRF) complexed with maize oil (MO) through heat-moisture treatment (HMT). The NRS-/NRF-MO complex displayed an increased pasting temperature and a decreased peak viscosity. After HMT, less ordered Maltese and more granule fragments were observed for NRS-/NRF-MO complex. Meanwhile, more aggregation was observed in the HMT samples with higher moisture contents. We found that higher onset temperature, lower enthalpy change and relative crystallinity of the NRS-/NRF-MO complex were associated with a higher moisture content of HMT samples. The higher moisture content of HMT was also favorable for the amylose-lipid complex formation. Differences in starch digestion properties were found for NRS-MO and NRF-MO complex. All of the NRS/NRF complexed MO after cooking showed lower rapidly digestible starch (RDS) contents compared with the control sample, therein NRS-/NRF- MO 20% exhibited the highest sum of the slowly digestible starch and resistant starch contents. In general, HMT had a greater impact on the in vitro digestion and physicochemical properties of flour samples compared with starch counterparts. Copyright © 2017 Elsevier B.V. All rights reserved.

Fractionation, physicochemical property and immunological activity of polysaccharides from Cassia obtusifolia.

PubMed

Feng, Lei; Yin, Junyi; Nie, Shaoping; Wan, Yiqun; Xie, Mingyong

2016-10-01

The seeds of Cassia obtusifolia are widely used as a drink in Asia and an additive in food industry. Considerable amounts of water-soluble polysaccharides were found in the whole seeds, while conflicting results on structure characteristics have been reported, and few studies have been reported on physicochemical properties and immunomodulatory activities. In the present study, gradient ethanol precipitation was applied to fractionate the water-soluble polysaccharide (CP), and two sub-fractions CP-30 (30% ethanol precipitate) and CP-40 (40% ethanol precipitate) were obtained. Different rheological properties for CP-30 and CP-40 were found, indicating the differences in structure characteristics between CP-30 and CP-40. Chemical properties, including molecular weight, monosaccharide composition, and glycosidic linkage were investigated. Compared with CP-30, CP-40 had lower molecular weight and higher content of xylose. The immunomodulatory effects of CP, CP-30 and CP-40 were assessed. All of them were found to possess significant immunomodulation activities, while varied effects of them on macrophage functions were observed. The aim of the present study was to develop a simple and efficient method to purify cassia polysaccharides, and investigate their physicochemical properties and biological activities, which was meaningful for their potential use in food industry and folk medicine. Copyright © 2016. Published by Elsevier B.V.

Physicochemical and morphological properties of plasticized poly(vinyl alcohol)-agar biodegradable films.

PubMed

Madera-Santana, T J; Freile-Pelegrín, Y; Azamar-Barrios, J A

2014-08-01

The effects of the addition of glycerol (GLY) on the physicochemical and morphological properties of poly(vinyl alcohol) (PVA)-agar films were reported. PVA-agar films were prepared by solution cast method, and the addition of GLY in PVA-agar films altered the optical properties, resulting in a decrease in opacity values and in the color difference (ΔE) of the films. Structural characterization using Fourier transformation infrared (FTIR) spectroscopy and X-ray diffraction (XRD) indicated that the presence of GLY altered the intensity of the bands (from 1200 to 800cm(-1)) and crystallinity. The characterization of the thermal properties indicated that an increase in the agar content produces a decrease in the melting temperature and augments the heat of fusion. Similar tendencies were observed in plasticized films, but at different magnification. The formulation that demonstrated the lowest mechanical properties contained 25wt.% agar, whereas the formulation that contained 75wt.% agar demonstrated a significant improvement. The water vapor transmission rate (WVTR) and surface morphology analysis demonstrated that the structure of PVA-agar films is reorganized upon GLY addition. The physicochemical properties of PVA-agar films using GLY as a plasticizer provide information for the application of this formulation as packaging material for specific food applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Structural characteristics and physicochemical properties of lotus seed resistant starch prepared by different methods.

PubMed

Zeng, Shaoxiao; Wu, Xiaoting; Lin, Shan; Zeng, Hongliang; Lu, Xu; Zhang, Yi; Zheng, Baodong

2015-11-01

Lotus seed resistant starch (LRS) is commonly known as resistant starch type 3 (LRS3). The objective of this study was to investigate the effect of different preparation methods on the structural characteristics and physicochemical properties of LRS3. The molar mass of LRS3 prepared by autoclaving method (GP-LRS3) and ultrasonic-autoclaving method (UP-LRS3) was mainly distributed in the range 1.0 × 10(4)-2 × 10(4) g/mol while a decrease of LRS3 prepared by microwave-moisture method (MP-LRS3) was observed. The particle of MP-LRS3 was smaller and relatively smoother while UP-LRS3 was bigger and rougher compared to GP-LRS3. Among these samples, GP-LRS3 exhibited the highest degree of ordered structure and crystallinity, the amorphous region of MP-LRS3 was the biggest and UP-LRS3 displayed the highest degree of double helical structure. Additionally, MP-LRS3 displayed the strongest solubility and swelling power while UP-LRS3 exhibited the strongest iodine absorption ability and thermostability, which were affected by their structural characteristics. Copyright © 2015 Elsevier Ltd. All rights reserved.

Substituent-directed structural and physicochemical controls of diruthenium catecholate complexes with ligand-unsupported Ru-Ru bonds.

PubMed

Chang, Ho-Chol; Mochizuki, Katsunori; Kitagawa, Susumu

2005-05-30

A family of diruthenium complexes with ligand-unsupported Ru-Ru bonds has been systematically synthesized, and their crystal structures and physical properties have been examined. A simple, useful reaction between Ru2(OAc)4Cl (OAc- = acetate) and catechol derivatives in the presence of bases afforded a variety of diruthenium complexes, generally formulated as [Na(n){Ru2(R4Cat)4}] (n = 2 or 3; R4 = -F4, -Cl4, -Br4, -H4, -3,5-di-t-Bu, and -3,6-di-t-Bu; Cat(2-) = catecholate). The most characteristic feature of the complexes is the formation of short ligand-unsupported Ru-Ru bonds (2.140-2.273 A). These comprehensive studies were carried out to evaluate the effects of the oxidation states and the substituents governing the molecular structures and physicochemical properties. The Ru-Ru bond distances, rotational conformations, and bending structures of the complexes were successfully varied. The results presented in this manuscript clearly demonstrate that the complexes with ligand-unsupported Ru-Ru bonds can sensitively respond to redox reactions and ligand substituents on the basis of the greater degree of freedom in their molecular structures.

Sludge Biochar Amendment and Alfalfa Revegetation Improve Soil Physicochemical Properties and Increase Diversity of Soil Microbes in Soils from a Rare Earth Element Mining Wasteland

PubMed Central

Inubushi, Kazuyuki; Liang, Jian; Zhu, Sipin; Wei, Zhenya; Guo, Xiaobin; Luo, Xianping

2018-01-01

Long-term unregulated mining of ion-adsorption clays (IAC) in China has resulted in severe ecological destruction and created large areas of wasteland in dire need of rehabilitation. Soil amendment and revegetation are two important means of rehabilitation of IAC mining wasteland. In this study, we used sludge biochar prepared by pyrolysis of municipal sewage sludge as a soil ameliorant, selected alfalfa as a revegetation plant, and conducted pot trials in a climate-controlled chamber. We investigated the effects of alfalfa revegetation, sludge biochar amendment, and their combined amendment on soil physicochemical properties in soil from an IAC mining wasteland as well as the impact of sludge biochar on plant growth. At the same time, we also assessed the impacts of these amendments on the soil microbial community by means of the Illumina Miseq sequences method. Results showed that alfalfa revegetation and sludge biochar both improved soil physicochemical properties and microbial community structure. When alfalfa revegetation and sludge biochar amendment were combined, we detected additive effects on the improvement of soil physicochemical properties as well as increases in the richness and diversity of bacterial and fungal communities. Redundancy analyses suggested that alfalfa revegetation and sludge biochar amendment significantly affected soil microbial community structure. Critical environmental factors consisted of soil available K, pH, organic matter, carbon–nitrogen ratio, bulk density, and total porosity. Sludge biochar amendment significantly promoted the growth of alfalfa and changed its root morphology. Combining alfalfa the revegetation with sludge biochar amendment may serve to not only achieve the revegetation of IAC mining wasteland, but also address the challenge of municipal sludge disposal by making the waste profitable. PMID:29751652

Sludge Biochar Amendment and Alfalfa Revegetation Improve Soil Physicochemical Properties and Increase Diversity of Soil Microbes in Soils from a Rare Earth Element Mining Wasteland.

PubMed

Luo, Caigui; Deng, Yangwu; Inubushi, Kazuyuki; Liang, Jian; Zhu, Sipin; Wei, Zhenya; Guo, Xiaobin; Luo, Xianping

2018-05-11

Long-term unregulated mining of ion-adsorption clays (IAC) in China has resulted in severe ecological destruction and created large areas of wasteland in dire need of rehabilitation. Soil amendment and revegetation are two important means of rehabilitation of IAC mining wasteland. In this study, we used sludge biochar prepared by pyrolysis of municipal sewage sludge as a soil ameliorant, selected alfalfa as a revegetation plant, and conducted pot trials in a climate-controlled chamber. We investigated the effects of alfalfa revegetation, sludge biochar amendment, and their combined amendment on soil physicochemical properties in soil from an IAC mining wasteland as well as the impact of sludge biochar on plant growth. At the same time, we also assessed the impacts of these amendments on the soil microbial community by means of the Illumina Miseq sequences method. Results showed that alfalfa revegetation and sludge biochar both improved soil physicochemical properties and microbial community structure. When alfalfa revegetation and sludge biochar amendment were combined, we detected additive effects on the improvement of soil physicochemical properties as well as increases in the richness and diversity of bacterial and fungal communities. Redundancy analyses suggested that alfalfa revegetation and sludge biochar amendment significantly affected soil microbial community structure. Critical environmental factors consisted of soil available K, pH, organic matter, carbon⁻nitrogen ratio, bulk density, and total porosity. Sludge biochar amendment significantly promoted the growth of alfalfa and changed its root morphology. Combining alfalfa the revegetation with sludge biochar amendment may serve to not only achieve the revegetation of IAC mining wasteland, but also address the challenge of municipal sludge disposal by making the waste profitable.

Structure-property relationship of quinuclidinium surfactants--Towards multifunctional biologically active molecules.

PubMed

Skočibušić, Mirjana; Odžak, Renata; Štefanić, Zoran; Križić, Ivana; Krišto, Lucija; Jović, Ozren; Hrenar, Tomica; Primožič, Ines; Jurašin, Darija

2016-04-01

Motivated by diverse biological and pharmacological activity of quinuclidine and oxime compounds we have synthesized and characterized novel class of surfactants, 3-hydroxyimino quinuclidinium bromides with different alkyl chains lengths (CnQNOH; n=12, 14 and 16). The incorporation of non conventional hydroxyimino quinuclidinium headgroup and variation in alkyl chain length affects hydrophilic-hydrophobic balance of surfactant molecule and thereby physicochemical properties important for its application. Therefore, newly synthesized surfactants were characterized by the combination of different experimental techniques: X-ray analysis, potentiometry, electrical conductivity, surface tension and dynamic light scattering measurements, as well as antimicrobial susceptibility tests. Comprehensive investigation of CnQNOH surfactants enabled insight into structure-property relationship i.e., way in which the arrangement of surfactant molecules in the crystal phase correlates with their solution behavior and biologically activity. The synthesized CnQNOH surfactants exhibited high adsorption efficiency and relatively low critical micelle concentrations. In addition, all investigated compounds showed very potent and promising activity against Gram-positive and clinically relevant Gram-negative bacterial strains compared to conventional antimicrobial agents: tetracycline and gentamicin. The overall results indicate that bicyclic headgroup with oxime moiety, which affects both hydrophilicity and hydrophobicity of CnQNOH molecule in addition to enabling hydrogen bonding, has dominant effect on crystal packing and physicochemical properties. The unique structural features of cationic surfactants with hydroxyimino quinuclidine headgroup along with diverse biological activity have made them promising structures in novel drug discovery. Obtained fundamental understanding how combination of different functionalities in a single surfactant molecule affects its physicochemical properties represents a good starting point for further biological research. Copyright © 2015 Elsevier B.V. All rights reserved.

Physicochemical characterization of mineral deposits in human ligamenta flava.

PubMed

Orzechowska, Sylwia; Wróbel, Andrzej; Kozieł, Marcin; Łasocha, Wiesław; Rokita, Eugeniusz

2018-05-01

The aim of our study was the detailed characterization of calcium deposits in ligamenta flava. The use of microcomputed tomography allowed extending the routine medical investigations to characterize mineral grains in the microscopic scale. A possible connection between spinal stenosis and ligament mineralization was investigated. The studies were carried out on 24 surgically removed ligamentum flavum samples divided into control and stenosis groups. Physicochemical characterization of the inorganic material was performed using X-ray fluorescence, X-ray diffraction, and Fourier transform infrared spectroscopy. The minerals were present in 14 of 24 ligament samples, both in stenosis and control groups. The inorganic substance constitutes on average ~0.1% of the sample volume. The minerals are scattered in the soft tissue matrix without any regular pattern. It was confirmed that minerals possess an internal structure and consist of the organic material and small inorganic grains mixture. The physicochemical analyses show that the predominant crystalline phase was hydroxyapatite (HAP). In the stenosis group calcium pyrophosphate dehydrate (CPPD) was identified. Both structures were never present in a single sample. Two different crystal structures suggest two independent processes of mineralization. The formation of CPPD may be treated as a more intense process since CPPD minerals are characterized by bigger values of the structural parameters and higher density than HAP deposits. The formation of HAP minerals is a soft tissue degeneration process that begins, in some cases, at early age or may not occur at all. Various density and volume of mineral grains indicate that the mineralization process does not occur in a constant environment and proceeds with various speeds. The formation of minerals in ligamenta flava is not directly associated with diagnosed spinal canal stenosis.

Structure and functions of keratin proteins in simple, stratified, keratinized and cornified epithelia

PubMed Central

Bragulla, Hermann H; Homberger, Dominique G

2009-01-01

Historically, the term ‘keratin’ stood for all of the proteins extracted from skin modifications, such as horns, claws and hooves. Subsequently, it was realized that this keratin is actually a mixture of keratins, keratin filament-associated proteins and other proteins, such as enzymes. Keratins were then defined as certain filament-forming proteins with specific physicochemical properties and extracted from the cornified layer of the epidermis, whereas those filament-forming proteins that were extracted from the living layers of the epidermis were grouped as ‘prekeratins’ or ‘cytokeratins’. Currently, the term ‘keratin’ covers all intermediate filament-forming proteins with specific physicochemical properties and produced in any vertebrate epithelia. Similarly, the nomenclature of epithelia as cornified, keratinized or non-keratinized is based historically on the notion that only the epidermis of skin modifications such as horns, claws and hooves is cornified, that the non-modified epidermis is a keratinized stratified epithelium, and that all other stratified and non-stratified epithelia are non-keratinized epithelia. At this point in time, the concepts of keratins and of keratinized or cornified epithelia need clarification and revision concerning the structure and function of keratin and keratin filaments in various epithelia of different species, as well as of keratin genes and their modifications, in view of recent research, such as the sequencing of keratin proteins and their genes, cell culture, transfection of epithelial cells, immunohistochemistry and immunoblotting. Recently, new functions of keratins and keratin filaments in cell signaling and intracellular vesicle transport have been discovered. It is currently understood that all stratified epithelia are keratinized and that some of these keratinized stratified epithelia cornify by forming a Stratum corneum. The processes of keratinization and cornification in skin modifications are different especially with respect to the keratins that are produced. Future research in keratins will provide a better understanding of the processes of keratinization and cornification of stratified epithelia, including those of skin modifications, of the adaptability of epithelia in general, of skin diseases, and of the changes in structure and function of epithelia in the course of evolution. This review focuses on keratins and keratin filaments in mammalian tissue but keratins in the tissues of some other vertebrates are also considered. PMID:19422428

FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects.

PubMed

Lagorce, David; Sperandio, Olivier; Galons, Hervé; Miteva, Maria A; Villoutreix, Bruno O

2008-09-24

Drug discovery and chemical biology are exceedingly complex and demanding enterprises. In recent years there are been increasing awareness about the importance of predicting/optimizing the absorption, distribution, metabolism, excretion and toxicity (ADMET) properties of small chemical compounds along the search process rather than at the final stages. Fast methods for evaluating ADMET properties of small molecules often involve applying a set of simple empirical rules (educated guesses) and as such, compound collections' property profiling can be performed in silico. Clearly, these rules cannot assess the full complexity of the human body but can provide valuable information and assist decision-making. This paper presents FAF-Drugs2, a free adaptable tool for ADMET filtering of electronic compound collections. FAF-Drugs2 is a command line utility program (e.g., written in Python) based on the open source chemistry toolkit OpenBabel, which performs various physicochemical calculations, identifies key functional groups, some toxic and unstable molecules/functional groups. In addition to filtered collections, FAF-Drugs2 can provide, via Gnuplot, several distribution diagrams of major physicochemical properties of the screened compound libraries. We have developed FAF-Drugs2 to facilitate compound collection preparation, prior to (or after) experimental screening or virtual screening computations. Users can select to apply various filtering thresholds and add rules as needed for a given project. As it stands, FAF-Drugs2 implements numerous filtering rules (23 physicochemical rules and 204 substructure searching rules) that can be easily tuned.

Classifying Nanomaterial Risks Using Multi-Criteria Decision Analysis

NASA Astrophysics Data System (ADS)

Linkov, I.; Steevens, J.; Chappell, M.; Tervonen, T.; Figueira, J. R.; Merad, M.

There is rapidly growing interest by regulatory agencies and stakeholders in the potential toxicity and other risks associated with nanomaterials throughout the different stages of the product life cycle (e.g., development, production, use and disposal). Risk assessment methods and tools developed and applied to chemical and biological material may not be readily adaptable for nanomaterials because of the current uncertainty in identifying the relevant physico-chemical and biological properties that adequately describe the materials. Such uncertainty is further driven by the substantial variations in the properties of the original material because of the variable manufacturing processes employed in nanomaterial production. To guide scientists and engineers in nanomaterial research and application as well as promote the safe use/handling of these materials, we propose a decision support system for classifying nanomaterials into different risk categories. The classification system is based on a set of performance metrics that measure both the toxicity and physico-chemical characteristics of the original materials, as well as the expected environmental impacts through the product life cycle. The stochastic multicriteria acceptability analysis (SMAA-TRI), a formal decision analysis method, was used as the foundation for this task. This method allowed us to cluster various nanomaterials in different risk categories based on our current knowledge of nanomaterial's physico-chemical characteristics, variation in produced material, and best professional judgement. SMAA-TRI uses Monte Carlo simulations to explore all feasible values for weights, criteria measurements, and other model parameters to assess the robustness of nanomaterial grouping for risk management purposes.1,2

A methodological approach to characterize the resilience of aquatic ecosystems with application to Lake Annecy, France

NASA Astrophysics Data System (ADS)

Pinault, J.-L.; Berthier, F.

2007-01-01

We propose a methodological approach to characterize the resilience of aquatic ecosystems with respect to the evolution of environmental parameters as well as their aptitude to adapt to forcings. This method that is applied to Lake Annecy, France, proceeds in three stages. First, according to the depth, variations of physicochemical parameters versus time are separated into three components related to (1) energy transfer through the surface of the lake, (2) the flow of rivers and springs that feed the lake, and (3) long-term evolution of the benthic zone as a consequence of mineral and organic matter loads. Second, dynamics of the lake are deduced by analyzing the physicochemical parameter components related to the three boundary conditions. Third, a stochastic process associated with the transfer models aims to characterize the resilience of the lakes according to forcings. For Lake Annecy, whose dynamics are representative of oligotrophic stratified lakes controlled by decarbonation processes where turnover and mixing occurring once a year in winter, the major consequence is the impoverishment of dissolved oxygen in deep water in autumn due to a temperature increase of the surface water in summer. The simulation raises relevant questions about whether a connection exists between physicochemical parameters and global warming, which should not induce harmful consequences on water quality and biodiversity in deep water. This methodological approach is general since it does not use any physical conceptual model to predict the hydrosystem behavior but uses directly observed data.

Medicinal flowers. IV. Marigold. (2): Structures of new ionone and sesquiterpene glycosides from Egyptian Calendula officinalis.

PubMed

Marukami, T; Kishi, A; Yoshikawa, M

2001-08-01

Following the characterization of hypoglycemic, gastric emptying inhibitory, and gastroprotective principles and the structure elucidation of calendasaponins A, B, C, and D, two new ionone glucosides (officinosides A and B), and two sesquiterpene oligoglycosides (officinosides C and D), were isolated from the flowers of Egyptian Calendula officinalis. The structures of the officinosides were elucidated on the basis of chemical and physicochemical evidence.

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015

PubMed Central

Galluzzi, L; Bravo-San Pedro, J M; Vitale, I; Aaronson, S A; Abrams, J M; Adam, D; Alnemri, E S; Altucci, L; Andrews, D; Annicchiarico-Petruzzelli, M; Baehrecke, E H; Bazan, N G; Bertrand, M J; Bianchi, K; Blagosklonny, M V; Blomgren, K; Borner, C; Bredesen, D E; Brenner, C; Campanella, M; Candi, E; Cecconi, F; Chan, F K; Chandel, N S; Cheng, E H; Chipuk, J E; Cidlowski, J A; Ciechanover, A; Dawson, T M; Dawson, V L; De Laurenzi, V; De Maria, R; Debatin, K-M; Di Daniele, N; Dixit, V M; Dynlacht, B D; El-Deiry, W S; Fimia, G M; Flavell, R A; Fulda, S; Garrido, C; Gougeon, M-L; Green, D R; Gronemeyer, H; Hajnoczky, G; Hardwick, J M; Hengartner, M O; Ichijo, H; Joseph, B; Jost, P J; Kaufmann, T; Kepp, O; Klionsky, D J; Knight, R A; Kumar, S; Lemasters, J J; Levine, B; Linkermann, A; Lipton, S A; Lockshin, R A; López-Otín, C; Lugli, E; Madeo, F; Malorni, W; Marine, J-C; Martin, S J; Martinou, J-C; Medema, J P; Meier, P; Melino, S; Mizushima, N; Moll, U; Muñoz-Pinedo, C; Nuñez, G; Oberst, A; Panaretakis, T; Penninger, J M; Peter, M E; Piacentini, M; Pinton, P; Prehn, J H; Puthalakath, H; Rabinovich, G A; Ravichandran, K S; Rizzuto, R; Rodrigues, C M; Rubinsztein, D C; Rudel, T; Shi, Y; Simon, H-U; Stockwell, B R; Szabadkai, G; Tait, S W; Tang, H L; Tavernarakis, N; Tsujimoto, Y; Vanden Berghe, T; Vandenabeele, P; Villunger, A; Wagner, E F; Walczak, H; White, E; Wood, W G; Yuan, J; Zakeri, Z; Zhivotovsky, B; Melino, G; Kroemer, G

2015-01-01

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as ‘accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. ‘Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death. PMID:25236395

Essential versus accessory aspects of cell death: recommendations of the NCCD 2015.

PubMed

Galluzzi, L; Bravo-San Pedro, J M; Vitale, I; Aaronson, S A; Abrams, J M; Adam, D; Alnemri, E S; Altucci, L; Andrews, D; Annicchiarico-Petruzzelli, M; Baehrecke, E H; Bazan, N G; Bertrand, M J; Bianchi, K; Blagosklonny, M V; Blomgren, K; Borner, C; Bredesen, D E; Brenner, C; Campanella, M; Candi, E; Cecconi, F; Chan, F K; Chandel, N S; Cheng, E H; Chipuk, J E; Cidlowski, J A; Ciechanover, A; Dawson, T M; Dawson, V L; De Laurenzi, V; De Maria, R; Debatin, K-M; Di Daniele, N; Dixit, V M; Dynlacht, B D; El-Deiry, W S; Fimia, G M; Flavell, R A; Fulda, S; Garrido, C; Gougeon, M-L; Green, D R; Gronemeyer, H; Hajnoczky, G; Hardwick, J M; Hengartner, M O; Ichijo, H; Joseph, B; Jost, P J; Kaufmann, T; Kepp, O; Klionsky, D J; Knight, R A; Kumar, S; Lemasters, J J; Levine, B; Linkermann, A; Lipton, S A; Lockshin, R A; López-Otín, C; Lugli, E; Madeo, F; Malorni, W; Marine, J-C; Martin, S J; Martinou, J-C; Medema, J P; Meier, P; Melino, S; Mizushima, N; Moll, U; Muñoz-Pinedo, C; Nuñez, G; Oberst, A; Panaretakis, T; Penninger, J M; Peter, M E; Piacentini, M; Pinton, P; Prehn, J H; Puthalakath, H; Rabinovich, G A; Ravichandran, K S; Rizzuto, R; Rodrigues, C M; Rubinsztein, D C; Rudel, T; Shi, Y; Simon, H-U; Stockwell, B R; Szabadkai, G; Tait, S W; Tang, H L; Tavernarakis, N; Tsujimoto, Y; Vanden Berghe, T; Vandenabeele, P; Villunger, A; Wagner, E F; Walczak, H; White, E; Wood, W G; Yuan, J; Zakeri, Z; Zhivotovsky, B; Melino, G; Kroemer, G

2015-01-01

Cells exposed to extreme physicochemical or mechanical stimuli die in an uncontrollable manner, as a result of their immediate structural breakdown. Such an unavoidable variant of cellular demise is generally referred to as 'accidental cell death' (ACD). In most settings, however, cell death is initiated by a genetically encoded apparatus, correlating with the fact that its course can be altered by pharmacologic or genetic interventions. 'Regulated cell death' (RCD) can occur as part of physiologic programs or can be activated once adaptive responses to perturbations of the extracellular or intracellular microenvironment fail. The biochemical phenomena that accompany RCD may be harnessed to classify it into a few subtypes, which often (but not always) exhibit stereotyped morphologic features. Nonetheless, efficiently inhibiting the processes that are commonly thought to cause RCD, such as the activation of executioner caspases in the course of apoptosis, does not exert true cytoprotective effects in the mammalian system, but simply alters the kinetics of cellular demise as it shifts its morphologic and biochemical correlates. Conversely, bona fide cytoprotection can be achieved by inhibiting the transduction of lethal signals in the early phases of the process, when adaptive responses are still operational. Thus, the mechanisms that truly execute RCD may be less understood, less inhibitable and perhaps more homogeneous than previously thought. Here, the Nomenclature Committee on Cell Death formulates a set of recommendations to help scientists and researchers to discriminate between essential and accessory aspects of cell death.

Age-Related Adaptation of Bone-PDL-Tooth Complex: Rattus-Norvegicus as a Model System

PubMed Central

Leong, Narita L.; Hurng, Jonathan M.; Djomehri, Sabra I.; Gansky, Stuart A.; Ryder, Mark I.; Ho, Sunita P.

2012-01-01

Functional loads on an organ induce tissue adaptations by converting mechanical energy into chemical energy at a cell-level. The transducing capacity of cells alters physico-chemical properties of tissues, developing a positive feedback commonly recognized as the form-function relationship. In this study, organ and tissue adaptations were mapped in the bone-tooth complex by identifying and correlating biomolecular expressions to physico-chemical properties in rats from 1.5 to 15 months. However, future research using hard and soft chow over relevant age groups would decouple the function related effects from aging affects. Progressive curvature in the distal root with increased root resorption was observed using micro X-ray computed tomography. Resorption was correlated to the increased activity of multinucleated osteoclasts on the distal side of the molars until 6 months using tartrate resistant acid phosphatase (TRAP). Interestingly, mononucleated TRAP positive cells within PDL vasculature were observed in older rats. Higher levels of glycosaminoglycans were identified at PDL-bone and PDL-cementum entheses using alcian blue stain. Decreasing biochemical gradients from coronal to apical zones, specifically biomolecules that can induce osteogenic (biglycan) and fibrogenic (fibromodulin, decorin) phenotypes, and PDL-specific negative regulator of mineralization (asporin) were observed using immunohistochemistry. Heterogeneous distribution of Ca and P in alveolar bone, and relatively lower contents at the entheses, were observed using energy dispersive X-ray analysis. No correlation between age and microhardness of alveolar bone (0.7±0.1 to 0.9±0.2 GPa) and cementum (0.6±0.1 to 0.8±0.3 GPa) was observed using a microindenter. However, hardness of cementum and alveolar bone at any given age were significantly different (P<0.05). These observations should be taken into account as baseline parameters, during development (1.5 to 4 months), growth (4 to 10 months), followed by a senescent phase (10 to 15 months), from which deviations due to experimentally induced perturbations can be effectively investigated. PMID:22558292

Acetaldehyde-induced structural and conformational alterations in human immunoglobulin G: A physicochemical and multi-spectroscopic study.

PubMed

Waris, Sana; Habib, Safia; Tantry, Irfan Qadir; Khan, Rizwan Hasan; Mahmood, Riaz; Ali, Asif

2018-07-01

Acetaldehyde is a reactive aldehyde produced as an intermediate of alcohol metabolism and tobacco pyrolysis. It has the potential to interact with different biomolecules in various tissues which results in the formation of stable, unstable and covalent adducts. This causes structural and functional modifications that may lead to severe complications such as cancer. This study has probed the structural modifications in human immunoglobulin G (IgG) as a function of different concentrations of acetaldehyde in the presence of reducing agent, sodium borohydride. Acetaldehyde mediated modifications in IgG have been characterised by various physicochemical techniques. UV-spectrophotometry showed that acetaldehyde modified IgG exhibited marked increase in hyperchromicity. Fluorescence studies revealed a significant quenching of tryptophan fluorescence which resulted in loss of β-sheet secondary structure that was confirmed by circular dichroic analysis. Gross structural changes in the morphology of IgG were confirmed by increase in mass and hydrodynamic radius of this glycoprotein along with the appearance of fibrillar structures in modified IgG, when compared to the granular structure of the native form of IgG observed by scanning electron microscope. The results indicate that acetaldehyde causes alterations in the secondary and tertiary structure of the protein leading to diminution of normal function of IgG molecule. Copyright © 2018 Elsevier B.V. All rights reserved.

Physico-chemical characterization of products from vacuum oil under delayed coking process by infrared spectroscopy and chemometrics methods

NASA Astrophysics Data System (ADS)

Meléndez, L. V.; Cabanzo, R.; Mejía-Ospino, E.; Guzmán, A.

2016-02-01

Eight vacuum residues and their delayed coking liquids products from Colombian crude were study by infrared spectroscopy with attenuated total reflectance (FTIR-ATR) and principal component analysis (PCA). For the samples the structural parameters of aromaticity factor (fa), alifaticity (A2500-3100cm-1), aromatic condensation degree (GCA), length of aliphatic chains (LCA) and aliphatic chain length associated with aromatic (LACAR) were determined through the development of a methodology, which includes the previous processing of spectroscopy data, identifying the regions in the IR spectra of greatest variance using PCA and molecules patterns. The parameters were compared with the results obtained from proton magnetic resonance (1H-NMR) and 13C-NMR. The results showed the influence and correlation of structural parameters with some physicochemical properties such as API gravity, weight percent sulphur (% S) and Conradson carbon content (% CCR)

Spatial variability of isoproturon mineralizing activity within an agricultural field: geostatistical analysis of simple physicochemical and microbiological soil parameters.

PubMed

El Sebai, T; Lagacherie, B; Soulas, G; Martin-Laurent, F

2007-02-01

We assessed the spatial variability of isoproturon mineralization in relation to that of physicochemical and biological parameters in fifty soil samples regularly collected along a sampling grid delimited across a 0.36 ha field plot (40 x 90 m). Only faint relationships were observed between isoproturon mineralization and the soil pH, microbial C biomass, and organic nitrogen. Considerable spatial variability was observed for six of the nine parameters tested (isoproturon mineralization rates, organic nitrogen, genetic structure of the microbial communities, soil pH, microbial biomass and equivalent humidity). The map of isoproturon mineralization rates distribution was similar to that of soil pH, microbial biomass, and organic nitrogen but different from those of structure of the microbial communities and equivalent humidity. Geostatistics revealed that the spatial heterogeneity in the rate of degradation of isoproturon corresponded to that of soil pH and microbial biomass.

The Adaptability of Life on Earth and the Diversity of Planetary Habitats.

PubMed

Schulze-Makuch, Dirk; Airo, Alessandro; Schirmack, Janosch

2017-01-01

The evolutionary adaptability of life to extreme environments is astounding given that all life on Earth is based on the same fundamental biochemistry. The range of some physicochemical parameters on Earth exceeds the ability of life to adapt, but stays within the limits of life for other parameters. Certain environmental conditions such as low water availability in hyperarid deserts on Earth seem to be close to the limit of biological activity. A much wider range of environmental parameters is observed on planetary bodies within our Solar System such as Mars or Titan, and presumably even larger outside of our Solar System. Here we review the adaptability of life as we know it, especially regarding temperature, pressure, and water activity. We use then this knowledge to outline the range of possible habitable environments for alien planets and moons and distinguish between a variety of planetary environment types. Some of these types are present in our Solar System, others are hypothetical. Our schematic categorization of alien habitats is limited to life as we know it, particularly regarding to the use of solvent (water) and energy source (light and chemical compounds).

The Adaptability of Life on Earth and the Diversity of Planetary Habitats

PubMed Central

Schulze-Makuch, Dirk; Airo, Alessandro; Schirmack, Janosch

2017-01-01

The evolutionary adaptability of life to extreme environments is astounding given that all life on Earth is based on the same fundamental biochemistry. The range of some physicochemical parameters on Earth exceeds the ability of life to adapt, but stays within the limits of life for other parameters. Certain environmental conditions such as low water availability in hyperarid deserts on Earth seem to be close to the limit of biological activity. A much wider range of environmental parameters is observed on planetary bodies within our Solar System such as Mars or Titan, and presumably even larger outside of our Solar System. Here we review the adaptability of life as we know it, especially regarding temperature, pressure, and water activity. We use then this knowledge to outline the range of possible habitable environments for alien planets and moons and distinguish between a variety of planetary environment types. Some of these types are present in our Solar System, others are hypothetical. Our schematic categorization of alien habitats is limited to life as we know it, particularly regarding to the use of solvent (water) and energy source (light and chemical compounds). PMID:29085352

Native and Reconstituted Plasma Lipoproteins in Nanomedicine: Physicochemical Determinants of Nanoparticle Structure, Stability, and Metabolism

PubMed Central

Pownall, Henry J.; Rosales, Corina; Gillard, Baiba K.; Ferrari, Mauro

2016-01-01

Although many acute and chronic diseases are managed via pharmacological means, challenges remain regarding appropriate drug targeting and maintenance of therapeutic levels within target tissues. Advances in nanotechnology will overcome these challenges through the development of lipidic particles, including liposomes, lipoproteins, and reconstituted high-density lipoproteins (rHDL) that are potential carriers of water-soluble, hydrophobic, and amphiphilic molecules. Herein we summarize the properties of human plasma lipoproteins and rHDL, identify the physicochemical determinants of lipid transfer between phospholipid surfaces, and discuss strategies for increasing the plasma half-life of lipoprotein- and liposome-associated molecules. PMID:27826368

Pharmaceutical Cocrystals and Their Physicochemical Properties

PubMed Central

2009-01-01

Over the last 20 years, the number of publications outlining the advances in design strategies, growing techniques, and characterization of cocrystals has continued to increase significantly within the crystal engineering field. However, only within the last decade have cocrystals found their place in pharmaceuticals, primarily due to their ability to alter physicochemical properties without compromising the structural integrity of the active pharmaceutical ingredient (API) and thus, possibly, the bioactivity. This review article will highlight and discuss the advances made over the last 10 years pertaining to physical and chemical property improvements through pharmaceutical cocrystalline materials and, hopefully, draw closer the fields of crystal engineering and pharmaceutical sciences. PMID:19503732

A simple approach to hybrid inorganic–organic step-growth hydrogels with scalable control of physicochemical properties and biodegradability† †Electronic supplementary information (ESI) available: Experimental details and characterization data as mentioned in the text. See DOI: 10.1039/c4py01789g Click here for additional data file.

PubMed Central

Alves, F.

2015-01-01

We prepared new and scalable, hybrid inorganic–organic step-growth hydrogels with polyhedral oligomeric silsesquioxane (POSS) network knot construction elements and hydrolytically degradable poly(ethylene glycol) (PEG) di-ester macromonomers by in situ radical-mediated thiol–ene photopolymerization. The physicochemical properties of the gels are fine-tailored over orders of magnitude including functionalization of their interior, a hierarchical gel structure, and biodegradability. PMID:25821524

Effects of volumetric expansion in molecular crystals: A quantum mechanical investigation on aspirin and paracetamol most stable polymorphs

NASA Astrophysics Data System (ADS)

Adhikari, Kapil; Flurchick, Kenneth M.; Valenzano, Loredana

2015-02-01

This work reports a study performed at hybrid semi-empirical density functional level (B3LYP-D2*) of the physico-chemical properties of aspirin (acetylsalicylic acid) and paracetamol (acetaminophen) in their most stable crystalline forms. It is shown how effects arising from volumetric expansions influence the properties of the materials. Structural, energetic, and vibrational properties are in good agreement with experimental values reported at temperatures far from 0 K. Results show that the proposed approach is reliable enough to reproduce effects of volumetric expansion on lattice energies and other measurable physico-chemical observables related to inter-molecular forces.

Preliminary results of water quality assessment using phytoplankton and physicochemical approaches in the Huai River Basin, China.

PubMed

Chen, Hao; Zuo, Qi-Ting; Zhang, Yong-Yong

2017-11-01

Water pollution has been a significant issue in the Huai River Basin (HRB) of China since the late 1970s. In July and December 2013, two field investigations were carried out at 10 sites along the main streams of the basin. The monitoring indices contained both physicochemical variables and the structure and composition of phytoplankton communities. The correlations between communities and physicochemical variables were analyzed using cluster analysis and redundancy analysis. Moreover, water quality was evaluated using the comprehensive nutrition state index (TLI) and Shannon-Wiener diversity index (H). Results indicated that more phytoplankton species were present in December than in July, but total density was less in December. Phytoplankton communities in the midstream of the Shaying River were affected by the same physicochemical factors throughout the year, but ammonia nitrogen and total phosphorus had the greatest influence on these sites in July and December, respectively. The water pollution status of the sampling sites was much greater in the Shaying River midstream than at other sites. TLI was more suitable than H for assessing water quality in the study area. These results provide valuable information for policy makers and stakeholders in water quality assessment, water ecosystem restoration, and sustainable basin management in the HRB.

Physicochemical properties and biocompatibility of N-trimethyl chitosan: effect of quaternization and dimethylation.

PubMed

Jintapattanakit, Anchalee; Mao, Shirui; Kissel, Thomas; Junyaprasert, Varaporn Buraphacheep

2008-10-01

The aim of this research was to investigate the effect of degrees of quaternization (DQ) and dimethylation (DD) on physicochemical properties and cytotoxicity of N-trimethyl chitosan (TMC). TMC was synthesized by reductive methylation of chitosan in the presence of a strong base at elevated temperature and polymer characteristics were investigated. The number of methylation process and duration of reaction were demonstrated to affect the DQ and DD. An increased number of reaction steps increased DQ and decreased DD, while an extended duration of reaction increased both DQ and DD. The molecular weight of TMC was in the range of 60-550kDa. From the Mark-Houwink equation, it was found that TMC in 2% acetic acid/0.2M sodium acetate behaved as a spherical structure, approximating a random coil. The highest solubility was found with TMC of an intermediate DQ (40%) regardless of DD and molecular weight. The effect of DD on the physicochemical properties and cytotoxicity was obviously observed when proportion of DD to DQ was higher than 1. TMC with relatively high DD showed reduction in both solubility and mucoadhesion and hence decreased cytotoxicity. However, the influence of DD was insignificant when DQ of TMC was higher than 40% at which physicochemical properties and cytotoxicity were mainly dependent upon DQ.

The microbial perspective of organic matter turnover and nutrient cycling in tropical soils

NASA Astrophysics Data System (ADS)

Rasche, Frank

2017-04-01

A primary goal of low-input small-holder farming systems in the tropics is the appropriate management of organic matter (OM) turnover and nutrient cycling via adapted agricultural practices. These emphasize the promotion of soil organic matter (SOM) turnover and carbon (C) sequestration, nutrient use efficiency and soil microbial activity. Since soil microbial communities are acknowledged as key players in the terrestrial C and nutrient (e.g., nitrogen (N), phosphorus (P)) cycles, they may respond sensitively to agricultural management with shifts in their community structure as well as functional traits (i.e., decomposition, mineralization). This may be in particular evident for tropical, agricultural soils which show an accelerated microbial decomposition activity induced by favourable climatic and unique physico-chemical soil conditions. While modern molecular techniques advanced primarily the understanding about the microbiome and their functional traits interacting closely with SOM dynamics in temperate soils, tropical soils under agricultural use have been still neglected to a great extent. The majority of available studies revealed mainly descriptive data on the structural composition of microbial communities rather than questioning if detected structural alterations of the soil microbiome influenced key processes in N and P cycling which actually maintain ecosystem functioning and soil productivity. This talk highlights latest efforts in deploying molecular techniques to study the compositional status of soil microbial decomposer communities and their functional attributes in response to land use change and OM management in tropical agro-ecosystems.

Influence of pectinase treatment on the physicochemical properties of potato flours.

PubMed

Kim, Eun-Jung; Kim, Hyun-Seok

2015-01-15

Untreated and pectinase-treated potato flours from Atlantic and Superior cultivars were characterised to identify the effects of pectinase treatment on their physicochemical properties. Steam-cooked potato whole-tissues were treated with and without pectinase to prepare the dehydrated potato flours. Untreated and pectinase-treated potato flours were investigated with respect to morphology, chemical composition, starch leaching, swelling power, gelatinization, and pasting viscosity. Upon viewing with scanning electron microscopy and light microscopy, the pectinase-treated (relative to untreated) potato flours revealed that the retrograded starch materials were present in intact parenchyma cells, apparently exhibiting granular structures. Their protein and ash contents were reduced through pectinase treatment. While starch leachate contents were lower for the pectinase-treated potato flours, the opposite trend in swelling powers was observed. Pectinase-treated potato flours exhibited higher melting temperatures and pasting viscosities than untreated counterparts. Overall, the modification of potato flour morphology by pectinase treatment may result in alteration of physicochemical properties of potato flours. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cytotoxicity screening of 23 engineered nanomaterials using a test matrix of ten cell lines and three different assays

PubMed Central

2011-01-01

Background Engineered nanomaterials display unique properties that may have impact on human health, and thus require a reliable evaluation of their potential toxicity. Here, we performed a standardized in vitro screening of 23 engineered nanomaterials. We thoroughly characterized the physicochemical properties of the nanomaterials and adapted three classical in vitro toxicity assays to eliminate nanomaterial interference. Nanomaterial toxicity was assessed in ten representative cell lines. Results Six nanomaterials induced oxidative cell stress while only a single nanomaterial reduced cellular metabolic activity and none of the particles affected cell viability. Results from heterogeneous and chemically identical particles suggested that surface chemistry, surface coating and chemical composition are likely determinants of nanomaterial toxicity. Individual cell lines differed significantly in their response, dependent on the particle type and the toxicity endpoint measured. Conclusion In vitro toxicity of the analyzed engineered nanomaterials cannot be attributed to a defined physicochemical property. Therefore, the accurate identification of nanomaterial cytotoxicity requires a matrix based on a set of sensitive cell lines and in vitro assays measuring different cytotoxicity endpoints. PMID:21345205

Sensory and physicochemical evaluation of low-fat chicken mortadella with added native and modified starches.

PubMed

Prestes, R C; Silva, L B; Torri, A M P; Kubota, E H; Rosa, C S; Roman, S S; Kempka, A P; Demiate, I M

2015-07-01

The objective of this work was to evaluate the effect of adding different starches (native and modified) on the physicochemical, sensory, structural and microbiological characteristics of low-fat chicken mortadella. Two formulations containing native cassava and regular corn starch, coded CASS (5.0 % of cassava starch) and CORN (5.0 % of regular corn starch), and one formulation produced with physically treated starch coded as MOD1 (2.5 % of Novation 2300) and chemically modified starch coded as MOD2 (2.5 % of Thermtex) were studied. The following tests were performed: physicochemical characterization (moisture, ash, protein, starch and lipid contents, and water activity); cooling, freezing and reheating losses; texture (texture profile test); color coordinates (L*, a*, b*, C and h); microbiological evaluation; sensory evaluation (multiple comparison and preference test); and histological evaluation (light microscopy). There was no significant difference (p > 0.05) for ash, protein, cooling loss, cohesiveness or in the preference test for the tested samples. The other evaluated parameters showed significant differences (p < 0.05). Histological study allowed for a qualitative evaluation between the physical properties of the food and its microscopic structure. The best results were obtained for formulation MOD2 (2.5 % Thermtex). The addition of modified starch resulted in a better performance than the native starch in relation to the evaluated technological parameters, mainly in relation to reheating losses, which demonstrated the good interaction between the modified starch in the structure of the product and the possibility of the application of this type of starch in other types of functional meat products.

Phosphorus promotion and poisoning in zeolite-based materials: synthesis, characterisation and catalysis

PubMed Central

van der Bij, Hendrik E.

2015-01-01

Phosphorus and microporous aluminosilicates, better known as zeolites, have a unique but poorly understood relationship. For example, phosphatation of the industrially important zeolite H-ZSM-5 is a well-known, relatively inexpensive and seemingly straightforward post-synthetic modification applied by the chemical industry not only to alter its hydrothermal stability and acidity, but also to increase its selectivity towards light olefins in hydrocarbon catalysis. On the other hand, phosphorus poisoning of zeolite-based catalysts, which are used for removing nitrogen oxides from exhaust fuels, poses a problem for their use in diesel engine catalysts. Despite the wide impact of phosphorus–zeolite chemistry, the exact physicochemical processes that take place require a more profound understanding. This review article provides the reader with a comprehensive and state-of-the-art overview of the academic literature, from the first reports in the late 1970s until the most recent studies. In the first part an in-depth analysis is undertaken, which will reveal universal physicochemical and structural effects of phosphorus–zeolite chemistry on the framework structure, accessibility, and strength of acid sites. The second part discusses the hydrothermal stability of zeolites and clarifies the promotional role that phosphorus plays. The third part of the review paper links the structural and physicochemical effects of phosphorus on zeolite materials with their catalytic performance in a variety of catalytic processes, including alkylation of aromatics, catalytic cracking, methanol-to-hydrocarbon processing, dehydration of bioalcohol, and ammonia selective catalytic reduction (SCR) of NOx. Based on these insights, we discuss potential applications and important directions for further research. PMID:26051875

Phosphorus promotion and poisoning in zeolite-based materials: synthesis, characterisation and catalysis.

PubMed

van der Bij, Hendrik E; Weckhuysen, Bert M

2015-10-21

Phosphorus and microporous aluminosilicates, better known as zeolites, have a unique but poorly understood relationship. For example, phosphatation of the industrially important zeolite H-ZSM-5 is a well-known, relatively inexpensive and seemingly straightforward post-synthetic modification applied by the chemical industry not only to alter its hydrothermal stability and acidity, but also to increase its selectivity towards light olefins in hydrocarbon catalysis. On the other hand, phosphorus poisoning of zeolite-based catalysts, which are used for removing nitrogen oxides from exhaust fuels, poses a problem for their use in diesel engine catalysts. Despite the wide impact of phosphorus-zeolite chemistry, the exact physicochemical processes that take place require a more profound understanding. This review article provides the reader with a comprehensive and state-of-the-art overview of the academic literature, from the first reports in the late 1970s until the most recent studies. In the first part an in-depth analysis is undertaken, which will reveal universal physicochemical and structural effects of phosphorus-zeolite chemistry on the framework structure, accessibility, and strength of acid sites. The second part discusses the hydrothermal stability of zeolites and clarifies the promotional role that phosphorus plays. The third part of the review paper links the structural and physicochemical effects of phosphorus on zeolite materials with their catalytic performance in a variety of catalytic processes, including alkylation of aromatics, catalytic cracking, methanol-to-hydrocarbon processing, dehydration of bioalcohol, and ammonia selective catalytic reduction (SCR) of NOx. Based on these insights, we discuss potential applications and important directions for further research.

General Platform for Systematic Quantitative Evaluation of Small-Molecule Permeability in Bacteria

PubMed Central

2015-01-01

The chemical features that impact small-molecule permeability across bacterial membranes are poorly understood, and the resulting lack of tools to predict permeability presents a major obstacle to the discovery and development of novel antibiotics. Antibacterials are known to have vastly different structural and physicochemical properties compared to nonantiinfective drugs, as illustrated herein by principal component analysis (PCA). To understand how these properties influence bacterial permeability, we have developed a systematic approach to evaluate the penetration of diverse compounds into bacteria with distinct cellular envelopes. Intracellular compound accumulation is quantitated using LC-MS/MS, then PCA and Pearson pairwise correlations are used to identify structural and physicochemical parameters that correlate with accumulation. An initial study using 10 sulfonyladenosines in Escherichia coli, Bacillus subtilis, and Mycobacterium smegmatis has identified nonobvious correlations between chemical structure and permeability that differ among the various bacteria. Effects of cotreatment with efflux pump inhibitors were also investigated. This sets the stage for use of this platform in larger prospective analyses of diverse chemotypes to identify global relationships between chemical structure and bacterial permeability that would enable the development of predictive tools to accelerate antibiotic drug discovery. PMID:25198656

Autogenous teeth used for bone grafting: a comparison with traditional grafting materials.

PubMed

Kim, Young-Kyun; Kim, Su-Gwan; Yun, Pil-Young; Yeo, In-Sung; Jin, Seung-Chan; Oh, Ji-Su; Kim, Heung-Joong; Yu, Sun-Kyoung; Lee, Sook-Young; Kim, Jae-Sung; Um, In-Woong; Jeong, Mi-Ae; Kim, Gyung-Wook

2014-01-01

This study evaluated the surface structures and physicochemical characteristics of a novel autogenous tooth bone graft material currently in clinical use. The material's surface structure was compared with a variety of other bone graft materials via scanning electron microscope (SEM). The crystalline structure of the autogenous tooth bone graft material from the crown (AutoBT crown) and root (AutoBT root), xenograft (BioOss), alloplastic material (MBCP), allograft (ICB), and autogenous mandibular cortical bone were compared using x-ray diffraction (XRD) analysis. The solubility of each material was measured with the Ca/P dissolution test. The results of the SEM analysis showed that the pattern associated with AutoBT was similar to that from autogenous cortical bones. In the XRD analysis, AutoBT root and allograft showed a low crystalline structure similar to that of autogenous cortical bones. In the CaP dissolution test, the amount of calcium and phosphorus dissolution in AutoBT was significant from the beginning, while displaying a pattern similar to that of autogenous cortical bones. In conclusion, autogenous tooth bone graft materials can be considered to have physicochemical characteristics similar to those of autogenous bones. Copyright © 2014 Elsevier Inc. All rights reserved.

Structural Modification of Fish Gelatin by the Addition of Gellan, κ-Carrageenan, and Salts Mimics the Critical Physicochemical Properties of Pork Gelatin.

PubMed

Sow, Li Cheng; Kong, Karmaine; Yang, Hongshun

2018-05-01

Pork gelatin is not suitable for halal and kosher application; however, fish gelatin (FG) can be modified for use as a pork gelatin (PG) mimetic. Herein, low-acyl gellan (GE), κ-carrageenan (KC), and salts (CaCl 2 or KCl) were combined with a 180 Bloom tilapia FG. A formulation comprising 5.925% (w/v) FG + 0.025% (w/v) GE + 3mM CaCl 2 best matched the physicochemical properties of PG. The modification increased the FG gel strength from 115 ± 2 to 149 ± 2 g (matching the 148 ± 2 of PG), while the T m increased from 27.9 ± 1.0 to 32.4 ± 0.8 °C (matching the 33.1 ± 0.3 °C of PG). Nanoaggregates (diameter between 150 and 300 nm) could be an important structural factor affecting the physicochemical properties, as both PG and GE-modified FG showed a similar frequency distribution in this size group (57.4 ± 1.6% (PG) compared with 56.3 ± 2.2% (modified FG)). To further explore the differences between KC and GE in modifying of FG's structure, the FG-KC and FG-GE gels were compared. The zeta potential and Fourier transform infrared (FTIR) spectroscopy results for the FG-KC gel supported an associative interaction with complex formation, as indicated from the large aggregates and amorphous phase under atomic force microscopy (AFM). Contrastingly, a segregative FG-GE interaction took place in presence of CaCl 2 . These structures and interaction differences between FG-GE and FG-KC influenced the macro-properties of FG, possibly explaining the differences in the modification of the melting temperature of FG. A diagram representing the interaction-structure-physicochemical properties was proposed to explain the differences between the FG-GE and FG-KC gels. Certain people cannot consume any pork product or derivatives for religious reasons, thus it is essential to find a pork gelatin (PG) substitute for food product development. The commonly used polysaccharides, gellan and carrageenan, together with salt, can be added to fish gelatin (FG) to match the textural properties of PG, representing a promising substitute for PG. The difference in the mechanism of gellan and carrageenan to improve properties of FG has been revealed from nanostructure level. The use of food grade ingredients and simple mixing process are favorable in the food industry. © 2018 Institute of Food Technologists®.

Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences.

PubMed

Chen, Peng; Li, Jinyan; Wong, Limsoon; Kuwahara, Hiroyuki; Huang, Jianhua Z; Gao, Xin

2013-08-01

Hot spot residues of proteins are fundamental interface residues that help proteins perform their functions. Detecting hot spots by experimental methods is costly and time-consuming. Sequential and structural information has been widely used in the computational prediction of hot spots. However, structural information is not always available. In this article, we investigated the problem of identifying hot spots using only physicochemical characteristics extracted from amino acid sequences. We first extracted 132 relatively independent physicochemical features from a set of the 544 properties in AAindex1, an amino acid index database. Each feature was utilized to train a classification model with a novel encoding schema for hot spot prediction by the IBk algorithm, an extension of the K-nearest neighbor algorithm. The combinations of the individual classifiers were explored and the classifiers that appeared frequently in the top performing combinations were selected. The hot spot predictor was built based on an ensemble of these classifiers and to work in a voting manner. Experimental results demonstrated that our method effectively exploited the feature space and allowed flexible weights of features for different queries. On the commonly used hot spot benchmark sets, our method significantly outperformed other machine learning algorithms and state-of-the-art hot spot predictors. The program is available at http://sfb.kaust.edu.sa/pages/software.aspx. Copyright © 2013 Wiley Periodicals, Inc.

Physico-Chemical Conversion of Lignocellulose: Inhibitor Effects and Detoxification Strategies: A Mini Review.

PubMed

Kim, Daehwan

2018-02-01

A pretreatment of lignocellulosic biomass to produce biofuels, polymers, and other chemicals plays a vital role in the biochemical conversion process toward disrupting the closely associated structures of the cellulose-hemicellulose-lignin molecules. Various pretreatment steps alter the chemical/physical structure of lignocellulosic materials by solubilizing hemicellulose and/or lignin, decreasing the particle sizes of substrate and the crystalline portions of cellulose, and increasing the surface area of biomass. These modifications enhance the hydrolysis of cellulose by increasing accessibilities of acids or enzymes onto the surface of cellulose. However, lignocellulose-derived byproducts, which can inhibit and/or deactivate enzyme and microbial biocatalysts, are formed, including furan derivatives, lignin-derived phenolics, and carboxylic acids. These generation of compounds during pretreatment with inhibitory effects can lead to negative effects on subsequent steps in sugar flat-form processes. A number of physico-chemical pretreatment methods such as steam explosion, ammonia fiber explosion (AFEX), and liquid hot water (LHW) have been suggested and developed for minimizing formation of inhibitory compounds and alleviating their effects on ethanol production processes. This work reviews the physico-chemical pretreatment methods used for various biomass sources, formation of lignocellulose-derived inhibitors, and their contributions to enzymatic hydrolysis and microbial activities. Furthermore, we provide an overview of the current strategies to alleviate inhibitory compounds present in the hydrolysates or slurries.

Bis-quaternary gemini surfactants as components of nonviral gene delivery systems: a comprehensive study from physicochemical properties to membrane interactions.

PubMed

Cardoso, Ana M; Morais, Catarina M; Silva, Sandra G; Marques, Eduardo F; de Lima, Maria C Pedroso; Jurado, Maria Amália S

2014-10-20

Gemini surfactants have been successfully used as components of gene delivery systems. In the present work, a family of gemini surfactants, represented by the general structure [CmH2m+1(CH3)2N(+)(CH2)sN(+)(CH3)2CmH2m+1]2Br(-), or simply m-s-m, was used to prepare cationic gene carriers, aiming at their application in transfection studies. An extensive characterization of the gemini surfactant-based complexes, produced with and without the helper lipids cholesterol and DOPE, was carried out in order to correlate their physico-chemical properties with transfection efficiency. The most efficient complexes were those containing helper lipids, which, combining amphiphiles with propensity to form structures with different intrinsic curvatures, displayed a morphologically labile architecture, putatively implicated in the efficient DNA release upon complex interaction with membranes. While complexes lacking helper lipids were translocated directly across the lipid bilayer, complexes containing helper lipids were taken up by cells also by macropinocytosis. This study contributes to shed light on the relationship between important physico-chemical properties of surfactant-based DNA vectors and their efficiency to promote gene transfer, which may represent a step forward to the rational design of gene delivery systems. Copyright © 2014 Elsevier B.V. All rights reserved.

Size effect of ZnO nanorods on physicochemical properties of plasticized starch composites.

PubMed

Guz, L; Famá, L; Candal, R; Goyanes, S

2017-02-10

This work demonstrates that the size of ZnO nanorods (ZnONR) with similar aspect ratio determines several physicochemical and microbiological properties of thermoplastic starch composites (TPS/ZnONR) at a given concentration of ZnONRs. A combination of sol-gel and hydrothermal methods was developed to synthesize ZnONR with different sizes but similar aspect ratios. Starch composites containing 1wt.% of ZnONR were prepared by casting. Composites with smaller size nanorods (ZnONR-S) showed more efficiency in shielding UVA radiation and had a higher solubility and water vapor permeability than those with larger nanorods (ZnONR-L). Mechanical properties, biodegradability and antibacterial activity were also influenced by the size of the ZnONR. X-ray diffraction analysis showed that composites with ZnONR-S maintained the typical B-V type starch structure, intensifying the V-type starch structure peaks, while composite with ZnONR-L induced the formation of an amorphous structure, preventing starch retrogradation during storage. Properties affected by nanorods size are fundamental in determining composite applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Preparation and physicochemical characterization of 5 niclosamide solvates and 1 hemisolvate.

PubMed

van Tonder, Elsa C; Mahlatji, Mabatane D; Malan, Sarel F; Liebenberg, Wilna; Caira, Mino R; Song, Mingna; de Villiers, Melgardt M

2004-02-23

The purpose of the study was to characterize the physicochemical, structural, and spectral properties of the 1:1 niclosamide and methanol, diethyl ether, dimethyl sulfoxide, N,N' dimethylformamide, and tetrahydrofuran solvates and the 2:1 niclosamide and tetraethylene glycol hemisolvate prepared by recrystallization from these organic solvents. Structural, spectral, and thermal analysis results confirmed the presence of the solvents and differences in the structural properties of these solvates. In addition, differences in the activation energy of desolvation, batch solution calorimetry, and the aqueous solubility at 25 degrees C, 24 hours, showed the stability of the solvates to be in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > methanol solvate > dimethyl sulfoxide solvate > N,N' dimethylformamide solvate. The intrinsic and powder dissolution rates of the solvates were in the order: anhydrate > diethyl ether solvate > tetraethylene glycol hemisolvate > N,N' dimethylformamide solvate > methanol solvate > dimethyl sulfoxide solvate. Although these nonaqueous solvates had higher solubility and dissolution rates than the monohydrous forms, they were unstable in aqueous media and rapidly transformed to one of the monohydrous forms.

Virtual screening applications: a study of ligand-based methods and different structure representations in four different scenarios.

PubMed

Hristozov, Dimitar P; Oprea, Tudor I; Gasteiger, Johann

2007-01-01

Four different ligand-based virtual screening scenarios are studied: (1) prioritizing compounds for subsequent high-throughput screening (HTS); (2) selecting a predefined (small) number of potentially active compounds from a large chemical database; (3) assessing the probability that a given structure will exhibit a given activity; (4) selecting the most active structure(s) for a biological assay. Each of the four scenarios is exemplified by performing retrospective ligand-based virtual screening for eight different biological targets using two large databases--MDDR and WOMBAT. A comparison between the chemical spaces covered by these two databases is presented. The performance of two techniques for ligand--based virtual screening--similarity search with subsequent data fusion (SSDF) and novelty detection with Self-Organizing Maps (ndSOM) is investigated. Three different structure representations--2,048-dimensional Daylight fingerprints, topological autocorrelation weighted by atomic physicochemical properties (sigma electronegativity, polarizability, partial charge, and identity) and radial distribution functions weighted by the same atomic physicochemical properties--are compared. Both methods were found applicable in scenario one. The similarity search was found to perform slightly better in scenario two while the SOM novelty detection is preferred in scenario three. No method/descriptor combination achieved significant success in scenario four.

Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

PubMed Central

Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

2015-01-01

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223

Sea ice microorganisms: environmental constraints and extracellular responses.

PubMed

Ewert, Marcela; Deming, Jody W

2013-03-28

Inherent to sea ice, like other high latitude environments, is the strong seasonality driven by changes in insolation throughout the year. Sea-ice organisms are exposed to shifting, sometimes limiting, conditions of temperature and salinity. An array of adaptations to survive these and other challenges has been acquired by those organisms that inhabit the ice. One key adaptive response is the production of extracellular polymeric substances (EPS), which play multiple roles in the entrapment, retention and survival of microorganisms in sea ice. In this concept paper we consider two main areas of sea-ice microbiology: the physico-chemical properties that define sea ice as a microbial habitat, imparting particular advantages and limits; and extracellular responses elicited in microbial inhabitants as they exploit or survive these conditions. Emphasis is placed on protective strategies used in the face of fluctuating and extreme environmental conditions in sea ice. Gaps in knowledge and testable hypotheses are identified for future research.

Sea Ice Microorganisms: Environmental Constraints and Extracellular Responses

PubMed Central

Ewert, Marcela; Deming, Jody W.

2013-01-01

Inherent to sea ice, like other high latitude environments, is the strong seasonality driven by changes in insolation throughout the year. Sea-ice organisms are exposed to shifting, sometimes limiting, conditions of temperature and salinity. An array of adaptations to survive these and other challenges has been acquired by those organisms that inhabit the ice. One key adaptive response is the production of extracellular polymeric substances (EPS), which play multiple roles in the entrapment, retention and survival of microorganisms in sea ice. In this concept paper we consider two main areas of sea-ice microbiology: the physico-chemical properties that define sea ice as a microbial habitat, imparting particular advantages and limits; and extracellular responses elicited in microbial inhabitants as they exploit or survive these conditions. Emphasis is placed on protective strategies used in the face of fluctuating and extreme environmental conditions in sea ice. Gaps in knowledge and testable hypotheses are identified for future research. PMID:24832800

Variability in the phytoplankton community of Kavaratti reef ecosystem (northern Indian Ocean) during peak and waning periods of El Niño 2016.

PubMed

Karati, Kusum Komal; Vineetha, G; Madhu, N V; Anil, P; Dayana, M; Shihab, B K; Muhsin, A I; Riyas, C; Raveendran, T V

2017-11-29

El Niño, an interannual climate event characterized by elevated oceanic temperature, is a prime threat for coral reef ecosystems worldwide, owing to their thermal threshold sensitivity. Phytoplankton plays a crucial role in the sustenance of reef trophodynamics. The cell size of the phytoplankton forms the "master morphological trait" with implications for growth, resource acquisition, and adaptability to nutrients. In the context of a strong El Niño prediction for 2015-2016, the present study was undertaken to evaluate the variations in the size-structured phytoplankton of Kavaratti reef waters, a major coral atoll along the southeast coast of India. The present study witnessed a remarkable change in the physicochemical environment of the reef water and massive coral bleaching with the progression of El Niño 2015-2016 from its peak to waning phase. The fluctuations observed in sea surface temperature, pH, and nutrient concentration of the reef water with the El Niño progression resulted in a remarkable shift in phytoplankton size structure, abundance, and community composition of the reef waters. Though low nutrient concentration of the waning phase resulted in lower phytoplankton biomass and abundance, the diazotroph Trichodesmium erythraeum predominated the reef waters, owing to its capability of the atmospheric nitrogen fixation and dissolved organic phosphate utilization.

Recent advances in tea polysaccharides: Extraction, purification, physicochemical characterization and bioactivities.

PubMed

Chen, Guijie; Yuan, Qingxia; Saeeduddin, Muhammad; Ou, Shiyi; Zeng, Xiaoxiong; Ye, Hong

2016-11-20

Tea has a long history of medicinal and dietary use. Tea polysaccharide (TPS) is regarded as one of the main bioactive constituents of tea and is beneficial for health. Over the last decades, considerable efforts have been devoted to the studies on TPS: extraction, structural feature and bioactivity of TPS. However, it has been received much less attention compared with tea polyphenols. In order to provide new insight for further development of TPS in functional foods, in present review we summarize the recent literature, update the information and put forward future perspectives on TPS covering its extraction, purification, quantitative determination techniques as well as physicochemical characterization and bioactivities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Direct Human Contact with Siloxanes (Silicones) – Safety or Risk Part 1. Characteristics of Siloxanes (Silicones)

PubMed Central

Mojsiewicz-Pieńkowska, Krystyna; Jamrógiewicz, Marzena; Szymkowska, Katarzyna; Krenczkowska, Dominika

2016-01-01

Siloxanes are commonly known as silicones. They belong to the organosilicon compounds and are exclusively obtained by synthesis. Their chemical structure determines a range of physicochemical properties which were recognized as unique. Due to the susceptibility to chemical modifications, ability to create short, long or complex polymer particles, siloxanes found an application in many areas of human life. Siloxanes differ in particle size, molecular weight, shape and chemical groups. As a result, this determines the different physico-chemical properties, that directly affect the safety or the risk of their use. The areas that can be a source of danger to human health will be commented in this paper. PMID:27303296

Assessing therapeutic relevance of biologically interesting, ampholytic substances based on their physicochemical and spectral characteristics with chemometric tools

NASA Astrophysics Data System (ADS)

Judycka, U.; Jagiello, K.; Bober, L.; Błażejowski, J.; Puzyn, T.

2018-06-01

Chemometric tools were applied to investigate the biological behaviour of ampholytic substances in relation to their physicochemical and spectral properties. Results of the Principal Component Analysis suggest that size of molecules and their electronic and spectral characteristics are the key properties required to predict therapeutic relevance of the compounds examined. These properties were used for developing the structure-activity classification model. The classification model allows assessing the therapeutic behaviour of ampholytic substances on the basis of solely values of descriptors that can be obtained computationally. Thus, the prediction is possible without necessity of carrying out time-consuming and expensive laboratory tests, which is its main advantage.

Effect of ultrasound treatment on the wet heating Maillard reaction between mung bean [Vigna radiate (L.)] protein isolates and glucose and on structural and physico-chemical properties of conjugates.

PubMed

Wang, Zhongjiang; Han, Feifei; Sui, Xiaonan; Qi, Baokun; Yang, Yong; Zhang, Hui; Wang, Rui; Li, Yang; Jiang, Lianzhou

2016-03-30

The objective of this study was to determine the effect of ultrasound treatment on the wet heating Maillard reaction between mung bean protein isolates (MBPIs) and glucose, and on structural and physico-chemical properties of the conjugates. The degree of glycosylation of MBPI-glucose conjugates treated by ultrasound treatment and wet heating (MBPI-GUH) was higher than that of MBPI-glucose conjugates only treated by wet heating (MBPI-GH). Solubility, emulsification activity, emulsification stability and surface hydrophobicity of MBPI-GUH were higher than that of MBPI-GH. Grafted MBPIs had a lower content of α-helix and unordered coil, but a higher content of β-sheet and β-turn structure than MBPIs. No significant structural changes were observed in β-turn and random coil structure of MBPI-GUH, while α-helix content increased with ultrasonic time, and decreased at 300 W ultrasonic power with the increase of β-sheet. MBPI-GUH had a less compact tertiary structure compared to MBPI-GH and MBPI. Grafting MBPIs with glucose formed conjugates of higher molecular weight, while no significant changes were observed in electrophoresis profiles of MBPI-GUH. Ultrasound-assisted wet heating Maillard reaction between MBPIs and glucose could be a promising way to improve functional properties of MBPIs. © 2015 Society of Chemical Industry.

Humic Substances in Organic Wastes and their Effects on Amended Soils

NASA Astrophysics Data System (ADS)

Senesi, N.; Ciavatta, C.; Plaza, C.

2009-04-01

Soil humic substances (HS) are universally recognized to play a major role in a wide number of agronomic and environmental processes. For example, soil HS are able to bind mineral particles together, thus promoting a good soil structure, constitute an important source of nutrients for plants and microorganisms, contribute largely to the acid-base buffering capacity of soils, and exert a marked control on the biological availability, physico-chemical behavior, and environmental fate of toxic metal ions and xenobiotics. For these reasons, the knowledge of the short- and long-term effects of organic amendments on the status, quality, and reactivity of indigenous soil HS is of paramount importance. The objective of this presentation is to provide an overview of the chemical and physico-chemical data available in the literature for the evaluation of the effects of organic wastes of various origin and nature used as soil amendments on the composition, structure, and chemical reactivity of native soil HS. In general, HS-like components of organic wastes are typically characterized by a relatively larger presence of aliphatic, amide, and polysaccharide structures, simple structural components of wide molecular heterogeneity, smaller contents of oxygen, acidic functional groups, and organic free radicals, and smaller degrees of aromatic ring polycondensation, polymerization, and humification than native soil HS. Further, with respect to native soil HS, HS-like fractions from organic wastes generally exhibit smaller binding capacities and affinities for metal ions and organic xenobiotics. Appropriate treatment processes of raw organic wastes able to produce environmentally safe and agronomically efficient soil amendments, such as composting, yield HS-like fractions characterized by chemical and physico-chemical features that approach those of native soil HS. In general, aliphatic, polysaccharide, and lignin structures and S- and N-containing groups of the HS-like fractions of organic wastes can be partially incorporated into native soil HS determining modifications at various extents of their composition, structure, and chemistry. The changes occurred in amended soil HS are more evident when untreated organic materials are used. However, with increasing time after land application, the effects observed become less and less apparent with a clear trend to approach the molecular properties typical of native soil HS.

ABIOTIC REDOX TRANSFORMATION OF ORGANIC COMPOUNDS AT THE CLAY-WATER INTERFACE

EPA Science Inventory

The interactions of clay, water and organic compounds considerably modify the structural and physico-chemical properties of all components and create a unique domain for biological and chemical species in environments. Previous research indicates that the nature and properties of...

CLINICALLY RELEVANT IGE-CROSS-REACTIVITY OF NUT ALLERGENS

EPA Science Inventory

All data resulting from this study will be catalogued in SDAP .This work will generate important information relating the structure/ physicochemical properties of cross-reactive IgE epitopes to clinical response, and model factors that underlie allergen recognition by the immu...

Principal Physicochemical Methods Used to Characterize Dendrimer Molecule Complexes Used as Genetic Therapy Agents, Nanovaccines or Drug Carriers.

PubMed

Alberto, Rodríguez Fonseca Rolando; Joao, Rodrigues; de Los Angeles, Muñoz-Fernández María; Alberto, Martínez Muñoz; Manuel Jonathan, Fragoso Vázquez; José, Correa Basurto

2017-08-30

Nanomedicine is the application of nanotechnology to medicine. This field is related to the study of nanodevices and nanomaterials applied to various medical uses, such as in improving the pharmacological properties of different molecules. Dendrimers are synthetic nanoparticles whose physicochemical properties vary according to their chemical structure. These molecules have been extensively investigated as drug nanocarriers to improve drug solubility and as sustained-release systems. New therapies such as gene therapy and the development of nanovaccines can be improved by the use of dendrimers. The biophysical and physicochemical characterization of nucleic acid/peptide-dendrimer complexes is crucial to identify their functional properties prior to biological evaluation. In that sense, it is necessary to first identify whether the peptide-dendrimer or nucleic aciddendrimer complexes can be formed and whether the complex can dissociate under the appropriate conditions at the target cells. In addition, biophysical and physicochemical characterization is required to determine how long the complexes remain stable, what proportion of peptide or nucleic acid is required to form the complex or saturate the dendrimer, and the size of the complex formed. In this review, we present the latest information on characterization systems for dendrimer-nucleic acid, dendrimer-peptide and dendrimer-drug complexes with several biotechnological and pharmacological applications. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Physicochemical and Immunomodulatory Properties of Gum Exudates Obtained from Astragalus myriacanthus and Some of Its Isolated Carbohydrate Biopolymers

PubMed Central

Hamedi, Azadeh; Yousefi, Gholamhossein; Farjadian, Shirin; Bour Bour, Mitra Saadat; Parhizkar, Elahenaz

2017-01-01

Plants gums are complex mixtures of different polysaccharides with a variety of biological activities and pharmaceutical applications. Few studies have focused on physicochemical and biological properties of gums obtained from different plants. This study was designed to determine potential pharmaceutical and pharmacological values of the gum exudates and its isolated biopolymers obtained from Astragalus myriacanthus Boiss [syn. Astracantha myriacantha (Boiss.) Podlech] (Fabaceae). The physicochemical, rheological, and mucoadhesion properties of the gum and its fractions was measured at 7, 27, and 37 °C with and without the presence of NaCl (1%). Also, the structural and immunomodulatory properties of several water soluble biopolymers isolated using ion exchange and size exclusion chromatographic methods were investigated on Jurkat cells at concentrations of 31.25, 62.5, 125, 250, 500 and 1000 μg/mL. The consistency and shear-thinning property of the gum and its fractions decreased as temperature increased. In the presence of NaCl, the consistency increased but no regular pattern was observed regarding to shear-thinning behavior. The mucoadhesion strength was 40.66 ± 2.08 g/cm2 which is suitable for use as a formulary mucoadhesive polymer. The isolated biopolymers had proteo-arabinoglycan structure. Their molecular weight was calculated to be 1.67-667 kDa. One biopolymer had a proliferative effect and others had dose dependent cytotoxic/proliferative properties. The crude gum and its insoluble fraction showed suitable mucoadhesion, swellability and rheological properties which makes them suitable for designing drug delivery systems. The gum proteo-arabinoglycans with different molecular weight and structures had different immunomodulatory properties. PMID:29552060

Influence of pH control in the formation of inclusion bodies during production of recombinant sphingomyelinase-D in Escherichia coli.

PubMed

Castellanos-Mendoza, Andrea; Castro-Acosta, Ricardo M; Olvera, Alejandro; Zavala, Guadalupe; Mendoza-Vera, Miguel; García-Hernández, Enrique; Alagón, Alejandro; Trujillo-Roldán, Mauricio A; Valdez-Cruz, Norma A

2014-09-12

Inclusion bodies (IBs) are aggregated proteins that form clusters when protein is overexpressed in heterologous expression systems. IBs have been considered as non-usable proteins, but recently they are being used as functional materials, catalytic particles, drug delivery agents, immunogenic structures, and as a raw material in recombinant therapeutic protein purification. However, few studies have been made to understand how culture conditions affect the protein aggregation and the physicochemical characteristics that lead them to cluster. The objective of our research was to understand how pH affects the physicochemical properties of IBs formed by the recombinant sphingomyelinase-D of tick expressed in E. coli BL21-Gold (DE3) by evaluating two pH culture strategies. Uncontrolled pH culture conditions favored recombinant sphingomyelinase-D aggregation and IB formation. The IBs of sphingomyelinase-D produced under controlled pH at 7.5 and after 24 h were smaller (<500 nm) than those produced under uncontrolled pH conditions (>500 nm). Furthermore, the composition, conformation and β-structure formation of the aggregates were different. Under controlled pH conditions in comparison to uncontrolled conditions, the produced IBs presented higher resistance to denaturants and proteinase-K degradation, presented β-structure, but apparently as time passes the IBs become compacted and less sensitive to amyloid dye binding. The manipulation of the pH has an impact on IB formation and their physicochemical characteristics. Particularly, uncontrolled pH conditions favored the protein aggregation and sphingomyelinase-D IB formation. The evidence may lead to find methodologies for bioprocesses to obtain biomaterials with particular characteristics, extending the application possibilities of the inclusion bodies.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

Integrating in Silico and in Vitro Approaches To Predict Drug Accessibility to the Central Nervous System.

PubMed

Zhang, Yan-Yan; Liu, Houfu; Summerfield, Scott G; Luscombe, Christopher N; Sahi, Jasminder

2016-05-02

Estimation of uptake across the blood-brain barrier (BBB) is key to designing central nervous system (CNS) therapeutics. In silico approaches ranging from physicochemical rules to quantitative structure-activity relationship (QSAR) models are utilized to predict potential for CNS penetration of new chemical entities. However, there are still gaps in our knowledge of (1) the relationship between marketed human drug derived CNS-accessible chemical space and preclinical neuropharmacokinetic (neuroPK) data, (2) interpretability of the selected physicochemical descriptors, and (3) correlation of the in vitro human P-glycoprotein (P-gp) efflux ratio (ER) and in vivo rodent unbound brain-to-blood ratio (Kp,uu), as these are assays routinely used to predict clinical CNS exposure, during drug discovery. To close these gaps, we explored the CNS druglike property boundaries of 920 market oral drugs (315 CNS and 605 non-CNS) and 846 compounds (54 CNS drugs and 792 proprietary GlaxoSmithKline compounds) with available rat Kp,uu data. The exact permeability coefficient (Pexact) and P-gp ER were determined for 176 compounds from the rat Kp,uu data set. Receiver operating characteristic curves were performed to evaluate the predictive power of human P-gp ER for rat Kp,uu. Our data demonstrates that simple physicochemical rules (most acidic pKa ≥ 9.5 and TPSA < 100) in combination with P-gp ER < 1.5 provide mechanistic insights for filtering BBB permeable compounds. For comparison, six classification modeling methods were investigated using multiple sets of in silico molecular descriptors. We present a random forest model with excellent predictive power (∼0.75 overall accuracy) using the rat neuroPK data set. We also observed good concordance between the structural interpretation results and physicochemical descriptor importance from the Kp,uu classification QSAR model. In summary, we propose a novel, hybrid in silico/in vitro approach and an in silico screening model for the effective development of chemical series with the potential to achieve optimal CNS exposure.

Influence of the physicochemical and aromatic properties on the chemical reactivity and its relation with carcinogenic and anticoagulant effect of 17β-aminoestrogens

NASA Astrophysics Data System (ADS)

Soriano-Correa, Catalina; Raya, Angélica; Barrientos-Salcedo, Carolina; Esquivel, Rodolfo O.

2014-06-01

Activity of steroid hormones is dependent upon a number of factors, as solubility, transport and metabolism. The functional differences caused by structural modifications could exert an influence on the chemical reactivity and biological effect. The goal of this work is to study the influence of the physicochemical and aromatic properties on the chemical reactivity and its relation with the carcinogenic risk that can associate with the anticoagulant effect of 17β-aminoestrogens using quantum-chemical descriptors at the DFT-B3LYP, BH&HLYP and M06-2X levels. The relative acidity of (H1) of the hydroxyl group increases with electron-withdrawing groups. Electron-donor groups favor the basicity. The steric hindrance of the substituents decreases the aromatic character and consequently diminution the carcinogenic effect. Density descriptors: hardness, electrophilic index, atomic charges, molecular orbitals, electrostatic potential and their geometric parameters permit analyses of the chemical reactivity and physicochemical features and to identify some reactive sites of 17β-aminoestrogens.

Effect of ultrasound-assisted freezing on the physico-chemical properties and volatile compounds of red radish.

PubMed

Xu, Bao-Guo; Zhang, Min; Bhandari, Bhesh; Cheng, Xin-Feng; Islam, Md Nahidul

2015-11-01

Power ultrasound, which can enhance nucleation rate and crystal growth rate, can also affect the physico-chemical properties of immersion frozen products. In this study, the influence of slow freezing (SF), immersion freezing (IF) and ultrasound-assisted freezing (UAF) on physico-chemical properties and volatile compounds of red radish was investigated. Results showed that ultrasound application significantly improved the freezing rate; the freezing time of ultrasound application at 0.26 W/cm(2) was shorten by 14% and 90%, compared to IF and SF, respectively. UAF products showed significant (p<0.05) reduction in drip loss and phytonutrients (anthocyanins, vitamin C and phenolics) loss. Compared to SF products, IF and UAF products showed better textural preservation and higher calcium content. The radish tissues exhibited better cellular structures under ultrasonic power intensities of 0.17 and 0.26 W/cm(2) with less cell separation and disruption. Volatile compound data revealed that radish aromatic profile was also affected in the freezing process. Copyright © 2015 Elsevier B.V. All rights reserved.

Cholinium-amino acid based ionic liquids: a new method of synthesis and physico-chemical characterization.

PubMed

De Santis, Serena; Masci, Giancarlo; Casciotta, Francesco; Caminiti, Ruggero; Scarpellini, Eleonora; Campetella, Marco; Gontrani, Lorenzo

2015-08-28

In the present work we report the synthesis and physico-chemical characterization in terms of the viscosity and density of a wide series of cholinium-amino acid based room temperature ionic liquids ([Ch][AA] RTILs). 18 different amino acids were used to obtain 14 room temperature ILs. Among the most common AAs, only valine did not form an RTIL but it is a liquid above 80 °C. With respect to the methods reported in the literature we propose a synthesis based on potentiometric titration which has several advantages such as shorter preparation time, stoichiometry within ±1%, very high yields (close to 100%), high reproducibility, and no use of organic solvents, thus being more environmentally friendly. We tried to prepare dianionic ILs with some AAs with two potentially ionisable groups but in all cases the salts were solids at room temperature. All the ILs were characterized by (1)H NMR to confirm the stoichiometry. Physico-chemical properties such as density, viscosity, refractive index and conductivity were measured as a function of temperature and correlated with empirical equations. The values were compared with the data already reported in the literature for some [Ch][AA] ILs. The thermal expansion coefficient αp and the molar volume Vm were also calculated from the experimental density values. Due to the high number of AAs explored and their structural heterogeneity we have been able to find some interesting correlations between the data obtained and the structural features of the AAs in terms of the alkyl chain length, hydrogen bonding ability, stacking and cyclization. Some parameters were also found to be in good agreement with those reported for other ILs. We think that these data can give an important contribution to the understanding of the structure-property relationship of ILs because they focused on the structural effect of the anions, while most data in the literature are focussed on the cations.

Effects of biochar blends on microbial community composition in two coastal plain soils

EPA Science Inventory

The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

A volumetric ablation model of EPDM considering complex physicochemical process in porous structure of char layer

NASA Astrophysics Data System (ADS)

Yang, Liu; Xiao-Jing, Yu; Jian-Ming, Ma; Yi-Wen, Guan; Jiang, Li; Qiang, Li; Sa, Yang

2017-06-01

A volumetric ablation model for EPDM (ethylene- propylene-diene monomer) is established in this paper. This model considers the complex physicochemical process in the porous structure of a char layer. An ablation physics model based on a porous structure of a char layer and another model of heterogeneous volumetric ablation char layer physics are then built. In the model, porosity is used to describe the porous structure of a char layer. Gas diffusion and chemical reactions are introduced to the entire porous structure. Through detailed formation analysis, the causes of the compact or loose structure in the char layer and chemical vapor deposition (CVD) reaction between pyrolysis gas and char layer skeleton are introduced. The Arrhenius formula is adopted to determine the methods for calculating carbon deposition rate C which is the consumption rate caused by thermochemical reactions in the char layer, and porosity evolution. The critical porosity value is used as a criterion for char layer porous structure failure under gas flow and particle erosion. This critical porosity value is obtained by fitting experimental parameters and surface porosity of the char layer. Linear ablation and mass ablation rates are confirmed with the critical porosity value. Results of linear ablation and mass ablation rate calculations generally coincide with experimental results, suggesting that the ablation analysis proposed in this paper can accurately reflect practical situations and that the physics and mathematics models built are accurate and reasonable.

Evaluation of SARs for the prediction of eye irritation/corrosion potential: structural inclusion rules in the BfR decision support system.

PubMed

Tsakovska, I; Saliner, A Gallegos; Netzeva, T; Pavan, M; Worth, A P

2007-01-01

The proposed REACH regulation within the European Union (EU) aims to minimise the number of laboratory animals used for human hazard and risk assessment while ensuring adequate protection of human health and the environment. One way to achieve this goal is to develop non-testing methods, such as (quantitative) structure-activity relationships ([Q]SARs), suitable for identifying toxicological hazard from chemical structure and physicochemical properties alone. A database containing data submitted within the EU New Chemicals Notification procedure was compiled by the German Bundesinstitut für Risikobewertung (BfR). On the basis of these data, the BfR built a decision support system (DSS) for the prediction of several toxicological endpoints. For the prediction of eye irritation and corrosion potential, the DSS contains 31 physicochemical exclusion rules evaluated previously by the European Chemicals Bureau (ECB), and 27 inclusion rules that define structural alerts potentially responsible for eye irritation and/or corrosion. This work summarises the results of a study carried out by the ECB to assess the performance of the BfR structural rulebase. The assessment included: (a) evaluation of the structural alerts by using the training set of 1341 substances with experimental data for eye irritation and corrosion; and (b) external validation by using an independent test set of 199 chemicals. Recommendations are made for the further development of the structural rules in order to increase the overall predictivity of the DSS.

Two Perspectives on the Origin of the Standard Genetic Code

NASA Astrophysics Data System (ADS)

Sengupta, Supratim; Aggarwal, Neha; Bandhu, Ashutosh Vishwa

2014-12-01

The origin of a genetic code made it possible to create ordered sequences of amino acids. In this article we provide two perspectives on code origin by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids. We determine the efficacy of the physico-chemical hypothesis of code origin in the absence and presence of horizontal gene transfer (HGT) by allowing a diverse collection of code-sequence sets to compete with each other. We find that in the absence of horizontal gene transfer, natural selection between competing codes distinguished by differences in the degree of physico-chemical optimization is unable to explain the structure of the standard genetic code. However, for certain probabilities of the horizontal transfer events, a universal code emerges having a structure that is consistent with the standard genetic code.

Physicochemical properties of black pepper (Piper nigrum) starch.

PubMed

Zhu, Fan; Mojel, Reuben; Li, Guantian

2018-02-01

Black pepper (Piper nigrum) is among the most popular spices around the world. Starch is the major component of black pepper. However, little is known about functional properties of this starch. In this study, swelling, solubility, thermal properties, rheology, and enzyme susceptibility of 2 black pepper starches were studied and compared with those of maize starch. Pepper starch had lower water solubility and swelling power than maize starch. It had higher viscosity during pasting event. In dynamic oscillatory analysis, pepper starch had lower storage modulus. Thermal analysis showed that pepper starch had much higher gelatinization temperatures (e.g., conclusion temperature of 94°C) than maize starch. The susceptibility to α-amylolysis of pepper starch was not very different from that of maize starch. Overall, the differences in the physicochemical properties of the 2 pepper starches are non-significant. The relationships between structure (especially amylopectin internal molecular structure) and properties of starch components are highlighted. Copyright © 2017 Elsevier Ltd. All rights reserved.

Study of heat-moisture treatment of potato starch granules by chemical surface gelatinization.

PubMed

Bartz, Josiane; da Rosa Zavareze, Elessandra; Dias, Alvaro Renato Guerra

2017-08-01

Native potato starch was subjected to heat-moisture treatment (HMT) at 12%, 15%, 18%, 21%, and 24% of moisture content at 110 °C for 1 h, and the effects on morphology, structure, and thermal and physicochemical properties were investigated. To reveal the internal structure, 30% and 50% of the granular surface were removed by chemical surface gelatinization in concentrated LiCl solution. At moisture contents of 12% and 15%, HTM reduced the gelatinization temperatures and relative crystallinity of the starches, while at moisture contents of 21% and 24 % both increased. The alterations on morphology, X-ray pattern, physicochemical properties, and increase of amylose content were more intense with the increase of moisture content of HMT. The removal of granular layers showed that the changes promoted by HMT occur throughout the whole granule and were pronounced at the core or peripheral region, depending of the moisture content applied during HMT. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Physicochemical properties of manganese oxides obtained via the sol-gel method: The reduction of potassium permanganate by polyvinyl alcohol

NASA Astrophysics Data System (ADS)

Ivanets, A. I.; Prozorovich, V. G.; Krivoshapkina, E. F.; Kuznetsova, T. F.; Krivoshapkin, P. V.; Katsoshvili, L. L.

2017-08-01

Experimental data on the sol-gel synthesis of manganese oxides formed during the reduction of potassium permanganate by polyvinyl alcohol in an aqueous medium are presented. The physicochemical properties of the obtained manganese oxide systems that depend on the conditions of the synthesis are studied by means of DTA, XRD, SEM, and the low temperature adsorption-desorption of nitrogen. It is found that the obtained samples have a mesoporous structure and predominantly consist of double potassium-manganese oxide K2Mn4O8 with a tunnel structure and impurities of oxides such as α-MnO2, MnO, α-Mn2O3, and Mn5O8. It is shown that the proposed method of synthesis allows us to regulate the size and volume of mesopores and, to a lesser extent, the texture of the obtained oxides, which can be considered promising sorbents for the selective extraction of strontium and cesium ions from multicomponent aqueous solutions.

The crucial effect of early-stage gelation on the mechanical properties of cement hydrates

NASA Astrophysics Data System (ADS)

Ioannidou, Katerina; Kanduč, Matej; Li, Lunna; Frenkel, Daan; Dobnikar, Jure; Del Gado, Emanuela

2016-07-01

Gelation and densification of calcium-silicate-hydrate take place during cement hydration. Both processes are crucial for the development of cement strength, and for the long-term evolution of concrete structures. However, the physicochemical environment evolves during cement formation, making it difficult to disentangle what factors are crucial for the mechanical properties. Here we use Monte Carlo and Molecular Dynamics simulations to study a coarse-grained model of cement formation, and investigate the equilibrium and arrested states. We can correlate the various structures with the time evolution of the interactions between the nano-hydrates during the preparation of cement. The novel emerging picture is that the changes of the physicochemical environment, which dictate the evolution of the effective interactions, specifically favour the early gel formation and its continuous densification. Our observations help us understand how cement attains its unique strength and may help in the rational design of the properties of cement and related materials.

Synthesis, characterization, bioactivity and potential application of phenolic acid grafted chitosan: A review.

PubMed

Liu, Jun; Pu, Huimin; Liu, Shuang; Kan, Juan; Jin, Changhai

2017-10-15

In recent years, increasing attention has been paid to the grafting of phenolic acid onto chitosan in order to enhance the bioactivity and widen the application of chitosan. Here, we present a comprehensive overview on the recent advances of phenolic acid grafted chitosan (phenolic acid-g-chitosan) in many aspects, including the synthetic method, structural characterization, biological activity, physicochemical property and potential application. In general, four kinds of techniques including carbodiimide based coupling, enzyme catalyzed grafting, free radical mediated grafting and electrochemical methods are frequently used for the synthesis of phenolic acid-g-chitosan. The structural characterization of phenolic acid-g-chitosan can be determined by several instrumental methods. The physicochemical properties of chitosan are greatly altered after grafting. As compared with chitosan, phenolic acid-g-chitosan exhibits enhanced antioxidant, antimicrobial, antitumor, anti-allergic, anti-inflammatory, anti-diabetic and acetylcholinesterase inhibitory activities. Notably, phenolic acid-g-chitosan shows potential applications in many fields as coating agent, packing material, encapsulation agent and bioadsorbent. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of electronic structure and physicochemical properties of antiparasitic nifurtimox analogues: A theoretical study

NASA Astrophysics Data System (ADS)

Soriano-Correa, Catalina; Raya, A.; Esquivel, Rodolfo O.

American trypanosomiasis, also known as Chagas' disease, is caused by Trypanosoma cruzi (T. cruzi). It is well known that trypanosomes, and particularly T. cruzi, are highly sensitive towards oxidative stress, i.e., to compounds than are able to produce free radicals. Generally, nifurtimox (NFX) and benznidazol are most effective in the acute phase of the disease; therefore, nitroheterocycles constitute good models to design other nitrocompounds with specific biological characteristics. Thus, we have performed an ab initio study at the Hartree-Fock and Density Functional Theory levels of theory of several NFX analogues recently synthesized, to characterize them by obtaining their electronic, structural, and physicochemical properties, which might be linked to the observed antichagasic activity. The antitrypanosomal activity scale previously reported for the NFX analogues studied in this work is in good agreement with our theoretical results, from which we can conclude that the activity seems to be related to the reactivity along with the acidity observed for the most active molecules.

The crucial effect of early-stage gelation on the mechanical properties of cement hydrates

PubMed Central

Ioannidou, Katerina; Kanduč, Matej; Li, Lunna; Frenkel, Daan; Dobnikar, Jure; Del Gado, Emanuela

2016-01-01

Gelation and densification of calcium–silicate–hydrate take place during cement hydration. Both processes are crucial for the development of cement strength, and for the long-term evolution of concrete structures. However, the physicochemical environment evolves during cement formation, making it difficult to disentangle what factors are crucial for the mechanical properties. Here we use Monte Carlo and Molecular Dynamics simulations to study a coarse-grained model of cement formation, and investigate the equilibrium and arrested states. We can correlate the various structures with the time evolution of the interactions between the nano-hydrates during the preparation of cement. The novel emerging picture is that the changes of the physicochemical environment, which dictate the evolution of the effective interactions, specifically favour the early gel formation and its continuous densification. Our observations help us understand how cement attains its unique strength and may help in the rational design of the properties of cement and related materials. PMID:27417911

Water Splitting Using Porous Silicon Photo-electrodes for Hydrogen Production

NASA Astrophysics Data System (ADS)

Ali, M.; Starkov, V. V.; Gosteva, E. A.; Druzhinin, A. V.; Sattar, S.

2017-11-01

This paper presents the efficiency study results of using gradient-porous silicon structures with different morphology, as photo-anodes for photo-electrochemical dissociation of water. The results of a study of the physicochemical properties of gradient-porous silicon structures show the relatively low cost and simplicity of the technological process, as well as the possibility of forming structures with predefined properties, allow the creation of effective devices for artificial photosynthesis based on porous silicon for subsequent use in hydrogen energy.

[Microeukaryotic biodiversity in the waste ore samples surrounding an acid mine drainage lake].

PubMed

Li, Si-Yuan; Hao, Chun-Bo; Wang, Li-Hua; Lü, Zheng; Zhang, Li-Na; Liu, Ying; Feng, Chuan-Ping

2013-10-01

The abandoned mineral samples were collected in an acid mine drainage area in Anhui Province. Molecular ecological methods were used to construct 18S rDNA clone libraries after analyzing the main physicochemical parameters, and then the microeukaryotic diversity and community structure in the acid mine drainage area were studied. The results showed that the region was strongly acidic (pH <3), and the concentrations of Fe, SO2-(4), P, NO-(3) -N showed the same trend, all higher in the bare waste ore samples PD and 1 M than in the vegetation covered samples LW and XC. Four eukaryotic phyla were detected in the abandoned mineral samples: Ascomycota, Basidiomycota, Glomeromycota and Arthropoda. Glomeromycota can form an absolute symbiotic relationship with the plant, and it was a key factor for early plant to adapt the terrestrial environment. The biodiversity of the vegetation covered samples LW and XC, which contained Glomeromycota, was much higher than that of the bare abandoned rock samples PD and 1 M. Moreover, many sequences in the libraries were closely related to some isolated strains, which are tolerant to low pH and heavy metals, such as Penicillium purpurogenum, Chaetothyriales sp. and Staninwardia suttonii.

Metagenomic covariation along densely sampled environmental gradients in the Red Sea

PubMed Central

Thompson, Luke R; Williams, Gareth J; Haroon, Mohamed F; Shibl, Ahmed; Larsen, Peter; Shorenstein, Joshua; Knight, Rob; Stingl, Ulrich

2017-01-01

Oceanic microbial diversity covaries with physicochemical parameters. Temperature, for example, explains approximately half of global variation in surface taxonomic abundance. It is unknown, however, whether covariation patterns hold over narrower parameter gradients and spatial scales, and extending to mesopelagic depths. We collected and sequenced 45 epipelagic and mesopelagic microbial metagenomes on a meridional transect through the eastern Red Sea. We asked which environmental parameters explain the most variation in relative abundances of taxonomic groups, gene ortholog groups, and pathways—at a spatial scale of <2000 km, along narrow but well-defined latitudinal and depth-dependent gradients. We also asked how microbes are adapted to gradients and extremes in irradiance, temperature, salinity, and nutrients, examining the responses of individual gene ortholog groups to these parameters. Functional and taxonomic metrics were equally well explained (75–79%) by environmental parameters. However, only functional and not taxonomic covariation patterns were conserved when comparing with an intruding water mass with different physicochemical properties. Temperature explained the most variation in each metric, followed by nitrate, chlorophyll, phosphate, and salinity. That nitrate explained more variation than phosphate suggested nitrogen limitation, consistent with low surface N:P ratios. Covariation of gene ortholog groups with environmental parameters revealed patterns of functional adaptation to the challenging Red Sea environment: high irradiance, temperature, salinity, and low nutrients. Nutrient-acquisition gene ortholog groups were anti-correlated with concentrations of their respective nutrient species, recapturing trends previously observed across much larger distances and environmental gradients. This dataset of metagenomic covariation along densely sampled environmental gradients includes online data exploration supplements, serving as a community resource for marine microbial ecology. PMID:27420030

Molecular Detection of Candidatus Scalindua pacifica and Environmental Responses of Sediment Anammox Bacterial Community in the Bohai Sea, China

PubMed Central

Dang, Hongyue; Zhou, Haixia; Zhang, Zhinan; Yu, Zishan; Hua, Er; Liu, Xiaoshou; Jiao, Nianzhi

2013-01-01

The Bohai Sea is a large semi-enclosed shallow water basin, which receives extensive river discharges of various terrestrial and anthropogenic materials such as sediments, nutrients and contaminants. How these terrigenous inputs may influence the diversity, community structure, biogeographical distribution, abundance and ecophysiology of the sediment anaerobic ammonium oxidation (anammox) bacteria was unknown. To answer this question, an investigation employing both 16S rRNA and hzo gene biomarkers was carried out. Ca. Scalindua bacteria were predominant in the surface sediments of the Bohai Sea, while non-Scalindua anammox bacteria were also detected in the Yellow River estuary and inner part of Liaodong Bay that received strong riverine and anthropogenic impacts. A novel 16S rRNA gene sequence clade was identified, putatively representing an anammox bacterial new candidate species tentatively named “Ca. Scalindua pacifica”. Several groups of environmental factors, usually with distinct physicochemical or biogeochemical natures, including general marine and estuarine physicochemical properties, availability of anammox substrates (inorganic N compounds), alternative reductants and oxidants, environmental variations caused by river discharges and associated contaminants such as heavy metals, were identified to likely play important roles in influencing the ecology and biogeochemical functioning of the sediment anammox bacteria. In addition to inorganic N compounds that might play a key role in shaping the anammox microbiota, organic carbon, organic nitrogen, sulfate, sulfide and metals all showed the potentials to participate in the anammox process, releasing the strict dependence of the anammox bacteria upon the direct availability of inorganic N nutrients that might be limiting in certain areas of the Bohai Sea. The importance of inorganic N nutrients and certain other environmental factors to the sediment anammox microbiota suggests that these bacteria were active for the in situ N transforming process and maintained a versatile life style well adapted to the varying environmental conditions of the studied coastal ocean. PMID:23577216

Bioactive constituents from Chinese natural medicines. XXII. Absolute structures of new megastigmane glycosides, sedumosides E1, E2, E3, F1, F2, and G, from Sedum sarmentosum (Crassulaceae).

PubMed

Morikawa, Toshio; Zhang, Yi; Nakamura, Seikou; Matsuda, Hisashi; Muraoka, Osamu; Yoshikawa, Masayuki

2007-03-01

Six new megastigmane glycosides, sedumosides E1, E2, E3, F1, F2, and G, were isolated from the whole plant of Sedum sarmentosum (Crassulaceae). The structures of new constituents including the absolute configuration were elucidated on the basis of chemical and physicochemical evidence.

Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Wei, Yu-Tuo; Pang, Zong-Wen; Du, Li-Qin; Chou, Kuo-Chen

2009-01-30

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus. (c) 2008 Wiley Periodicals, Inc.

Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine.

PubMed

Bonilla, José O; Kurth, Daniel G; Cid, Fabricio D; Ulacco, José H; Gil, Raúl A; Villegas, Liliana B

2018-04-28

The acid mine drainage that originates in the abandoned gold mine in San Luis, Argentina, is released into La Carolina stream. The aim of this study was to determine the influence of this mine drainage on the physicochemical parameters of the area studied and on both prokaryotic and eukaryotic community structure. In addition, specific relationships between microbial taxonomic groups and physicochemical parameters were established. The drainage that flows into La Carolina stream acidifies the stream and increases its sulfate, Zn, Cd and Te concentrations. Microbial analysis showed that prokaryotic community structure is mainly affected by pH values. Actinobacteria and Gammaproteobacteria were abundant in samples characterized by low pH values, while Nitrospirae, Chloroflexi, Deltaproteobacteria, Thaumarchaeota and Euryarchaeota were associated with high concentrations of heavy metals. Otherwise, Alphaproteobacteria was present in samples taken in sunlit areas. Regarding eukaryotic community structure, the sunlight had the greatest impact. Inside the mine, in the absence of light, fungi and protists members were the most abundant microorganisms, while those samples taken in the presence of light displayed algae (green algae and diatoms) as the most abundant ones. After receiving the mine drainage, the stream showed a decrease in the diatom abundance and green algae predominated.

Noncoded amino acids in protein engineering: Structure-activity relationship studies of hirudin-thrombin interaction.

PubMed

De Filippis, Vincenzo; Acquasaliente, Laura; Pontarollo, Giulia; Peterle, Daniele

2018-01-01

The advent of recombinant DNA technology allowed to site-specifically insert, delete, or mutate almost any amino acid in a given protein, significantly improving our knowledge of protein structure, stability, and function. Nevertheless, a quantitative description of the physical and chemical basis that makes a polypeptide chain to efficiently fold into a stable and functionally active conformation is still elusive. This mainly originates from the fact that nature combined, in a yet unknown manner, different properties (i.e., hydrophobicity, conformational propensity, polarizability, and hydrogen bonding capability) into the 20 standard natural amino acids, thus making difficult, if not impossible, to univocally relate the change in protein stability or function to the alteration of physicochemical properties caused by amino acid exchange(s). In this view, incorporation of noncoded amino acids with tailored side chains, allowing to finely tune the structure at a protein site, would facilitate to dissect the effects of a given mutation in terms of one or a few physicochemical properties, thus much expanding the scope of physical organic chemistry in the study of proteins. In this review, relevant applications from our laboratory will be presented on the use of noncoded amino acids in structure-activity relationships studies of hirudin binding to thrombin. © 2017 International Union of Biochemistry and Molecular Biology, Inc.

Influence of calcium-induced droplet heteroaggregation on the physicochemical properties of oppositely charged lactoferrin coated lutein droplets and whey protein isolate-coated DHA droplets.

PubMed

Li, Xin; Wang, Xu; Xu, Duoxia; Cao, Yanping; Wang, Shaojia; Wang, Bei; Wang, Chengtao; Sun, Baoguo

2017-08-01

The influence of calcium-induced droplet heteroaggregation on the formation and physicochemical stability of mixed lutein and DHA emulsions was studied. Heteroaggregation was induced by mixing oppositely charged lactoferrin (LF)-coated lutein and whey protein isolate (WPI)-coated DHA emulsions with different CaCl 2 concentrations at pH 6.0. The droplet size, zeta-potential, transmission-physical stability and microstructure behavior (CLSM and Cryo-SEM) of single-protein emulsions and mixed emulsions were measured as a function of different CaCl 2 concentrations. Lutein degradation and DHA oxidation by measurement of lipid hydroperoxides and thiobarbituric acid reactive substances were determined during storage. The physical stability of the mixed emulsions could be modulated by controlling CaCl 2 concentrations. Microstructure behavior indicated that a mixed emulsion with 30 mM CaCl 2 promoted more droplets to form a special three-dimensional network and microcluster structures. The chemical stability of the mixed lutein and DHA emulsions was obviously enhanced by the addition of 30 mM CaCl 2 . The decreased surface areas of the DHA and lutein droplets and the physical barrier of the network of heteroaggregates against transition metals and free radicals could mainly explain the improvement in chemical stability. Calcium-induced droplet aggregation may be useful for creating specific food structures that lead to desirable physicochemical properties of multiple functional components.

Preparation and biological properties of a novel composite scaffold of nano-hydroxyapatite/chitosan/carboxymethyl cellulose for bone tissue engineering

PubMed Central

Liuyun, Jiang; Yubao, Li; Chengdong, Xiong

2009-01-01

In this study, we report the physico-chemical and biological properties of a novel biodegradable composite scaffold made of nano-hydroxyapatite and natural derived polymers of chitosan and carboxymethyl cellulose, namely, n-HA/CS/CMC, which was prepared by freeze-drying method. The physico-chemical properties of n-HA/CS/CMC scaffold were tested by infrared absorption spectra (IR), transmission electron microscope(TEM), scanning electron microscope(SEM), universal material testing machine and phosphate buffer solution (PBS) soaking experiment. Besides, the biological properties were evaluated by MG63 cells and Mesenchymal stem cells (MSCs) culture experiment in vitro and a short period implantation study in vivo. The results show that the composite scaffold is mainly formed through the ionic crossing-linking of the two polyions between CS and CMC, and n-HA is incorporated into the polyelectrolyte matrix of CS-CMC without agglomeration, which endows the scaffold with good physico-chemical properties such as highly interconnected porous structure, high compressive strength and good structural stability and degradation. More important, the results of cells attached, proliferated on the scaffold indicate that the scaffold is non-toxic and has good cell biocompatibility, and the results of implantation experiment in vivo further confirm that the scaffold has good tissue biocompatibility. All the above results suggest that the novel degradable n-HA/CS/CMC composite scaffold has a great potential to be used as bone tissue engineering material. PMID:19594953

Solid-state characterization and impurities determination of fluconazol generic products marketed in Morocco

PubMed Central

Bourichi, Houda; Brik, Youness; Hubert, Philipe; Cherrah, Yahia; Bouklouze, Abdelaziz

2012-01-01

In this paper, we report the results of quality control based in physicochemical characterization and impurities determination of three samples of fluconazole drug substances marketed in Morocco. These samples were supplied by different pharmaceuticals companies. The sample A, as the discovered product, was supplied by Pfizer, while samples B and C (generics), were manufactured by two different Indian industries. Solid-state characterization of the three samples was realized with different physicochemical methods as: X-ray powder diffraction, Fourier-transformation infrared spectroscopy, differential scanning calorimetry. High performance liquid chromatography was used to quantify the impurities in the different samples. The results from the physicochemical methods cited above, showed difference in polymorph structure of the three drug substances. Sample A consisted in pure polymorph III, sample B consisted in pure polymorph II, sample C consisted in a mixture of fluconazole Form III, form II and the monohydrate. This result was confirmed by differential scanning calorimetry. Also it was demonstrated that solvents used during the re-crystallization step were among the origins of these differences in the structure form. On the other hand, the result of the stability study under humidity and temperature showed that fluconazole polymorphic transformation could be owed to the no compliance with the conditions of storage. The HPLC analysis of these compounds showed the presence of specific impurities for each polymorphic form, and a possible relationship could be exist between impurities and crystalline form of fluconazole. PMID:29403776

High-dilution effects revisited. 1. Physicochemical aspects.

PubMed

Bellavite, Paolo; Marzotto, Marta; Olioso, Debora; Moratti, Elisabetta; Conforti, Anita

2014-01-01

Several lines of evidence suggest that homeopathic high dilutions (HDs) can effectively have a pharmacological action, and so cannot be considered merely placebos. However, until now there has been no unified explanation for these observations within the dominant paradigm of the dose-response effect. Here the possible scenarios for the physicochemical nature of HDs are reviewed. A number of theoretical and experimental approaches, including quantum physics, conductometric and spectroscopic measurements, thermoluminescence, and model simulations investigated the peculiar features of diluted/succussed solutions. The heterogeneous composition of water could be affected by interactive phenomena such as coherence, epitaxy and formation of colloidal nanobubbles containing gaseous inclusions of oxygen, nitrogen, carbon dioxide, silica and, possibly, the original material of the remedy. It is likely that the molecules of active substance act as nucleation centres, amplifying the formation of supramolecular structures and imparting order to the solvent. Three major models for how this happens are currently being investigated: the water clusters or clathrates, the coherent domains postulated by quantum electrodynamics, and the formation of nanoparticles from the original solute plus solvent components. Other theoretical approaches based on quantum entanglement and on fractal-type self-organization of water clusters are more speculative and hypothetical. The problem of the physicochemical nature of HDs is still far from to be clarified but current evidence strongly supports the notion that the structuring of water and its solutes at the nanoscale can play a key role. Copyright © 2013 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Real-Time Optical Monitoring of Pt Catalyst Under the Potentiodynamic Conditions

NASA Astrophysics Data System (ADS)

Song, Hyeon Don; Lee, Minzae; Kim, Gil-Pyo; Choi, Inhee; Yi, Jongheop

2016-12-01

In situ monitoring of electrode materials reveals detailed physicochemical transition in electrochemical device. The key challenge is to explore the localized features of electrode surfaces, since the performance of an electrochemical device is determined by the summation of local architecture of the electrode material. Adaptive in situ techniques have been developed for numerous investigations; however, they require restricted measurement environments and provide limited information, which has impeded their widespread application. In this study, we realised an optics-based electrochemical in situ monitoring system by combining a dark-field micro/spectroscopy with an electrochemical workstation to investigate the physicochemical behaviours of Pt catalyst. We found that the localized plasmonic trait of a Pt-decorated Au nanoparticle as a model system varied in terms of its intensity and wavelength during the iterations of a cyclic voltammetry test. Furthermore, we show that morphological and compositional changes of the Pt catalyst can be traced in real time using changes in quantified plasmonic characteristics, which is a distinct advantage over the conventional electrochemistry-based in situ monitoring systems. These results indicate the substantial promise of online operando observation in a wide range of electrical energy conversion systems and electrochemical sensing areas.

Sorption of benzotriazoles under the conditions of RP HPLC

NASA Astrophysics Data System (ADS)

Dzhabieva, S. A.; Kurbatova, S. V.; Belousova, Z. P.

2016-02-01

The results of a chromatographic study of sorption of several benzotriazole derivatives on octadecyl silica gel were reported. The physicochemical and electronic parameters of benzotriazoles were calculated. The effect of the structure of analyte molecules and eluent composition on chromatographic retention of these substances was analyzed.

PREDICTING THE ADSORPTION CAPACITY OF ACTIVATED CARBON FOR ORGANIC CONTAMINANTS FROM ADSORBENT AND ADSORBATE PROPERTIES

EPA Science Inventory

A quantitative structure-property relationship (QSPR) was developed and combined with the Polanyi-Dubinin-Manes model to predict adsorption isotherms of emerging contaminants on activated carbons with a wide range of physico-chemical properties. Affinity coefficients (β_l

Measuring Physicochemical Properties to Inform the Scope of Existing QSAR/QSPR Models (SOT annual meeting)

EPA Science Inventory

Chemical structures and their properties are important for determining their potential toxicological effects, toxicokinetics, and route of exposure. These data are needed to prioritize thousands of environmental chemicals, but are often lacking. In order to fill data gaps, robust...

Changes in resistant starch from two banana cultivars during postharvest storage.

PubMed

Wang, Juan; Tang, Xue Juan; Chen, Ping Sheng; Huang, Hui Hua

2014-08-01

Banana resistant starch samples were extracted and isolated from two banana cultivars (Musa AAA group, Cavendish subgroup and Musa ABB group, Pisang Awak subgroup) at seven ripening stages during postharvest storage. The structures of the resistant starch samples were analysed by light microscopy, polarising microscopy, scanning electron microscopy, X-ray diffraction, and infrared spectroscopy. Physicochemical properties (e.g., water-holding capacity, solubility, swelling power, transparency, starch-iodine absorption spectrum, and Brabender microviscoamylograph profile) were determined. The results revealed significant differences in microstructure and physicochemical characteristics among the banana resistant starch samples during different ripening stages. The results of this study provide valuable information for the potential applications of banana resistant starches. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synthesis of mouse centromere-targeted polyamides and physico-chemical studies of their interaction with the target double-stranded DNA.

PubMed

Nozeret, Karine; Bonan, Marc; Yarmoluk, Serguiy M; Novopashina, Darya S; Boutorine, Alexandre S

2015-09-01

Synthetic minor groove-binding pyrrole-imidazole polyamides labeled by fluorophores are promising candidates for fluorescence imaging of double-stranded DNA in isolated chromosomes or fixed and living cells. We synthesized nine hairpin and two head-to-head tandem polyamides targeting repeated sequences from mouse major satellites. Their interaction with synthetic target dsDNA has been studied by physico-chemical methods in vitro before and after coupling to various fluorophores. Great variability in affinities and fluorescence properties reveals a conclusion that these properties do not only rely on recognition rules, but also on other known and unknown structural factors. Individual testing of each probe is needed before cellular applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Physicochemical properties and ion-solvent interactions in aqueous sodium, ammonium, and lead acetate solution

NASA Astrophysics Data System (ADS)

Deosarkar, S. D.; Mendkudle, M. S.

2014-09-01

Densities (ρ), viscosities (η) and refractive indices ( n D) of aqueous sodium acetate (SA), ammonium acetate (AA), and lead acetate (LA) solutions have been measured for different concentrations of salts at 302.15 K. Apparent molar volumes (φv) for studied solutions were calculated from density data, and fitted to Masson's relation and partial molar volume (φ{v/o}) was determined. Viscosity data were fitted to Jones-Dole equation and viscosity A- and B-coefficients were determined. Refractive index and density data were fitted to Lorentz and Lorenz equation and specific refraction ( R D) were calculated. Behavior of various physicochemical properties indicated presence of strong ion-solvent interactions in present systems and the acetate salts structure maker in water.

Improving Physical Properties via C–H Oxidation: Chemical and Enzymatic Approaches

PubMed Central

Michaudel, Quentin; Journot, Guillaume; Regueiro-Ren, Alicia; Goswami, Animesh; Guo, Zhiwei; Tully, Thomas P.; Zou, Lufeng; Ramabhadran, Raghunath O.; Houk, Kendall N.

2014-01-01

Physicochemical properties constitute a key factor for the success of a drug candidate. Whereas many strategies to improve the physicochemical properties of small heterocycle-type leads exist, complex hydrocarbon skeletons are more challenging to derivatize due to the absence of functional groups. A variety of C–H oxidation methods have been explored on the betulin skeleton to improve the solubility of this very bioactive, yet poorly water soluble, natural product. Capitalizing on the innate reactivity of the molecule, as well as the few molecular handles present on the core, allowed for oxidations at different positions across the pentacyclic structure. Enzymatic oxidations afforded several orthogonal oxidations to chemical methods. Solubility measurements showed an enhancement for many of the synthesized compounds. PMID:25244630

Interspecies quantitative structure-activity relationships (QSARs) for eco-toxicity screening of chemicals: the role of physicochemical properties.

PubMed

Furuhama, A; Hasunuma, K; Aoki, Y

2015-01-01

In addition to molecular structure profiles, descriptors based on physicochemical properties are useful for explaining the eco-toxicities of chemicals. In a previous study we reported that a criterion based on the difference between the partition coefficient (log POW) and distribution coefficient (log D) values of chemicals enabled us to identify aromatic amines and phenols for which interspecies relationships with strong correlations could be developed for fish-daphnid and algal-daphnid toxicities. The chemicals that met the log D-based criterion were expected to have similar toxicity mechanisms (related to membrane penetration). Here, we investigated the applicability of log D-based criteria to the eco-toxicity of other kinds of chemicals, including aliphatic compounds. At pH 10, use of a log POW - log D > 0 criterion and omission of outliers resulted in the selection of more than 100 chemicals whose acute fish toxicities or algal growth inhibition toxicities were almost equal to their acute daphnid toxicities. The advantage of log D-based criteria is that they allow for simple, rapid screening and prioritizing of chemicals. However, inorganic molecules and chemicals containing certain structural elements cannot be evaluated, because calculated log D values are unavailable.

Application of a Dense Gas Technique for Sterilizing Soft Biomaterials

PubMed Central

Karajanagi, Sandeep S.; Yoganathan, Roshan; Mammucari, Raffaella; Park, Hyoungshin; Cox, Julian; Zeitels, Steven M.; Langer, Robert; Foster, Neil R.

2017-01-01

Sterilization of soft biomaterials such as hydrogels is challenging because existing methods such as gamma irradiation, steam sterilization, or ethylene oxide sterilization, while effective at achieving high sterility assurance levels (SAL), may compromise their physicochemical properties and biocompatibility. New methods that effectively sterilize soft biomaterials without compromising their properties are therefore required. In this report, a dense-carbon dioxide (CO2)-based technique was used to sterilize soft polyethylene glycol (PEG)-based hydrogels while retaining their structure and physicochemical properties. Conventional sterilization methods such as gamma irradiation and steam sterilization severely compromised the structure of the hydrogels. PEG hydrogels with high water content and low elastic shear modulus (a measure of stiffness) were deliberately inoculated with bacteria and spores and then subjected to dense CO2. The dense CO2-based methods effectively sterilized the hydrogels achieving a SAL of 10−7 without compromising the viscoelastic properties, pH, water-content, and structure of the gels. Furthermore, dense CO2-treated gels were biocompatible and non-toxic when implanted subcutaneously in ferrets. The application of novel dense CO2-based methods to sterilize soft biomaterials has implications in developing safe sterilization methods for soft biomedical implants such as dermal fillers and viscosupplements. PMID:21337339

Soil cover of gas-bearing areas

NASA Astrophysics Data System (ADS)

Mozharova, N. V.

2010-08-01

Natural soils with disturbed functioning parameters compared to the background soils with conservative technogenic-pedogenic features were distinguished on vast areas above the artificial underground gas storages in the zones of spreading and predominant impact of hydrocarbon gases. The disturbance of the functioning parameters is related to the increase in the methane concentration, the bacterial oxidation intensity and destruction, and the complex microbiological and physicochemical synthesis of iron oxides. The technogenic-pedogenic features include neoformations of bacteriomorphic microdispersed iron oxides. The impurity components consist of elements typical for biogenic structures. New soil layers, horizons, specific anthropogenically modified soils, and soil-like structures were formed on small areas in the industrial zones of underground gas storages due to the mechanical disturbance, the deposition of drilling sludge, and the chemical contamination. Among the soils, postlithogenic formations were identified—chemotechnosols (soddy-podzolic soils and chernozems), as well as synlithogenic ones: strato-chemotechnosols and stratochemoembryozems. The soil-like bodies included postlithogenic soil-like structures (chemotechnozems) and synlithogenic ones (strato-chemotechnozems). A substantive approach was used for the soil diagnostics. The morphological and magnetic profiles and the physical, chemical, and physicochemical properties of the soils were analyzed. The micromorphological composition of the soil magnetic fraction was used as a magnetic label.

Chemometric analysis of correlations between electronic absorption characteristics and structural and/or physicochemical parameters for ampholytic substances of biological and pharmaceutical relevance.

PubMed

Judycka-Proma, U; Bober, L; Gajewicz, A; Puzyn, T; Błażejowski, J

2015-03-05

Forty ampholytic compounds of biological and pharmaceutical relevance were subjected to chemometric analysis based on unsupervised and supervised learning algorithms. This enabled relations to be found between empirical spectral characteristics derived from electronic absorption data and structural and physicochemical parameters predicted by quantum chemistry methods or phenomenological relationships based on additivity rules. It was found that the energies of long wavelength absorption bands are correlated through multiparametric linear relationships with parameters reflecting the bulkiness features of the absorbing molecules as well as their nucleophilicity and electrophilicity. These dependences enable the quantitative analysis of spectral features of the compounds, as well as a comparison of their similarities and certain pharmaceutical and biological features. Three QSPR models to predict the energies of long-wavelength absorption in buffers with pH=2.5 and pH=7.0, as well as in methanol, were developed and validated in this study. These models can be further used to predict the long-wavelength absorption energies of untested substances (if they are structurally similar to the training compounds). Copyright © 2014 Elsevier B.V. All rights reserved.

Black Carbon (Biochar) In Water/Soil Environments: Molecular Structure, Sorption, Stability, and Potential Risk.

PubMed

Lian, Fei; Xing, Baoshan

2017-12-05

Black carbon (BC) is ubiquitous in the environments and participates in various biogeochemical processes. Both positive and negative effects of BC (especially biochar) on the ecosystem have been identified, which are mainly derived from its diverse physicochemical properties. Nevertheless, few studies systematically examined the linkage between the evolution of BC molecular structure with the resulted BC properties, environmental functions as well as potential risk, which is critical for understanding the BC environmental behavior and utilization as a multifunctional product. Thus, this review highlights the molecular structure evolution of BC during pyrolysis and the impact of BC physicochemical properties on its sorption behavior, stability, and potential risk in terrestrial and aqueous ecosystems. Given the wide application of BC and its important role in biogeochemical processes, future research should focus on the following: (1) establishing methodology to more precisely predict and design BC properties on the basis of pyrolysis and phase transformation of biomass; (2) developing an assessment system to evaluate the long-term effect of BC on stabilization and bioavailability of contaminants, agrochemicals, and nutrient elements in soils; and (3) elucidating the interaction mechanisms of BC with plant roots, microorganisms, and soil components.

Physicochemical characterization of native and modified sodium caseinate- Vitamin A complexes.

PubMed

Gupta, Chitra; Arora, Sumit; Syama, M A; Sharma, Apurva

2018-04-01

Native and modified sodium caseinate- Vitamin A complexes {Sodium caseinate- Vit A complex by stirring (NaCas-VA ST), succinylated sodium caseinate- Vit A complex by stirring (SNaCas-VA ST), reassembled sodium caseinate- Vit A complex (RNaCas-VA) and reassembled succinylated sodium caseinate- Vit A complex (RSNaCas-VA)} were prepared and characterized for their physicochemical characteristics e.g. particle size, zeta potential, turbidity analysis and tryptophan intensities which confirmed structural modification of both native (NaCas-VA ST) and modified (SNaCas-VA ST, RNaCas-VA and RSNaCas- VA) proteins upon complex formation with vitamin A. Binding of vitamin A to milk protein reduced the turbidity caused by vitamin A, however, the particle size and zeta potential of milk protein increased after complexation. Microstructure details of NaCas (spray dried) showed uniform spherical structure, however, other milk proteins and milk protein- Vit A complexes (freeze dried) showed broken glass and flaky structures. Tiny particles were observed on the surface of reassembled protein and reassembled protein- Vit A complexes. Binding of vitamin A to milk protein did not have an influence on the electrophoretic mobility and elution profile (RP-HPLC). Copyright © 2018 Elsevier Ltd. All rights reserved.

Process signatures in glatiramer acetate synthesis: structural and functional relationships.

PubMed

Campos-García, Víctor R; Herrera-Fernández, Daniel; Espinosa-de la Garza, Carlos E; González, German; Vallejo-Castillo, Luis; Avila, Sandra; Muñoz-García, Leslie; Medina-Rivero, Emilio; Pérez, Néstor O; Gracia-Mora, Isabel; Pérez-Tapia, Sonia Mayra; Salazar-Ceballos, Rodolfo; Pavón, Lenin; Flores-Ortiz, Luis F

2017-09-21

Glatiramer Acetate (GA) is an immunomodulatory medicine approved for the treatment of multiple sclerosis, whose mechanisms of action are yet to be fully elucidated. GA is comprised of a complex mixture of polypeptides with different amino acid sequences and structures. The lack of sensible information about physicochemical characteristics of GA has contributed to its comprehensiveness complexity. Consequently, an unambiguous determination of distinctive attributes that define GA is of highest relevance towards dissecting its identity. Herein we conducted a study of characteristic GA heterogeneities throughout its manufacturing process (process signatures), revealing a strong impact of critical process parameters (CPPs) on the reactivity of amino acid precursors; reaction initiation and polymerization velocities; and peptide solubility, susceptibility to hydrolysis, and size-exclusion properties. Further, distinctive GA heterogeneities were correlated to defined immunological and toxicological profiles, revealing that GA possesses a unique repertoire of active constituents (epitopes) responsible of its immunological responses, whose modification lead to altered profiles. This novel approach established CPPs influence on intact GA peptide mixture, whose physicochemical identity cannot longer rely on reduced properties (based on complete or partial GA degradation), providing advanced knowledge on GA structural and functional relationships to ensure a consistent manufacturing of safe and effective products.

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

Assessment of physico-chemical quality of borehole and spring water sources supplied to Robe Town, Oromia region, Ethiopia

NASA Astrophysics Data System (ADS)

Shigut, Dagim Abera; Liknew, Geremew; Irge, Dejene Disasa; Ahmad, Tanweer

2017-03-01

The study was carried out to find the physico-chemical water quality of borehole and spring water supplied to Robe Town. For this study, a total of six water samples were collected from three borehole and three spring water sources. The analyses for 14 physico-chemical parameters, pH, turbidity, electrical conductivity, total dissolved solids, total suspended solids total hardness cations (Ca2+, Mg2+), anions (NO2 -, NO3 -, SO4 2- and PO4 3-) and heavy metals (Fe and Mn), were done in the laboratory by adopting standard procedures suggested by the American Public Health Association (APHA). Descriptive statistics were used to describe data, while Pearson correlation was used to determine the influences of the physico-chemical variables. The single factor analysis of variance ( t test) was used to determine possible differences between the borehole and spring water, while means plots were used for further structure detection. From the total samples analyzed, most of the samples comply with the water quality guidelines of Ethiopian limit, WHO and U.SEPA. The pH of the water samples from borehole groundwater source was found to be slightly acidic and bove the maximum permissible limit (MPL). High concentration of Fe and Mn that exceeds the MPL set by WHO was found in the three boreholes. The spring water sources were found to be better for drinking than borehole water sources.

OPERA: A free and open source QSAR tool for predicting physicochemical properties and environmental fate endpoints

EPA Science Inventory

Collecting the chemical structures and data for necessary QSAR modeling is facilitated by available public databases and open data. However, QSAR model performance is dependent on the quality of data and modeling methodology used. This study developed robust QSAR models for physi...

PREDICTING THE ADSORPTION CAPACITY OF ACTIVATED CARBON FOR EMERGING ORGANIC CONTAMINANTS FROM FUNDAMENTAL ADSORBENT AND ADSORBATE PROPERTIES - PRESENTATION

EPA Science Inventory

A quantitative structure-property relationship (QSPR) was developed and combined with the Polanyi-Dubinin-Manes model to predict adsorption isotherms of emerging contaminants on activated carbons with a wide range of physico-chemical properties. Affinity coefficients (β_l

OPERA: A QSAR tool for physicochemical properties and environmental fate predictions (ACS Spring meeting)

EPA Science Inventory

The collection of chemical structures and associated experimental data for QSAR modeling is facilitated by the increasing number and size of public databases. However, the performance of QSAR models highly depends on the quality of the data used and the modeling methodology. The ...

Applications of positron annihilation spectroscopy in materials research

NASA Technical Reports Server (NTRS)

Singh, Jag J.

1988-01-01

Positron Annihilation Spectroscopy (PAS) has emerged as a powerful technique for research in condensed matter. It has been used extensively in the study of metals, ionic crystals, glasses and polymers. The present review concentrates on applications of positron lifetime measurements for elucidation of the physicochemical structure of polymers.

21 CFR 320.33 - Criteria and evidence to assess actual or potential bioequivalence problems.

Code of Federal Regulations, 2012 CFR

2012-04-01

... bioavailability. (4) Certain physical structural characteristics of the active drug ingredient, e.g., polymorphic... effective use of the drug products requires careful dosage titration and patient monitoring. (d) Competent... or prevention of a serious disease or condition. (e) Physicochemical evidence that: (1) The active...

21 CFR 320.33 - Criteria and evidence to assess actual or potential bioequivalence problems.

Code of Federal Regulations, 2011 CFR

2011-04-01

... bioavailability. (4) Certain physical structural characteristics of the active drug ingredient, e.g., polymorphic... effective use of the drug products requires careful dosage titration and patient monitoring. (d) Competent... or prevention of a serious disease or condition. (e) Physicochemical evidence that: (1) The active...

21 CFR 320.33 - Criteria and evidence to assess actual or potential bioequivalence problems.

Code of Federal Regulations, 2010 CFR

2010-04-01

... bioavailability. (4) Certain physical structural characteristics of the active drug ingredient, e.g., polymorphic... effective use of the drug products requires careful dosage titration and patient monitoring. (d) Competent... or prevention of a serious disease or condition. (e) Physicochemical evidence that: (1) The active...

21 CFR 320.33 - Criteria and evidence to assess actual or potential bioequivalence problems.

Code of Federal Regulations, 2014 CFR

2014-04-01

... bioavailability. (4) Certain physical structural characteristics of the active drug ingredient, e.g., polymorphic... effective use of the drug products requires careful dosage titration and patient monitoring. (d) Competent... or prevention of a serious disease or condition. (e) Physicochemical evidence that: (1) The active...

21 CFR 320.33 - Criteria and evidence to assess actual or potential bioequivalence problems.

Code of Federal Regulations, 2013 CFR

2013-04-01

... bioavailability. (4) Certain physical structural characteristics of the active drug ingredient, e.g., polymorphic... effective use of the drug products requires careful dosage titration and patient monitoring. (d) Competent... or prevention of a serious disease or condition. (e) Physicochemical evidence that: (1) The active...

PHYSICOCHEMICAL PROPERTIES AS PREDICTORS OF ORGANIC CHEMICAL EFFECTS ON SOIL MICROBIAL RESPIRATION

EPA Science Inventory

Structure-activity analysis was used to evaluate the effects of 19 hazardous organic chemicals on microbial respiration in two slightly acidic soils (a Captina silt loam from Roane County Tennessee, and a McLaurin sandy loam from Stone County, Mississippi), both low in organic ca...

Influence of the Structure of Molecules of Derivatives of 1,2,4-Triazole and 1,2,4-Triazine on Chromatographic Retention Under Conditions of Reversed Phase HPLC

NASA Astrophysics Data System (ADS)

Karaseva, I. N.; Karasev, M. O.; Nechaeva, O. N.; Kurbatova, S. V.

2018-07-01

The dependence of the chromatographic retention of 1,2,4-triazine and 1,2,4-triazole derivatives from water-acetonitrile solutions over octadecyl silica on the structure of sorbate molecules is studied. The effect the physicochemical parameters and topology of heterocycle molecules have on the retention characteristics under RP HPLC conditions is analyzed.

Physical aspects of dexibuprofen and racemic ibuprofen.

PubMed

Leising, G; Resel, R; Stelzer, F; Tasch, S; Lanziner, A; Hantich, G

1996-12-01

This article presents a comparative study of ibuprofen materials in their solid state. Ibuprofen crystallizes into two different structures for the S(+) enantiomer (dexibuprofen) and racemic ibuprofen. The crystal structure of ibuprofen, its optical absorption and photoluminescence, and the thermodynamic results (melting point and heat of fusion) are discussed. From these physicochemical properties, the authors conclude that dexibuprofen, which is the most active species pharmaceutically, and racemic ibuprofen are inherently different solid-state materials.

Alkanols and chlorophenols cause different physiological adaptive responses on the level of cell surface properties and membrane vesicle formation in Pseudomonas putida DOT-T1E.

PubMed

Baumgarten, Thomas; Vazquez, José; Bastisch, Christian; Veron, Wilfried; Feuilloley, Marc G J; Nietzsche, Sandor; Wick, Lukas Y; Heipieper, Hermann J

2012-01-01

In order to cope with the toxicity imposed by the exposure to environmental hydrocarbons, many bacteria have developed specific adaptive responses such as modifications in the cell envelope. Here we compared the influence of n-alkanols and chlorophenols on the surface properties of the solvent-tolerant bacterium Pseudomonas putida DOT-T1E. In the presence of toxic concentrations of n-alkanols, this strain significantly increased its cell surface charge and hydrophobicity with changes depending on the chain length of the added n-alkanols. The adaptive response occurred within 10 min after the addition of the solvent and was demonstrated to be of physiological nature. Contrary to that, chlorophenols of similar hydrophobicity and potential toxicity as the corresponding alkanols caused only minor effects in the surface properties. To our knowledge, this is the first observation of differences in the cellular adaptive response of bacteria to compound classes of quasi equal hydrophobicity and toxicity. The observed adaptation of the physico-chemical surface properties of strain DOT-T1E to the presence of alkanols was reversible and correlated with changes in the composition of the lipopolysaccharide content of the cells. The reaction is explained by previously described reactions allowing the release of membrane vesicles that was demonstrated for cells affected by 1-octanol and heat shock, whereas no membrane vesicles were released after the addition of chlorophenols.

Cloning and Stress-Induced Expression Analysis of Calmodulin in the Antarctic Alga Chlamydomonas sp. ICE-L.

PubMed

He, Ying-Ying; Wang, Yi-Bin; Zheng, Zhou; Liu, Fang-Ming; An, Mei-Ling; He, Xiao-Dong; Qu, Chang-Feng; Li, Lu-Lu; Miao, Jin-Lai

2017-08-01

Calmodulin (CaM) is a Ca 2+ -binding protein that plays a role in several Ca 2+ signaling pathways, which dynamically regulates the activities of hundreds of proteins. The ice alga Chlamydomonas sp. ICE-L, which has the ability to adapt to extreme polar conditions, is a crucial primary producer in Antarctic ecosystem. This study hypothesized that Cam helps the ICE-L to adapt to the fluctuating conditions in the polar environment. It first verified the overall length of Cam, through RT-PCR and RACE-PCR, based on partial Cam transcriptome library of ICE-L. Then, the nucleotide and predicted amino acid sequences were, respectively, analyzed by various bioinformatics approaches to gain more insights into the computed physicochemical properties of the CaM. Potential involvements of Cam in responding to certain stimuli (i.e., UVB radiation, high salinity, and temperature) were investigated by differential expression, measuring its transcription levels by means of quantitative RT-PCR. Results showed that CaM was indeed inducible and regulated by high UVB radiation, high salinity, and nonoptimal temperature conditions. Different conditions had different expression tendencies, which provided an important basis for investigating the adaptation mechanism of Cam in ICE-L.

Influences of heating temperature, pH, and soluble solids on the decimal reduction times of acid-adapted and non-adapted Escherichia coli O157:H7 (HCIPH 96055) in a defined liquid heating medium.

PubMed

Gabriel, Alonzo A

2012-11-01

The study characterized the influences of various combinations of process and product parameters namely, heating temperature (53, 55, 57.5, 60, 62 °C), pH (2.0, 3.0, 4.5, 6.0, 7.0), and soluble solids (SS) (1.4, 15, 35, 55, 69°Brix) on the thermal inactivation of non-adapted and acid-adapted E. coli O157:H7 (HCIPH 96055) in a defined liquid heating medium (LHM). Acid adaptation was conducted by propagating cells in a gradually acidifying nutrient broth medium, supplemented with 1% glucose. The D values of non-adapted cells ranged from 1.43 s (0.02 min) to 304.89 s (5.08 min). Acid-adapted cells had D values that ranged from 1.33 s (0.02 min) to 2628.57 s (43.81 min). Adaptation did not always result in more resistant cells as indicated by the Log (D(adapted)/D(non-adapted)) values calculated in all combinations tested, with values ranging from -1.10 to 1.40. The linear effects of temperature and pH, and the joint effects of pH and SS significantly influenced the thermal resistance of non-adapted cells. Only the linear and quadratic effects of both pH and SS significantly influenced the D values of acid-adapted cells. Generally, the D values of acid-adapted cells decreased at SS greater than 55 °Brix, suggesting the possible cancelation of thermal cross protection by acid habituation at such SS levels. The relatively wide ranges of LHM pH and SS values tested in the study allowed for better examination of the effects of these factors on the thermal death of the pathogen. The results established in this work may be used in the evaluation, control and improvement of safety of juice products; and of other liquid foods with physicochemical properties that fall within the ranges tested in this work. Copyright © 2012 Elsevier B.V. All rights reserved.

Current trends in protein crystallization.

PubMed

Gavira, José A

2016-07-15

Proteins belong to the most complex colloidal system in terms of their physicochemical properties, size and conformational-flexibility. This complexity contributes to their great sensitivity to any external change and dictate the uncertainty of crystallization. The need of 3D models to understand their functionality and interaction mechanisms with other neighbouring (macro)molecules has driven the tremendous effort put into the field of crystallography that has also permeated other fields trying to shed some light into reluctant-to-crystallize proteins. This review is aimed at revising protein crystallization from a regular-laboratory point of view. It is also devoted to highlight the latest developments and achievements to produce, identify and deliver high-quality protein crystals for XFEL, Micro-ED or neutron diffraction. The low likelihood of protein crystallization is rationalized by considering the intrinsic polypeptide nature (folded state, surface charge, etc) followed by a description of the standard crystallization methods (batch, vapour diffusion and counter-diffusion), including high throughput advances. Other methodologies aimed at determining protein features in solution (NMR, SAS, DLS) or to gather structural information from single particles such as Cryo-EM are also discussed. Finally, current approaches showing the convergence of different structural biology techniques and the cross-methodologies adaptation to tackle the most difficult problems, are presented. Current advances in biomacromolecules crystallization, from nano crystals for XFEL and Micro-ED to large crystals for neutron diffraction, are covered with special emphasis in methodologies applicable at laboratory scale. Copyright © 2015 Elsevier Inc. All rights reserved.

Juniper wood structure under the microscope.

PubMed

Bogolitsyn, Konstantin G; Zubov, Ivan N; Gusakova, Maria A; Chukhchin, Dmitry G; Krasikova, Anna A

2015-05-01

The investigations confirm the physicochemical nature of the structure and self-assembly of wood substance and endorse its application in plant species. The characteristic morphological features, ultra-microstructure, and submolecular structure of coniferous wood matrix using junipers as the representative tree were investigated by scanning electron (SEM) and atomic-force microscopy (AFM). Novel results on the specific composition and cell wall structure features of the common juniper (Juniperus Communis L.) were obtained. These data confirm the possibility of considering the wood substance as a nanobiocomposite. The cellulose nanofibrils (20-50 nm) and globular-shaped lignin-carbohydrate structures (diameter of 5-60 nm) form the base of such a nanobiocomposite.

Real-time control of geometry and stiffness in adaptive structures

NASA Technical Reports Server (NTRS)

Ramesh, A. V.; Utku, S.; Wada, B. K.

1991-01-01

The basic theory is presented for the geometry, stiffness, and damping control of adaptive structures, with emphasis on adaptive truss structures. Necessary and sufficient conditions are given for stress-free geometry control in statically determinate and indeterminate adaptive discrete structures. Two criteria for selecting the controls are proposed, and their use in real-time control is illustrated by numerical simulation results. It is shown that the stiffness and damping control of adaptive truss structures for vibration suppression is possible by elongation and elongation rate dependent feedback forces from the active elements.

Sea ice, extremophiles and life on extra-terrestrial ocean worlds

NASA Astrophysics Data System (ADS)

Martin, Andrew; McMinn, Andrew

2018-01-01

The primary aim of this review is to highlight that sea-ice microbes would be capable of occupying ice-associated biological niches on Europa and Enceladus. These moons are compelling targets for astrobiological exploration because of the inferred presence of subsurface oceans that have persisted over geological timescales. Although potentially hostile to life in general, Europa and Enceladus may still harbour biologically permissive domains associated with the ice, ocean and seafloor environments. However, validating sources of free energy is challenging, as is qualifying possible metabolic processes or ecosystem dynamics. Here, the capacity for biological adaptation exhibited by microorganisms that inhabit sea ice is reviewed. These ecosystems are among the most relevant Earth-based analogues for considering life on ocean worlds because microorganisms must adapt to multiple physicochemical extremes. In future, these organisms will likely play a significant role in defining the constraints on habitability beyond Earth and developing a mechanistic framework that contrasts the limits of Earth's biosphere with extra-terrestrial environments of interest.

Nanoparticle Exposure and Hormetic Dose–Responses: An Update

PubMed Central

Leso, Veruscka; Fontana, Luca; Calabrese, Edward J.

2018-01-01

The concept of hormesis, as an adaptive response of biological systems to moderate environmental challenges, has raised considerable nano-toxicological interests in view of the rapid pace of production and application of even more innovative nanomaterials and the expected increasing likelihood of environmental and human exposure to low-dose concentrations. Therefore, the aim of this review is to provide an update of the current knowledge concerning the biphasic dose–responses induced by nanoparticle exposure. The evidence presented confirmed and extended our previous findings, showing that hormesis is a generalized adaptive response which may be further generalized to nanoscale xenobiotic challenges. Nanoparticle physico-chemical properties emerged as possible features affecting biphasic relationships, although the molecular mechanisms underlining such influences remain to be fully understood, especially in experimental settings resembling long-term and low-dose realistic environmental exposure scenarios. Further investigation is necessary to achieve helpful information for a suitable assessment of nanomaterial risks at the low-dose range for both the ecosystem function and the human health. PMID:29534471

Evaluation of extra virgin olive oil stability by artificial neural network.

PubMed

Silva, Simone Faria; Anjos, Carlos Alberto Rodrigues; Cavalcanti, Rodrigo Nunes; Celeghini, Renata Maria dos Santos

2015-07-15

The stability of extra virgin olive oil in polyethylene terephthalate bottles and tinplate cans stored for 6 months under dark and light conditions was evaluated. The following analyses were carried out: free fatty acids, peroxide value, specific extinction at 232 and 270 nm, chlorophyll, L(∗)C(∗)h color, total phenolic compounds, tocopherols and squalene. The physicochemical changes were evaluated by artificial neural network (ANN) modeling with respect to light exposure conditions and packaging material. The optimized ANN structure consists of 11 input neurons, 18 hidden neurons and 5 output neurons using hyperbolic tangent and softmax activation functions in hidden and output layers, respectively. The five output neurons correspond to five possible classifications according to packaging material (PET amber, PET transparent and tinplate can) and light exposure (dark and light storage). The predicted physicochemical changes agreed very well with the experimental data showing high classification accuracy for test (>90%) and training set (>85). Sensitivity analysis showed that free fatty acid content, peroxide value, L(∗)Cab(∗)hab(∗) color parameters, tocopherol and chlorophyll contents were the physicochemical attributes with the most discriminative power. Copyright © 2015 Elsevier Ltd. All rights reserved.

Evaluation of Fe-containing Li2CuO2 on CO2 capture performed at different physicochemical conditions.

PubMed

Yañez-Aulestia, Ana; Ovalle-Encinia, Oscar; Pfeiffer, Heriberto

2018-06-05

Li 2 CuO 2 and different iron-containing Li 2 CuO 2 samples were synthesized by solid state reaction. On iron-containing samples, atomic sites of copper are substituted by iron ions in the lattice (XRD and Rietveld analyses). Iron addition induces copper release from Li 2 CuO 2 , which produce cationic vacancies and CuO, due to copper (Cu 2+ ) and iron (Fe 3+ ) valence differences. Two different physicochemical conditions were used for analyzing CO 2 capture on these samples; (i) high temperature and (ii) low temperature in presence of water vapor. At high temperatures, iron addition increased CO 2 chemisorption, due to structural and chemical variations on Li 2 CuO 2 . Kinetic analysis performed by first order reaction and Eyring models evidenced that iron addition on Li 2 CuO 2 induced a faster CO 2 chemisorption but a higher thermal dependence. Conversely, CO 2 chemisorption at low temperature in water vapor presence practically did not vary by iron addition, although hydration and hydroxylation processes were enhanced. Moreover, under these physicochemical conditions the whole sorption process became slower on iron-containing samples, due to metal oxides presence.

Relationship between potency and boiling point of general anesthetics: a thermodynamic consideration.

PubMed

Dastmalchi, S; Barzegar-Jalali, M

2000-07-20

The most important group of nonspecific drugs is that of the general anesthetics. These nonspecific compounds vary greatly in structure, from noble gases such as Ar or Xe to complex steroids. Since the development of clinical anesthesia over a century ago, there has been a vast amount of research and speculation concerning the mechanism of action of general anesthetics. Despite these efforts, the exact mechanism remains unknown. Many theories of narcosis do not explain how unconsciousness is produced at a molecular level, but instead relate some physicochemical property of anesthetic agents to their anesthetic potencies. In this paper, we address some of those physicochemical properties, with more emphasis on correlating the anesthetic potency of volatile anesthetics to their boiling points based on thermodynamic principles.

Charge-switching amino acids-based cationic lipids for efficient gene delivery.

PubMed

Zheng, Li-Ting; Yi, Wen-Jing; Liu, Qiang; Su, Rong-Chuan; Zhao, Zhi-Gang

2015-12-15

A series of charge-switching amino acids-based cationic lipids 4a-4e bearing a benzyl ester at the terminus of the acyl chain, but differing in the polar-head group were prepared. The physicochemical properties of these lipids, including size, zeta potential and cellular uptake of the lipoplexes formed from with DNA, as well as the transfection efficiency (TE), were investigated. The results showed that the chemical structure of the cationic head-group clearly affects the physicochemical parameters of the amino acid-based lipids and especially the TE. The selected lipid, 4c gave 2.1 times higher TE than bPEI 25k in the presence of 10% serum in HeLa cells, with little toxicity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improving physical properties via C-H oxidation: chemical and enzymatic approaches.

PubMed

Michaudel, Quentin; Journot, Guillaume; Regueiro-Ren, Alicia; Goswami, Animesh; Guo, Zhiwei; Tully, Thomas P; Zou, Lufeng; Ramabhadran, Raghunath O; Houk, Kendall N; Baran, Phil S

2014-11-03

Physicochemical properties constitute a key factor for the success of a drug candidate. Whereas many strategies to improve the physicochemical properties of small heterocycle-type leads exist, complex hydrocarbon skeletons are more challenging to derivatize because of the absence of functional groups. A variety of C-H oxidation methods have been explored on the betulin skeleton to improve the solubility of this very bioactive, yet poorly water-soluble, natural product. Capitalizing on the innate reactivity of the molecule, as well as the few molecular handles present on the core, allowed oxidations at different positions across the pentacyclic structure. Enzymatic oxidations afforded several orthogonal oxidations to chemical methods. Solubility measurements showed an enhancement for many of the synthesized compounds. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perylene and Perylene-Derivative Nano-Cocrystals: Preparation and Physicochemical Property

NASA Astrophysics Data System (ADS)

Baba, Koichi; Konta, Sayaka; Oliveira, Daniel; Sugai, Kenji; Onodera, Tsunenobu; Masuhara, Akito; Kasai, Hitoshi; Oikawa, Hidetoshi; Nakanishi, Hachiro

2012-12-01

Organic nano-cocrystals of functional dyes of perylene and a perylene derivative were successfully prepared by the reprecipitation method. The particle sizes, optical properties, and powder X-ray diffraction patterns of nano-cocrystals were evaluated. Typically, the size with size distribution of nano-cocrystals was 55±15 nm when the molar ratio of perylene to the perylene derivative was 50:50. The particular intermolecular electronic interaction between perylene and the perylene derivative in the nano-cocrystal state was observed by absorption and fluorescence spectra measurements. The powder X-ray diffraction pattern analysis confirmed that the structure of nano-cocrystals was different from those prepared from perylene and the perylene derivative. The nano-cocrystal having unique physicochemical properties will be potentially classified as a new type of functional nanomaterial.

Physicochemical Investigation of 2,4,5-Trimethoxybenzylidene Propanedinitrile (TMPN) Dye as Fluorescence off-on Probe for Critical Micelle Concentration (CMC) of SDS and CTAB.

PubMed

Khan, Salman A; Asiri, Abdullah M

2015-11-01

2,4,5-trimethoxybenzylidene propanedinitrile (TMPN) was synthesized by Knoevenagel condensation. Structure of the TMPN was conformed by the elemental analysis and EI-MS, FT-IR, (1)H-NMR, (13)C-NMR spectroscopy. Absorbance and emission spectrum of the TMPN was studied in different solvent provide that TMPN is good absorbent and emission red shift in absorbance and emission spectra as polarity of the solvents increase. Photophysical properties including, oscillator strength, extinction coefficient, transition dipole moment, stokes shift and fluorescence quantum yield were investigated in order to investigate the physicochemical behaviors of TMPN. Dye undergoes solubilization in different micelles and may be used as a probe to determine the critical micelle concentration (CMC) of SDS and CTAB.

Contribution of Circulatory Disturbances in Subchondral Bone to the Pathophysiology of Osteoarthritis.

PubMed

Aaron, Roy K; Racine, Jennifer; Dyke, Jonathan P

2017-08-01

This review describes the contributions of abnormal bone circulation to the pathophysiology of osteoarthritis. Combining dynamic imaging with MRI and PET with previous observations reveals that venous stasis and a venous outlet syndrome is most likely the key circulatory pathology associated with the initiation or progression of osteoarthritis. MRI and PET have revealed that venous outflow obstruction results in physicochemical changes in subchondral bone to which osteoblasts are responsive. The osteoblasts express an altered pattern of cytokines, many of which can serve as structural or signaling molecules contributing to both bone remodeling and cartilage degeneration. The patterns of circulatory changes are associated with alterations in the physicochemical environment of subchondral bone, including hypoxia. Osteoblast cytokines can transit the subchondral bone plate and calcified cartilage and communicate with chondrocytes.

Engineered Nanomaterials: Their Physicochemical Characteristics and How to Measure Them.

PubMed

Atluri, Rambabu; Jensen, Keld Alstrup

2017-01-01

Numerous types of engineered nanomaterials (ENMs) are commercially available and developments move towards producing more advanced nanomaterials with tailored properties. Such advanced nanomaterials may include chemically doped or modified derivatives with specific surface chemistries; also called higher generation or multiconstituent nanomaterials. To fully enjoy the benefits of nanomaterials, appropriate characterisation of ENMs is necessary for many aspects of their production, use, testing and reporting to regulatory bodies. This chapter introduces both structural and textural properties of nanomaterials with a focus on demonstrating the information that can be achieved by analysis of primary physicochemical characteristics and how such information is critical to understand or assess the possible toxicity of engineered nanomaterials. Many of characterization methods are very specific to obtain particular characteristics and therefore the most widely used techniques are explained and demonstrated.

A physicochemical mechanism of chemical gas sensors using an AC analysis.

PubMed

Moon, Jaehyun; Park, Jin-Ah; Lee, Su-Jae; Lee, Jeong-Ik; Zyung, Taehyong; Shin, Eui-Chol; Lee, Jong-Sook

2013-06-21

Electrical modeling of the chemical gas sensors was successfully applied to TiO2 nanofiber gas sensors by developing an equivalent circuit model where the junction capacitance as well as the resistance can be separated from the comparable stray capacitance. The Schottky junction impedance exhibited a characteristic skewed arc described by a Cole-Davidson function, and the variation of the fit and derived parameters with temperature, bias, and NO2 gas concentration indicated definitely a physicochemical sensing mechanism based on the Pt|TiO2 Schottky junctions against the conventional supposition of the enhanced sensitivity in nanostructured gas sensors with high grain boundary/surface area. Analysis on a model Pt|TiO2|Pt structure also confirmed the characteristic impedance response of TiO2 nanofiber sensors.

Unveiling the Molecular Structure of Pulmonary Surfactant Corona on Nanoparticles.

PubMed

Hu, Qinglin; Bai, Xuan; Hu, Guoqing; Zuo, Yi Y

2017-07-25

The growing risk of human exposure to airborne nanoparticles (NPs) causes a general concern on the biosafety of nanotechnology. Inhaled NPs can deposit in the deep lung at which they interact with the pulmonary surfactant (PS). Despite the increasing study of nano-bio interactions, detailed molecular mechanisms by which inhaled NPs interact with the natural PS system remain unclear. Using coarse-grained molecular dynamics simulation, we studied the interaction between NPs and the PS system in the alveolar fluid. It was found that regardless of different physicochemical properties, upon contacting the PS, both silver and polystyrene NPs are immediately coated with a biomolecular corona that consists of both lipids and proteins. Structure and molecular conformation of the PS corona depend on the hydrophobicity of the pristine NPs. Quantitative analysis revealed that lipid composition of the corona formed on different NPs is relatively conserved and is similar to that of the bulk phase PS. However, relative abundance of the surfactant-associated proteins, SP-A, SP-B, and SP-C, is notably affected by the hydrophobicity of the NP. The PS corona provides the NPs with a physicochemical barrier against the environment, equalizes the hydrophobicity of the pristine NPs, and may enhance biorecognition of the NPs. These modifications in physicochemical properties may play a crucial role in affecting the biological identity of the NPs and hence alter their subsequent interactions with cells and other biological entities. Our results suggest that all studies of inhalation nanotoxicology or NP-based pulmonary drug delivery should consider the influence of the PS corona.

Theoretical Studies for Dendrimer-Based Drug Delivery.

PubMed

Bello, Martiniano; Fragoso-Vázquez, Jonathan; Correa-Basurto, José

2017-01-01

Numerous theoretical studies have been performed to iteratively optimize the physicochemical properties such as dendrimer size and surface constituents in solution, as well as their molecular recognition properties for drugs, lipid membranes, nucleic acids and proteins, etc. Molecular modeling approaches such as docking and molecular dynamic (MD) simulations have supported experimental efforts by providing important insights into the structural properties of dendrimers in solution and possible binding properties of drugs at the atomic level. We review the utilization of molecular modelling tools to obtain insight into the study and design of dendrimers, with particular importance placed on the improvement of binding properties of dendrimers for their use as drug nanocarriers and to increase the water solubility properties and drug delivery. The modeling studies discussed in this review have provided substantial insight into the physicochemical properties of dendrimers in solution, including solvent pH and counterion distribution, at the atomic level, as well as the elucidation of some of the key interactions in solution of unmodified and modified dendrimers with some drugs of pharmaceutics interest and biological systems such as nucleic acids, proteins and lipid membranes. the described studies illustrate that whether simulations will be run at the all-atom or coarse-grained level, physicochemical conditions such as the type of force field, the treatment of electrostatics effects, counterion distribution, protonation state of dendrimers, and dendrimer concentrations which have been probed to play a crucial role in the structural behavior and binding properties must be prudently incorporated in the simulations. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Comparison of the applicability domain of a quantitative structure-activity relationship for estrogenicity with a large chemical inventory.

PubMed

Netzeva, Tatiana I; Gallegos Saliner, Ana; Worth, Andrew P

2006-05-01

The aim of the present study was to illustrate that it is possible and relatively straightforward to compare the domain of applicability of a quantitative structure-activity relationship (QSAR) model in terms of its physicochemical descriptors with a large inventory of chemicals. A training set of 105 chemicals with data for relative estrogenic gene activation, obtained in a recombinant yeast assay, was used to develop the QSAR. A binary classification model for predicting active versus inactive chemicals was developed using classification tree analysis and two descriptors with a clear physicochemical meaning (octanol-water partition coefficient, or log Kow, and the number of hydrogen bond donors, or n(Hdon)). The model demonstrated a high overall accuracy (90.5%), with a sensitivity of 95.9% and a specificity of 78.1%. The robustness of the model was evaluated using the leave-many-out cross-validation technique, whereas the predictivity was assessed using an artificial external test set composed of 12 compounds. The domain of the QSAR training set was compared with the chemical space covered by the European Inventory of Existing Commercial Chemical Substances (EINECS), as incorporated in the CDB-EC software, in the log Kow / n(Hdon) plane. The results showed that the training set and, therefore, the applicability domain of the QSAR model covers a small part of the physicochemical domain of the inventory, even though a simple method for defining the applicability domain (ranges in the descriptor space) was used. However, a large number of compounds are located within the narrow descriptor window.

Breakdown of the Debye polarization ansatz at protein-water interfaces

NASA Astrophysics Data System (ADS)

Fernández Stigliano, Ariel

2013-06-01

The topographical and physico-chemical complexity of protein-water interfaces scales down to the sub-nanoscale range. At this level of confinement, we demonstrate that the dielectric structure of interfacial water entails a breakdown of the Debye ansatz that postulates the alignment of polarization with the protein electrostatic field. The tendencies to promote anomalous polarization are determined for each residue type and a particular kind of structural defect is shown to provide the predominant causal context.

Using Theoretical Descriptors in Structural Activity Relationships: 4. Molecular Orbital Basicity and Electrostatic Basicity

DTIC Science & Technology

1988-11-01

rates.6 The Hammet equation , also called the Linear Free Energy Relationship (LFER) because of the relationship of the Gibb’s Free Energy to the... equations for numerous biological and physicochemical properties. Linear Solvation Enery Relationship (LSER), a sub-set of QSAR have been used by...originates from thermodynamics, where Hammet recognized the relationship of structure to the Gibb’s Free Energy, and ultimately to equilibria and reaction

Probing binding hot spots at protein-RNA recognition sites.

PubMed

Barik, Amita; Nithin, Chandran; Karampudi, Naga Bhushana Rao; Mukherjee, Sunandan; Bahadur, Ranjit Prasad

2016-01-29

We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein-RNA interfaces to probe the binding hot spots at protein-RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein-protein and protein-RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein-RNA recognition sites with desired affinity. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Medicinal flowers. XXX. Eight new glycosides, everlastosides F-M, from the flowers of Helichrysum arenarium.

PubMed

Morikawa, Toshio; Wang, Li-Bo; Ninomiya, Kiyofumi; Nakamura, Seikou; Matsuda, Hisashi; Muraoka, Osamu; Wu, Li-Jun; Yoshikawa, Masayuki

2009-08-01

Eight new glycosides, everlastosides F (1), G (2), H (3), I (4), J (5), K (6), L (7), and M (8), were isolated from the methanolic extract of the flowers of Helichrysum arenarium. Their structures were elucidated on the basis of chemical and physicochemical evidence.

Physico-chemical studies of hardened cement paste structure with micro-reinforcing fibers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steshenko, Aleksei, E-mail: steshenko.alexey@gmail.com; Kudyakov, Aleksander; Konusheva, Viktoriya

The results of physico-chemical studies of modified hardened cement paste with micro-reinforcing fibers are given in this article. The goal was to study the reasons of the increase of strength properties of modified hardened cement paste by the method of X-ray diffraction and electron microscopy. It is shown that the use of mineral fibers in the production of cement based material has positive effect on its properties. The study found out that the increase in the strength of the hardened cement paste with micro-reinforcing fibers is due to the increase of the rate of hydration of cement without a significantmore » change in the phase composition in comparison with hardened cement paste without additive. The results of microstructure investigation (of control samples and samples of the reinforced hardened cement paste) have shown that introduction of mineral fibers in the amount of 0.1-2 % by weight of cement provides the structure of the homogeneous microporous material with uniform distribution of the crystalline phase provided by densely packed hydrates.« less

A comparative analysis on the physicochemical properties of tick-borne encephalitis virus envelope protein residues that affect its antigenic properties.

PubMed

Bukin, Yu S; Dzhioev, Yu P; Tkachev, S E; Kozlova, I V; Paramonov, A I; Ruzek, D; Qu, Z; Zlobin, V I

2017-06-15

This work is dedicated to the study of the variability of the main antigenic envelope protein E among different strains of tick-borne encephalitis virus at the level of physical and chemical properties of the amino acid residues. E protein variants were extracted from then NCBI database. Four amino acid residues properties in the polypeptide sequences were investigated: the average volume of the amino acid residue in the protein tertiary structure, the number of amino acid residue hydrogen bond donors, the charge of amino acid residue lateral radical and the dipole moment of the amino acid residue. These physico-chemical properties are involved in antigen-antibody interactions. As a result, 103 different variants of the antigenic determinants of the tick-borne encephalitis virus E protein were found, significantly different by physical and chemical properties of the amino acid residues in their structure. This means that some strains among the natural variants of tick-borne encephalitis virus can potentially escape the immune response induced by the standard vaccine. Copyright © 2017 Elsevier B.V. All rights reserved.

Dynamic and structural evidence of mesoscopic aggregation in phosphonium ionic liquids

NASA Astrophysics Data System (ADS)

Cosby, T.; Vicars, Z.; Heres, M.; Tsunashima, K.; Sangoro, J.

2018-05-01

Mesoscopic aggregation in aprotic ionic liquids due to the microphase separation of polar and non-polar components is expected to correlate strongly with the physicochemical properties of ionic liquids and therefore their potential applications. The most commonly cited experimental evidence of such aggregation is the observation of a low-q pre-peak in the x-ray and neutron scattering profiles, attributed to the polarity alternation of polar and apolar phases. In this work, a homologous series of phosphonium ionic liquids with the bis(trifluoromethylsulfonyl)imide anion and systematically varying alkyl chain lengths on the phosphonium cation are investigated by small and wide-angle x-ray scattering, dynamic-mechanical spectroscopy, and broadband dielectric spectroscopy. A comparison of the real space correlation distance corresponding to the pre-peak and the presence or absence of the slow sub-α dielectric relaxation previously associated with the motion of mesoscale aggregates reveals a disruption of mesoscale aggregates with increasing symmetry of the quaternary phosphonium cation. These findings contribute to the broader understanding of the interplay of molecular structures, mesoscale aggregation, and physicochemical properties in aprotic ionic liquids.

Nanocrystalline hydroxyapatite enriched in selenite and manganese ions: physicochemical and antibacterial properties

NASA Astrophysics Data System (ADS)

Kolmas, Joanna; Groszyk, Ewa; Piotrowska, Urszula

2015-07-01

In this work, we used the co-precipitation method to synthesize hydroxyapatite (Mn-SeO3-HA) containing both selenium IV (approximately 3.60 wt.%) and manganese II (approximately 0.29 wt.%). Pure hydroxyapatite (HA), hydroxyapatite-containing manganese (II) ions (Mn-HA), and hydroxyapatite-containing selenite ions alone (SeO3-HA), prepared with the same method, were used as reference materials. The structures and physicochemical properties of all the obtained samples were investigated. PXRD studies showed that the obtained materials were homogeneous and consisted of apatite phase. Introducing selenites into the hydroxyapatite crystals considerably affects the size and degree of ordering. Experiments with transmission electron microscopy (TEM) showed that Mn-SeO3-HA crystals are very small, needle-like, and tend to form agglomerates. Fourier transform infrared spectroscopy (FT-IR) and solid-state nuclear magnetic resonance (ssNMR) were used to analyze the structure of the obtained material. Preliminary microbiological tests showed that the material demonstrated antibacterial activity against Staphylococcus aureus, yet such properties were not confirmed regarding Escherichia coli. PACS codes: 61, 76, 81

Food grade microemulsion systems: Sunflower oil/castor oil derivative-ethanol/water. Rheological and physicochemical analysis.

PubMed

Mori Cortés, Noelia; Lorenzo, Gabriel; Califano, Alicia N

2018-05-01

Microemulsions are thermodynamically stable systems that have attracted considerable attention in the food industry as delivery systems for many hydrophobic nutrients. These spontaneous systems are highly dependent on ingredients and composition. In this work phase diagrams were constructed using two surfactants (Kolliphor RH40 and ELP), water, sunflower oil, and ethanol as cosurfactant, evaluating their physicochemical properties. Stability of the systems was studied at 25 and 60 °C, monitoring turbidity at 550 nm for over a month to identify the microemulsion region. Conductivity was measured to classify between water-in-oil and oil-in-water microemulsions. The phase diagram constructed with Kolliphor RH40 exhibited a larger microemulsion area than that formulated with Kolliphor ELP. All formulations showed a monomodal droplet size distribution with low polydispersity index (<0.30) and a mean droplet size below 20 nm. Systems with higher water content presented a Newtonian behavior; increasing the dispersed phase content produced a weak gel-like structure with pseudoplastic behavior under flow conditions that was satisfactorily modeled to obtain structural parameters. Copyright © 2018 Elsevier Ltd. All rights reserved.

Insights into the structural and physicochemical properties of small granular starches from two hydrophyte duckweeds, Spirodela oligorrhiza and Lemna minor.

PubMed

Chen, Lei; Yu, Changjiang; Ma, Yubin; Xu, Hua; Wang, Shumin; Wang, Yu; Liu, Xingxun; Zhou, Gongke

2016-11-29

The structure and physicochemical properties of starches from two hydrophyte duckweeds, Spirodela oligorrhiza and Lemna minor, were investigated and compared in this study. The amylose content and average size of starches were determined to be 20.85%, 4.70 μm and 27.77%, 6.17 μm for Spirodela oligorrhiza and Lemna minor, respectively. The average chain length of two duckweed starches was measured to be around DP 28. The chain length distribution was observed to be greatly different from other reported starches for the high proportion of long chains (DP ≥ 37) over 50%. Wide-angle X-ray diffraction profiles of the two starch samples displayed typical B-type diffraction pattern. The gelatinization enthalpy-changes (ΔH gel ) of two starch samples was about 10.40 J/g for two duckweed starches. The present results suggested the potential utilization of small granular starches from duckweed in functional foods and dietary supplement products. Copyright © 2016 Elsevier Ltd. All rights reserved.

Physicochemical and functional properties of coconut (Cocos nucifera L) cake dietary fibres: Effects of cellulase hydrolysis, acid treatment and particle size distribution.

PubMed

Zheng, Yajun; Li, Yan

2018-08-15

Effects of cellulase hydrolysis, acid treatment and particle size distribution on the structure, physicochemical and functional properties of coconut cake dietary fiber (DCCDF) were studied. Results showed that both the cellulase hydrolysis and acid treatment contributed to the structural modification of DCCDF as evident from XRD, FT-IR and SEM analysis. Moreover, the cellulase hydrolysis enhanced soluble carbohydrate content, water holding capacity (WHC) and swelling capacity (WSC), α-amylase inhibition activity (α-AAIR), glucose dialysis retardation index (GDRI) and cation-exchange capacity (CEC) of DCCDF; but it had undesirable effects on colour, oil holding capacity (OHC) and emulsifying capacity (EC). On other hand, acid treatment decreased the WHC, WSC and GDRI, but improved the colour, CEC, OHC and emulsion stability of DCCDF. Furthermore, the WHC, WSC and EC of DCCDF increased as the particle size reduced from 250 to 167 μm, while the GDRI, OHC, α-AAIR and emulsion stability decreased with decreasing particle size. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effect of different temperature-time combinations on physicochemical, microbiological, textural and structural features of sous-vide cooked lamb loins.

PubMed

Roldán, Mar; Antequera, Teresa; Martín, Alberto; Mayoral, Ana Isabel; Ruiz, Jorge

2013-03-01

Lamb loins were subjected to sous-vide cooking at different combinations of temperature (60, 70, and 80 °C) and time (6, 12, and 24 h). Different physicochemical, histological and structural parameters were studied. Increasing cooking temperatures led to higher weight losses and lower moisture contents, whereas the effect of cooking time on these variables was limited. Samples cooked at 60 °C showed the highest lightness and redness, while increasing cooking temperature and cooking time produced higher yellowness values. Most textural variables in a texture profile analysis showed a marked interaction between cooking temperature and time. Samples cooked for 24h showed significantly lower values for most of the studied textural parameters for all the temperatures considered. Connective tissue granulation at 60 °C and gelation at 70 °C were observed in the SEM micrographs. The sous-vide cooking of lamb loins dramatically reduced microbial population even with the less intense heat treatment studied (60 °C-6 h). Copyright © 2012 Elsevier Ltd. All rights reserved.

Chain conformational and physicochemical properties of fucoidans from sea cucumber.

PubMed

Xu, Xiaoqi; Xue, Changhu; Chang, Yaoguang; Wang, Jun; Jiang, Kunhao

2016-11-05

Although fucoidans from sea cucumber (SC-FUCs) have been proven as potential bioactive polysaccharides and functional food ingridents, their chain conformation and physicochemical properties were still poorly understood. This study investigated the chain conformation of fucoidans from sea cucumber Acaudina molpadioides (Am-FUC), Isostichopus badionotus (Ib-FUC) and Apostichopus japonicus (Aj-FUC), of which primary structure has been recently clarified. Chain conformation parameters demonstrated that studied SC-FUCs adopted random coil conformation in 150mM NaCl solution (pH 7.4). Based on the worm-like cylinder model and atomic force microscopy, the chain stiffness of SC-FUCs was further evaluated as Am-FUC≈Ib-FUC>Aj-FUC. It was suggested that the existence of branch structure increased the chain flexibility, while sulfated pattern exerted limited influence. SC-FUCs demonstrated shear-thinning rheological behavior and negative charge. Am-FUC possessed a higher thermostability than Ib-FUC and Aj-FUC. These results have important implications for understanding the molecular characteristics of SC-FUCs, which could facilitate their further application. Copyright © 2016 Elsevier Ltd. All rights reserved.

Statistical mechanics of protein structural transitions: Insights from the island model

PubMed Central

Kobayashi, Yukio

2016-01-01

The so-called island model of protein structural transition holds that hydrophobic interactions are the key to both the folding and function of proteins. Herein, the genesis and statistical mechanical basis of the island model of transitions are reviewed, by presenting the results of simulations of such transitions. Elucidating the physicochemical mechanism of protein structural formation is the foundation for understanding the hierarchical structure of life at the microscopic level. Based on the results obtained to date using the island model, remaining problems and future work in the field of protein structures are discussed, referencing Professor Saitô’s views on the hierarchic structure of science. PMID:28409078

Physicochemical and biological characterization of SB2, a biosimilar of Remicade® (infliximab)

PubMed Central

Hong, Juyong; Lee, Yuhwa; Lee, Changsoo; Eo, Suhyeon; Kim, Soyeon; Park, Seungkyu; Seo, Donghyuck; Lee, Youngji; Yeon, Soojeong; Bou-Assaf, George; Sosic, Zoran; Zhang, Wei

2017-01-01

ABSTRACT A biosimilar is a biological medicinal product that contains a version of the active substance of an already authorized original biological medicinal product. Biosimilarity to the reference product (RP) in terms of quality characteristics, such as physicochemical and biological properties, safety, and efficacy, based on a comprehensive comparability exercise needs to be established. SB2 (Flixabi® and Renflexis®) is a biosimilar to Remicade® (infliximab). The development of SB2 was performed in accordance with relevant guidelines of the International Conference on Harmonisation, the European Medicines Agency, and the United States Food and Drug Administration. To determine whether critical quality attributes meet quality standards, an extensive characterization test was performed with more than 80 lots of EU- and US-sourced RP. The physicochemical characterization study results revealed that SB2 was similar to the RP. Although a few differences in physicochemical attributes were observed, the evidence from the related literature, structure-activity relationship studies, and comparative biological assays showed that these differences were unlikely to be clinically meaningful. The biological characterization results showed that SB2 was similar to the RP in terms of tumor necrosis factor–α (TNF-α) binding and TNF-α neutralization activities as a main mode of action. SB2 was also similar in Fc-related biological activities including antibody-dependent cell-mediated cytotoxicity, complement-dependent cytotoxicity, neonatal Fc receptor binding, C1q binding, and Fc gamma receptor binding activities. These analytical findings support that SB2 is similar to the RP and also provide confidence of biosimilarity in terms of clinical safety and efficacy. PMID:28005456

Physicochemical properties of collagen solutions cross-linked by glutaraldehyde.

PubMed

Tian, Zhenhua; Li, Conghu; Duan, Lian; Li, Guoying

2014-06-01

The physicochemical properties of collagen solutions (5 mg/ml) cross-linked by various amounts of glutaraldehyde (GTA) [GTA/collagen (w/w) = 0-0.5] under acidic condition (pH 4.00) were examined. Based on the results of the determination of residual amino group content, sodium dodecyl sulphate-polyacrylamide gel electrophoresis, dynamic rheological measurements, differential scanning calorimetry and atomic force microscopy (AFM), it was proved that the collagen solutions possessed strikingly different physicochemical properties depending on the amount of GTA. At low GTA amounts [GTA/collagen (w/w) ≤ 0.1], the residual amino group contents of the cross-linked collagens decreased largely from 100% to 32.76%, accompanied by an increase in the molecular weight. Additionally, increases of the fiber diameter and the values of G', G″ and η* were measured, while the thermal denaturation temperature (Td) did not change visibly and the fluidity of collagen samples was still retained with increasing the GTA amount. When the ratio of GTA to collagen exceeded 0.1, although the residual amino group content only decreased by ~8.2%, the cross-linked collagen solution [GTA/collagen (w/w) = 0.3] displayed a clear loss of flow and a sudden rise (~2.0 °C) of the Td value compared to the uncross-linked collagen solution, probably illustrating that the collagen solution was converted into a gel with mature network structure-containing nuclei observed in AFM image. It was conjectured that the physicochemical properties of the collagen solutions might be in connection with the cross-linking between collagen molecules from the same aggregate or different aggregates.

Enhancing physicochemical properties of emulsions by heteroaggregation of oppositely charged lactoferrin coated lutein droplets and whey protein isolate coated DHA droplets.

PubMed

Li, Xin; Wang, Xu; Xu, Duoxia; Cao, Yanping; Wang, Shaojia; Wang, Bei; Sun, Baoguo; Yuan, Fang; Gao, Yanxiang

2018-01-15

The formation and physicochemical stability of mixed functional components (lutein & DHA) emulsions through heteroaggregation were studied. It was formed by controlled heteroaggregation of oppositely charged lutein and DHA droplets coated by cationic lactoferrin (LF) and anionic whey protein isolate (WPI), respectively. Heteroaggregation was induced by mixing the oppositely charged LF-lutein and WPI-DHA emulsions together at pH 6.0. Droplet size, zeta-potential, transmission-physical stability, microrheological behavior and microstructure of the heteroaggregates formed were measured as a function of LF-lutein to WPI-DHA droplet ratio. Lutein degradation and DHA oxidation by measurement of lipid hydroperoxides and thiobarbituric acid reactive substances were determined. Upon mixing the two types of bioactive compounds droplets together, it was found that the largest aggregates and highest physical stability occurred at a droplet ratio of 40% LF-lutein droplets to 60% WPI-DHA droplets. Heteroaggregates formation altered the microrheological properties of the mixed emulsions mainly by the special network structure of the droplets. When LF-coated lutein droplets ratios were more than 30% and less than 60%, the mixed emulsions exhibited distinct decreases in the Mean Square Displacement, which indicated that their limited scope of Brownian motion and stable structure. Mixed emulsions with LF-lutein/WPI-DHA droplets ratio of 4:6 exhibited Macroscopic Viscosity Index with 13 times and Elasticity Index with 3 times of magnitudes higher than the individual emulsions from which they were prepared. Compared with the WPI-DHA emulsion or LF-lutein emulsion, the oxidative stability of the heteroaggregate of LF-lutein/WPI-DHA emulsions was improved. Heteroaggregates formed by oppositely charged bioactive compounds droplets may be useful for creating specific food structures that lead to desirable physicochemical properties, such as microrheological property, physical and chemical stabilities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Physicochemical characterization and structural evaluation of a specific 2:1 cocrystal of naproxen-nicotinamide.

PubMed

Ando, Shigeru; Kikuchi, Junko; Fujimura, Yuko; Ida, Yasuo; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2012-09-01

Physicochemical characterization and structural evaluation of a 2:1 naproxen-nicotinamide cocrystal were performed. The 2:1 cocrystal showed rapid naproxen dissolution and less water vapor adsorption, indicating better pharmaceutical properties of naproxen. The unique 2:1 cocrystal formation was evaluated by solid-state nuclear magnetic resonance (NMR). The assignments of all H and (13) C peaks for naproxen and the cocrystal were performed using dipolar-insensitive nuclei enhanced by polarization transfer and (1) H-(13) C cross-polarization (CP)-heteronuclear correlation (HETCOR) NMR measurements. The (13) C chemical shift revealed that two naproxen molecules and one nicotinamide molecule existed in the asymmetric unit of the cocrystal. The (1) H chemical shifts indicated that the carboxylic group of the naproxen in the cocrystal was nonionized, and the CH-π interaction between naproxens was very strong. From the (1) H-(13) C CP-HETCOR NMR spectrum with contact time of 5 ms, two different synthons, carboxylic acid-amide and carboxylic acid-pyridine ring, were found between naproxen and nicotinamide. Single-crystal X-ray analysis, which supported the solid-state NMR results, clarified the geometry and intermolecular interactions in more detail. The structure is unique among pharmaceutical cocrystals because each carboxyl group of the two naproxens formed different intermolecular synthons. Copyright © 2012 Wiley Periodicals, Inc.

Structural and physicochemical characterization of pyridine derivative salts of anti-inflammatory drugs

NASA Astrophysics Data System (ADS)

Nechipadappu, Sunil Kumar; Trivedi, Darshak R.

2017-08-01

Salts of common anti-inflammatory drugs mefenamic acid (MFA), tolfenamic acid (TFA) and naproxen (NPX) with various pyridine derivatives (4-amino pyridine (4AP), 4-dimethylaminopyridine (DMAP) and 2-amino pyridine (2AP)) were synthesized by crystal engineering approach based on the pKa values of API's and the salt former. All the salts were characterized systematically by various spectroscopic methods including FT-IR and 1H NMR and the crystal structure was determined by single-crystal X-ray diffraction techniques (SCXRD). DMAP salt of NPX and 2AP salts of MFA and TFA were not obtained in the salt screening experiments. All the molecular salts exhibited 1:1 molecular stoichiometry in the asymmetric unit and except NPX-2AP salt, all the molecular salts included a water molecule in the crystal lattice. Physicochemical and structural properties between drug-drug molecular salts of MFA-4AP, TFA-4AP and NPX-4AP have been evaluated and it was found that these molecular salts were found to be stable for a time period of six months at ambient condition and further hydration of molecular salts were not observed even at accelerated humid conditions (∼75% RH). It was found that 4AP salts of MFA and TFA and DMAP salts of MFA and TFA are isostructural.

Toward Understanding Drug Incorporation and Delivery from Biocompatible Metal-Organic Frameworks in View of Cutaneous Administration.

PubMed

Rojas, Sara; Colinet, Isabel; Cunha, Denise; Hidalgo, Tania; Salles, Fabrice; Serre, Christian; Guillou, Nathalie; Horcajada, Patricia

2018-03-31

Although metal-organic frameworks (MOFs) have widely demonstrated their convenient performances as drug-delivery systems, there is still work to do to fully understand the drug incorporation/delivery processes from these materials. In this work, a combined experimental and computational investigation of the main structural and physicochemical parameters driving drug adsorption/desorption kinetics was carried out. Two model drugs (aspirin and ibuprofen) and three water-stable, biocompatible MOFs (MIL-100(Fe), UiO-66(Zr), and MIL-127(Fe)) have been selected to obtain a variety of drug-matrix couples with different structural and physicochemical characteristics. This study evidenced that the drug-loading and drug-delivery processes are mainly governed by structural parameters (accessibility of the framework and drug volume) as well as the MOF/drug hydrophobic/hydrophilic balance. As a result, the delivery of the drug under simulated cutaneous conditions (aqueous media at 37 °C) demonstrated that these systems fulfill the requirements to be used as topical drug-delivery systems, such as released payload between 1 and 7 days. These results highlight the importance of the rational selection of MOFs, evidencing the effect of geometrical and chemical parameters of both the MOF and the drug on the drug adsorption and release.

Toward Understanding Drug Incorporation and Delivery from Biocompatible Metal–Organic Frameworks in View of Cutaneous Administration

PubMed Central

2018-01-01

Although metal–organic frameworks (MOFs) have widely demonstrated their convenient performances as drug-delivery systems, there is still work to do to fully understand the drug incorporation/delivery processes from these materials. In this work, a combined experimental and computational investigation of the main structural and physicochemical parameters driving drug adsorption/desorption kinetics was carried out. Two model drugs (aspirin and ibuprofen) and three water-stable, biocompatible MOFs (MIL-100(Fe), UiO-66(Zr), and MIL-127(Fe)) have been selected to obtain a variety of drug–matrix couples with different structural and physicochemical characteristics. This study evidenced that the drug-loading and drug-delivery processes are mainly governed by structural parameters (accessibility of the framework and drug volume) as well as the MOF/drug hydrophobic/hydrophilic balance. As a result, the delivery of the drug under simulated cutaneous conditions (aqueous media at 37 °C) demonstrated that these systems fulfill the requirements to be used as topical drug-delivery systems, such as released payload between 1 and 7 days. These results highlight the importance of the rational selection of MOFs, evidencing the effect of geometrical and chemical parameters of both the MOF and the drug on the drug adsorption and release. PMID:29623304

Benefits of statistical molecular design, covariance analysis, and reference models in QSAR: a case study on acetylcholinesterase

NASA Astrophysics Data System (ADS)

Andersson, C. David; Hillgren, J. Mikael; Lindgren, Cecilia; Qian, Weixing; Akfur, Christine; Berg, Lotta; Ekström, Fredrik; Linusson, Anna

2015-03-01

Scientific disciplines such as medicinal- and environmental chemistry, pharmacology, and toxicology deal with the questions related to the effects small organic compounds exhort on biological targets and the compounds' physicochemical properties responsible for these effects. A common strategy in this endeavor is to establish structure-activity relationships (SARs). The aim of this work was to illustrate benefits of performing a statistical molecular design (SMD) and proper statistical analysis of the molecules' properties before SAR and quantitative structure-activity relationship (QSAR) analysis. Our SMD followed by synthesis yielded a set of inhibitors of the enzyme acetylcholinesterase (AChE) that had very few inherent dependencies between the substructures in the molecules. If such dependencies exist, they cause severe errors in SAR interpretation and predictions by QSAR-models, and leave a set of molecules less suitable for future decision-making. In our study, SAR- and QSAR models could show which molecular sub-structures and physicochemical features that were advantageous for the AChE inhibition. Finally, the QSAR model was used for the prediction of the inhibition of AChE by an external prediction set of molecules. The accuracy of these predictions was asserted by statistical significance tests and by comparisons to simple but relevant reference models.

The Hydric Effect in Inorganic Nanomaterials for Nanoelectronics and Energy Applications.

PubMed

Sun, Xu; Guo, Yuqiao; Wu, Changzheng; Xie, Yi

2015-07-08

Protons, as one of the world's smallest ions, are able to trigger the charge effect without obvious lattice expansion inside inorganic materials, offering a unique and important test-bed for controlling their diverse functionalities. Arising from the high chemical reactivity of hydrogen (easily losing an electron) with various main group anions (easily accepting a proton), the hydric effect provides a convenient and environmentally benign route to bring about fascinating new physicochemical properties, as well as to create new inorganic structures based on the "old lattice" without dramatically destroying the pristine structure, covering most inorganic materials. Moreover, hydrogen atoms tend to bond with anions or to produce intrinsic defects, both of which are expected to inject extra electrons into lattice framework, promising advances in control of bandgap, spin behavior, and carrier concentration, which determine functionality for wide applications. In this review article, recently developed effective hydric strategies are highlighted, which include the conventional hydric reaction under high temperature or room temperature, proton irradiation or hydrogen plasma treatment, and gate-electrolyte-driven adsorption or doping. The diverse physicochemical properties brought by the hydric effect via modulation of the intrinsic electronic structure are also summarized, finding wide applications in nanoelectronics, energy applications, and catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Arginine-based poly(ester amide) nanoparticle platform: From structure-property relationship to nucleic acid delivery.

PubMed

You, Xinru; Gu, Zhipeng; Huang, Jun; Kang, Yang; Chu, Chih-Chang; Wu, Jun

2018-05-25

Many different types of polycations have been vigorously studied for nucleic acid delivery, but a systematical investigation of the structure-property relationships of polycations for nucleic acid delivery is still lacking. In this study, a new library of biodegradable and biocompatible arginine-based poly(ester amide) (Arg-PEA) biomaterials was designed and synthesized with a tunable structure for such a comprehensive structure-property research. Nanoparticle (NP) complexes were formed through the electrostatic interactions between the polycationic Arg-PEAs and anionic nucleic acids. The following structure effects of the Arg-PEAs on the transfection efficiency of nucleic acids were investigated: 1) the linker/spacer length (length effect and odd-even effect); 2) salt type of arginine; 3) the side chain; 4) chain stiffness; 5) molecular weight (MW). The data obtained revealed that a slight change in the Arg-PEA structure could finely tune its physicochemical property such as hydrophobicity, and this could subsequently affect the nanoparticle size and zeta potential, which, in turn, regulate the transfection efficiency and silencing outcomes. A further study of the Arg-PEA/CpG oligodeoxynucleotide NP complexes indicated that the polymer structure could precisily regulate the immune response of CpG, thus providing a new potential nano-immunotherapy strategy. The in vitro data have further confirmed that the Arg-PEA NPs showed a satisfactory delivery performance for a variety of nucleic acids. Therefore, the data from the current study provide comprehensive information about the Arg-PEA structure-transfection property relationship; the tunable property of the library of Arg-PEA biomaterials can be one of the promising candidates for nucleic acid delivery and other biomedical applications. Polycations have being intensive utilized for nucleic acid delivery. However, there has not been elucidated about the relationship between polycation's structure and the physicochemical properties/biological function. In this timely report, an arginine based poly(ester amide) (Arg-PEA) library was prepared with finely tunable structure to systematically investigate the structure-property relationships of polycations for nucleic acid delivery. The results revealed that slight change of Arg-PEA structure could finely tune the physicochemical property (such as hydrophobicity), which subsequently affect the size and zeta potential of Arg-PEA/nucleic acid nanoparticles(NPs), and finally regulate the resulting transfection or silencing outcomes. Further study of Arg-PEA/CpG NPs indicated that the polymer structure could precisely regulate immuno response of CpG, providing new potential nano-immunotherapy strategy. In vitro evaluations confirmed that the NPs showed satisfied delivery performance for a variety types of nucleic acids. Therefore, these studies provide comprehensive information of Arg-PEA structure-property relationship, and the tunable properties of Arg-PEAs make them promising candidates for nucleic acid delivery and other biomedical applications. Overall, we have shown enough significance and novelty in terms of nucleic acid delivery, biomaterials, pharmaceutical science and nanomedicine. Copyright © 2018. Published by Elsevier Ltd.

Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens.

PubMed

Al Qaraghuli, Mohammed M; Ferro, Valerie A

2017-04-01

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes. Copyright © 2016 John Wiley & Sons, Ltd.

Energy as a Constraint on Habitability in the Subsurface

NASA Astrophysics Data System (ADS)

Hoehler, T.

2008-12-01

All living things must obtain energy from the environment to grow, to maintain a metabolic steady state, or simply to preserve viability. The availability of energy sources in the environment thus represents a key factor in determining the size, distribution, and activity of biological populations, and ultimately constrains the possibility for life itself. Lacking the abundant energy provided by solar radiation or the products of oxygenic photosynthesis, life in subsurface environments may be limited by energy availability as much as any other factor. The biological requirement for energy is expressed in two dimensions - analogous to the power and voltage requirements of electrical devices - and consideration and quantification of these requirements establishes quantitative boundary conditions on subsurface habitability. The magnitude of these requirements depends significantly on physicochemical environment, as does the provision of biologically-accessible energy from subsurface sources. With this conceptual basis, we are developing an 'energy balance' model that is designed to ultimately predict the habitability of a given environment, with respect to a given metabolism, in quantitative terms (as 'biomass density potential'). The model will develop from conceptual to quantitative as experimental and observational work constrains and quantifies, in natural populations adapted to low energy conditions, the magnitude of the biological energy requirements and the impacts of physicochemical environmental conditions on energy demand and supply.

Quantum Chemical and Physicochemical Studies of Oximes (Prophylactics against and Reactivators of Phosphorylated AChE).

DTIC Science & Technology

1984-10-25

crystal structure of nicotinic acid ,. and we used the ether bridge from the crystal structure of dimethyl ether. We are investigating various rotamers...observations were made: - The titration curve (after the subtraction of the blank curve) shows only one titrable group, i.e. the oxime moiety. - The...subtraction of the blank curve, shows two titrable groups, i.e. the two oxime moieties. The results are as follows: Temperature Conditions PKa pK2

Atomic force microscopy of starch systems.

PubMed

Zhu, Fan

2017-09-22

Atomic force microscopy (AFM) generates information on topography, adhesion, and elasticity of sample surface by touching with a tip. Under suitable experimental settings, AFM can image biopolymers of few nanometers. Starch is a major food and industrial component. AFM has been used to probe the morphology, properties, modifications, and interactions of starches from diverse botanical origins at both micro- and nano-structural levels. The structural information obtained by AFM supports the blocklet structure of the granules, and provides qualitative and quantitative basis for some physicochemical properties of diverse starch systems. It becomes evident that AFM can complement other microscopic techniques to provide novel structural insights for starch systems.

[Some aspects of lifestyle and health status in students].

PubMed

Khisamov, E N; Musalimova, R S

2004-01-01

To study the lifestyle of students, the spread of bad habits and the self-appraisal of their health status, a sociological survey was made among the indigenous dwellers of a large industrial town and nonresident students. A slight deterioration of health indices was revealed in the students residing in a chemically polluted area of the town and in those who had come from other environmentally unfavorable areas of the republic. These changes may be associated not only with the known reorganization of the pattern of academic activities and lifestyle, but also with the adverse physicochemical influence of a new environment. Changing the environment may promote the strain of mechanisms responsible for adaptation and health destabilization.

Chitosan-coated mesoporous MIL-100(Fe) nanoparticles as improved bio-compatible oral nanocarriers

PubMed Central

Hidalgo, T.; Giménez-Marqués, M.; Bellido, E.; Avila, J.; Asensio, M. C.; Salles, F.; Lozano, M. V.; Guillevic, M.; Simón-Vázquez, R.; González-Fernández, A.; Serre, C.; Alonso, M. J.; Horcajada, P.

2017-01-01

Nanometric biocompatible Metal-Organic Frameworks (nanoMOFs) are promising candidates for drug delivery. Up to now, most studies have targeted the intravenous route, related to pain and severe complications; whereas nanoMOFs for oral administration, a commonly used non-invasive and simpler route, remains however unexplored. We propose here the biofriendly preparation of a suitable oral nanocarrier based on the benchmarked biocompatible mesoporous iron(III) trimesate nanoparticles coated with the bioadhesive polysaccharide chitosan (CS). This method does not hamper the textural/structural properties and the sorption/release abilities of the nanoMOFs upon surface engineering. The interaction between the CS and the nanoparticles has been characterized through a combination of high resolution soft X-ray absorption and computing simulation, while the positive impact of the coating on the colloidal and chemical stability under oral simulated conditions is here demonstrated. Finally, the intestinal barrier bypass capability and biocompatibility of CS-coated nanoMOF have been assessed in vitro, leading to an increased intestinal permeability with respect to the non-coated material, maintaining an optimal biocompatibility. In conclusion, the preservation of the interesting physicochemical features of the CS-coated nanoMOF and their adapted colloidal stability and progressive biodegradation, together with their improved intestinal barrier bypass, make these nanoparticles a promising oral nanocarrier. PMID:28256600

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu, Tianfeng

The goal of the proposed research is to create computational flame diagnostics (CFLD) that are rigorous numerical algorithms for systematic detection of critical flame features, such as ignition, extinction, and premixed and non-premixed flamelets, and to understand the underlying physicochemical processes controlling limit flame phenomena, flame stabilization, turbulence-chemistry interactions and pollutant emissions etc. The goal has been accomplished through an integrated effort on mechanism reduction, direct numerical simulations (DNS) of flames at engine conditions and a variety of turbulent flames with transport fuels, computational diagnostics, turbulence modeling, and DNS data mining and data reduction. The computational diagnostics are primarily basedmore » on the chemical explosive mode analysis (CEMA) and a recently developed bifurcation analysis using datasets from first-principle simulations of 0-D reactors, 1-D laminar flames, and 2-D and 3-D DNS (collaboration with J.H. Chen and S. Som at Argonne, and C.S. Yoo at UNIST). Non-stiff reduced mechanisms for transportation fuels amenable for 3-D DNS are developed through graph-based methods and timescale analysis. The flame structures, stabilization mechanisms, local ignition and extinction etc., and the rate controlling chemical processes are unambiguously identified through CFLD. CEMA is further employed to segment complex turbulent flames based on the critical flame features, such as premixed reaction fronts, and to enable zone-adaptive turbulent combustion modeling.« less

Obesity-driven disruption of haematopoiesis and the bone marrow niche.

PubMed

Adler, Benjamin J; Kaushansky, Kenneth; Rubin, Clinton T

2014-12-01

Obesity markedly increases susceptibility to a range of diseases and simultaneously undermines the viability and fate selection of haematopoietic stem cells (HSCs), and thus the kinetics of leukocyte production that is critical to innate and adaptive immunity. Considering that blood cell production and the differentiation of HSCs and their progeny is orchestrated, in part, by complex interacting signals emanating from the bone marrow microenvironment, it is not surprising that conditions that disturb bone marrow structure inevitably disrupt both the numbers and lineage-fates of these key blood cell progenitors. In addition to the increased adipose burden in visceral and subcutaneous compartments, obesity causes a marked increase in the size and number of adipocytes encroaching into the bone marrow space, almost certainly disturbing HSC interactions with neighbouring cells, which include osteoblasts, osteoclasts, mesenchymal cells and endothelial cells. As the global obesity pandemic grows, the short-term and long-term consequences of increased bone marrow adiposity on HSC lineage selection and immune function remain uncertain. This Review discusses the differentiation and function of haematopoietic cell populations, the principal physicochemical components of the bone marrow niche, and how this environment influences HSCs and haematopoiesis in general. The effect of adipocytes and adiposity on HSC and progenitor cell populations is also discussed, with the goal of understanding how obesity might compromise the core haematopoietic system.

Human, vector and parasite Hsp90 proteins: A comparative bioinformatics analysis.

PubMed

Faya, Ngonidzashe; Penkler, David L; Tastan Bishop, Özlem

2015-01-01

The treatment of protozoan parasitic diseases is challenging, and thus identification and analysis of new drug targets is important. Parasites survive within host organisms, and some need intermediate hosts to complete their life cycle. Changing host environment puts stress on parasites, and often adaptation is accompanied by the expression of large amounts of heat shock proteins (Hsps). Among Hsps, Hsp90 proteins play an important role in stress environments. Yet, there has been little computational research on Hsp90 proteins to analyze them comparatively as potential parasitic drug targets. Here, an attempt was made to gain detailed insights into the differences between host, vector and parasitic Hsp90 proteins by large-scale bioinformatics analysis. A total of 104 Hsp90 sequences were divided into three groups based on their cellular localizations; namely cytosolic, mitochondrial and endoplasmic reticulum (ER). Further, the parasitic proteins were divided according to the type of parasite (protozoa, helminth and ectoparasite). Primary sequence analysis, phylogenetic tree calculations, motif analysis and physicochemical properties of Hsp90 proteins suggested that despite the overall structural conservation of these proteins, parasitic Hsp90 proteins have unique features which differentiate them from human ones, thus encouraging the idea that protozoan Hsp90 proteins should be further analyzed as potential drug targets.

Approaching Pharmacological Space: Events and Components.

PubMed

Vistoli, Giulio; Pedretti, Alessandro; Mazzolari, Angelica; Testa, Bernard

2018-01-01

With a view to introducing the concept of pharmacological space and its potential applications in investigating and predicting the toxic mechanisms of xenobiotics, this opening chapter describes the logical relations between conformational behavior, physicochemical properties and binding spaces, which are seen as the three key elements composing the pharmacological space. While the concept of conformational space is routinely used to encode molecular flexibility, the concepts of property spaces and, particularly, of binding spaces are more innovative. Indeed, their descriptors can find fruitful applications (a) in describing the dynamic adaptability a given ligand experiences when inserted into a specific environment, and (b) in parameterizing the flexibility a ligand retains when bound to a biological target. Overall, these descriptors can conveniently account for the often disregarded entropic factors and as such they prove successful when inserted in ligand- or structure-based predictive models. Notably, and although binding space parameters can clearly be derived from MD simulations, the chapter will illustrate how docking calculations, despite their static nature, are able to evaluate ligand's flexibility by analyzing several poses for each ligand. Such an approach, which represents the founding core of the binding space concept, can find various applications in which the related descriptors show an impressive enhancing effect on the statistical performances of the resulting predictive models.

Chitosan-coated mesoporous MIL-100(Fe) nanoparticles as improved bio-compatible oral nanocarriers

NASA Astrophysics Data System (ADS)

Hidalgo, T.; Giménez-Marqués, M.; Bellido, E.; Avila, J.; Asensio, M. C.; Salles, F.; Lozano, M. V.; Guillevic, M.; Simón-Vázquez, R.; González-Fernández, A.; Serre, C.; Alonso, M. J.; Horcajada, P.

2017-03-01

Nanometric biocompatible Metal-Organic Frameworks (nanoMOFs) are promising candidates for drug delivery. Up to now, most studies have targeted the intravenous route, related to pain and severe complications; whereas nanoMOFs for oral administration, a commonly used non-invasive and simpler route, remains however unexplored. We propose here the biofriendly preparation of a suitable oral nanocarrier based on the benchmarked biocompatible mesoporous iron(III) trimesate nanoparticles coated with the bioadhesive polysaccharide chitosan (CS). This method does not hamper the textural/structural properties and the sorption/release abilities of the nanoMOFs upon surface engineering. The interaction between the CS and the nanoparticles has been characterized through a combination of high resolution soft X-ray absorption and computing simulation, while the positive impact of the coating on the colloidal and chemical stability under oral simulated conditions is here demonstrated. Finally, the intestinal barrier bypass capability and biocompatibility of CS-coated nanoMOF have been assessed in vitro, leading to an increased intestinal permeability with respect to the non-coated material, maintaining an optimal biocompatibility. In conclusion, the preservation of the interesting physicochemical features of the CS-coated nanoMOF and their adapted colloidal stability and progressive biodegradation, together with their improved intestinal barrier bypass, make these nanoparticles a promising oral nanocarrier.

Impact of abiotic factors on development of the community of arbuscular mycorrhizal fungi in the soil: a Review

NASA Astrophysics Data System (ADS)

Jamiołkowska, Agnieszka; Księżniak, Andrzej; Gałązka, Anna; Hetman, Beata; Kopacki, Marek; Skwaryło-Bednarz, Barbara

2018-01-01

Arbuscular mycorrhizal fungi inhabiting soil play an important role for vascular plants. Interaction between arbuscular mycorrhizal fungi, plants and soil microorganisms leads to many mutual advantages. However, the effectiveness of mycorrhizal fungi depends not only on biotic, but also abiotic factors such as physico-chemical properties of the soil, availability of water and biogenic elements, agricultural practices, and climatic conditions. First of all, it is important to adapt the arbuscular mycorrhizal fungi species to changing environmental conditions. The compactness of the soil and its structure have a huge impact on its biological activity. Soil pH reaction has a substantial impact on the mobility of ions in soil dilutions and their uptake by plants and soil microflora. Water excess can be a factor negatively affecting arbuscular mycorrhizal fungi because these microorganisms are sensitive to a lower availability of oxygen. Mechanical cultivation of the soil has a marginal impact on the arbuscular mycorrhizal fungi spores. However, soil translocation can cause changes to the population of the arbuscular mycorrhizal fungi abundance in the soil profile. The geographical location and topographic differentiation of cultivated soils, as well as the variability of climatic factors affect the population of the arbuscular mycorrhizal fungi in the soils and their symbiotic activity.

Assessment of thermal stress adaptation by monitoring Hsp70 and MnSOD in the freshwater gastropod, Bellamya bengalensis (Lamark 1882).

PubMed

Dutta, Sangita Maiti; Mustafi, Soumyajit Banerjee; Raha, Sanghamitra; Chakraborty, Susanta Kumar

2014-12-01

Expression of the stress biomarkers 70-kDa heat shock proteins (Hsp70) and manganese superoxide dismutase (MnSOD) was measured as the molecular basis of adaptive response against increased experimental temperatures (32-40 °C for a span of 24-72 h) on the fresh water molluscan species, Bellamya bengalensis (Lamark 1882). The experimental snail specimens were collected during summer and winter seasons from two contrasting wetlands: an ecorestored (free from human interference) site (SI) and other experiencing anthropogenic stresses (SII). The mortality rate of the B. bengalensis and the immunoblotting of MnSOD and Hsp70 of their digestive glands were performed at regular intervals during the period of heat stress. The SI provided a lower stress environment based on physicochemical parameters such as pH, dissolved oxygen (DO), biological oxygen demand (BOD), chemical oxygen demand (COD), and alkalinity for the survival of test species, although both sites experienced mortality due to thermal stresses. The parity in protein expressions displayed a uniform mode of adaptive impact to temperature elevations in both field and laboratory exposure. The Hsp70 expression was minimal at lower thermal stress, but increased with a rise in temperature. It is very likely that higher Hsp70 levels are not directly related to survival or adaptation. In contrast, MnSOD levels appeared to be an indicator of adaptive responses vis-a-vis survival of the animals. So, the expression levels of a universal free radical scavenger like MnSOD are recognized as a potential biomarker in a bioindicator species like Bellamya.

Adaptive and neutral markers both show continent-wide population structure of mountain pine beetle (Dendroctonus ponderosae).

PubMed

Batista, Philip D; Janes, Jasmine K; Boone, Celia K; Murray, Brent W; Sperling, Felix A H

2016-09-01

Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single-nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range-wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

Conformational interpretation of vescalagin and castalagin physicochemical properties.

PubMed

Vivas, Nicolas; Laguerre, Michel; Pianet de Boissel, Isabelle; Vivas de Gaulejac, Nathalie; Nonier, Marie-Françoise

2004-04-07

Vescalagin and castalagin are two diastereoisomers. The variability of their principal physicochemical properties, compared with their small structural differences, suggests important conformational variations. This study shows, experimentally, that vescalagin has a greater effect on polarity, oxidizability in solution, and thermodegradability than castalagin. Conformational analysis by molecular mechanics demonstrated that vescalagin was more hydrophilic and was more reactive to electrophilic reagents than castalagin. Experimental results were thus explained and demonstrated the distinct behaviors of vescalagin and castalagin. These results were attributed to the C1 position of the two compounds because vescalin and castalin have comparable characteristics. Experimental data were confirmed and interpreted by molecular mechanics. This work represents one of the first attempts to correlate conformation and the properties of phenolic compounds. This step constitutes a predictive method for the pharmacology or chemistry of new compounds.

[Chemical constituents of Pileostegia viburnoides var. glabrescens].

PubMed

Zou, Ju-ying; Chen, Sheng-huang; Li, Qin-wen; Ou, Yang-wen; Chen, Han-jun; Wang, Wei

2012-05-01

To study the chemical constituents of Pileostegia viburnoides var. glabrescens. The compounds were isolated and purified by various techniques. Their structures were determined by physicochemical properties and spectral analysis. Five compounds were isolated and identified as friedelin (1), beta-sitosterol (2), umbelliferone (3), daucosterol (4) and skimmin (5). All the compounds were isolated from this genus for the first time.

Urbanization alters the functional composition, but not taxonomic diversity, of the soil nematode community

Treesearch

Mitchell A. Pavao-Zuckerman; David C. Coleman

2007-01-01

We evaluated the response of riparian forest soil nematode community structure to the physico-chemical environment associated with urban land use. Soils were sampled seasonally between December 2000 and October 2002 along an urban-rural transect in Asheville, North Carolina. We characterized the taxonomic (to genus) and functional composition (trophic groups) of the...

Regularities of the sorption of 1,2,3,4-tetrahydroquinoline derivatives under conditions of reversed phase HPLC

NASA Astrophysics Data System (ADS)

Nekrasova, N. A.; Kurbatova, S. V.; Zemtsova, M. N.

2016-12-01

Regularities of the sorption of 1,2,3,4-tetrahydroquinoline derivatives on octadecylsilyl silica gel and porous graphitic carbon from aqueous acetonitrile solutions were investigated. The effect the molecular structure and physicochemical parameters of the sorbates have on their retention characteristics under conditions of reversed phase HPLC are analyzed.

Life Origination and Development Hydrate theory (LOH-Theory): new approaches to the problems of the optimal nutrition and life prolongation

NASA Astrophysics Data System (ADS)

Kadyshevich, E. A.; Ostrovskii, V. E.

2014-04-01

Life Origination Hydrate Theory (LOH-Theory) and Mitosis and Replication Hydrate Theory (MRHTheory), both grounded on the notion of honeycomb gas-hydrate structures formation/destruction as the physicochemical phenomenon governing the DNA origination and replication, allow new approaches to the optimal nutrition and life prolongation problems.

Structure-Based Drug Design of Novel Potent and Selective Tetrahydropyrazolo[1,5- a ]pyrazines as ATR Inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barsanti, Paul A.; Aversa, Robert J.; Jin, Xianming

A saturation strategy focused on improving the selectivity and physicochemical properties of ATR inhibitor HTS hit 1 led to a novel series of highly potent and selective tetrahydropyrazolo[1,5-a]pyrazines. Use of PI3Kα mutants as ATR crystal structure surrogates was instrumental in providing cocrystal structures to guide the medicinal chemistry designs. Detailed DMPK studies involving cyanide and GSH as trapping agents during microsomal incubations, in addition to deuterium-labeled compounds as mechanistic probes uncovered the molecular basis for the observed CYP3A4 TDI in the series.

[Strategy of molecular design of drugs: the unification of macro-properties and micro-structures of a molecule].

PubMed

Guo, Zong-Ru

2008-03-01

The interaction of a drug with the organism involves both the disposition of a drug by the organism and the action of a drug on the organism. The disposition of various exogenous substances, including drugs, complies with general rules. The underlying physical and chemical changes to different drugs in view of time and space, i. e. pharmacokinetics, share common characteristics, that is the tout ensemble of a molecule and its macroscopic properties convey direct effect on the pharmacokinetic behavior as the tendency and consequence of biological evolution. The action of a drug on the organism, on the other hand, implicates the physico-chemical binding of a drug molecule to the target protein, which induces pharmacological and toxicological effects. The biological reactions, no matter beneficial or adverse, are all specific and individual manifestation of the drug molecule and determined by the interactive binding between definitive atoms or groups of the drug molecule and the macromolecular target in three-dimension. Such critical atoms, groups, or fragments responsible for the interaction reflect the microscopic structures of drug molecules and are called pharmacophore. In this context, a drug molecule is presumed as an assembly of macroscopic property and microscopic structure, with the macroscopic properties determining the absorption, distribution, metabolism and elimination of drugs and the microscopic structure coining pharmacological action. The knowledge of the internal relationship between macroscopy/microscopy and PK/PD conduces to comprehension of drug action and guides molecular drug design, because this conception facilitates the identification of structural features necessary for biological response, and the determination of factors modulating the physico-chemical and pharmacokinetic properties. The factors determining macro-properties include molecular weight, solubility, charge, lipophilicity (partition), and polar surface area, etc., which are destined by molecular scaffolds and/or side chain(s) apart from pharmacophore. The features of micro-structures contributing to specific activity contain hydrogen bonding donor and acceptor, positive and negative charge centers, hydrophobic centers and centers of aromatic rings. Different combinations and spacial arrangements of these features determine the distinct activity presented. The macro-property and micro-structure are integrated into a single molecule, and are inseparable. The macro-property reflects overall contribution of atoms and groups in the micro-structure. On the other hand, structural changes aimed to adjust macroscopic property usually alter the relative position of the microscopic structure. The goal of molecular drug design is to integrate the macroscopic and microscopic factors in optimized manner. In the early stage of molecular design, both macroscopic property and microscopic structure should be considered to make pharmacodynamics, pharmacokinetics, and physico-chemical properties in optimal match. Therefore, it required the existence of structural overlapping among acceptable pharmacokinetics, visible developing potential and specific pharmacodynamics. The larger the scope of overlapping, the higher the possibility to be a drug.

Succession and diversity of microorganisms and their association with physicochemical properties during green waste thermophilic composting.

PubMed

Liu, Ling; Wang, Shuqi; Guo, Xiaoping; Zhao, Tingning; Zhang, Bolin

2018-03-01

A comprehensive characterization of the bacterial diversity associated to thermophilic stages of green waste composting was achieved. In this study, eight different treatments (T1-T8) and three replicated lab-scale green waste composting were carried out to compare the effect of the cellulase (i.e. 0, 2%), microbial inoculum (i.e. 0, 2 and 4%) and particle size (i.e. 2 and 5 mm) on bacterial community structure. Physicochemical properties and bacterial communities of T1-T8 composts were observed, and the bacterial structure and diversity were examined by high-throughput sequencing via a MiSeq platform. The results showed that the most abundant phyla among the treatments were the Firmicutes, Chloroflexi and Proteobacteria. The shannon index and non-metric multidimensional scaling (NMDS) showed higher bacterial abundance and diversity at the metaphase of composting. Comparing with 5-mm treatments, particle size of 2-mm had a richer diversity of bacterial communities. The addition of cellulase and a microbial inoculum could promote the fermentation temperature, reduce the compost pH and C/N ratio and result in higher GI index. The humic substance (HS) and humic acid (HA) contents for 2-mm particle size treatments were higher than those of 5-mm treatments. Canonical correspondence analysis suggested that differences in bacterial abundance and diversity significantly correlated with HA, E 4 /E 6 and temperature, and the relationship between bacterial diversity and environmental parameters was affected by composting stages. Based on these results, the application of cellulase to promote green waste composting was feasible, and particle size was identified as a potential control of composting physicochemical properties and bacterial diversity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Readers generalize adaptation to newly-encountered dialectal structures to other unfamiliar structures

PubMed Central

Fraundorf, Scott H.; Jaeger, T. Florian

2016-01-01

Growing evidence suggests that syntactic processing may be guided in part by expectations about the statistics of the input that comprehenders have encountered; however, these statistics and even the syntactic structures themselves vary from situation to situation. Some recent work suggests that readers can adapt to variability in the frequencies of known, but infrequent syntactic structures. But, the relation between adaptation to altered frequencies of familiar structures and learning to process unfamiliar, never-before-seen structures is under-explored. In two self-paced reading experiments, we investigated readers’ adaptation to an unfamiliar structure used in some regional dialects of American English: the needs+past participle structure, such as using The car needs washed to mean The car needs to be washed. Study 1 used a novel Web-based recruitment method to target regions where participants were likely to be familiar (Ohio, western Pennsylvania) or unfamiliar (Colorado) with the needs+past participle structure. Participants unfamiliar with the structure initially read the structure more slowly, but over the course of the experiment came to read it more like the familiar participants. Study 2 further demonstrated that participants who have adapted to needs+past participle generalize this adaptation to a different, but related structure. These results suggest (a) that readers adapt to unfamiliar syntactic structures, (b) that, in doing so, they become more like existing users of those structures, and (c) that they can generalize this other structures that they may also be more likely to encounter. We discuss these results in the context of implicit learning accounts of exposure effects on syntactic processing. PMID:28377640

A novel method based on new adaptive LVQ neural network for predicting protein-protein interactions from protein sequences.

PubMed

Yousef, Abdulaziz; Moghadam Charkari, Nasrollah

2013-11-07

Protein-Protein interaction (PPI) is one of the most important data in understanding the cellular processes. Many interesting methods have been proposed in order to predict PPIs. However, the methods which are based on the sequence of proteins as a prior knowledge are more universal. In this paper, a sequence-based, fast, and adaptive PPI prediction method is introduced to assign two proteins to an interaction class (yes, no). First, in order to improve the presentation of the sequences, twelve physicochemical properties of amino acid have been used by different representation methods to transform the sequence of protein pairs into different feature vectors. Then, for speeding up the learning process and reducing the effect of noise PPI data, principal component analysis (PCA) is carried out as a proper feature extraction algorithm. Finally, a new and adaptive Learning Vector Quantization (LVQ) predictor is designed to deal with different models of datasets that are classified into balanced and imbalanced datasets. The accuracy of 93.88%, 90.03%, and 89.72% has been found on S. cerevisiae, H. pylori, and independent datasets, respectively. The results of various experiments indicate the efficiency and validity of the method. © 2013 Published by Elsevier Ltd.

Ontogenetic changes in helminth membrane function.

PubMed

Arme, C

1988-01-01

During their life-cycle many parasites experience a wide range of environments including free living and those provided by a variety of intermediate and final hosts. The nutritional requirements of parasites are met by physiological processes adapted to exploit the physicochemical characteristics provided by different hosts. In helminth parasites these adaptations are frequently expressed on the tegumentary surface. As an example of adaptations within the Trematoda, the control of monosaccharide transport in Proterometra sp. is described. Environmental sodium, although not directly involved in the uptake process, nevertheless regulates the expression of transport capabilities. In the Cestoda, the uptake of monosaccharides and amino acids is described for Hymenolepis diminuta. The metacestode of this tapeworm inhabits the blood system of an arthropod, and the adult the gut of a mammal. There are quantitative and qualitative differences in the amino acids and monosaccharides in these two environments and these are reflected in the transport mechanisms exhibited by the two forms of the life-cycle. In Echinococcus granulosus the transfer of amino acids, sugars and macromolecules across the membranes of hydatid cysts and protoscoleces is described. The major difference between these two stages in the life-cycle relates to the ability of hydatid cysts to absorb macromolecules, whereas protoscoleces are impermeable to these compounds. The potential for future work is emphasized.

Adaptive structures for precision controlled large space systems

NASA Technical Reports Server (NTRS)

Garba, John A.; Wada, Ben K.; Fanson, James L.

1991-01-01

The stringent accuracy and ground test validation requirements of some of the future space missions will require new approaches in structural design. Adaptive structures, structural systems that can vary their geometric congiguration as well as their physical properties, are primary candidates for meeting the functional requirements for such missions. Research performed in the development of such adaptive structural systems is described.

The Architecture of Iron Microbial Mats Reflects the Adaptation of Chemolithotrophic Iron Oxidation in Freshwater and Marine Environments

PubMed Central

Chan, Clara S.; McAllister, Sean M.; Leavitt, Anna H.; Glazer, Brian T.; Krepski, Sean T.; Emerson, David

2016-01-01

Microbes form mats with architectures that promote efficient metabolism within a particular physicochemical environment, thus studying mat structure helps us understand ecophysiology. Despite much research on chemolithotrophic Fe-oxidizing bacteria, Fe mat architecture has not been visualized because these delicate structures are easily disrupted. There are striking similarities between the biominerals that comprise freshwater and marine Fe mats, made by Beta- and Zetaproteobacteria, respectively. If these biominerals are assembled into mat structures with similar functional morphology, this would suggest that mat architecture is adapted to serve roles specific to Fe oxidation. To evaluate this, we combined light, confocal, and scanning electron microscopy of intact Fe microbial mats with experiments on sheath formation in culture, in order to understand mat developmental history and subsequently evaluate the connection between Fe oxidation and mat morphology. We sampled a freshwater sheath mat from Maine and marine stalk and sheath mats from Loihi Seamount hydrothermal vents, Hawaii. Mat morphology correlated to niche: stalks formed in steeper O2 gradients while sheaths were associated with low to undetectable O2 gradients. Fe-biomineralized filaments, twisted stalks or hollow sheaths, formed the highly porous framework of each mat. The mat-formers are keystone species, with nascent marine stalk-rich mats comprised of novel and uncommon Zetaproteobacteria. For all mats, filaments were locally highly parallel with similar morphologies, indicating that cells were synchronously tracking a chemical or physical cue. In the freshwater mat, cells inhabited sheath ends at the growing edge of the mat. Correspondingly, time lapse culture imaging showed that sheaths are made like stalks, with cells rapidly leaving behind an Fe oxide filament. The distinctive architecture common to all observed Fe mats appears to serve specific functions related to chemolithotrophic Fe oxidation, including (1) removing Fe oxyhydroxide waste without entombing cells or clogging flow paths through the mat and (2) colonizing niches where Fe(II) and O2 overlap. This work improves our understanding of Fe mat developmental history and how mat morphology links to metabolism. We can use these results to interpret biogenicity, metabolism, and paleoenvironmental conditions of Fe microfossil mats, which would give us insight into Earth's Fe and O2 history. PMID:27313567

Bio-NCs--the marriage of ultrasmall metal nanoclusters with biomolecules.

PubMed

Goswami, Nirmal; Zheng, Kaiyuan; Xie, Jianping

2014-11-21

Ultrasmall metal nanoclusters (NCs) have attracted increasing attention due to their fascinating physicochemical properties. Today, functional metal NCs are finding growing acceptance in biomedical applications. To achieve a better performance in biomedical applications, metal NCs can be interfaced with biomolecules, such as proteins, peptides, and DNA, to form a new class of biomolecule-NC composites (or bio-NCs in short), which typically show synergistic or novel physicochemical and physiological properties. This feature article focuses on the recent studies emerging at the interface of metal NCs and biomolecules, where the interactions could impart unique physicochemical properties to the metal NCs, as well as mutually regulate biological functions of the bio-NCs. In this article, we first provide a broad overview of key concepts and developments in the novel biomolecule-directed synthesis of metal NCs. A special focus is placed on the key roles of biomolecules in metal NC synthesis. In the second part, we describe how the encapsulated metal NCs affect the structure and function of biomolecules. Followed by that, we discuss several unique synergistic effects observed in the bio-NCs, and illustrate them with examples highlighting their potential biomedical applications. Continued interdisciplinary efforts are required to build up in-depth knowledge about the interfacial chemistry and biology of bio-NCs, which could further pave their ways toward biomedical applications.

Characterization of physicochemical and thermal properties and crystallization behavior of krabok (Irvingia Malayana ) and rambutan seed fats.

PubMed

Sonwai, Sopark; Ponprachanuvut, Punnee

2012-01-01

Fatty acid composition, physicochemical and thermal properties and crystallization behavior of fats extracted from the seeds of krabok (Irvingia Malayana) and rambutan (Nephelium lappaceum L.) trees grown in Thailand were studied and compared with cocoa butter (CB). The krabok seed fat, KSF, consisted of 46.9% lauric and 40.3% myristic acids. It exhibited the highest saponification value and slip melting point but the lowest iodine values. The three fats displayed different crystallization behavior at 25°C. KSF crystallized into a mixture of β' and pseudo-β' structures with a one-step crystallization curve and high solid fat content (SFC). The fat showed simple DSC crystallization and melting thermograms with one distinct peak. The rambutan seed fat, RSF, consisted of 42.5% arachidic and 33.1% oleic acids. Its crystallization behavior was more similar to CB than KSF, displaying a two-step crystallization curve with SFC lower than that of KSF. RSF solidified into a mixture of β' and pseudo-β' before transforming to β after 24 h. The large spherulitic microstructures were observed in both KSF and RSF. According to these results, the Thai KSF and RSF exhibited physicochemical, thermal characteristics and crystallization behavior that could be suitable for specific applications in several areas of the food, cosmetic and pharmaceutical industries.

Physicochemical Changes and Resistant-Starch Content of Extruded Cornstarch with and without Storage at Refrigerator Temperatures.

PubMed

Neder-Suárez, David; Amaya-Guerra, Carlos A; Quintero-Ramos, Armando; Pérez-Carrillo, Esther; Alanís-Guzmán, María G de J; Báez-González, Juan G; García-Díaz, Carlos L; Núñez-González, María A; Lardizábal-Gutiérrez, Daniel; Jiménez-Castro, Jorge A

2016-08-15

Effects of extrusion cooking and low-temperature storage on the physicochemical changes and resistant starch (RS) content in cornstarch were evaluated. The cornstarch was conditioned at 20%-40% moisture contents and extruded in the range 90-130 °C and at screw speeds in the range 200-360 rpm. The extrudates were stored at 4 °C for 120 h and then at room temperature. The water absorption, solubility index, RS content, viscoelastic, thermal, and microstructural properties of the extrudates were evaluated before and after storage. The extrusion temperature and moisture content significantly affected the physicochemical properties of the extrudates before and after storage. The RS content increased with increasing moisture content and extrusion temperature, and the viscoelastic and thermal properties showed related behaviors. Microscopic analysis showed that extrusion cooking damaged the native starch structure, producing gelatinization and retrogradation and forming RS. The starch containing 35% moisture and extruded at 120 °C and 320 rpm produced the most RS (1.13 g/100 g) after to storage at low temperature. Although the RS formation was low, the results suggest that extrusion cooking could be advantageous for RS production and application in the food industry since it is a pollution less, continuous process requiring only a short residence time.

Physicochemical and Rheological Properties of a Dairy Dessert, Enriched with Chickpea Flour.

PubMed

Aguilar-Raymundo, Victoria Guadalupe; Vélez-Ruiz, Jorge Fernando

2018-02-18

Dairy desserts are complex mixtures and matrices including main components such as milk, sugar, starch, hydrocolloids, colorants and flavors, with a proteinaceous structure; they are widely consumed and present a semisolid consistency. In this work, the physicochemical and rheological properties of a dairy dessert with the addition of chickpea flour (raw and cooked, at four concentrations) were studied to determine the effect of the flour. The results indicated that luminosity (L*: 62.75-83.29), pH (6.35-7.11) and acidity (1.56-3.56) changed with the type of flour. The flow properties of the custards exhibited a non-Newtonian behavior that was well fitted by three flow models. The studied custard systems were stored for twelve days at 4 °C. The physicochemical and flow properties of the custards changed notably as a function of flour addition and storage time. From all samples, only four were analyzed with oscillatory tests, showing their mechanical spectra with elastic behavior. The dessert texture was also measured, founding that those formulated with Blanco Noroeste chickpea flour exhibited the highest values of hardness (0.356-0.391 Newton (N)) through the twelve days. It can be concluded that those custard systems with the highest content of flour presented a very good response as a potential new dairy product.

High similarity in physicochemical properties of chitin and chitosan from nymphs and adults of a grasshopper.

PubMed

Erdogan, Sevil; Kaya, Murat

2016-08-01

This is the first study to explain the differences in the physicochemical properties of chitin and chitosan obtained from the nymphs and adults of Dociostaurus maroccanus using the same method. Fourier transform infrared spectroscopy, thermogravimetric analysis and x-ray diffraction analysis results demonstrated that the chitins from both the adults and nymphs were in the α-form. The chitin contents of the adults (14%) and nymphs (12%) were of the same order of magnitude. The crystalline index values of chitins from the adult and nymph grasshoppers were 71% and 74%, respectively. Thermal stabilities of the chitins and chitosans from adult and nymph grasshoppers were close to each other. Both the adult (7.2kDa) and nymph (5.6kDa) chitosans had low molar masses. Environmental scanning electron microscopy revealed that the surface morphologies of both chitins consisted of nanofibers and nanopores together, and they were very similar to each other. Consequently, it was determined that the physicochemical properties of the chitins and chitosans from adults and nymphs of D. maroccanus were not very different, so it can be hypothesized that the development of the chitin structure in the nymph has almost been completed and the nymph chitin has the same characteristics as the adult. Copyright © 2016 Elsevier B.V. All rights reserved.

Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions.

PubMed

Du, Q S; Ma, Y; Xie, N Z; Huang, R B

2014-01-01

In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.

Investigation of Methylene Blue Release from Functional Polymeric Systems Using Dielectric Analysis.

PubMed

Bruschi, Marcos Luciano; Junqueira, Mariana Volpato; Borghi-Pangoni, Fernanda Belincanta; Yu, Tao; Andrews, Gavin Paul; Jones, David Simon

2018-01-01

Methylene blue (MB) is a photosensitizer used in photodynamic therapy (PDT) to treat colorectal cancer tumors and leishmaniasis infection. The clinical efficacy of PDT using MB is dependent on the physicochemical characteristics of the formulation. Bioadhesive thermoresponsive systems containing poloxamer 407 and Carbopol 934P have been proposed as platforms for PDT. However, the effect of MB on the physicochemical properties of these platforms is not fully understood, particularly in light of the MB availability. The aim of this study was to investigate the dielectric characteristics of functional polymeric systems containing MB and their influence on mucoadhesion and drug release. Binary polymeric systems containing different concentrations of poloxamer 407, Carbopol 934P and MB were evaluated as dielectric and mucoadhesive properties, as well as in vitro drug release profile. MB, temperature and polymeric composition influenced the physicochemical properties of the systems. The presence of MB altered the supramolecular structure of the preparations. The mucoadhesive properties of systems were influenced by MB presence and the formulation with the lowest amount of MB displayed faster release. The lower MB concentration in the systems displayed better results in terms of ionic mobility and drug release, and is indicative of a suitable clinical performance. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The physicochemical properties and catalytic performance of carbon-covered alumina for oxidative dehydrogenation of ethylbenzene with CO2

NASA Astrophysics Data System (ADS)

Wang, Tehua; Chong, Siying; Wang, Tongtong; Lu, Huiyi; Ji, Min

2018-01-01

In order to correlate the physicochemical properties of carbon-covered alumina (CCA) materials with their catalytic performance for oxidative dehydrogenation of ethylbenzene with CO2 (CO2-ODEB), a series of CCA materials with diverse carbon contents (8.7-31.3 wt%) and pyrolysis temperatures (600-800 °C), which were synthesized via an impregnation method followed by pyrolysis, were applied. These catalytic materials were characterized by TGA, N2 physisorption, XRD, Raman spectroscopy and XPS techniques. It was found that the catalytic performance of these CCA materials highly depended on their physicochemical properties, and the optimum CCA catalyst exhibited much better catalytic stability than conventional hydroxyl carbon nanotubes. Below an optimum value of carbon content, the CCA catalyst preserved the main pore characteristics of the Al2O3 support and its catalytic activity increased with the carbon content. Excessive carbon loading resulted in significant textural alterations and thereby decreased both the ethylbenzene conversion and styrene selectivity. On the other hand, high pyrolysis temperature was detrimental to the ordered graphitic structure of the carbon species within the Al2O3 pore. The decreased ordered graphitic degree was found to be associated with the loss of the surface active carbonyl groups, consequently hampering the catalytic efficiency of the CCA catalyst.

Bio-NCs - the marriage of ultrasmall metal nanoclusters with biomolecules

NASA Astrophysics Data System (ADS)

Goswami, Nirmal; Zheng, Kaiyuan; Xie, Jianping

2014-10-01

Ultrasmall metal nanoclusters (NCs) have attracted increasing attention due to their fascinating physicochemical properties. Today, functional metal NCs are finding growing acceptance in biomedical applications. To achieve a better performance in biomedical applications, metal NCs can be interfaced with biomolecules, such as proteins, peptides, and DNA, to form a new class of biomolecule-NC composites (or bio-NCs in short), which typically show synergistic or novel physicochemical and physiological properties. This feature article focuses on the recent studies emerging at the interface of metal NCs and biomolecules, where the interactions could impart unique physicochemical properties to the metal NCs, as well as mutually regulate biological functions of the bio-NCs. In this article, we first provide a broad overview of key concepts and developments in the novel biomolecule-directed synthesis of metal NCs. A special focus is placed on the key roles of biomolecules in metal NC synthesis. In the second part, we describe how the encapsulated metal NCs affect the structure and function of biomolecules. Followed by that, we discuss several unique synergistic effects observed in the bio-NCs, and illustrate them with examples highlighting their potential biomedical applications. Continued interdisciplinary efforts are required to build up in-depth knowledge about the interfacial chemistry and biology of bio-NCs, which could further pave their ways toward biomedical applications.

Dynamic mesh adaption for triangular and tetrahedral grids

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Strawn, Roger

1993-01-01

The following topics are discussed: requirements for dynamic mesh adaption; linked-list data structure; edge-based data structure; adaptive-grid data structure; three types of element subdivision; mesh refinement; mesh coarsening; additional constraints for coarsening; anisotropic error indicator for edges; unstructured-grid Euler solver; inviscid 3-D wing; and mesh quality for solution-adaptive grids. The discussion is presented in viewgraph form.

Toward the Understanding of MNEI Sweetness from Hydration Map Surfaces

PubMed Central

De Simone, Alfonso; Spadaccini, Roberta; Temussi, Piero A.; Fraternali, Franca

2006-01-01

The binding mechanism of sweet proteins to their receptor, a G-protein-coupled receptor, is not supported by direct structural information. In principle, the key groups responsible for biological activity (glucophores) can be localized on a small structural unit (sweet finger) or spread on a larger surface area. A recently proposed model, called “wedge model”, implies a large surface of interaction with the receptor. To explore this model in greater detail, it is necessary to examine the physicochemical features of the surfaces of sweet proteins, since their interaction with the receptor, with respect to that of small sweeteners, is more dependent on general physicochemical properties of the interface, such as electrostatic potential and hydration. In this study, we performed exhaustive molecular dynamics simulations in explicit water of the sweet protein MNEI and of its structural mutant G-16A, whose sweetness is one order of magnitude lower than that of MNEI. Solvent density and self-diffusion calculated from molecular dynamics simulations suggest a likely area of interaction delimited by four stretches arranged as a tetrahedron whose shape is complementary to that of a cavity on the surface of the receptor, in agreement with the wedge model. The suggested area of interaction is amazingly consistent with known mutagenesis data. In addition, the asymmetric hydration of the only helix in both proteins hints at a specific role for this secondary structure element in orienting the protein during the binding process. PMID:16461400

Atomic Force Microscopy of virus capsids uncover the interplay between mechanics, structure and function

NASA Astrophysics Data System (ADS)

de Pablo, Pedro J.

The basic architecture of a virus consists of the capsid, a shell made up of repeating protein subunits, which packs, shuttles and delivers their genome at the right place and moment. Viral particles are endorsed with specific physicochemical properties which confer to their structures certain meta-stability whose modulation permits fulfilling each task of the viral cycle. These natural designed capabilities have impelled using viral capsids as protein containers of artificial cargoes (drugs, polymers, enzymes, minerals) with applications in biomedical and materials sciences. Both natural and artificial protein cages have to protect their cargo against a variety of physicochemical aggressive environments, including molecular impacts of highly crowded media, thermal and chemical stresses, and osmotic shocks. Viral cages stability under these ambiences depend not only on the ultimate structure of the external capsid, which rely on the interactions between protein subunits, but also on the nature of the cargo. During the last decade our lab has focused on the study of protein cages with Atomic Force Microscopy (AFM) (figure 1). We are interested in stablishing links of their mechanical properties with their structure and function. In particular, mechanics provide information about the cargo storage strategies of both natural and virus-derived protein cages. Mechanical fatigue has revealed as a nanosurgery tool to unveil the strength of the capisd subunit bonds. We also interrogated the electrostatics of individual protein shells. Our AFM-fluorescence combination provided information about DNA diffusing out cracked-open protein cages in real time.

Microbiological and physicochemical factors affecting Aspergillus section Flavi incidence in Cavendish banana (Musa cavendishii) chips production in Southern Philippines.

PubMed

Sales, A C; Azanza, P V; Yoshizawa, T

2005-01-01

Microbiological and physicochemical factors affecting the incidence of Aspergillus section Flavi in dried Cavendish banana (Musa cavendishii) chips production in Southern Philippines were examined. The average counts of Aspergillus section Flavi (AFC) in fresh and dried Cavendish bananas from 10 production batches of the Philippine Agro-Industrial Development Cooperative in Davao del Norte, Southern Philippines were 1.2 x 10(2) and 1.6 x 10(2) cfu/g, respectively. Isolates from both samples were identified to be Aspergillus flavus based on spore type and conidial structure of isolates. An increasing trend in the AFC of Cavendish bananas was observed during dried banana chips processing. Variability in the AFC between production batches was attributed to differences in aerobic and fungal populations and physicochemical characteristics of the fruits, peel damage of the raw materials, concentration of AFC in the air and food-contact surfaces of the production area, and temperature and relative humidity (RH) conditions of the environment during production and storage. Physicochemical characteristics of Cavendish bananas from the receipt of raw materials up to the first day of drying were within the reported range of values allowing growth and toxin production by aflatoxigenic fungi. Air-borne AFC varied depending on the section of the production area examined. The close proximity of the waste disposal area from the production operation to the preparation, drying and storage areas suggests that cross-contamination, probably air-borne or insect-borne was a likely occurrence. The hands of workers were also identified as AFC sources. Results of this study highlight the need for the development of strategies to control aflatoxigenic fungi and aflatoxin contamination in Philippine dried Cavendish bananas.

[Studies on the triterpenoids of Cyclocarya paliurus (Batal.) Iljinsk].

PubMed

Shu, Rengeng; Liu, Yufeng; Chen, Jie; Shu, Jicheng

2005-07-01

Three triterpenes (I-II) were obtained from the leaves of Cyclocarya paliurus (Batal.) Iljinsk. By means of physicochemical and spectral methods, the structures of the three triterpenes were identified as oleanolic acid (I), ursolic acid (II) and epikatonic acid (III) respectively. All of the three triterpenes were isolated for the first time from the plant of Cyclocarya paliurus (Batal.) Iljinsk.

[Studies on chemical constituents from Elaeocarpus sylvestris].

PubMed

Zhang, Hong-Chao; Shi, Hai-Ming

2008-10-01

To study the chemical constituents of Elaeocarpus sylvestris. The compounds were isolated by chromatographic methods and their structures were elucidated by physico-chemical properties and spectral analysis. Six compounds were isolated and identified as: 2-hydroxy-benzaldehyde (1), coniferyl alcohol (2), umbelliferone (3), scopoletin (4), beta-sitosterol (5), daucosterol (6). All above compounds are isolated from Elaeocarpus Genus for the first time.

Effect of the physicochemical parameters of benzimidazole molecules on their retention by a nonpolar sorbent from an aqueous acetonitrile solution

NASA Astrophysics Data System (ADS)

Shafigulin, R. V.; Safonova, I. A.; Bulanova, A. V.

2015-09-01

The effect of the structure of benzimidazoles on their chromatographic retention on octadecyl silica gel from an aqueous acetonitrile eluent was studied. One- and many-parameter correlation equations were obtained by linear regression analysis, and their prognostic potential in determining the retention factors of benzimidazoles under study was analyzed.

Stationarity conditions for physicochemical processes in the interior ballistics of a gun

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lipanov, A.M.

1995-09-01

An original method is proposed for ensuring time-invariant (stationary) interior ballistic parameters in the postprojectile space of a gun barrel. Stationarity of the parameters is achieved by investing the solid-propellant charge with highly original structures that produce the required pressure condition and linear growth of the projectile velocity. Simple relations are obtained for calculating the principal characteristics.

Interactive effects of body-size structure and adaptive foraging on food-web stability.

PubMed

Heckmann, Lotta; Drossel, Barbara; Brose, Ulrich; Guill, Christian

2012-03-01

Body-size structure of food webs and adaptive foraging of consumers are two of the dominant concepts of our understanding how natural ecosystems maintain their stability and diversity. The interplay of these two processes, however, is a critically important yet unresolved issue. To fill this gap in our knowledge of ecosystem stability, we investigate dynamic random and niche model food webs to evaluate the proportion of persistent species. We show that stronger body-size structures and faster adaptation stabilise these food webs. Body-size structures yield stabilising configurations of interaction strength distributions across food webs, and adaptive foraging emphasises links to resources closer to the base. Moreover, both mechanisms combined have a cumulative effect. Most importantly, unstructured random webs evolve via adaptive foraging into stable size-structured food webs. This offers a mechanistic explanation of how size structure adaptively emerges in complex food webs, thus building a novel bridge between these two important stabilising mechanisms. © 2012 Blackwell Publishing Ltd/CNRS.

Physicochemical properties of mucus and their impact on transmucosal drug delivery.

PubMed

Leal, Jasmim; Smyth, Hugh D C; Ghosh, Debadyuti

2017-10-30

Mucus is a selective barrier to particles and molecules, preventing penetration to the epithelial surface of mucosal tissues. Significant advances in transmucosal drug delivery have recently been made and have emphasized that an understanding of the basic structure, viscoelastic properties, and interactions of mucus is of great value in the design of efficient drug delivery systems. Mucins, the primary non-aqueous component of mucus, are polymers carrying a complex and heterogeneous structure with domains that undergo a variety of molecular interactions, such as hydrophilic/hydrophobic, hydrogen bonds and electrostatic interactions. These properties are directly relevant to the numerous mucin-associated diseases, as well as delivering drugs across the mucus barrier. Therefore, in this review we discuss regional differences in mucus composition, mucus physicochemical properties, such as pore size, viscoelasticity, pH, and ionic strength. These factors are also discussed with respect to changes in mucus properties as a function of disease state. Collectively, the review seeks to provide a state of the art roadmap for researchers who must contend with this critical barrier to drug delivery. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Fluorophore labeling of a cell-penetrating peptide induces differential effects on its cellular distribution and affects cell viability.

PubMed

Birch, Ditlev; Christensen, Malene Vinther; Staerk, Dan; Franzyk, Henrik; Nielsen, Hanne Mørck

2017-12-01

Cell-penetrating peptides constitute efficient delivery vectors, and studies of their uptake and mechanism of translocation typically involve fluorophore-labeled conjugates. In the present study, the influence of a number of specific fluorophores on the physico-chemical properties and uptake-related characteristics of penetratin were studied. An array of seven fluorophores belonging to distinct structural classes was examined, and the impact of fluorophore labeling on intracellular distribution and cytotoxicity was correlated to the physico-chemical properties of the conjugates. Exposure of several mammalian cell types to fluorophore-penetratin conjugates revealed a strong structure-dependent reduction in viability (1.5- to 20-fold lower IC 50 values as compared to those of non-labeled penetratin). Also, the degree of less severe effects on membrane integrity, as well as intracellular distribution patterns differed among the conjugates. Overall, neutral hydrophobic fluorophores or negatively charged fluorophores conferred less cytotoxicity as compared to the effect exerted by positively charged, hydrophobic fluorophores. The latter conjugates, however, exhibited less membrane association and more clearly defined intracellular distribution patterns. Thus, selection of the appropriate flurophore is critical. Copyright © 2017 Elsevier B.V. All rights reserved.

Structural, morphological, and thermal characterization of kraft lignin and its charcoals obtained at different heating rates

NASA Astrophysics Data System (ADS)

Rodrigues Brazil, Tayra; Nunes Costa, Rogeria; Massi, Marcos; Cerqueira Rezende, Mirabel

2018-04-01

Biomass is a renewable resource that is becoming more import due to environmental concerns and possible oil crisis. Thus, optimizing its use is a current challenge for many researchers. Lignin, which is a macromolecule with complex chemical structure, valuable physicochemical properties, and varied chemical composition, is available in large quantities in pulp and paper companies. The objective of this work is the physicochemical characterization of two Kraft lignin samples with different purities, and the study of its thermal conversion into charcoal. The lignin characterization was based on chemical, TGA, DSC, FT-IR, particle sizes, and FEG-SEM analyses. These analyses show that the lignins are mainly composed of guaiacyl and syringyl units, with residues of 30–36 wt.%, in inert atmosphere, depending on the lignin purity. From these results, the more purified lignin with higher carbon yield (%C) was selected for charcoal production. The heat treatment (HT) for carbonization of lignin, at different times (90, 180, and 420 min), resulted in different %C (41–44 wt.%). Longer HT resulted in higher %C and in charcoals with smaller pore sizes. Nanopores (∼50 nm) are observed for the charcoal obtained with the longest HT.

Thermodynamic and transport properties of spiro-(1,1')-bipyrrolidinium tetrafluoroborate and acetonitrile mixtures: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Qing-Yin, Zhang; Peng, Xie; Xin, Wang; Xue-Wen, Yu; Zhi-Qiang, Shi; Shi-Huai, Zhao

2016-06-01

Organic salts such as spiro-(1,1')-bipyrrolidinium tetrafluoroborate ([SBP][BF4]) dissolved in liquid acetonitrile (ACN) are a new kind of organic salt solution, which is expected to be used as an electrolyte in electrical double layer capacitors (EDLCs). To explore the physicochemical properties of the solution, an all-atom force field is established on the basis of AMBER parameter values and quantum mechanical calculations. Molecular dynamics (MD) simulations are carried out to explore the liquid structure and physicochemical properties of [SBP][BF4] electrolyte at room temperature. The computed thermodynamic and transport properties match the available experimental results very well. The microscopic structures of [SBP][BF4] salt solution are also discussed in detail. The method used in this work provides an efficient way of predicting the properties of organic salt solvent as an electrolyte in EDLCs. Project supported by the National Natural Science Foundation of China (Grant Nos. 21476172 and 51172160), the National High Technology Research and Development Program of China (Grant No. 2013AA050905), and the Natural Science Foundation of Tianjin, China (Grant Nos. 12JCZDJC28400, 14RCHZGX00859, 14JCTPJC00484, and 14JCQNJC07200).

Investigation of relationships between removals of tetracycline and degradation products and physicochemical parameters in municipal wastewater treatment plant.

PubMed

Topal, Murat; Uslu Şenel, Gülşad; Öbek, Erdal; Arslan Topal, E Işıl

2016-05-15

Determination of the effect of physicochemical parameters on the removal of tetracycline (TC) and degradation products is important because of the importance of the removal of antibiotics in Wastewater Treatment Plant (WWTP). Therefore, the purpose of this study was to investigate the relationships between removals of TC and degradation products and physicochemical parameters in Municipal Wastewater Treatment Plant (MWWTP). For this aim, (i) the removals of physicochemical parameters in a MWWTP located in Elazığ city (Turkey) were determined (ii) the removals of TC and degradation products in MWWTP were determined (iii) the relationships between removals of TC and degradation products and physicochemical parameters were investigated. TC, 4-epitetracycline (ETC), 4-epianhydrotetracycline (EATC), anhydrotetracycline (ATC), and physicochemical parameters (pH, temperature, electrical conductivity (EC), suspended solids (SS), BOD5, COD, total organic carbon (TOC), NH4(+)-N, NO2(-)-N, NO3(-)-N and O-PO4(-3)) were determined. The calculation of the correlation coefficients of relationships between the physicochemical parameters and TC, EATC, ATC showed that, among the investigated parameters, EATC and SS most correlated. The removals of other physicochemical parameters were not correlated with TC, EATC and ATC. Copyright © 2016 Elsevier Ltd. All rights reserved.

Adaptive management of rangeland systems

USGS Publications Warehouse

Allen, Craig R.; Angeler, David G.; Fontaine, Joseph J.; Garmestani, Ahjond S.; Hart, Noelle M.; Pope, Kevin L.; Twidwell, Dirac

2017-01-01

Adaptive management is an approach to natural resource management that uses structured learning to reduce uncertainties for the improvement of management over time. The origins of adaptive management are linked to ideas of resilience theory and complex systems. Rangeland management is particularly well suited for the application of adaptive management, having sufficient controllability and reducible uncertainties. Adaptive management applies the tools of structured decision making and requires monitoring, evaluation, and adjustment of management. Adaptive governance, involving sharing of power and knowledge among relevant stakeholders, is often required to address conflict situations. Natural resource laws and regulations can present a barrier to adaptive management when requirements for legal certainty are met with environmental uncertainty. However, adaptive management is possible, as illustrated by two cases presented in this chapter. Despite challenges and limitations, when applied appropriately adaptive management leads to improved management through structured learning, and rangeland management is an area in which adaptive management shows promise and should be further explored.

Invertebrate Metacommunity Structure and Dynamics in an Andean Glacial Stream Network Facing Climate Change

PubMed Central

Cauvy-Fraunié, Sophie; Espinosa, Rodrigo; Andino, Patricio; Jacobsen, Dean; Dangles, Olivier

2015-01-01

Under the ongoing climate change, understanding the mechanisms structuring the spatial distribution of aquatic species in glacial stream networks is of critical importance to predict the response of aquatic biodiversity in the face of glacier melting. In this study, we propose to use metacommunity theory as a conceptual framework to better understand how river network structure influences the spatial organization of aquatic communities in glacierized catchments. At 51 stream sites in an Andean glacierized catchment (Ecuador), we sampled benthic macroinvertebrates, measured physico-chemical and food resource conditions, and calculated geographical, altitudinal and glaciality distances among all sites. Using partial redundancy analysis, we partitioned community variation to evaluate the relative strength of environmental conditions (e.g., glaciality, food resource) vs. spatial processes (e.g., overland, watercourse, and downstream directional dispersal) in organizing the aquatic metacommunity. Results revealed that both environmental and spatial variables significantly explained community variation among sites. Among all environmental variables, the glacial influence component best explained community variation. Overland spatial variables based on geographical and altitudinal distances significantly affected community variation. Watercourse spatial variables based on glaciality distances had a unique significant effect on community variation. Within alpine catchment, glacial meltwater affects macroinvertebrate metacommunity structure in many ways. Indeed, the harsh environmental conditions characterizing glacial influence not only constitute the primary environmental filter but also, limit water-borne macroinvertebrate dispersal. Therefore, glacier runoff acts as an aquatic dispersal barrier, isolating species in headwater streams, and preventing non-adapted species to colonize throughout the entire stream network. Under a scenario of glacier runoff decrease, we expect a reduction in both environmental filtering and dispersal limitation, inducing a taxonomic homogenization of the aquatic fauna in glacierized catchments as well as the extinction of specialized species in headwater groundwater and glacier-fed streams, and consequently an irreversible reduction in regional diversity. PMID:26308853

Synthesis, physico-chemical properties and complexing abilities of new amphiphilic ligands from D-galacturonic acid.

PubMed

Allam, Anas; Behr, Jean-Bernard; Dupont, Laurent; Nardello-Rataj, Véronique; Plantier-Royon, Richard

2010-04-19

This paper describes a convenient and efficient synthesis of new complexing surfactants from d-galacturonic acid and n-octanol as renewable raw materials in a two-step sequence. In the first step, simultaneous O-glycosidation-esterification under Fischer conditions was achieved. The anomeric ratio of the products was studied based on the main experimental parameters and the activation mode (thermal or microwave). In the second step, aminolysis of the n-octyl ester was achieved with various functionalized primary amines under standard thermal or microwave activation. The physico-chemical properties of these new amphiphilic ligands were measured and these compounds were found to exhibit interesting surface properties. Complexing abilities of one uronamide ligand functionalized with a pyridine moiety toward Cu(II) ions was investigated in solution by EPR titrations. A solid compound was also synthesized and characterized, its relative structure was deduced from spectroscopic data. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

New physicochemical interpretations for the adsorption of food dyes on chitosan films using statistical physics treatment.

PubMed

Dotto, G L; Pinto, L A A; Hachicha, M A; Knani, S

2015-03-15

In this work, statistical physics treatment was employed to study the adsorption of food dyes onto chitosan films, in order to obtain new physicochemical interpretations at molecular level. Experimental equilibrium curves were obtained for the adsorption of four dyes (FD&C red 2, FD&C yellow 5, FD&C blue 2, Acid Red 51) at different temperatures (298, 313 and 328 K). A statistical physics formula was used to interpret these curves, and the parameters such as, number of adsorbed dye molecules per site (n), anchorage number (n'), receptor sites density (NM), adsorbed quantity at saturation (N asat), steric hindrance (τ), concentration at half saturation (c1/2) and molar adsorption energy (ΔE(a)) were estimated. The relation of the above mentioned parameters with the chemical structure of the dyes and temperature was evaluated and interpreted. Copyright © 2014 Elsevier Ltd. All rights reserved.

Investigation of Physico-Chemical Properties of Sand-Lime Products Modified of Diabase Aggregate and Chalcedonite Meal

NASA Astrophysics Data System (ADS)

Dachowski, Ryszard; Komisarczyk, Katarzyna

2017-10-01

In the era of rapid development in the construction industry, particular attention is focused on harmless and natural materials. Some of the best materials for building masonry walls are sand-lime products. Silicates are obtained from a mixture of quartz, sand and a small amount of water. They emerge as a result of the hydrothermal treatment conducted under high pressure and at a temperature of app. 203 °C. Silicates were modified of different kinds of aggregates, glass or plastics, and the content of dry ingredients was changed because of this fact. The paper describes the studies where the combination of diabase aggregate and chalcedonite meal was used. Microstructure of the products was analyzed with the use of mercury intrusion porosimetry, SEM and XRD methods. Variable content of chalcedonite meal changes the internal structure and the physico-chemical properties.

Recent Advances for the Detection of Ochratoxin A.

PubMed

Ha, Tai Hwan

2015-12-04

Ochratoxin A (OTA) is one of the mycotoxins secreted by Aspersillus and Penicillium that can easily colonize various grains like coffee, peanut, rice, and maize. Since OTA is a chemically stable compound that can endure the physicochemical conditions of modern food processing, additional research efforts have been devoted to develop sensitive and cost-effective surveillance solutions. Although traditional chromatographic and immunoassays appear to be mature enough to attain sensitivity up to the regulation levels, alternative detection schemes are still being enthusiastically pursued in an attempt to meet the requirements of rapid and cost-effective detections. Herein, this review presents recent progresses in OTA detections with minimal instrumental usage, which have been facilitated by the development of OTA aptamers and by the innovations in functional nanomaterials. In addition to the introduction of aptamer-based OTA detection techniques, OTA-specific detection principles are also presented, which exclusively take advantage of the unique chemical structure and related physicochemical characteristics.

Profiling the Serum Protein Corona of Fibrillar Human Islet Amyloid Polypeptide.

PubMed

Pilkington, Emily H; Gustafsson, Ove J R; Xing, Yanting; Hernandez-Fernaud, Juan; Zampronio, Cleidi; Kakinen, Aleksandr; Faridi, Ava; Ding, Feng; Wilson, Paul; Ke, Pu Chun; Davis, Thomas P

2018-05-16

Amyloids may be regarded as native nanomaterials that form in the presence of complex protein mixtures. By drawing an analogy with the physicochemical properties of nanoparticles in biological fluids, we hypothesized that amyloids should form a protein corona in vivo that would imbue the underlying amyloid with a modified biological identity. To explore this hypothesis, we characterized the protein corona of human islet amyloid polypeptide (IAPP) fibrils in fetal bovine serum using two complementary methodologies developed herein: quartz crystal microbalance and "centrifugal capture", coupled with nanoliquid chromatography tandem mass spectroscopy. Clear evidence for a significant protein corona was obtained. No trends were identified for amyloid corona proteins based on their physicochemical properties, whereas strong binding with IAPP fibrils occurred for linear proteins or multidomain proteins with structural plasticity. Proteomic analysis identified amyloid-enriched proteins that are known to play significant roles in mediating cellular machinery and processing, potentially leading to pathological outcomes and therapeutic targets.

The xylooligosaccharide addition and sodium reduction in requeijão cremoso processed cheese.

PubMed

Ferrão, Luana L; Ferreira, Marcus Vinícius S; Cavalcanti, Rodrigo N; Carvalho, Ana Flávia A; Pimentel, Tatiana C; Silva, Hugo L A; Silva, Ramon; Esmerino, Erick A; Neto, Roberto P C; Tavares, Maria Inês B; Freitas, Mônica Q; Menezes, Jaqueline C V; Cabral, Lúcio M; Moraes, Jeremias; Silva, Márcia C; Mathias, Simone P; Raices, Renata S L; Pastore, Gláucia M; Cruz, Adriano G

2018-05-01

The addition of xylooligosaccharide (XOS), sodium reduction and flavor enhancers (arginine and yeast extract) on the manufacture of requeijão cremoso processed cheese was investigated. The addition of XOS resulted in a denser and compact structure, with increased apparent viscosity, elasticity (G') and firmness (G*). The addition of XOS and yeast extract improved the rheological and physicochemical properties (decrease in viscosity and particle size and increase in melting rate) and sensory characteristics (improvement in salty and acid taste, greater homogeneity, and lower bitter taste). In addition, a positive effect of arginine was observed in the sensory characteristics of the requeijão cremoso processed cheese, but without improvements in the physicochemical and rheological characteristics. Overall, the XOS addition and sodium reduction proportionated the development of a healthier processed cheese formulation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Physicochemical and Critical Micelle Concentration (CMC) of Cationic (CATB) and Anionic (SDS) Surfactants with Environmentally Benign Blue Emitting TTQC Dye.

PubMed

Khan, Salman A; Asiri, Abdullah M

2015-11-01

4-(3,4,5-trimethoxyphenyl)-8-methoxy-2-oxo-1,2,5,6 tetrahydrobenzo[h]quinoline-3-carbonitrile (TTQC) dye has synthesized by one-pot multicomponent reactions (MCRs) of 3,4,5-trimethoxybenzaldehyd, ethyl cyanoacetate, 6-methoxy-1,2,3,4-tetrahydro-naphthalin-1-one and ammonium acetate under microwave irradiation. The structures of the synthesized compound was established by spectroscopic (FT-IR, (1)H-NMR, (13)C-NMR, EI-MS) and elemental analyses. In addition, spectroscopic and physicochemical parameters, including electronic absorption, excitation coefficient, Stokes shift, oscillator strength, transition dipole moment and fluorescence quantum yield were investigated in order to explore the analytical potential of synthesized compound. TTQC dye undergoes solubilization in different micelles and may be used as a probe to determine the critical micelle concentration (CMC) of CTAB and SDS.

Physicochemical and Nonlinear Optical Properties of Novel Environmentally Benign Heterocyclic Azomethine Dyes: Experimental and Theoretical Studies

PubMed Central

Afzal, S. M.; Razvi, M. A. N.; Khan, Salman A.; Osman, Osman I.; Bakry, Ahmed H.; Asiri, Abdullah M.

2016-01-01

Novel heterocyclic azomethine dyes were prepared by the reaction of anthracene-9-carbaldehyde with different heterocyclic amines under microwave irradiation. Structures of the azomethine dyes were confirmed by the elemental analysis, mass spectrometry and several spectroscopic techniques. We studied absorbance and fluorescence spectra of the azomethine dyes in various solvents. They are found to be good absorbers and emitters. We also report photophysical properties like, extinction coefficient, oscillator strength, stokes shift and transition dipole moment. This reflects physicochemical behaviors of synthesized dyes. In addition, their intramolecular charge transfer and nonlinear optical properties, supported by natural bond orbital technique, were also studied computationally by density functional theory. The negative nonlinear refractive index and nonlinear absorption coefficient were measured for these dyes using the closed and open aperture Z-scan technique with a continuous wave helium-neon laser. These are found to vary linearly with solution concentration. PMID:27631371

Factors contributing to the immunogenicity of meningococcal conjugate vaccines

PubMed Central

Bröker, Michael; Berti, Francesco; Costantino, Paolo

2016-01-01

ABSTRACT Various glycoprotein conjugate vaccines have been developed for the prevention of invasive meningococcal disease, having significant advantages over pure polysaccharide vaccines. One of the most important features of the conjugate vaccines is the induction of a T-cell dependent immune response, which enables both the induction of immune memory and a booster response after repeated immunization. The nature of the carrier protein to which the polysaccharides are chemically linked, is often regarded as the main component of the vaccine in determining its immunogenicity. However, other factors can have a significant impact on the vaccine's profile. In this review, we explore the physico-chemical properties of meningococcal conjugate vaccines, which can significantly contribute to the vaccine's immunogenicity. We demonstrate that the carrier is not the sole determining factor of the vaccine's profile, but, moreover, that the conjugate vaccine's immunogenicity is the result of multiple physico-chemical structures and characteristics. PMID:26934310

Effects of gamma irradiation on physicochemical properties of native and acetylated wheat starches.

PubMed

Kong, Xiangli; Zhou, Xin; Sui, Zhongquan; Bao, Jinsong

2016-10-01

Effects of gamma irradiation on the physicochemical and crystalline properties of the native and acetylated wheat starches were investigated. Peak, hot paste, cool paste and setback viscosities of both native and acetylated wheat starches decreased continuously and significantly with the increase of the irradiation dose, whereas breakdown viscosity increased after irradiation. However, gamma irradiation only exerted slight effects on thermal and retrogradation properties of both native and acetylated wheat starches. X-ray diffraction and fourier transform infrared spectroscopy revealed that acetylation modification had considerable effects on the molecular structure of wheat starch, and the crystallinity of both untreated and acetylated starches increased slightly with the increase of irradiation dose. However, the V-type crystallinity of amylose-lipid complex was not affected by gamma irradiation treatments with doses up to 9kGy. Copyright © 2016 Elsevier B.V. All rights reserved.

How Proteins Bind Macrocycles

PubMed Central

Villar, Elizabeth A.; Beglov, Dmitri; Chennamadhavuni, Spandan; Porco, John A.; Kozakov, Dima; Vajda, Sandor; Whitty, Adrian

2014-01-01

The potential utility of synthetic macrocycles as drugs, particularly against low druggability targets such as protein-protein interactions, has been widely discussed. There is little information, however, to guide the design of macrocycles for good target protein-binding activity or bioavailability. To address this knowledge gap we analyze the binding modes of a representative set of macrocycle-protein complexes. The results, combined with consideration of the physicochemical properties of approved macrocyclic drugs, allow us to propose specific guidelines for the design of synthetic macrocycles libraries possessing structural and physicochemical features likely to favor strong binding to protein targets and also good bioavailability. We additionally provide evidence that large, natural product derived macrocycles can bind to targets that are not druggable by conventional, drug-like compounds, supporting the notion that natural product inspired synthetic macrocycles can expand the number of proteins that are druggable by synthetic small molecules. PMID:25038790

Structure determination and total synthesis of a novel antibacterial substance, AB0022A, produced by a cellular slime mold.

PubMed

Sawada, T; Aono, M; Asakawa, S; Ito, A; Awano, K

2000-09-01

A novel antibacterial substance, AB0022A, was isolated from the cellular slime mold Dictyostelium purpureum K1001. It inhibited the growth of Gram-positive bacteria, and its MICs ranged from 0.39 to 50 microg/ml. Because AB0022A was a highly substituted aromatic compound, we could not determine its structure based on only its physico-chemical and spectral data. We therefore used a dehalogenated derivative from AB0022A and deduced that its structure was 1,9-dihydroxy-3,7-dimethoxy-2-hexanoyl-4,6,8-trichlorodibenzofuran . To confirm this structure, we synthesized the compound having the deduced structure. The synthetic compound was identical to naturally occurring AB0022A.

Towards a molecular understanding of cellulose dissolution in ionic liquids: anion/cation effect, synergistic mechanism and physicochemical aspects.

PubMed

Li, Yao; Wang, Jianji; Liu, Xiaomin; Zhang, Suojiang

2018-05-07

Cellulose is one of the most abundant bio-renewable materials on the earth and its conversion to biofuels provides an appealing way to satisfy the increasing global energy demand. However, before carrying out the process of enzymolysis to glucose or polysaccharides, cellulose needs to be pretreated to overcome its recalcitrance. In recent years, a variety of ionic liquids (ILs) have been found to be effective solvents for cellulose, providing a new, feasible pretreatment strategy. A lot of experimental and computational studies have been carried out to investigate the dissolution mechanism. However, many details are not fully understood, which highlights the necessity to overview the current knowledge of cellulose dissolution and identify the research trend in the future. This perspective summarizes the mechanistic studies and microscopic insights of cellulose dissolution in ILs. Recent investigations of the synergistic effect of cations/anions and the distinctive structural changes of cellulose microfibril in ILs are also reviewed. Besides, understanding the factors controlling the dissolution process, such as the structure of anions/cations, viscosity of ILs, pretreatment temperature, heating rate, etc. , has been discussed from a structural and physicochemical viewpoint. At the end, the existing problems are discussed and future prospects are given. We hope this article would be helpful for deeper understanding of the cellulose dissolution process in ILs and the rational design of more efficient and recyclable ILs.

Optimization of a sponge cake formulation with inulin as fat replacer: structure, physicochemical, and sensory properties.

PubMed

Rodríguez-García, Julia; Puig, Ana; Salvador, Ana; Hernando, Isabel

2012-02-01

The effects of several fat replacement levels (0%, 35%, 50%, 70%, and 100%) by inulin in sponge cake microstructure and physicochemical properties were studied. Oil substitution for inulin decreased significantly (P < 0.05) batter viscosity, giving heterogeneous bubbles size distributions as it was observed by light microscopy. Using confocal laser scanning microscopy the fat was observed to be located at the bubbles' interface, enabling an optimum crumb cake structure development during baking. Cryo-SEM micrographs of cake crumbs showed a continuous matrix with embedded starch granules and coated with oil; when fat replacement levels increased, starch granules appeared as detached structures. Cakes with fat replacement up to 70% had a high crumb air cell values; they were softer and rated as acceptable by an untrained sensory panel (n = 51). So, the reformulation of a standard sponge cake recipe to obtain a new product with additional health benefits and accepted by consumers is achieved. Practical Application:  In this study, fat is replaced by inulin in cakes, which is a fiber mainly obtained from chicory roots. Sponge cake formulations with reductions in fat content up to 70% are achieved. These high-quality products can be labeled as "reduced in fat" according to U.S. FDA (2009) and EU regulations (European-Union 2006). © 2012 Institute of Food Technologists®

An in-depth understanding of biomass recalcitrance using natural poplar variants as the feedstock

DOE PAGES

Meng, Xianzhi; Pu, Yunqiao; Yoo, Chang Geun; ...

2016-12-12

Here, in an effort to better understand the biomass recalcitrance, six natural poplar variants were selected as feedstocks based on previous sugar release analysis. Compositional analysis and physicochemical characterizations of these poplars were performed and the correlations between these physicochemical properties and enzymatic hydrolysis yield were investigated. Gel permeation chromatography (GPC) and 13C solid state NMR were used to determine the degree of polymerization (DP) and crystallinity index (CrI) of cellulose, and the results along with the sugar release study indicated that cellulose DP likely played a more important role in enzymatic hydrolysis. Simons’ stain revealed that the accessible surface area of substrate significantly varied among these variants from 17.3 to 33.2 mg gmore » $$–1\\atop{biomass}$$ as reflected by dye adsorption, and cellulose accessibility was shown as one of the major factors governing substrates digestibility. HSQC and 31P NMR analysis detailed the structural features of poplar lignin variants. Overall, cellulose relevant factors appeared to have a stronger correlation with glucose release, if any, than lignin structural features. Lignin structural features, such as a phenolic hydroxyl group and the ratio of syringyl and guaiacyl (S/G), were found to have a more convincing impact on xylose release. Low lignin content, low cellulose DP, and high cellulose accessibility generally favor enzymatic hydrolysis; however, recalcitrance cannot be simply judged on any single substrate factor.« less

An in-depth understanding of biomass recalcitrance using natural poplar variants as the feedstock

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meng, Xianzhi; Pu, Yunqiao; Yoo, Chang Geun

Here, in an effort to better understand the biomass recalcitrance, six natural poplar variants were selected as feedstocks based on previous sugar release analysis. Compositional analysis and physicochemical characterizations of these poplars were performed and the correlations between these physicochemical properties and enzymatic hydrolysis yield were investigated. Gel permeation chromatography (GPC) and 13C solid state NMR were used to determine the degree of polymerization (DP) and crystallinity index (CrI) of cellulose, and the results along with the sugar release study indicated that cellulose DP likely played a more important role in enzymatic hydrolysis. Simons’ stain revealed that the accessible surface area of substrate significantly varied among these variants from 17.3 to 33.2 mg gmore » $$–1\\atop{biomass}$$ as reflected by dye adsorption, and cellulose accessibility was shown as one of the major factors governing substrates digestibility. HSQC and 31P NMR analysis detailed the structural features of poplar lignin variants. Overall, cellulose relevant factors appeared to have a stronger correlation with glucose release, if any, than lignin structural features. Lignin structural features, such as a phenolic hydroxyl group and the ratio of syringyl and guaiacyl (S/G), were found to have a more convincing impact on xylose release. Low lignin content, low cellulose DP, and high cellulose accessibility generally favor enzymatic hydrolysis; however, recalcitrance cannot be simply judged on any single substrate factor.« less

Synthesis of Nanoscale TiO2 and Study of the Effect of Their Crystal Structure on Single Cell Response

PubMed Central

Ismagilov, Z. R.; Shikina, N. V.; Mazurkova, N. A.; Tsikoza, L. T.; Tuzikov, F. V.; Ushakov, V. A.; Ishchenko, A. V.; Rudina, N. A.; Korneev, D. V.; Ryabchikova, E. I.

2012-01-01

To study the effect of nanoscale titanium dioxide (TiO2) on cell responses, we synthesized four modifications of the TiO2 (amorphous, anatase, brookite, and rutile) capable of keeping their physicochemical characteristics in a cell culture medium. The modifications of nanoscale TiO2 were obtained by hydrolysis of TiCl4 and Ti(i-OC3H7)4 (TIP) upon variation of the synthesis conditions; their textural, morphological, structural, and dispersion characteristics were examined by a set of physicochemical methods: XRD, BET, SAXS, DLS, AFM, SEM, and HR-TEM. The effect of synthesis conditions (nature of precursor, pH, temperature, and addition of a complexing agent) on the structural-dispersion properties of TiO2 nanoparticles was studied. The hydrolysis methods providing the preparation of amorphous, anatase, brookite, and rutile modifications of TiO2 nanoparticles 3–5 nm in size were selected. Examination of different forms of TiO2 nanoparticles interaction with MDCK cells by transmission electron microscopy of ultrathin sections revealed different cell responses after treatment with different crystalline modifications and amorphous form of TiO2. The obtained results allowed us to conclude that direct contact of the nanoparticles with cell plasma membrane is the primary and critical step of their interaction and defines a subsequent response of the cell. PMID:22623903

Responses of Bacterial Communities in Arable Soils in a Rice-Wheat Cropping System to Different Fertilizer Regimes and Sampling Times

PubMed Central

Zhao, Jun; Ni, Tian; Li, Yong; Xiong, Wu; Ran, Wei; Shen, Biao; Shen, Qirong; Zhang, Ruifu

2014-01-01

Soil physicochemical properties, soil microbial biomass and bacterial community structures in a rice-wheat cropping system subjected to different fertilizer regimes were investigated in two seasons (June and October). All fertilizer regimes increased the soil microbial biomass carbon and nitrogen. Both fertilizer regime and time had a significant effect on soil physicochemical properties and bacterial community structure. The combined application of inorganic fertilizer and manure organic-inorganic fertilizer significantly enhanced the bacterial diversity in both seasons. The bacterial communities across all samples were dominated by Proteobacteria, Acidobacteria and Chloroflexi at the phylum level. Permutational multivariate analysis confirmed that both fertilizer treatment and season were significant factors in the variation of the composition of the bacterial community. Hierarchical cluster analysis based on Bray-Curtis distances further revealed that bacterial communities were separated primarily by season. The effect of fertilizer treatment is significant (P = 0.005) and accounts for 7.43% of the total variation in bacterial community. Soil nutrients (e.g., available K, total N, total P and organic matter) rather than pH showed significant correlation with the majority of abundant taxa. In conclusion, both fertilizer treatment and seasonal changes affect soil properties, microbial biomass and bacterial community structure. The application of NPK plus manure organic-inorganic fertilizer may be a sound fertilizer practice for sustainable food production. PMID:24465530

The Effect of Physicochemical Modification on the Function of Antibodies Induced by Anti-Nicotine Vaccine in Mice

PubMed Central

Thorn, Jennifer M.; Bhattacharya, Keshab; Crutcher, Renata; Sperry, Justin; Isele, Colleen; Kelly, Barbara; Yates, Libbey; Zobel, James; Zhang, Ningli; Davis, Heather L.; McCluskie, Michael J.

2017-01-01

Smoking remains one of the major causes of morbidity and mortality worldwide. One approach to assisting smoking cessation is via anti-nicotine vaccines, composed of nicotine-like haptens conjugated to a carrier protein plus adjuvant(s). We have previously shown that the carrier, hapten, linker, hapten load, degree of conjugate aggregation, and presence of adducts can each influence the function (nicotine-binding capacity) of the antibody (Ab) induced. Herein, we extend those findings and show that tertiary structure is also critical to the induction of functional immune responses and that this can be influenced by conjugation conditions. We evaluated immunogenicity in mice using six lots of NIC7-CRM, a conjugate of 5-aminoethoxy-nicotine (Hapten 7), and a single point (glycine 52 to glutamic acid) mutant nontoxic form of diphtheria toxin, cross-reactive material 197 (CRM197), which were synthesized under different reaction conditions resulting in conjugates with equivalent molecular characteristics (hapten load, aggregates, adducts), but a different tertiary structure. When tested in mice, better functional responses (reduced nicotine in the brain of immunized animals relative to non-immunized controls) were obtained with conjugates with a more closed structure than those with an open conformation. These studies highlight the need for a better understanding of the physicochemical properties of small molecule conjugate vaccines. PMID:28513561

Quantitative structure-retention relationship studies with immobilized artificial membrane chromatography II: partial least squares regression.

PubMed

Li, Jie; Sun, Jin; He, Zhonggui

2007-01-26

We aimed to establish quantitative structure-retention relationship (QSRR) with immobilized artificial membrane (IAM) chromatography using easily understood and obtained physicochemical molecular descriptors and to elucidate which descriptors are critical to affect the interaction process between solutes and immobilized phospholipid membranes. The retention indices (logk(IAM)) of 55 structurally diverse drugs were determined on an immobilized artificial membrane column (IAM.PC.DD2) directly or obtained by extrapolation method for highly hydrophobic compounds. Ten simple physicochemical property descriptors (clogP, rings, rotatory bond, hydro-bond counting, etc.) of these drugs were collected and used to establish QSRR and predict the retention data by partial least squares regression (PLSR). Five descriptors, clogP, rotatory bond (RotB), rings, molecular weight (MW) and total surface area (TSA), were reserved by using the Variable Importance for Projection (VIP) values as criterion to build the final PLSR model. An external test set was employed to verify the QSRR based on the training set with the five variables, and QSRR by PLSR exhibited a satisfying predictive ability with R(p)=0.902 and RMSE(p)=0.400. Comparison of coefficients of centered and scaled variables by PLSR demonstrated that, for the descriptors studied, clogP and TSA have the most significant positive effect but the rotatable bond has significant negative effect on drug IAM chromatographic retention.

Morphology, structural and physicochemical properties of starch from the root of Cynanchum auriculatum Royle ex Wight.

PubMed

Liu, Jun; Wang, Xingchi; Wen, Fanting; Zhang, Shurong; Shen, Ruru; Jiang, Wei; Kan, Juan; Jin, Changhai

2016-12-01

The root of Cynanchum auriculatum Royle ex Wight is a traditional Chinese herbal medicine and healthy food. Although C. auriculatum has already been processed into starch for human consumption in China, the structural characterizations of C. auriculatum starch is still unknown. Therefore, the morphology, structural and physicochemical properties of C. auriculatum starch were investigated in this study. C. auriculatum starch exhibited both spherical and polygonal shapes with granule size ranging from 2 to 12μm. Some void cavities and serpentine channels were observed in the inner of starch granules. X-ray powder diffraction pattern revealed that C. auriculatum starch was a C B -type with relative crystallinity of 25.19%. Small-angle X-ray scattering spectrum indicated C. auriculatum starch had a lamellar repeat distance of 9.21nm. The proportions of single helix, double helix and amorphous components in C. auriculatum starch were 3.42%, 27.11% and 69.47%, respectively. The amylose content of C. auriculatum starch was 28.0% with the gelatinization temperature ranging from 59.3 to 70.1°C. The maximum weight loss rate of C. auriculatum starch appeared at 309°C. In addition, C. auriculatum starch showed higher swelling power than other starches tested. Our results suggest C. auriculatum starch will have wide applications in food industry. Copyright © 2016 Elsevier B.V. All rights reserved.

Towards a molecular understanding of cellulose dissolution in ionic liquids: anion/cation effect, synergistic mechanism and physicochemical aspects

PubMed Central

Li, Yao; Wang, Jianji

2018-01-01

Cellulose is one of the most abundant bio-renewable materials on the earth and its conversion to biofuels provides an appealing way to satisfy the increasing global energy demand. However, before carrying out the process of enzymolysis to glucose or polysaccharides, cellulose needs to be pretreated to overcome its recalcitrance. In recent years, a variety of ionic liquids (ILs) have been found to be effective solvents for cellulose, providing a new, feasible pretreatment strategy. A lot of experimental and computational studies have been carried out to investigate the dissolution mechanism. However, many details are not fully understood, which highlights the necessity to overview the current knowledge of cellulose dissolution and identify the research trend in the future. This perspective summarizes the mechanistic studies and microscopic insights of cellulose dissolution in ILs. Recent investigations of the synergistic effect of cations/anions and the distinctive structural changes of cellulose microfibril in ILs are also reviewed. Besides, understanding the factors controlling the dissolution process, such as the structure of anions/cations, viscosity of ILs, pretreatment temperature, heating rate, etc., has been discussed from a structural and physicochemical viewpoint. At the end, the existing problems are discussed and future prospects are given. We hope this article would be helpful for deeper understanding of the cellulose dissolution process in ILs and the rational design of more efficient and recyclable ILs. PMID:29780532

A fragment-based approach applied to a highly flexible target: Insights and challenges towards the inhibition of HSP70 isoforms

NASA Astrophysics Data System (ADS)

Jones, Alan M.; Westwood, Isaac M.; Osborne, James D.; Matthews, Thomas P.; Cheeseman, Matthew D.; Rowlands, Martin G.; Jeganathan, Fiona; Burke, Rosemary; Lee, Diane; Kadi, Nadia; Liu, Manjuan; Richards, Meirion; McAndrew, Craig; Yahya, Norhakim; Dobson, Sarah E.; Jones, Keith; Workman, Paul; Collins, Ian; van Montfort, Rob L. M.

2016-10-01

The heat shock protein 70s (HSP70s) are molecular chaperones implicated in many cancers and of significant interest as targets for novel cancer therapies. Several HSP70 inhibitors have been reported, but because the majority have poor physicochemical properties and for many the exact mode of action is poorly understood, more detailed mechanistic and structural insight into ligand-binding to HSP70s is urgently needed. Here we describe the first comprehensive fragment-based inhibitor exploration of an HSP70 enzyme, which yielded an amino-quinazoline fragment that was elaborated to a novel ATP binding site ligand with different physicochemical properties to known adenosine-based HSP70 inhibitors. Crystal structures of amino-quinazoline ligands bound to the different conformational states of the HSP70 nucleotide binding domain highlighted the challenges of a fragment-based approach when applied to this particular flexible enzyme class with an ATP-binding site that changes shape and size during its catalytic cycle. In these studies we showed that Ser275 is a key residue in the selective binding of ATP. Additionally, the structural data revealed a potential functional role for the ATP ribose moiety in priming the protein for the formation of the ATP-bound pre-hydrolysis complex by influencing the conformation of one of the phosphate binding loops.

Slip-additive migration, surface morphology, and performance on injection moulded high-density polyethylene closures.

PubMed

Dulal, Nabeen; Shanks, Robert; Gengenbach, Thomas; Gill, Harsharn; Chalmers, David; Adhikari, Benu; Pardo Martinez, Isaac

2017-11-01

The amount and distribution of slip agents, erucamide, and behenamide, on the surface of high-density polyethene, is determined by integral characteristics of slip agent structure and polymer morphology. A suite of surface analysis techniques was applied to correlate physicochemical properties with slip-additive migration behaviour and their surface morphology. The migration, surface morphology and physicochemical properties of the slip additives, crystallinity and orientation of polyethene spherulites and interaction between slip additives and high-density polyethene influence the surface characteristics. The high-density polyethene closures were produced with erucamide and behenamide separately and stored until they produced required torque. Surface composition was determined employing spectroscopy and gas chromatography. The distribution of additives was observed under optical, scanning electron and atomic force microscopes. The surface energy, crystallinity and application torque were measured using contact angle, differential scanning calorimeter and a torque force tester respectively. Each slip additive produced a characteristic amide peak at 1645cm -1 in infrared spectroscopy and peaks of oxygen and nitrogen in X-ray photoelectron spectroscopy, suggesting their presence on the surface. The erucamide produced placoid scale-like structures and behenamide formed denticulate structures. The surface erucamide and behenamide responsible for reducing the torque was found to be 15.7µg/cm 2 and 1.7µg/cm 2 . Copyright © 2017 Elsevier Inc. All rights reserved.

Growth of the Facultative Anaerobes from Antarctica, Alaska, and Patagonia at Low Temperatures

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.

2004-01-01

Psychotolerance, as an adaptation for surviving in extreme environments, is widespread among mesophilic microorganisms. Physico-chemical factors such as pressure, red-ox potential, pH and salinity could significantly alter the features of ecosystems by providing liquid water at subzero temperatures. Furthermore, organisms can respond to temperature changes by several known mechanisms, including changing the conformation capacities of constitutional proteins or by the synthesis of mucopolysaccharides around the cell wall and membrane. Such protective mechanisms make it possible for cells to not only passively survive low temperatures in a state of anabiosis, but also to be capable of actively metabolizing substrates and reproducing normally. The physiological and biochemical characteristics of the species, as well as genetics, could be remarkably changed due to adaptation and surviving in extreme environments. The cold shock genes of some of the studied strains of psychotolerant facultative anaerobes were reported previously. In this paper we present experimental data for psychotolerant, non spore-forming, facultative anaerobes isolated from geographically different cold regions of our planet. We show the growth response on changing from anaerobic conditions to aerobic with cultivation at low temperatures.

[Studies on the chemical constituents of the fruit of Xylocarpus granatum].

PubMed

Cheng, Fan; Zhou, Yuan; Zou, Kun; Wu, Jun

2009-08-01

To study the chemical constituents of the fruit of Xylocarpus granatum. The chemical constituents were isolated by chromatographic methods and their structures were elucidated by NMR spectra and physicochemical properties. Ten compounds were isolated from the fruit of Xylocarpus granatum and the structures of them were identified as spicatin (1), xyloccensin K(2), 6-acetoxycedrodorin (3), aurantiamide acetate (4), (+)-catechin (5), alpha-tocopherol (6), abscisic acid (7), daucosterol (8), 4-hydroxybenzoic acid (9) and ethyl 3,4-dihydroxybenzoate (10). Compound 4 -10 are isolated from this plant for the first time.

Precise replication of antireflective nanostructures from biotemplates

NASA Astrophysics Data System (ADS)

Gao, Hongjun; Liu, Zhongfan; Zhang, Jin; Zhang, Guoming; Xie, Guoyong

2007-03-01

The authors report herein a new type of nanonipple structures on the cicada's eye and the direct structural replication of the complex micro- and nanostructures for potential functional emulation. A two-step direct molding process is developed to replicate these natural micro- and nanostructures using epoxy resin with high fidelity, which demonstrates a general way of fabricating functional nanostructures by direct replication of natural biotemplates via a suitable physicochemical process. Measurements of spectral reflectance showed that this kind of replicated nanostructure has remarkable antireflective property, suggestive of its potential applications to optical devices.

PLS-based quantitative structure-activity relationship for substituted benzamides of clebopride type. Application of experimental design in drug design.

PubMed

Norinder, U; Högberg, T

1992-04-01

The advantageous approach of using an experimentally designed training set as the basis for establishing a quantitative structure-activity relationship with good predictive capability is described. The training set was selected from a fractional factorial design scheme based on a principal component description of physico-chemical parameters of aromatic substituents. The derived model successfully predicts the activities of additional substituted benzamides of 6-methoxy-N-(4-piperidyl)salicylamide type. The major influence on activity of the 3-substituent is demonstrated.

Bioactive constituents from Chinese natural medicines. XXXII. aminopeptidase N and aldose reductase inhibitors from Sinocrassula indica: structures of sinocrassosides B(4), B(5), C(1), and D(1)-D(3).

PubMed

Morikawa, Toshio; Xie, Haihui; Wang, Tao; Matsuda, Hisashi; Yoshikawa, Masayuki

2008-10-01

From the methanolic extract of the whole plant of Sinocrassula indica (Crassulaceae), six new flavonol glycosides, sinocrassosides B(4) (1), B(5) (2), C(1) (3), D(1) (4), D(2) (5), and D(3) (6), were isolated together with 30 compounds. The structures of 1-6 were elucidated on the basis of chemical and physicochemical evidence. In addition, several constituents were found to show inhibitory effects on aminopeptidase N and aldose reductase.

ACToR – Aggregated Computational Toxicology Resource ...

EPA Pesticide Factsheets

ACToR (Aggregated Computational Toxicology Resource) is a collection of databases collated or developed by the US EPA National Center for Computational Toxicology (NCCT). More than 200 sources of publicly available data on environmental chemicals have been brought together and made searchable by chemical name and other identifiers, and by chemical structure. Data includes chemical structure, physico-chemical values, in vitro assay data and in vivo toxicology data. Chemicals include, but are not limited to, high and medium production volume industrial chemicals, pesticides (active and inert ingredients), and potential ground and drinking water contaminants.

Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes.

PubMed

Papaleo, Elena; Tiberti, Matteo; Invernizzi, Gaetano; Pasi, Marco; Ranzani, Valeria

2011-11-01

The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.

A mechanical adapter for installing mission equipment on large space structures

NASA Technical Reports Server (NTRS)

Lefever, A. E.; Totah, R. S.

1980-01-01

A mechanical attachment adapter was designed, constructed, and tested. The adapter was was included in a simulation program that investigated techniques for assembling erectable structures under simulated zero-g conditions by pressure-suited subjects in a simulated EVA mode. The adapter was utilized as an interface attachment between a simulated equipment module and one node point of a tetrahedral structural cell. The mating performance of the adapter, a self-energized mechanism, was easily and quickly demonstrated and required little effort on the part of the test subjects.

Breath Figure Method for Construction of Honeycomb Films

PubMed Central

Dou, Yingying; Jin, Mingliang; Zhou, Guofu; Shui, Lingling

2015-01-01

Honeycomb films with various building units, showing potential applications in biological, medical, physicochemical, photoelectric, and many other areas, could be prepared by the breath figure method. The ordered hexagonal structures formed by the breath figure process are related to the building units, solvents, substrates, temperature, humidity, air flow, and other factors. Therefore, by adjusting these factors, the honeycomb structures could be tuned properly. In this review, we summarized the development of the breath figure method of fabricating honeycomb films and the factors of adjusting honeycomb structures. The organic-inorganic hybrid was taken as the example building unit to discuss the preparation, mechanism, properties, and applications of the honeycomb films. PMID:26343734

Optimal descriptor as a translator of eclectic information into the prediction of membrane damage by means of various TiO(2) nanoparticles.

PubMed

Toropova, Alla P; Toropov, Andrey A

2013-11-01

The increasing use of nanomaterials incorporated into consumer products leads to the need for developing approaches to establish "quantitative structure-activity relationships" (QSARs) for various nanomaterials. However, the molecular structure as rule is not available for nanomaterials at least in its classic meaning. An possible alternative of classic QSAR (based on the molecular structure) is the using of data on physicochemical features of TiO(2) nanoparticles. The damage to cellular membranes (units L(-1)) by means of various TiO(2) nanoparticles is examined as the endpoint. Copyright © 2013 Elsevier Ltd. All rights reserved.

Role of Physicochemical Properties in Nanoparticle Toxicity

PubMed Central

Shin, Seung Won; Song, In Hyun; Um, Soong Ho

2015-01-01

With the recent rapid growth of technological comprehension in nanoscience, researchers have aimed to adapt this knowledge to various research fields within engineering and applied science. Dramatic advances in nanomaterials marked a new epoch in biomedical engineering with the expectation that they would have huge contributions to healthcare. However, several questions regarding their safety and toxicity have arisen due to numerous novel properties. Here, recent studies of nanomaterial toxicology will be reviewed from several physiochemical perspectives. A variety of physiochemical properties such as size distribution, electrostatics, surface area, general morphology and aggregation may significantly affect physiological interactions between nanomaterials and target biological areas. Accordingly, it is very important to finely tune these properties in order to safely fulfill a bio-user’s purpose. PMID:28347068

Phage Display Derived IgNAR V Region Binding Domains for Therapeutic Development.

PubMed

Ubah, Obinna C; Barelle, Caroline J; Buschhaus, Magdalena J; Porter, Andrew J

2016-01-01

Phage display technology has revolutionized the science of drug discovery by transforming the generation and manipulation of ligands, such as antibody fragments, enzymes, and peptides. The basis of this technology is the expression of recombinant proteins or peptides fused to a phage coat protein, and subsequent isolation of ligands based on a variety of catalytic, physicochemical/binding kinetic and/or biological characteristics. An incredible number of diagnostic and therapeutic domains have been successfully isolated using phage display technology. The variable domain of the New Antigen Receptors (VNAR) found in cartilaginous fish, is also amenable to phage display selection. Whilst not an antibody, VNARs are unquestionable the oldest (450 million years), and smallest antigen binding, single-domains so far identified in the vertebrate kingdom. Their role as an integral part of the adaptive immune system of sharks has been well established, enhancing our understanding of the evolutionary origins of humoral immunity and the unusual but divergent ancestry of the VNARs themselves. VNARs exhibit remarkable physicochemical properties, such as small size, stability in extreme conditions, solubility, molecular flexibility, high affinity and selectivity for target. The purpose of this review is to illustrate the important role phage display has played in the isolation and characterization of potent therapeutic and diagnostic VNAR domains. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Exploring the Structure of Adaptive Behavior: Project Report Number 87-1.

ERIC Educational Resources Information Center

Bruininks, Robert H.; McGrew, Kevin

This report presents results from three research studies that were designed to explore both the definition and the structure of the adaptive behavior construct. The first study investigated the structure of adaptive behavior as a function of age, developmental level, and type of handicap through an exploratory factor analysis of both the…

Structure and photochromic properties of molybdenum-containing silica gels obtained by molecular-lamination method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Belotserkovskaya, N.G.; Dobychin, D.P.; Pak, V.N.

1992-05-10

The structure and physicochemical properties of molybdenum-containing silica gels obtained by molecular lamination have been studied quite extensively. Up to the present, however, no studies have been made of the influence of the pore structure of the original silica gel on the structure and properties of molybdenum-containing silica gels (MSG). The problem is quite important, since molybdenum silicas obtained by molecular lamination may find applications in catalysis and as sensors of UV radiation. In either case, the structure of the support is not a factor to be ignored. Here, the authors are reporting on an investigation of the structure ofmore » MSG materials with different pore structures and their susceptibility to reduction of the Mo(VI) oxide groupings when exposed to UV radiation. 16 refs., 2 figs., 2 tabs.« less

[Study on the chemical constituents of Rhizoma Cyperi].

PubMed

Wu, Xi; Xia, Hou-Lin; Huang, Li-Hua; Chen, Dan-Dan; Chen, Jin-Yu; Weng, Hai-Ting

2008-07-01

To study the chemical constituents of Rhizoma Cyperi. The constituents were separated and purified by silica gel column chromatography, their structures were identified on the basis of physico-chemical properties and spectral data. Six compounds were isolated and identified as physicion (1), hexadecanoic acid (2), beta-sitosterol (3), stigmasterol (4), catenarin (5), daucosterol (6). Compounds 1, 4, 5 were isolated from this plant for the first fime.

Physico-chemical study of some areas of fundamental significance to biophysics. Final report, 1974--1977

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGlynn, S.P.

1977-08-18

The comprehensive report includes a complete list of publications resulting from the work and a review of studies made in the vacuum ultraviolet, photoelectron spectroscopy, excited states and electron structure of inorganic salts, a model for polar molecules, application of abstract mathematics to the genetic code, the orbital approximation in which orbital properties are related to state properties. (JSR)

[HEALTH-IMPROVING REMEDIES ON THE BASIS OF SMECTITE®].

PubMed

Shirobokov, V; Yankovskii, D; Dyment, G

2015-01-01

The review is devoted to the issues of using smectites in medicine. Modern information concerning smectite composition, structure, physico-chemical properties and reasonability of using them with health-improving purposes is presented. Special attention is given to smectite sorbtional and ionic properties and their unique mineral composition. Characterization is given to modern preparation based on smectites, including developed in Ukraine dietary additives of the series Smectovit®.

Joint U.S./Japan Conference on Adaptive Structures, 1st, Maui, HI, Nov. 13-15, 1990, Proceedings

NASA Technical Reports Server (NTRS)

Wada, Ben K. (Editor); Fanson, James L. (Editor); Miura, Koryo (Editor)

1991-01-01

The present volume of adaptive structures discusses the development of control laws for an orbiting tethered antenna/reflector system test scale model, the sizing of active piezoelectric struts for vibration suppression on a space-based interferometer, the control design of a space station mobile transporter with multiple constraints, and optimum configuration control of an intelligent truss structure. Attention is given to the formulation of full state feedback for infinite order structural systems, robustness issues in the design of smart structures, passive piezoelectric vibration damping, shape control experiments with a functional model for large optical reflectors, and a mathematical basis for the design optimization of adaptive trusses in precision control. Topics addressed include approaches to the optimal adaptive geometries of intelligent truss structures, the design of an automated manufacturing system for tubular smart structures, the Sandia structural control experiments, and the zero-gravity dynamics of space structures in parabolic aircraft flight.

Joint U.S./Japan Conference on Adaptive Structures, 1st, Maui, HI, Nov. 13-15, 1990, Proceedings

NASA Astrophysics Data System (ADS)

Wada, Ben K.; Fanson, James L.; Miura, Koryo

1991-11-01

The present volume of adaptive structures discusses the development of control laws for an orbiting tethered antenna/reflector system test scale model, the sizing of active piezoelectric struts for vibration suppression on a space-based interferometer, the control design of a space station mobile transporter with multiple constraints, and optimum configuration control of an intelligent truss structure. Attention is given to the formulation of full state feedback for infinite order structural systems, robustness issues in the design of smart structures, passive piezoelectric vibration damping, shape control experiments with a functional model for large optical reflectors, and a mathematical basis for the design optimization of adaptive trusses in precision control. Topics addressed include approaches to the optimal adaptive geometries of intelligent truss structures, the design of an automated manufacturing system for tubular smart structures, the Sandia structural control experiments, and the zero-gravity dynamics of space structures in parabolic aircraft flight.

Effects of a nanoceria fuel additive on the physicochemical properties of diesel exhaust particles.

PubMed

Zhang, Junfeng Jim; Lee, Ki-Bum; He, Linchen; Seiffert, Joanna; Subramaniam, Prasad; Yang, Letao; Chen, Shu; Maguire, Pierce; Mainelis, Gediminas; Schwander, Stephan; Tetley, Teresa; Porter, Alexandra; Ryan, Mary; Shaffer, Milo; Hu, Sheng; Gong, Jicheng; Chung, Kian Fan

2016-10-12

Nanoceria (i.e., CeO 2 nanoparticles) fuel additives have been used in Europe and elsewhere to improve fuel efficiency. Previously we have shown that the use of a commercial fuel additive Envirox™ in a diesel-powered electricity generator reduced emissions of diesel exhaust particle (DEP) mass and other pollutants. However, such additives are currently not permitted for use in on-road vehicles in North America, largely due to limited data on the potential health impact. In this study, we characterized a variety of physicochemical properties of DEPs emitted from the same engine. Our methods include novel techniques such as Raman spectrometry for analyzing particle surface structure and an assay for DEP oxidative potential. Results show that with increasing Envirox™ concentrations in the fuel (0×, 0.1×, 1×, and 10× of manufacturer recommended 0.5 mL Envirox™ per liter fuel), DEP sizes decreased from 194.6 ± 20.1 to 116.3 ± 14.8 nm; the zeta potential changed from -28.4 mV to -22.65 mV; DEP carbon content decreased from 91.8% to 79.4%; cerium and nitrogen contents increased from 0.3% to 6.5% and 0.2% to 0.6%, respectively; the ratio of organic carbon (OC) to elemental carbon (EC) increased from 22.9% to 38.7%; and the ratio of the disordered carbon structure to the ordered carbon structure (graphitized carbon) in DEPs decreased. Compared to DEPs emitted from 0×, 0.1×, and 1× fuels, DEPs from the 10× fuel had a lower oxidative potential likely due to the increased ceria content because pure ceria nanoparticles exhibited the lowest oxidative potential compared to all the DEPs. Since the physicochemical parameters tested here are among the determinants of particle toxicity, our findings imply that adding ceria nanoparticles into diesel may alter the toxicity of DEPs. The findings from the present study, hence, can help future studies that will examine the impact of nanoceria additives on DEP toxicities.

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types.

PubMed

Ji, Yang; Angel, Roey; Klose, Melanie; Claus, Peter; Marotta, Humberto; Pinho, Luana; Enrich-Prast, Alex; Conrad, Ralf

2016-12-01

Tropical lake sediments are a significant source for the greenhouse gas methane. We studied function (pathway, rate) and structure (abundance, taxonomic composition) of the microbial communities (Bacteria, Archaea) leading to methane formation together with the main physicochemical characteristics in the sediments of four clear water, six white water and three black water lakes of the Amazon River system. Concentrations of sulfate and ferric iron, pH and δ 13 C of organic carbon were usually higher, while concentrations of carbon, nitrogen and rates of CH 4 production were generally lower in white water versus clear water or black water sediments. Copy numbers of bacterial and especially archaeal ribosomal RNA genes also tended to be relatively lower in white water sediments. Hydrogenotrophic methanogenesis contributed 58 ± 16% to total CH 4 production in all systems. Network analysis identified six communities, of which four were comprised mostly of bacteria found in all sediment types, while two were mostly in clear water sediment. Terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing showed that the compositions of the communities differed between the different sediment systems, statistically related to the particular physicochemical conditions and to CH 4 production rates. Among the archaea, clear water, white water, and black water sediments contained relatively more Methanomicrobiales, Methanosarcinaceae and Methanocellales, respectively, while Methanosaetaceae were common in all systems. Proteobacteria, Deltaproteobacteria (Myxococcales, Syntrophobacterales, sulfate reducers) in particular, Acidobacteria and Firmicutes were the most abundant bacterial phyla in all sediment systems. Among the other important bacterial phyla, clear water sediments contained relatively more Alphaproteobacteria and Planctomycetes, whereas white water sediments contained relatively more Betaproteobacteria, Firmicutes, Actinobacteria, and Chloroflexi than the respective other sediment systems. The data showed communities of bacteria common to all sediment types, but also revealed microbial groups that were significantly different between the sediment types, which also differed in physicochemical conditions. Our study showed that function of the microbial communities may be understood on the basis of their structures, which in turn are determined by environmental heterogeneity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Linking the structures, free volumes, and properties of ionic liquid mixtures† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01407d

PubMed Central

Brooks, Nicholas J.; Castiglione, Franca; Doherty, Cara M.; Dolan, Andrew; Hill, Anita J.; Hunt, Patricia A.; Matthews, Richard P.; Mauri, Michele; Mele, Andrea; Simonutti, Roberto; Villar-Garcia, Ignacio J.; Weber, Cameron C.

2017-01-01

The formation of ionic liquid (IL) mixtures has been proposed as an approach to rationally fine-tune the physicochemical properties of ILs for a variety of applications. However, the effects of forming such mixtures on the resultant properties of the liquids are only beginning to be understood. Towards a more complete understanding of both the thermodynamics of mixing ILs and the effect of mixing these liquids on their structures and physicochemical properties, the spatial arrangement and free volume of IL mixtures containing the common [C4C1im]+ cation and different anions have been systematically explored using small angle X-ray scattering (SAXS), positron annihilation lifetime spectroscopy (PALS) and 129Xe NMR techniques. Anion size has the greatest effect on the spatial arrangement of the ILs and their mixtures in terms of the size of the non-polar domains and inter-ion distances. It was found that differences in coulombic attraction between oppositely charged ions arising from the distribution of charge density amongst the atoms of the anion also significantly influences these inter-ion distances. PALS and 129Xe NMR results pertaining to the free volume of these mixtures were found to strongly correlate with each other despite the vastly different timescales of these techniques. Furthermore, the excess free volumes calculated from each of these measurements were in excellent agreement with the excess volumes of mixing measured for the IL mixtures investigated. The correspondence of these techniques indicates that the static and dynamic free volume of these liquid mixtures are strongly linked. Consequently, fluxional processes such as hydrogen bonding do not significantly contribute to the free volumes of these liquids compared to the spatial arrangement of ions arising from their size, shape and coulombic attraction. Given the relationship between free volume and transport properties such as viscosity and conductivity, these results provide a link between the structures of IL mixtures, the thermodynamics of mixing and their physicochemical properties. PMID:29619199

A Short Review of the Generation of Molecular Descriptors and Their Applications in Quantitative Structure Property/Activity Relationships.

PubMed

Sahoo, Sagarika; Adhikari, Chandana; Kuanar, Minati; Mishra, Bijay K

2016-01-01

Synthesis of organic compounds with specific biological activity or physicochemical characteristics needs a thorough analysis of the enumerable data set obtained from literature. Quantitative structure property/activity relationships have made it simple by predicting the structure of the compound with any optimized activity. For that there is a paramount data set of molecular descriptors (MD). This review is a survey on the generation of the molecular descriptors and its probable applications in QSP/AR. Literatures have been collected from a wide class of research journals, citable web reports, seminar proceedings and books. The MDs were classified according to their generation. The applications of the MDs on the QSP/AR have also been reported in this review. The MDs can be classified into experimental and theoretical types, having a sub classification of the later into structural and quantum chemical descriptors. The structural parameters are derived from molecular graphs or topology of the molecules. Even the pixel of the molecular image can be used as molecular descriptor. In QSPR studies the physicochemical properties include boiling point, heat capacity, density, refractive index, molar volume, surface tension, heat of formation, octanol-water partition coefficient, solubility, chromatographic retention indices etc. Among biological activities toxicity, antimalarial activity, sensory irritant, potencies of local anesthetic, tadpole narcosis, antifungal activity, enzyme inhibiting activity are some important parameters in the QSAR studies. The classification of the MDs is mostly generic in nature. The application of the MDs in QSP/AR also has a generic link. Experimental MDs are more suitable in correlation analysis than the theoretical ones but are more expensive for generation. In advent of sophisticated computational tools and experimental design proliferation of MDs is inevitable, but for a highly optimized MD, studies on generation of MD is an unending process.

Evaluating habitat associations of a fish assemblage at multiple spatial scales in a minimally disturbed stream using low-cost remote sensing

USGS Publications Warehouse

Cheek, Brandon D.; Grabowski, Timothy B.; Bean, Preston T.; Groeschel, Jillian R.; Magnelia, Stephan J.

2016-01-01

Habitat heterogeneity at multiple scales is a major factor affecting fish assemblage structure. However, assessments that examine these relationships at multiple scales concurrently are lacking. The lack of assessments at these scales is a critical gap in understanding as conservation and restoration efforts typically work at these levels.A combination of low-cost side-scan sonar surveys, aerial imagery using an unmanned aerial vehicle, and fish collections were used to evaluate the relationship between physicochemical and landscape variables at various spatial scales (e.g. micro-mesohabitat, mesohabitat, channel unit, stream reach) and stream–fish assemblage structure and habitat associations in the South Llano River, a spring-fed second-order stream on the Edwards Plateau in central Texas during 2012–2013.Low-cost side-scan sonar surveys have not typically been used to generate data for riverscape assessments of assemblage structure, thus the secondary objective was to assess the efficacy of this approach.The finest spatial scale (micro-mesohabitat) and the intermediate scale (channel unit) had the greatest explanatory power for variation in fish assemblage structure.Many of the fish endemic to the Edwards Plateau showed similar associations with physicochemical and landscape variables suggesting that conservation and restoration actions targeting a single endemic species may provide benefits to a large proportion of the endemic species in this system.Low-cost side-scan sonar proved to be a cost-effective means of acquiring information on the habitat availability of the entire river length and allowed the assessment of how a full suite of riverscape-level variables influenced local fish assemblage structure.

Calculation of phase diagrams for the FeCl2, PbCl2, and ZnCl2 binary systems by using molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Seo, Won-Gap; Matsuura, Hiroyuki; Tsukihashi, Fumitaka

2006-04-01

Recently, molecular dynamics (MD) simulation has been widely employed as a very useful method for the calculation of various physicochemical properties in the molten slags and fluxes. In this study, MD simulation has been applied to calculate the structural, transport, and thermodynamic properties for the FeCl2, PbCl2, and ZnCl2 systems using the Born—Mayer—Huggins type pairwise potential with partial ionic charges. The interatomic potential parameters were determined by fitting the physicochemical properties of iron chloride, lead chloride, and zinc chloride systems with experimentally measured results. The calculated structural, transport, and thermodynamic properties of pure FeCl2, PbCl2, and ZnCl2 showed the same tendency with observed results. Especially, the calculated structural properties of molten ZnCl2 and FeCl2 show the possibility of formation of polymeric network structures based on the ionic complexes of ZnCl{4/2-}, ZnCl{3/-}, FeCl{4/2-}, and FeCl{3/-}, and these calculations have successfully reproduced the measured results. The enthalpy, entropy, and Gibbs energy of mixing for the PbCl2-ZnCl2, FeCl2-PbCl2, and FeCl2-ZnCl2 systems were calculated based on the thermodynamic and structural parameters of each binary system obtained from MD simulation. The phase diagrams of the PbCl2-ZnCl2, FeCl2-PbCl2, and FeCl2-ZnCl2 systems estimated by using the calculated Gibbs energy of mixing reproduced the experimentally measured ones reasonably well.

The Science of Biometeorology

ERIC Educational Resources Information Center

Maxey, E. Stanton

1977-01-01

Biometeorology is the study of the relations between meteorological factors, physico-chemical systems and living organisms, and the indirect effects of the physical, chemical, and physico-chemical environments of the earth's atmosphere and of similar extraterrestrial space upon physico-chemical systems and living organisms. This article discusses…

Non-Fourier thermal transport induced structural hierarchy and damage to collagen ultrastructure subjected to laser irradiation.

PubMed

Sahoo, Nilamani; Narasimhan, Arunn; Dhar, Purbarun; Das, Sarit K

2018-05-01

Comprehending the mechanism of thermal transport through biological tissues is an important factor for optimal ablation of cancerous tissues and minimising collateral tissue damage. The present study reports detailed mapping of the rise in internal temperature within the tissue mimics due to NIR (1064 nm) laser irradiation, both for bare mimics and with gold nanostructures infused. Gold nanostructures such as mesoflowers and nanospheres have been synthesised and used as photothermal converters to enhance the temperature rise, resulting in achieving the desired degradation of malignant tissue in targeted region. Thermal history was observed experimentally and simulated considering non-Fourier dual phase lag (DPL) model incorporated Pennes bio-heat transfer equation using COMSOL Multiphysics software. The gross deviation in temperature i.e. rise from the classical Fourier model for bio-heat conduction suggests additional effects of temperature rise on the secondary structures and morphological and physico-chemical changes to the collagen ultrastructures building the tissue mass. The observed thermal denaturation in the collagen fibril morphologies have been explained based on the physico-chemical structure of collagen and its response to thermal radiation. The large shift in frequency of amides A and B is pronounced at a depth of maximum temperature rise compared with other positions in tissue phantom. Observations for change in band of amide I, amide II, and amide III are found to be responsible for damage to collagen ultra-structure. Variation in the concentration of gold nanostructures shows the potentiality of localised hyperthermia treatment subjected to NIR radiation through a proposed free radical mechanism.

Assessing Analytical Similarity of Proposed Amgen Biosimilar ABP 501 to Adalimumab.

PubMed

Liu, Jennifer; Eris, Tamer; Li, Cynthia; Cao, Shawn; Kuhns, Scott

2016-08-01

ABP 501 is being developed as a biosimilar to adalimumab. Comprehensive comparative analytical characterization studies have been conducted and completed. The objective of this study was to assess analytical similarity between ABP 501 and two adalimumab reference products (RPs), licensed by the United States Food and Drug Administration (adalimumab [US]) and authorized by the European Union (adalimumab [EU]), using state-of-the-art analytical methods. Comprehensive analytical characterization incorporating orthogonal analytical techniques was used to compare products. Physicochemical property comparisons comprised the primary structure related to amino acid sequence and post-translational modifications including glycans; higher-order structure; primary biological properties mediated by target and receptor binding; product-related substances and impurities; host-cell impurities; general properties of the finished drug product, including strength and formulation; subvisible and submicron particles and aggregates; and forced thermal degradation. ABP 501 had the same amino acid sequence and similar post-translational modification profiles compared with adalimumab RPs. Primary structure, higher-order structure, and biological activities were similar for the three products. Product-related size and charge variants and aggregate and particle levels were also similar. ABP 501 had very low residual host-cell protein and DNA. The finished ABP 501 drug product has the same strength with regard to protein concentration and fill volume as adalimumab RPs. ABP 501 and the RPs had a similar stability profile both in normal storage and thermal stress conditions. Based on the comprehensive analytical similarity assessment, ABP 501 was found to be similar to adalimumab with respect to physicochemical and biological properties.

Comparison of Two Xenograft Materials Used in Sinus Lift Procedures: Material Characterization and In Vivo Behavior

PubMed Central

Ramírez Fernández, María Piedad; Mazón, Patricia; Gehrke, Sergio A.; Calvo-Guirado, Jose Luis; De Aza, Piedad N.

2017-01-01

Detailed information about graft material characteristic is crucial to evaluate their clinical outcomes. The present study evaluates the physico-chemical characteristics of two xenografts manufactured on an industrial scale deproteinized at different temperatures (non-sintered and sintered) in accordance with a protocol previously used in sinus lift procedures. It compares how the physico-chemical properties influence the material’s performance in vivo by a histomorphometric study in retrieved bone biopsies following maxillary sinus augmentation in 10 clinical cases. An X-ray diffraction analysis revealed the typical structure of hydroxyapatite (HA) for both materials. Both xenografts were porous and exhibited intraparticle pores. Strong differences were observed in terms of porosity, crystallinity, and calcium/phosphate. Histomorphometric measurements on the bone biopsies showed statistically significant differences. The physic-chemical assessment of both xenografts, made in accordance with the protocol developed on an industrial scale, confirmed that these products present excellent biocompatibilitity, with similar characteristics to natural bone. The sintered HA xenografts exhibited greater osteoconductivity, but were not completely resorbable (30.80 ± 0.88% residual material). The non-sintered HA xenografts induced about 25.92 ± 1.61% of new bone and a high level of degradation after six months of implantation. Differences in the physico-chemical characteristics found between the two HA xenografts determined a different behavior for this material. PMID:28772984

Isolation and connectivity: Relationships between periodic connection to the ocean and environmental variables in intermittently closed estuaries

NASA Astrophysics Data System (ADS)

Lill, Adrian Wilfred Thomas; Schallenberg, Marc; Lal, Aparna; Savage, Candida; Closs, Gerard Patrick

2013-08-01

Morphometric and physicochemical variables are key determinants of biotic community structure in estuaries and are influenced by changes to estuary mouth state (open/closed). This study examined and compared the consequences of intermittent connection to the ocean on environmental gradients among estuaries; specifically, how estuary morphology and hydrology relate to physical connection to the sea, and the influence of this relationship on the physicochemical environment. By sampling 20 estuaries across New Zealand and using historical aerial photographs, a continuous index of estuarine connection to the ocean was developed and independently validated using berm elevation derived from Airborne Laser Scanning (ALS) data. Using published literature, this index was compared to equivalent indices in South Africa and Australia. A clear relationship between connections to the ocean, freshwater flow and productivity indices underlie the environmental differences between permanently open and intermittently closed estuaries. Consistent patterns across the Southern Hemisphere, albeit with regional variations in estuarine characteristics, suggest that remote sensing is useful for predicting the physicochemical environment of small estuaries across regions. Principal components analysis for Otago estuaries showed that 40% of measured variation in the environment could be attributed to the gradient of relative connectivity (EOI), or isolation (berm elevation) to the ocean. Evaluating these relationships is central to understanding how global and local environmental changes may affect estuarine connectivity regimes and, ultimately, the functioning of estuarine ecosystems.

Physicochemical and Rheological Properties of a Dairy Dessert, Enriched with Chickpea Flour

PubMed Central

Aguilar-Raymundo, Victoria Guadalupe; Vélez-Ruiz, Jorge Fernando

2018-01-01

Dairy desserts are complex mixtures and matrices including main components such as milk, sugar, starch, hydrocolloids, colorants and flavors, with a proteinaceous structure; they are widely consumed and present a semisolid consistency. In this work, the physicochemical and rheological properties of a dairy dessert with the addition of chickpea flour (raw and cooked, at four concentrations) were studied to determine the effect of the flour. The results indicated that luminosity (L*: 62.75–83.29), pH (6.35–7.11) and acidity (1.56–3.56) changed with the type of flour. The flow properties of the custards exhibited a non-Newtonian behavior that was well fitted by three flow models. The studied custard systems were stored for twelve days at 4 °C. The physicochemical and flow properties of the custards changed notably as a function of flour addition and storage time. From all samples, only four were analyzed with oscillatory tests, showing their mechanical spectra with elastic behavior. The dessert texture was also measured, founding that those formulated with Blanco Noroeste chickpea flour exhibited the highest values of hardness (0.356–0.391 N) through the twelve days. It can be concluded that those custard systems with the highest content of flour presented a very good response as a potential new dairy product. PMID:29463036

Morphing wing structure with controllable twist based on adaptive bending-twist coupling

NASA Astrophysics Data System (ADS)

Raither, Wolfram; Heymanns, Matthias; Bergamini, Andrea; Ermanni, Paolo

2013-06-01

A novel semi-passive morphing airfoil concept based on variable bending-twist coupling induced by adaptive shear center location and torsional stiffness is presented. Numerical parametric studies and upscaling show that the concept relying on smart materials permits effective twist control while offering the potential of being lightweight and energy efficient. By means of an experimental characterization of an adaptive beam and a scaled adaptive wing structure, effectiveness and producibility of the structural concept are demonstrated.

Band structure engineering strategies of metal oxide semiconductor nanowires and related nanostructures: A review

NASA Astrophysics Data System (ADS)

Piyadasa, Adimali; Wang, Sibo; Gao, Pu-Xian

2017-07-01

The electronic band structure of a solid state semiconductor determines many of its physical and chemical characteristics such as electrical, optical, physicochemical, and catalytic activity. Alteration or modification of the band structure could lead to significant changes in these physical and chemical characteristics, therefore we introduce new mechanisms of creating novel solid state materials with interesting properties. Over the past three decades, research on band structure engineering has allowed development of various methods to modify the band structure of engineered materials. Compared to bulk counterparts, nanostructures generally exhibit higher band structure modulation capabilities due to the quantum confinement effect, prominent surface effect, and higher strain limit. In this review we will discuss various band structure engineering strategies in semiconductor nanowires and other related nanostructures, mostly focusing on metal oxide systems. Several important strategies of band structure modulation are discussed in detail, such as doping, alloying, straining, interface and core-shell nanostructuring.

Characterization and 2D structural model of corn straw and poplar leaf biochars.

PubMed

Zhao, Nan; Lv, YiZhong; Yang, XiXiang; Huang, Feng; Yang, JianWen

2017-12-22

The integrated experimental methods were used to analyze the physicochemical properties and structural characteristics and to build the 2D structural model of two kinds of biochars. Corn straw and poplar leaf biochars were gained by pyrolysing the raw materials slowly in a furnace at 300, 500, and 700 °C under oxygen-deficient conditions. Scanning electron microscope was applied to observe the surface morphology of the biochars. High temperatures destroyed the pore structures of the biochars, forming a particle mixture of varying sizes. The ash content, yield, pH, and surface area were also observed to describe the biochars' properties. The yield decreases as the pyrolysis temperature increases. The biochars are neutral to alkaline. The biggest surface area is 251.11 m 2 /g for 700 °C corn straw biochar. Elemental analysis, infrared microspectroscopy, solid-state C-13 NMR spectroscopy, and pyrolysis gas chromatography-mass spectrometry (Py-GC-MS) were also used to study the structural characteristics and build the 2D structural models of biochars. The C content in the corn straw and poplar leaf biochars increases with the increase of the pyrolysis temperature. A higher pyrolysis temperature makes the aryl carbon increase, and C=O, OH, and aliphatic hydrocarbon content decrease in the IR spectra. Solid-state C-13 NMR spectra show that a higher pyrolysis temperature makes the alkyl carbon and alkoxy carbon decrease and the aryl carbon increase. The results of IR microspectra and solid-state C-13 NMR spectra reveal that some noticeable differences exist in these two kinds of biochars and in the same type of biochar but under different pyrolysis temperatures. The conceptual elemental compositions of 500 °C corn straw and poplar leaf biochars are C 61 H 33 NO 13 and C 59 H 41 N 3 O 12 , respectively. Significant differences exist in the SEM images, physicochemical properties, and structural characteristics of corn straw and poplar leaf biochars.

Citrus fruit extracts with carvacrol and thymol eliminated 7-log acid-adapted Escherichia coli O157:H7, Salmonella typhimurium, and Listeria monocytogenes: A potential of effective natural antibacterial agents.

PubMed

Chung, Doohyun; Cho, Tae Jin; Rhee, Min Suk

2018-05-01

Despite the widespread belief that citrus fruit extracts (CFEs) are microbiologically safe due to their acidity, limited bactericidal effect results in low applicability as antibacterial agent and outbreaks occurred by acid-adapted pathogens. Here, we examined the antibacterial effects of CFEs [lime (Citrus medica), lemon (Citrus limon), calamansi (Citrus microcarpa)] combined with essential oil components (EOCs; carvacrol and thymol) against non-acid-adapted/acid-adapted Escherichia coli O157:H7, Salmonella Typhimurium, and Listeria monocytogenes under 22 °C for 5 min. CFEs (<20%) alone or small amounts of EOCs (2.0 mM; 0.032%) alone could not inactivate the target bacteria effectively. However, combined treatments exhibited marked synergy: CFE + EOCs eliminated all the bacteria (>6.9 log CFU/ml). Among the CFEs tested, the highest synergism was shown by calamansi, an exotic citrus fruit previously unrecognized as an antibacterial agent. Although acid-adaptation improved bacterial survival, calamansi (<20%) + EOCs (<0.032%) completely inactivated even the most resistant pathogen (E. coli O157:H7). Validation test also showed that all tested commercial juice products also eliminated acid-adapted pathogens when used with EOCs. Physicochemical analysis of tested CFEs (pH measurement and HPLC analysis of components) revealed that low pH and flavanone (hesperidin) did not contribute to the synergistic bactericidal effects. Rather, the high citric acid content is likely to contribute to the strong synergistic effect with EOCs by damaging susceptible bacterial membranes. Sensory scores for CFEs were not altered by addition of EOCs at concentrations up to 1.5 mM. This study provides new insight into the utility of CFEs with EOCs to improve not only the microbiological safety of food products containing CFEs but also their applicability as natural antibacterial complex. Copyright © 2018 Elsevier Ltd. All rights reserved.

Adaptive wing static aeroelastic roll control

NASA Astrophysics Data System (ADS)

Ehlers, Steven M.; Weisshaar, Terrence A.

1993-09-01

Control of the static aeroelastic characteristics of a swept uniform wing in roll using an adaptive structure is examined. The wing structure is modeled as a uniform beam with bending and torsional deformation freedom. Aerodynamic loads are obtained from strip theory. The structure model includes coefficients representing torsional and bending actuation provided by embedded piezoelectric material layers. The wing is made adaptive by requiring the electric field applied to the piezoelectric material layers to be proportional to the wing root loads. The proportionality factor, or feedback gain, is used to control static aeroelastic rolling properties. Example wing configurations are used to illustrate the capabilities of the adaptive structure. The results show that rolling power, damping-in-roll and aileron effectiveness can be controlled by adjusting the feedback gain. And that dynamic pressure affects the gain required. Gain scheduling can be used to set and maintain rolling properties over a range of dynamic pressures. An adaptive wing provides a method for active aeroelastic tailoring of structural response to meet changing structural performance requirements during a roll maneuver.

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps

PubMed Central

Meola, Marco; Lazzaro, Anna; Zeyer, Josef

2015-01-01

Deposition of Sahara dust (SD) particles is a frequent phenomenon in Europe, but little is known about the viability and composition of the bacterial community transported with SD. The goal of this study was to characterize SD-associated bacteria transported to the European Alps, deposited and entrapped in snow. During two distinct events in February and May 2014, SD particles were deposited and promptly covered by falling snow, thus preserving them in distinct ochre layers within the snowpack. In June 2014, we collected samples at different depths from a snow profile at the Jungfraujoch (Swiss Alps; 3621 m a.s.l.). After filtration, we performed various microbiological and physicochemical analyses of the snow and dust particles therein that originated in Algeria. Our results show that bacteria survive and are metabolically active after the transport to the European Alps. Using high throughput sequencing, we observed distinct differences in bacterial community composition and structure in SD-layers as compared to clean snow layers. Sporulating bacteria were not enriched in the SD-layers; however, phyla with low abundance such as Gemmatimonadetes and Deinococcus-Thermus appeared to be specific bio-indicators for SD. Since many members of these phyla are known to be adapted to arid oligotrophic environments and UV radiation, they are well suited to survive the harsh conditions of long-range airborne transport. PMID:26733988

Synergistic effect of polyaniline coverage and surface microstructure on the inhibition of Pseudomonas aeruginosa biofilm formation.

PubMed

Gallarato, L A; Mulko, L E; Dardanelli, M S; Barbero, C A; Acevedo, D F; Yslas, E I

2017-02-01

Biofilm Formation is a survival strategy for microorganisms to adapt to their environment. Microbial cells in biofilm become tolerant and resistant to antibiotics and immune responses, increasing the difficulties for the clinical treatment of microbial infections. The surface chemistry and the micro/nano-topography of solid interfaces play a major role in mediating microorganism activity and adhesion. The effect of the surface chemical composition and topography on the adhesion and viability of Pseudomonas aeruginosa was studied. Polymeric (polyethylene terephthalate) surfaces were covered with a conducting polymer (polyaniline, PANI) film by in-situ polymerization and microstructured by Direct Laser Interference Patterning (DLIP). The viability of Pseudomonas aeruginosa on the different surfaces was investigated. The physicochemical properties of the surfaces were characterized by water contact angle measurements, scanning electron microscopy and atomic force microscopy. Bacterial biofilms were imaged by atomic force and scanning electron microscopies. The bacterial viability decreased on PANI compared with the substrate (polyethylene terephthalate) and it decreased even more upon micro-structuring the PANI films. In addition, the biofilm reduction could be improved using polymers with different chemical composition and/or the same polymer with different topographies. Both methods presented diminish the bacterial attachment and biofilm formation. These findings present a high impact related to materials for biomedical engineer applications regarding medical devices, as prostheses or catheters. Copyright © 2016 Elsevier B.V. All rights reserved.

Assessing and Developing the Adaptive Functioning of Handicapped Children and Youth. Final Report [October 1984-September 1987].

ERIC Educational Resources Information Center

Bruininks, Robert H.

The project sought to clarify the nature and structure of adaptive functioning and to address methodological issues in its assessment, in order to improve placement, evaluation, and instructional decision-making related to adaptive functioning. Project components included: (1) exploration of the structure of adaptive behavior; (2) comparison of…

Comparative analysis of machine learning methods in ligand-based virtual screening of large compound libraries.

PubMed

Ma, Xiao H; Jia, Jia; Zhu, Feng; Xue, Ying; Li, Ze R; Chen, Yu Z

2009-05-01

Machine learning methods have been explored as ligand-based virtual screening tools for facilitating drug lead discovery. These methods predict compounds of specific pharmacodynamic, pharmacokinetic or toxicological properties based on their structure-derived structural and physicochemical properties. Increasing attention has been directed at these methods because of their capability in predicting compounds of diverse structures and complex structure-activity relationships without requiring the knowledge of target 3D structure. This article reviews current progresses in using machine learning methods for virtual screening of pharmacodynamically active compounds from large compound libraries, and analyzes and compares the reported performances of machine learning tools with those of structure-based and other ligand-based (such as pharmacophore and clustering) virtual screening methods. The feasibility to improve the performance of machine learning methods in screening large libraries is discussed.

Physicochemical properties of quinoa starch.

PubMed

Li, Guantian; Wang, Sunan; Zhu, Fan

2016-02-10

Physicochemical properties of quinoa starches isolated from 26 commercial samples from a wide range of collection were studied. Swelling power (SP), water solubility index (WSI), amylose leaching (AML), enzyme susceptibility, pasting, thermal and textural properties were analyzed. Apparent amylose contents (AAM) ranged from 7.7 to 25.7%. Great variations in the diverse physicochemical properties were observed. Correlation analysis showed that AAM was the most significant factor related to AML, WSI, and pasting parameters. Correlations among diverse physicochemical parameters were analyzed. Principal component analysis using twenty three variables were used to visualize the difference among samples. Six principal components were extracted which could explain 88.8% of the total difference. The wide variations in physicochemical properties could contribute to innovative utilization of quinoa starch for food and non-food applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Can benthic foraminifera be used as bio-indicators of pollution in areas with a wide range of physicochemical variability?

NASA Astrophysics Data System (ADS)

Martins, Maria Virgínia Alves; Pinto, Anita Fernandes Souza; Frontalini, Fabrizio; da Fonseca, Maria Clara Machado; Terroso, Denise Lara; Laut, Lazaro Luiz Mattos; Zaaboub, Noureddine; da Conceição Rodrigues, Maria Antonieta; Rocha, Fernando

2016-12-01

The Ria de Aveiro, a lagoon located in the NW coast of Portugal, presents a wide range of changes to the natural hydrodynamical and physicochemical conditions induced for instance by works of port engineering and pollution. In order to evaluate the response of living benthic foraminifera to the fluctuations in physicochemical parameters and pollution (metals and TOC), eight sediment samples were collected from canals and salt pans within the Aveiro City, in four different sampling events. During the sampling events, salinity showed the most significant fluctuations among the physicochemical parameters with the maximum range of variation at Troncalhada and Santiago salt pans. Species such as Haynesina germanica, Trochammina inflata and Entzia macrescens were found inhabiting these hypersaline environments with the widest fluctuations of physicochemical parameters. In contrast, Ammonia tepida dominated zones with high concentrations of metals and organic matter and in lower salinity waters. Parameters related to benthic foraminiferal assemblages (i.e., diversity and evenness) were found to significantly decline in stations polluted by metals and characterized by higher TOC content. Foraminiferal density reduced significantly in locations with a wide range of physicochemical temporal variability. This work shows that, even under extreme conditions caused by highly variable physicochemical parameters, benthic foraminiferal assemblages might be used as valuable bioindicators of environmental stress.

Adaptation to implied tilt: extensive spatial extrapolation of orientation gradients

PubMed Central

Roach, Neil W.; Webb, Ben S.

2013-01-01

To extract the global structure of an image, the visual system must integrate local orientation estimates across space. Progress is being made toward understanding this integration process, but very little is known about whether the presence of structure exerts a reciprocal influence on local orientation coding. We have previously shown that adaptation to patterns containing circular or radial structure induces tilt-aftereffects (TAEs), even in locations where the adapting pattern was occluded. These spatially “remote” TAEs have novel tuning properties and behave in a manner consistent with adaptation to the local orientation implied by the circular structure (but not physically present) at a given test location. Here, by manipulating the spatial distribution of local elements in noisy circular textures, we demonstrate that remote TAEs are driven by the extrapolation of orientation structure over remarkably large regions of visual space (more than 20°). We further show that these effects are not specific to adapting stimuli with polar orientation structure, but require a gradient of orientation change across space. Our results suggest that mechanisms of visual adaptation exploit orientation gradients to predict the local pattern content of unfilled regions of space. PMID:23882243

Fragment-Based Discovery of Pyrimido[1,2-b]indazole PDE10A Inhibitors.

PubMed

Chino, Ayaka; Seo, Ryushi; Amano, Yasushi; Namatame, Ichiji; Hamaguchi, Wataru; Honbou, Kazuya; Mihara, Takuma; Yamazaki, Mayako; Tomishima, Masaki; Masuda, Naoyuki

2018-01-01

In this study, we report the identification of potent pyrimidoindazoles as phosphodiesterase10A (PDE10A) inhibitors by using the method of fragment-based drug discovery (FBDD). The pyrazolopyridine derivative 2 was found to be a fragment hit compound which could occupy a part of the binding site of PDE10A enzyme by using the method of the X-ray co-crystal structure analysis. On the basis of the crystal structure of compound 2 and PDE10A protein, a number of compounds were synthesized and evaluated, by means of structure-activity relationship (SAR) studies, which culminated in the discovery of a novel pyrimidoindazole derivative 13 having good physicochemical properties.

On Topological Indices of Certain Dendrimer Structures

NASA Astrophysics Data System (ADS)

Aslam, Adnan; Bashir, Yasir; Ahmad, Safyan; Gao, Wei

2017-05-01

A topological index can be considered as transformation of chemical structure in to real number. In QSAR/QSPR study, physicochemical properties and topological indices such as Randić, Zagreb, atom-bond connectivity ABC, and geometric-arithmetic GA index are used to predict the bioactivity of chemical compounds. Dendrimers are highly branched, star-shaped macromolecules with nanometer-scale dimensions. Dendrimers are defined by three components: a central core, an interior dendritic structure (the branches), and an exterior surface with functional surface groups. In this paper we determine generalised Randić, general Zagreb, general sum-connectivity indices of poly(propyl) ether imine, porphyrin, and zinc-Porphyrin dendrimers. We also compute ABC and GA indices of these families of dendrimers.

Integrating structure-based and ligand-based approaches for computational drug design.

PubMed

Wilson, Gregory L; Lill, Markus A

2011-04-01

Methods utilized in computer-aided drug design can be classified into two major categories: structure based and ligand based, using information on the structure of the protein or on the biological and physicochemical properties of bound ligands, respectively. In recent years there has been a trend towards integrating these two methods in order to enhance the reliability and efficiency of computer-aided drug-design approaches by combining information from both the ligand and the protein. This trend resulted in a variety of methods that include: pseudoreceptor methods, pharmacophore methods, fingerprint methods and approaches integrating docking with similarity-based methods. In this article, we will describe the concepts behind each method and selected applications.

Towards the discovery of drug-like RNA ligands?

PubMed

Foloppe, Nicolas; Matassova, Natalia; Aboul-Ela, Fareed

2006-11-01

Targeting RNA with small molecule drugs is an area of great potential for therapeutic treatment of infections and possibly genetic and autoimmune diseases. However, a mature set of precedents and established methodology is lacking. The physicochemical properties of RNA raise specific issues and obstacles to development, and contribute to explain the distinct characteristics of natural RNA ligands, including antibiotics. Yet, RNA-targeting strategies are being implemented to reinvigorate antibacterial discovery by using the ribosomal X-ray structures to modify known antibiotics. To exploit further these structures, we suggest the use of existing protein kinase-directed libraries of drug-like compounds to target the A-site of the bacterial ribosome, on the basis of a specific structural hypothesis.

Macromolecular metal carboxylates

NASA Astrophysics Data System (ADS)

Dzhardimalieva, G. I.; Pomogailo, A. D.

2008-03-01

Data on the synthesis and physicochemical studies of salts of mono- or dibasic unsaturated carboxylic acids and unsaturated metal oxo-carboxylates are generalised and described systematically. The structures and properties of the COO group in various compounds and characteristic features of the structures of carboxylate complexes are analysed. The main routes and kinetics of polymerisation transformations of unsaturated metal carboxylates are considered. The attention is focused on the effect of the metal ion on the monomer reactivity and the polymer morphology and structure. The possibility of stereochemical control of radical polymerisation of unsaturated metal carboxylates is demonstrated. The electronic, magnetic, optical, absorption and thermal properties of metal (co)polymers and nanocomposites and their main applications are considered.

Description of recovery method used for curdlan produced by Agrobacterium sp. IFO 13140 and its relation to the morphology and physicochemical and technological properties of the polysaccharide

PubMed Central

Mangolim, Camila Sampaio; da Silva, Thamara Thaiane; Fenelon, Vanderson Carvalho; Koga, Luciana Numata; Ferreira, Sabrina Barbosa de Souza; Bruschi, Marcos Luciano; Matioli, Graciette

2017-01-01

Curdlan is a linear polysaccharide considered a dietary fiber and with gelation properties. This study evaluated the structure, morphology and the physicochemical and technological properties of curdlan produced by Agrobacterium sp. IFO 13140 recovered by pre-gelation and precipitation methods. Commercial curdlan submitted or otherwise to the pre-gelation process was also evaluated. The data obtained from structural analysis revealed a similarity between the curdlan produced by Agrobacterium sp. IFO 13140 (recovered by both methods) and the commercial curdlans. The results showed that the curdlans evaluated differed significantly in terms of dispersibility and gelation, and only the pre-gelled ones had significant potential for food application, because this method influence on the size of the particles and in the presence of NaCl. In terms of technological properties, the curdlan produced by Agrobacterium sp. IFO 13140 (pre-gelation method) had a greater water and oil holding capacity (64% and 98% greater, respectively) and a greater thickening capacity than the pre-gelled commercial curdlan. The pre-gelled commercial curdlan displayed a greater gelling capacity at 95°C than the others. When applied to food, only the pre-gelled curdlans improved the texture parameters of yogurts and reduced syneresis. The curdlan gels, which are rigid and stable in structure, demonstrated potential for improving the texture of food products, with potential industrial use. PMID:28245244

WRF-TMH: predicting transmembrane helix by fusing composition index and physicochemical properties of amino acids.

PubMed

Hayat, Maqsood; Khan, Asifullah

2013-05-01

Membrane protein is the prime constituent of a cell, which performs a role of mediator between intra and extracellular processes. The prediction of transmembrane (TM) helix and its topology provides essential information regarding the function and structure of membrane proteins. However, prediction of TM helix and its topology is a challenging issue in bioinformatics and computational biology due to experimental complexities and lack of its established structures. Therefore, the location and orientation of TM helix segments are predicted from topogenic sequences. In this regard, we propose WRF-TMH model for effectively predicting TM helix segments. In this model, information is extracted from membrane protein sequences using compositional index and physicochemical properties. The redundant and irrelevant features are eliminated through singular value decomposition. The selected features provided by these feature extraction strategies are then fused to develop a hybrid model. Weighted random forest is adopted as a classification approach. We have used two benchmark datasets including low and high-resolution datasets. tenfold cross validation is employed to assess the performance of WRF-TMH model at different levels including per protein, per segment, and per residue. The success rates of WRF-TMH model are quite promising and are the best reported so far on the same datasets. It is observed that WRF-TMH model might play a substantial role, and will provide essential information for further structural and functional studies on membrane proteins. The accompanied web predictor is accessible at http://111.68.99.218/WRF-TMH/ .

Spreading properties of cosmetic emollients: Use of synthetic skin surface to elucidate structural effect.

PubMed

Douguet, Marine; Picard, Céline; Savary, Géraldine; Merlaud, Fabien; Loubat-Bouleuc, Nathalie; Grisel, Michel

2017-06-01

The study focuses on the impact of structural and physicochemical properties of emollients on their spreadability. Fifty-three emollients, among which esters, silicones, vegetable and mineral oils, have been characterized. Their viscosity, surface tension, density and spreadability have been measured. Vitro-skin ® , an artificial skin substitute, was used as an artificial porous substrate to measure spreadability. Two different methods have been selected to characterize spreadability, namely contact angle and spreading value. Dynamic contact angle measurements showed that emollient spreadability is first governed by spontaneous spreading and that, in a second phase, absorption and migration into the porous substrate becomes the driver of the extension of the spreading area. Statistical analysis of physicochemical and spreading value data revealed that viscosity has a major impact on the spreading behavior of emollients whatever their chemical type. A special emphasis was placed on the ester family in which chemical diversity is very wide. The results highlighted a difference between "high viscosity esters" for which viscosity is the main factor impacting spreadability and "low viscosity esters" for which structural variations (mono/diester, saturated/unsaturated chain, linear/branched chain) have to be considered in addition to viscosity. Linear regressions were used to express spreading value as a function of viscosity for each of the four emollient families tested (esters, silicones, vegetable and mineral oils). These regressions allowed the development of reliable predictive models as a powerful tool for formulators to forecast spreadability of emollients. Copyright © 2017 Elsevier B.V. All rights reserved.

Description of recovery method used for curdlan produced by Agrobacterium sp. IFO 13140 and its relation to the morphology and physicochemical and technological properties of the polysaccharide.

PubMed

Mangolim, Camila Sampaio; Silva, Thamara Thaiane da; Fenelon, Vanderson Carvalho; Koga, Luciana Numata; Ferreira, Sabrina Barbosa de Souza; Bruschi, Marcos Luciano; Matioli, Graciette

2017-01-01

Curdlan is a linear polysaccharide considered a dietary fiber and with gelation properties. This study evaluated the structure, morphology and the physicochemical and technological properties of curdlan produced by Agrobacterium sp. IFO 13140 recovered by pre-gelation and precipitation methods. Commercial curdlan submitted or otherwise to the pre-gelation process was also evaluated. The data obtained from structural analysis revealed a similarity between the curdlan produced by Agrobacterium sp. IFO 13140 (recovered by both methods) and the commercial curdlans. The results showed that the curdlans evaluated differed significantly in terms of dispersibility and gelation, and only the pre-gelled ones had significant potential for food application, because this method influence on the size of the particles and in the presence of NaCl. In terms of technological properties, the curdlan produced by Agrobacterium sp. IFO 13140 (pre-gelation method) had a greater water and oil holding capacity (64% and 98% greater, respectively) and a greater thickening capacity than the pre-gelled commercial curdlan. The pre-gelled commercial curdlan displayed a greater gelling capacity at 95°C than the others. When applied to food, only the pre-gelled curdlans improved the texture parameters of yogurts and reduced syneresis. The curdlan gels, which are rigid and stable in structure, demonstrated potential for improving the texture of food products, with potential industrial use.

[Studies on chemical constituents from leaves and stems of Aconitum coreanum].

PubMed

Li, Yan; Liang, Shuai

2009-05-01

To study the chemical constituents in the leaves and stems of Aconitum coreanum. The isolation and purification of chemical constituents were carried out on silica gel and polyamide column chromatographic. Their structures were identified by physico-chemical properties and spectral analysis. Five compounds were obtained and their structures were identified as guan-fu base I (1), guan-fu base R (2), beta-sitosterol (3), D-mannitol (4), daucosterol (5). Compound 2 is a new compound. Compounds 1 and 3, 4 are isolated from the leaves and stems of A. coreanum for the first time.

Triterpenoid saponins from Echinopsis macrogona (Cactaceae).

PubMed

Okazaki, Sachie; Kinoshita, Kaoru; Ito, Satoru; Koyama, Kiyotaka; Yuasa, Hiroshi; Takahashi, Kunio

2011-01-01

Triterpene saponins, pachanosides C1, E1, F1 and G1 (1-4), and bridgesides A1, C1, C2, D1, D2, E1 and E2 (5-11) were isolated from Echinopsis macrogona. Compounds 1-4 were saponins with pachanane type triterpene saponins, while the others (5-11) were oleanane type triterpene saponins. While the aglycones of 2-4 and 8-11 were hitherto unknown, the structure of pachanol C was revised in this paper. Their structures were elucidated on the basis of chemical and physicochemical evidence. Copyright © 2010 Elsevier Ltd. All rights reserved.

A new hydrocarbon material based on seabuckthorn ( Hippophae rhamnoides) sawdust: A structural promoter of cobalt catalyst for Fischer-Tropsch synthesis

NASA Astrophysics Data System (ADS)

Pankina, G. V.; Chernavskii, P. A.; Lunin, V. V.

2016-09-01

Aspects of the physicochemical properties of a hydrocarbon material based on seabuckthorn ( Hippophae rhamnoides) sawdust are studied. The use of a hydrocarbon material based on sea buckthorn sawdust as a structural promoter of Co/CHip cobalt catalyst in the reaction of CO hydrogenation is shown to require an additional cycling stage in the mode of reduction and oxidation. The resulting mean size of the Co particles is found to be 18-19 nm and is considered acceptable for the synthesis of C5+ liquid hydrocarbons.

Principal component analysis as a tool for library design: a case study investigating natural products, brand-name drugs, natural product-like libraries, and drug-like libraries.

PubMed

Wenderski, Todd A; Stratton, Christopher F; Bauer, Renato A; Kopp, Felix; Tan, Derek S

2015-01-01

Principal component analysis (PCA) is a useful tool in the design and planning of chemical libraries. PCA can be used to reveal differences in structural and physicochemical parameters between various classes of compounds by displaying them in a convenient graphical format. Herein, we demonstrate the use of PCA to gain insight into structural features that differentiate natural products, synthetic drugs, natural product-like libraries, and drug-like libraries, and show how the results can be used to guide library design.

Chemical structures of constituents from the whole plant of Bacopa monniera.

PubMed

Ohta, Tomoe; Nakamura, Seikou; Nakashima, Souichi; Oda, Yoshimi; Matsumoto, Takahiro; Fukaya, Masashi; Yano, Mamiko; Yoshikawa, Masayuki; Matsuda, Hisashi

2016-07-01

Two new dammarane-type triterpene oligoglycosides, bacomosaponins A and B, and three new phenylethanoid glycosides, bacomosides A, B1, and B2, were isolated from the whole plant of Bacopa monniera Wettst. The chemical structures of the new constituents were characterized on the basis of chemical and physicochemical evidence. In the present study, bacomosaponins A and B with acyl groups were obtained from the whole plant of B. monniera. This is the first report of acylated dammarane-type triterpene oligoglycosides isolated from B. monniera. In addition, dammarane-type triterpene saponins significantly inhibited the aggregation of 42-mer amyloid β-protein.

The effect of nanofiber based filter morphology on bacteria deactivation during water filtration

NASA Astrophysics Data System (ADS)

Kimmer, Dusan; Vincent, Ivo; Lev, Jaroslav; Kalhotka, Libor; Mikula, Premysl; Korinkova, Radka; Sambaer, Wannes; Zatloukal, Martin

2013-04-01

Procedures permitting to prepare homogeneous functionalized nanofibre structures based on polyurethanes modified by phthalocyanines (PCs) by employing a suitable combination of variables during the electrospinning process are presented. Compared are filtration and bacteria deactivation properties of open and planar nanostructures with PCs embedded into polyurethane chain by a covalent bond protecting the release of active organic compound during the filtration process. Finding that the morphology of functionalized nanofibre structures have an effect on bacterial growth was confirmed by microbiological and physico-chemical analyses, such as the inoculation in a nutrient agar culture medium and flow cytometry.

B-535a, b and c, new sphingosine kinase inhibitors, produced by a marine bacterium; taxonomy, fermentation, isolation, physico-chemical properties and structure determination.

PubMed

Kono, K; Tanaka, M; Mizuno, T; Kodama, K; Ogita, T; Kohama, T

2000-08-01

In the course of our screening for inhibitors of sphingosine kinase, we found a series of active compounds in a culture broth of a novel marine bacterium, SANK 71896. The structures of the compounds, named B-5354a, b and c, were elucidated by a combination of spectroscopic analyses to be new esters of 4-amino-3-hydroxybenzoic acid with long-chain unsaturated alcohols. B-5354a, b and c inhibit sphingosine kinase activity with IC50 values of 21, 58 and 38 microm, respectively.

Structures, properties, modifications, and uses of oat starch.

PubMed

Zhu, Fan

2017-08-15

There has been increasing interest to utilise oats and their components to formulate healthy food products. Starch is the major component of oat kernels and may account up to 60% of the dry weight. Starch properties may greatly determine the product quality. As a by-product of oat processing and fractionation, the starch may also be utilised for food and non-food applications. This mini-review updates the recent advances in the isolation, chemical and granular structures, physicochemical properties, chemical and physical modifications, and food and non-food uses of oat starch. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cytotoxicity of Aporphine, Protoberberine, and Protopine Alkaloids from Dicranostigma leptopodum (Maxim.) Fedde.

PubMed

Sun, Ruiqi; Jiang, Haiyan; Zhang, Wenjuan; Yang, Kai; Wang, Chengfang; Fan, Li; He, Qing; Feng, Jiangbin; Du, Shushan; Deng, Zhiwei; Geng, Zhufeng

2014-01-01

Nine alkaloids with three different structural skeletons were isolated from Dicranostigma leptopodum (Maxim.) Fedde (Papaveraceae) by repeated silica gel column chromatography. Their chemical structures were identified on the basic of physicochemical and spectroscopic data. Among them, 10-O-methylhernovine (1), nantenine (2), corytuberine (3), lagesianine A (4), and dihydrocryptopine (9) were first isolated from this plant. With a series of cytotoxic tests, compounds 2, 3, and 7 displayed cytotoxicity against SMMC-7721 with IC50 values of 70.08 ± 4.63, 73.22 ± 2.35, and 27.77 ± 2.29 μ M, respectively.

Cytotoxicity of Aporphine, Protoberberine, and Protopine Alkaloids from Dicranostigma leptopodum (Maxim.) Fedde

PubMed Central

Jiang, Haiyan; Zhang, Wenjuan; Yang, Kai; Wang, Chengfang; Fan, Li; Feng, Jiangbin; Du, Shushan; Deng, Zhiwei; Geng, Zhufeng

2014-01-01

Nine alkaloids with three different structural skeletons were isolated from Dicranostigma leptopodum (Maxim.) Fedde (Papaveraceae) by repeated silica gel column chromatography. Their chemical structures were identified on the basic of physicochemical and spectroscopic data. Among them, 10-O-methylhernovine (1), nantenine (2), corytuberine (3), lagesianine A (4), and dihydrocryptopine (9) were first isolated from this plant. With a series of cytotoxic tests, compounds 2, 3, and 7 displayed cytotoxicity against SMMC-7721 with IC50 values of 70.08 ± 4.63, 73.22 ± 2.35, and 27.77 ± 2.29 μM, respectively. PMID:24963327

The Influence of the Surface Neutralization of Active Impurities on the Field-Electron Emission Properties of p-Type Silicon Crystals

NASA Astrophysics Data System (ADS)

Yafarov, R. K.

2017-12-01

Correlation dependences between variations of the structural-phase composition, morphology characteristics, and field-electron-emission (FEE) properties of surface-structured p-type silicon singlecrystalline (100)-oriented wafers have been studied during their stepwise high-dose carbon-ion-beam irradiation. It is established that the stepwise implantation of carbon decreases the FEE threshold and favors an increase in the maximum FEE-current density by more than two orders of magnitude. Physicochemical mechanisms involved in this modification of the properties of near-surface layers of silicon under carbon-ion implantation are considered.

Principal Component Analysis as a Tool for Library Design: A Case Study Investigating Natural Products, Brand-Name Drugs, Natural Product-Like Libraries, and Drug-Like Libraries

PubMed Central

Wenderski, Todd A.; Stratton, Christopher F.; Bauer, Renato A.; Kopp, Felix; Tan, Derek S.

2015-01-01

Principal component analysis (PCA) is a useful tool in the design and planning of chemical libraries. PCA can be used to reveal differences in structural and physicochemical parameters between various classes of compounds by displaying them in a convenient graphical format. Herein, we demonstrate the use of PCA to gain insight into structural features that differentiate natural products, synthetic drugs, natural product-like libraries, and drug-like libraries, and show how the results can be used to guide library design. PMID:25618349

In silico ribozyme evolution in a metabolically coupled RNA population.

PubMed

Könnyű, Balázs; Szilágyi, András; Czárán, Tamás

2015-05-27

The RNA World hypothesis offers a plausible bridge from no-life to life on prebiotic Earth, by assuming that RNA, the only known molecule type capable of playing genetic and catalytic roles at the same time, could have been the first evolvable entity on the evolutionary path to the first living cell. We have developed the Metabolically Coupled Replicator System (MCRS), a spatially explicit simulation modelling approach to prebiotic RNA-World evolution on mineral surfaces, in which we incorporate the most important experimental facts and theoretical considerations to comply with recent knowledge on RNA and prebiotic evolution. In this paper the MCRS model framework has been extended in order to investigate the dynamical and evolutionary consequences of adding an important physico-chemical detail, namely explicit replicator structure - nucleotide sequence and 2D folding calculated from thermodynamical criteria - and their possible mutational changes, to the assumptions of a previously less detailed toy model. For each mutable nucleotide sequence the corresponding 2D folded structure with minimum free energy is calculated, which in turn is used to determine the fitness components (degradation rate, replicability and metabolic enzyme activity) of the replicator. We show that the community of such replicators providing the monomer supply for their own replication by evolving metabolic enzyme activities features an improved propensity for stable coexistence and structural adaptation. These evolutionary advantages are due to the emergent uniformity of metabolic replicator fitnesses imposed on the community by local group selection and attained through replicator trait convergence, i.e., the tendency of replicator lengths, ribozyme activities and population sizes to become similar between the coevolving replicator species that are otherwise both structurally and functionally different. In the most general terms it is the surprisingly high extra viability of the metabolic replicator system that the present model adds to the MCRS concept of the origin of life. Surface-bound, metabolically coupled RNA replicators tend to evolve different, enzymatically active sites within thermodynamically stable secondary structures, and the system as a whole evolves towards the robust coexistence of a complete set of such ribozymes driving the metabolism producing monomers for their own replication.

Prediction of Physicochemical Properties of Energetic Materials for Identification of Treatment Technologies for Waste Streams

DTIC Science & Technology

2010-11-01

estimate the pharmacokinetics of potential drugs (Horning and Klamt 2005). QSPR/ QSARs also have potential applications in the fuel science field...group contribution methods, and (2) quantitative structure-property/activity relationships (QSPR/ QSAR ). The group contribution methods are primarily...development of QSPR/ QSARs is the identification of the ap- propriate set of descriptors that allow the desired attribute of the compound to be adequately

Research and Development of Methods for Estimating Physicochemical Properties of Organic Compounds of Environmental Concern

DTIC Science & Technology

1979-02-01

coefficient (at equilibrium) when hysteresis is apparent. 6. Coefficient n in Freundlich equation for 1/n soil or sediment adsorption isotherms ýX - KC . 7...Biodegradation Chemical structures cal clasaes (e.g., Diffusion Correlations phenols). General Diffusion coefficients Equations terms for organic...OF THE FATE AND TRANSPORT OF ORGANIC CHEMICALS Adsorption coefficients: K, n* from Freundlich equation + Desorption coefficients: K’*, n’* from

Effect of lipophilicity modulation on inhibition of human rhinovirus capsid binders.

PubMed

Morley, Andrew; Tomkinson, Nicholas; Cook, Andrew; MacDonald, Catherine; Weaver, Richard; King, Sarah; Jenkinson, Lesley; Unitt, John; McCrae, Christopher; Phillips, Tim

2011-10-15

To try and generate broad spectrum human rhinovirus VP1 inhibitors with more attractive physicochemical, DMPK and safety profiles, we explored the current SAR of known VP1 compounds. This lead to the identification of specific structural regions where reduction in polarity can be achieved, so guiding chemistry to analogues with significantly superior profiles to previously reported inhibitors. Copyright © 2011 Elsevier Ltd. All rights reserved.

Residual-QSAR. Implications for genotoxic carcinogenesis

PubMed Central

2011-01-01

Introduction Both main types of carcinogenesis, genotoxic and epigenetic, were examined in the context of non-congenericity and similarity, respectively, for the structure of ligand molecules, emphasizing the role of quantitative structure-activity relationship ((Q)SAR) studies in accordance with OECD (Organization for Economic and Cooperation Development) regulations. The main purpose of this report involves electrophilic theory and the need for meaningful physicochemical parameters to describe genotoxicity by a general mechanism. Residual-QSAR Method The double or looping multiple linear correlation was examined by comparing the direct and residual structural information against the observed activity. A self-consistent equation of observed-computed activity was assumed to give maximum correlation efficiency for those situations in which the direct correlations gave non-significant statistical information. Alternatively, it was also suited to describe slow and apparently non-noticeable cancer phenomenology, with special application to non-congeneric molecules involved in genotoxic carcinogenesis. Application and Discussions The QSAR principles were systematically applied to a given pool of molecules with genotoxic activity in rats to elucidate their carcinogenic mechanisms. Once defined, the endpoint associated with ligand-DNA interaction was used to select variables that retained the main Hansch physicochemical parameters of hydrophobicity, polarizability and stericity, computed by the custom PM3 semiempirical quantum method. The trial and test sets of working molecules were established by implementing the normal Gaussian principle of activities that applies when the applicability domain is not restrained to the congeneric compounds, as in the present study. The application of the residual, self-consistent QSAR method and the factor (or average) method yielded results characterized by extremely high and low correlations, respectively, with the latter resembling the direct activity to parameter QSARs. Nevertheless, such contrasted correlations were further incorporated into the advanced statistical minimum paths principle, which selects the minimum hierarchy from Euclidean distances between all considered QSAR models for all combinations and considered molecular sets (i.e., school and validation). This ultimately led to a mechanistic picture based on the identified alpha, beta and gamma paths connecting structural indicators (i.e., the causes) to the global endpoint, with all included causes. The molecular mechanism preserved the self-consistent feature of the residual QSAR, with each descriptor appearing twice in the course of one cycle of ligand-DNA interaction through inter-and intra-cellular stages. Conclusions Both basal features of the residual-QSAR principle of self-consistency and suitability for non-congeneric molecules make it appropriate for conceptually assessing the mechanistic description of genotoxic carcinogenesis. Additionally, it could be extended to enriched physicochemical structural indices by considering the molecular fragments or structural alerts (or other molecular residues), providing more detailed maps of chemical-biological interactions and pathways. PMID:21668999

Physicochemical and immunochemical assays for monitoring consistent production of tetanus toxoid.

PubMed

Metz, Bernard; Tilstra, Wichard; van der Put, Robert; Spruit, Nanda; van den Ijssel, Jan; Robert, Jolanda; Hendriksen, Coenraad; Kersten, Gideon

2013-07-01

The detoxification of tetanus toxin by formaldehyde is a crucial step in the production of tetanus toxoid. The inactivation results in chemically modified proteins and it determines largely the ultimate efficacy and safety of the vaccine. Currently, the quality of tetanus toxoid lots is evaluated in potency and safety tests performed in animals. As a possible alternative, this article describes a panel of in vitro methods, which provides detailed information about the quality of tetanus toxoid. Ten experimental lots of tetanus toxoid were prepared using increasing concentrations of formaldehyde and glycine to obtain tetanus toxoids having differences in antigenicity, immunogenicity, residual toxicity and protein structure. The structural properties of each individual toxoid were determined using immunochemical and physicochemical methods, including biosensor analysis, ELISA, circular dichroism, TNBS assay, differential scanning calorimetry, fluorescence and SDS-PAGE. The quality of a tetanus toxoid lot can be assessed by these set of analytical techniques. Based on antigenicity, immunogenicity and residual toxicity data, criteria are formulated that tetanus toxoids lot have to meet in order to have a high quality. The in vitro methods are a valuable selection of techniques for monitoring consistency of production of tetanus toxoid, especially for the detoxification process of tetanus toxin. Copyright © 2013 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.

Recent advances in the application of microbial transglutaminase crosslinking in cheese and ice cream products: A review.

PubMed

Taghi Gharibzahedi, Seyed Mohammad; Koubaa, Mohamed; Barba, Francisco J; Greiner, Ralf; George, Saji; Roohinejad, Shahin

2018-02-01

Microbial transglutaminase (MTGase) has been currently utilized to form new food structures and matrices with high physicochemical stability. Incorporation of this multi-functional enzyme into structural composition of milk protein-based products, such as cheese and ice cream, can not only be a successful strategy to improve their nutritional and technological characteristics through intramolecular cross-linking, but also to reduce the production cost by decreasing fat and stabilizer contents. The recent research developments and promising results of MTGase application in producing functional formulations of cheese and ice cream with higher quality characteristics are reviewed. New interesting insights and future perspectives are also presented. The addition of MTGase to cheese led to significant improvements in moisture, yield, texture, rheology and sensory properties, without changes in the chemical composition. Furthermore, pH value of ice cream is not affected by the MTGase treatment. Compared to untreated ice creams, application of MTGase significantly promotes consistency, fat destabilization, overrun and organoleptic acceptance, while a substantial reduction in firmness and melting rate of samples was observed. The addition of MTGase to cheese and ice cream-milk provides reinforcement to the protein matrix and can be considered as a novel additive for improving the physicochemical and organoleptic properties of final products. Copyright © 2017 Elsevier B.V. All rights reserved.

Bioactivity tests of calcium phosphates with variant molar ratios of main components.

PubMed

Pluta, Klaudia; Sobczak-Kupiec, Agnieszka; Półtorak, Olga; Malina, Dagmara; Tyliszczak, Bożena

2018-03-09

Calcium phosphates constitute attractive materials of biomedical applications. Among them particular attention is devoted to bioactive hydroxyapatite (HAp) and bioresorbable tricalcium phosphate (TCP) that possess ability to bind to living bones and can be used clinically as important bone substitutes. Notably, in vivo bone bioactivity can be predicted from apatite formation of bone immersed in SBF fluids. Thus, analyses of behavior of calcium phosphates immersed in various bio fluids are of great importance. Recently, stoichiometric HAp and TCP structures have been widely studied, whereas only limited number of publications have been devoted to analyses of nonstoichiometric calcium phosphates. Here, we report physicochemical analysis of natural and synthetic phosphates with variable Ca/P molar ratios. Subsequently attained structures were subjected to incubation in either artificial saliva or Ringer's fluids. Both pH and conductivity of such fluids were determined before and after incubation. Furthermore, the influence of the Ca/P values on such parameters was exemplified. Physicochemical analysis of received materials was performed by XRD and FT-IR characterization techniques. Their potential antibacterial activity and behavior in the presence of infectious microorganisms as Escherichia coli and Staphylococcus aureus was also evaluated. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A, 2018. © 2018 Wiley Periodicals, Inc.

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

PubMed Central

Wang, Shang; Dong, Hailiang; Hou, Weiguo; Jiang, Hongchen; Huang, Qiuyuan; Briggs, Brandon R.; Huang, Liuqin

2014-01-01

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts. PMID:25524763

On the optimal design of molecular sensing interfaces with lipid bilayer assemblies - A knowledge based approach

NASA Astrophysics Data System (ADS)

Siontorou, Christina G.

2012-12-01

Biosensors are analytic devices that incorporate a biochemical recognition system (biological, biologicalderived or biomimic: enzyme, antibody, DNA, receptor, etc.) in close contact with a physicochemical transducer (electrochemical, optical, piezoelectric, conductimetric, etc.) that converts the biochemical information, produced by the specific biological recognition reaction (analyte-biomolecule binding), into a chemical or physical output signal, related to the concentration of the analyte in the measuring sample. The biosensing concept is based on natural chemoreception mechanisms, which are feasible over/within/by means of a biological membrane, i.e., a structured lipid bilayer, incorporating or attached to proteinaceous moieties that regulate molecular recognition events which trigger ion flux changes (facilitated or passive) through the bilayer. The creation of functional structures that are similar to natural signal transduction systems, correlating and interrelating compatibly and successfully the physicochemical transducer with the lipid film that is self-assembled on its surface while embedding the reconstituted biological recognition system, and at the same time manage to satisfy the basic conditions for measuring device development (simplicity, easy handling, ease of fabrication) is far from trivial. The aim of the present work is to present a methodological framework for designing such molecular sensing interfaces, functioning within a knowledge-based system built on an ontological platform for supplying sub-systems options, compatibilities, and optimization parameters.

Effects of heat-moisture treatment reaction conditions on the physicochemical and structural properties of maize starch: moisture and length of heating.

PubMed

Sui, Zhongquan; Yao, Tianming; Zhao, Yue; Ye, Xiaoting; Kong, Xiangli; Ai, Lianzhong

2015-04-15

Changes in the properties of normal maize starch (NMS) and waxy maize starch (WMS) after heat-moisture treatment (HMT) under various reaction conditions were investigated. NMS and WMS were adjusted to moisture levels of 20%, 25% and 30% and heated at 100 °C for 2, 4, 8 and 16 h. The results showed that moisture content was the most important factor in determining pasting properties for NMS, whereas the heating length was more important for WMS. Swelling power decreased in NMS but increased in WMS, and while the solubility index decreased for both samples, the changes were largely determined by moisture content. The gelatinisation temperatures of both samples increased with increasing moisture content but remained unchanged with increasing heating length. The Fourier transform infrared (FT-IR) absorbance ratio was affected to different extents by the moisture levels but remained constant with increasing the heating length. The X-ray intensities increased but relative crystallinity decreased to a greater extent with increasing moisture content. This study showed that the levels of moisture content and length of heating had significant impacts on the structural and physicochemical properties of normal and waxy maize starches but to different extents. Copyright © 2014 Elsevier Ltd. All rights reserved.

Recovering actives in multi-antitarget and target design of analogs of the myosin II inhibitor blebbistatin

NASA Astrophysics Data System (ADS)

Roman, Bart I.; Guedes, Rita C.; Stevens, Christian V.; García-Sosa, Alfonso T.

2018-05-01

In multitarget drug design, it is critical to identify active and inactive compounds against a variety of targets and antitargets. Multitarget strategies thus test the limits of available technology, be that in screening large databases of compounds versus a large number of targets, or in using in silico methods for understanding and reliably predicting these pharmacological outcomes. In this paper, we have evaluated the potential of several in silico approaches to predict the target, antitarget and physicochemical profile of (S)-blebbistatin, the best-known myosin II ATPase inhibitor, and a series of analogs thereof. Standard and augmented structure-based design techniques could not recover the observed activity profiles. A ligand-based method using molecular fingerprints was, however, able to select actives for myosin II inhibition. Using further ligand- and structure-based methods, we also evaluated toxicity through androgen receptor binding, affinity for an array of antitargets and the ADME profile (including assay-interfering compounds) of the series. In conclusion, in the search for (S)-blebbistatin analogs, the dissimilarity distance of molecular fingerprints to known actives and the computed antitarget and physicochemical profile of the molecules can be used for compound design for molecules with potential as tools for modulating myosin II and motility-related diseases.

Fuzzy cluster analysis of simple physicochemical properties of amino acids for recognizing secondary structure in proteins.

PubMed Central

Mocz, G.

1995-01-01

Fuzzy cluster analysis has been applied to the 20 amino acids by using 65 physicochemical properties as a basis for classification. The clustering products, the fuzzy sets (i.e., classical sets with associated membership functions), have provided a new measure of amino acid similarities for use in protein folding studies. This work demonstrates that fuzzy sets of simple molecular attributes, when assigned to amino acid residues in a protein's sequence, can predict the secondary structure of the sequence with reasonable accuracy. An approach is presented for discriminating standard folding states, using near-optimum information splitting in half-overlapping segments of the sequence of assigned membership functions. The method is applied to a nonredundant set of 252 proteins and yields approximately 73% matching for correctly predicted and correctly rejected residues with approximately 60% overall success rate for the correctly recognized ones in three folding states: alpha-helix, beta-strand, and coil. The most useful attributes for discriminating these states appear to be related to size, polarity, and thermodynamic factors. Van der Waals volume, apparent average thickness of surrounding molecular free volume, and a measure of dimensionless surface electron density can explain approximately 95% of prediction results. hydrogen bonding and hydrophobicity induces do not yet enable clear clustering and prediction. PMID:7549882

An Innovations-Based Noise Cancelling Technique on Inverse Kepstrum Whitening Filter and Adaptive FIR Filter in Beamforming Structure

PubMed Central

Jeong, Jinsoo

2011-01-01

This paper presents an acoustic noise cancelling technique using an inverse kepstrum system as an innovations-based whitening application for an adaptive finite impulse response (FIR) filter in beamforming structure. The inverse kepstrum method uses an innovations-whitened form from one acoustic path transfer function between a reference microphone sensor and a noise source so that the rear-end reference signal will then be a whitened sequence to a cascaded adaptive FIR filter in the beamforming structure. By using an inverse kepstrum filter as a whitening filter with the use of a delay filter, the cascaded adaptive FIR filter estimates only the numerator of the polynomial part from the ratio of overall combined transfer functions. The test results have shown that the adaptive FIR filter is more effective in beamforming structure than an adaptive noise cancelling (ANC) structure in terms of signal distortion in the desired signal and noise reduction in noise with nonminimum phase components. In addition, the inverse kepstrum method shows almost the same convergence level in estimate of noise statistics with the use of a smaller amount of adaptive FIR filter weights than the kepstrum method, hence it could provide better computational simplicity in processing. Furthermore, the rear-end inverse kepstrum method in beamforming structure has shown less signal distortion in the desired signal than the front-end kepstrum method and the front-end inverse kepstrum method in beamforming structure. PMID:22163987

A Structure-Adaptive Hybrid RBF-BP Classifier with an Optimized Learning Strategy

PubMed Central

Wen, Hui; Xie, Weixin; Pei, Jihong

2016-01-01

This paper presents a structure-adaptive hybrid RBF-BP (SAHRBF-BP) classifier with an optimized learning strategy. SAHRBF-BP is composed of a structure-adaptive RBF network and a BP network of cascade, where the number of RBF hidden nodes is adjusted adaptively according to the distribution of sample space, the adaptive RBF network is used for nonlinear kernel mapping and the BP network is used for nonlinear classification. The optimized learning strategy is as follows: firstly, a potential function is introduced into training sample space to adaptively determine the number of initial RBF hidden nodes and node parameters, and a form of heterogeneous samples repulsive force is designed to further optimize each generated RBF hidden node parameters, the optimized structure-adaptive RBF network is used for adaptively nonlinear mapping the sample space; then, according to the number of adaptively generated RBF hidden nodes, the number of subsequent BP input nodes can be determined, and the overall SAHRBF-BP classifier is built up; finally, different training sample sets are used to train the BP network parameters in SAHRBF-BP. Compared with other algorithms applied to different data sets, experiments show the superiority of SAHRBF-BP. Especially on most low dimensional and large number of data sets, the classification performance of SAHRBF-BP outperforms other training SLFNs algorithms. PMID:27792737

Resilience of Adapting Networks: Results from a Stylized Infrastructure Model.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beyeler, Walter E.; Vugrin, Eric D.; Forden, Geoffrey Ethan

2015-01-01

Adaptation is believed to be a source of resilience in systems. It has been difficult to measure the contribution of adaptation to resilience, unlike other resilience mechanisms such as restoration and recovery. One difficulty comes from treating adaptation as a deus ex machina that is interjected after a disruption. This provides no basis for bounding possible adaptive responses. We can bracket the possible effects of adaptation when we recognize that it occurs continuously, and is in part responsible for the current system’s properties. In this way the dynamics of the system’s pre-disruption structure provides information about post-disruption adaptive reaction. Seenmore » as an ongoing process, adaptation has been argued to produce “robust-yet-fragile” systems. Such systems perform well under historical stresses but become committed to specific features of those stresses in a way that makes them vulnerable to system-level collapse when those features change. In effect adaptation lessens the cost of disruptions within a certain historical range, at the expense of increased cost from disruptions outside that range. Historical adaptive responses leave a signature in the structure of the system. Studies of ecological networks have suggested structural metrics that pick out systemic resilience in the underlying ecosystems. If these metrics are generally reliable indicators of resilience they provide another strategy for gaging adaptive resilience. To progress in understanding how the process of adaptation and the property of resilience interrelate in infrastructure systems, we pose some specific questions: Does adaptation confer resilience?; Does it confer resilience to novel shocks as well, or does it tune the system to fragility?; Can structural features predict resilience to novel shocks?; Are there policies or constraints on the adaptive process that improve resilience?.« less

Effect of infrared and conventional drying methods on physicochemical characteristics of stored white rice

USDA-ARS?s Scientific Manuscript database

The objective of this study was to investigate the effect of infrared (IR) drying followed by tempering and natural cooling on the change of physicochemical characteristics of white rice during up to 10 months of storage. The physicochemical characteristics of IR dried rice was also compared with th...

A modeling assessment of the physicochemical properties and environmental fate of emerging and novel per- and polyfluoroalkyl substances.

PubMed

Gomis, Melissa Ines; Wang, Zhanyun; Scheringer, Martin; Cousins, Ian T

2015-02-01

Long-chain perfluoroalkyl carboxylic acids (PFCAs) and perfluoroalkane sulfonic acids (PFSAs) are persistent, bioaccumulative, and toxic contaminants that are globally present in the environment, wildlife and humans. Phase-out actions and use restrictions to reduce the environmental release of long-chain PFCAs, PFSAs and their precursors have been taken since 2000. In particular, long-chain poly- and perfluoroalkyl substances (PFASs) are being replaced with shorter-chain homologues or other fluorinated or non-fluorinated alternatives. A key question is: are these alternatives, particularly the structurally similar fluorinated alternatives, less hazardous to humans and the environment than the substances they replace? Several fluorinated alternatives including perfluoroether carboxylic acids (PFECAs) and perfluoroether sulfonic acids (PFESAs) have been recently identified. However, the scarcity of experimental data prevents hazard and risk assessments for these substances. In this study, we use state-of-the-art in silico tools to estimate key properties of these newly identified fluorinated alternatives. [i] COSMOtherm and SPARC are used to estimate physicochemical properties. The US EPA EPISuite software package is used to predict degradation half-lives in air, water and soil. [ii] In combination with estimated chemical properties, a fugacity-based multimedia mass-balance unit-world model - the OECD Overall Persistence (POV) and Long-Range Transport Potential (LRTP) Screening Tool - is used to assess the likely environmental fate of these alternatives. Even though the fluorinated alternatives contain some structural differences, their physicochemical properties are not significantly different from those of their predecessors. Furthermore, most of the alternatives are estimated to be similarly persistent and mobile in the environment as the long-chain PFASs. The models therefore predict that the fluorinated alternatives will become globally distributed in the environment similar to their predecessors. Although such in silico methods are coupled with uncertainties, this preliminary assessment provides enough cause for concern to warrant experimental work to better determine the properties of these fluorinated alternatives. Copyright © 2014 Elsevier B.V. All rights reserved.

The CoRR hypothesis for genes in organelles.

PubMed

Allen, John F

2017-12-07

Chloroplasts and mitochondria perform energy transduction in photosynthesis and respiration. These processes can be described in physico-chemical terms with no obvious requirement for co-located genetic systems, separat from those of the rest of the cell. Accordingly, biochemists once tended to regard endosymbiosis as untestable evolutionary speculation. Lynn Sagan's seminal 1967 paper "On the Origin of Mitosing Cells" outlined the evolution of eukaryotic cells by endosymbiosis of prokaryotes. The endosymbiont hypothesis is consistent with presence of DNA in chloroplasts and mitochondria, but does not assign it a function. Biochemistry and molecular biology now show that Sagan's proposal has an explanatory reach far beyond that originally envisaged. Prokaryotic origins of photosynthetic and respiratory mechanisms are apparent in protein structural insights into energy coupling. Genome sequencing confirms the underlying, prokaryotic architecture of chloroplasts and mitochondria and illustrates the profound influence of the original mergers of their ancestors' genes and proteins with those of their host cells. Peter Mitchell's 1961 chemiosmotic hypothesis applied the concept of vectorial catalysis that underlies biological energy transduction and cell structure, function, and origins. Continuity of electrical charge separation and membrane sidedness requires compartments within compartments, together with intricate mechanisms for transport within and between them. I suggest that the reason for the persistence of distinct genetic systems within bioenergetic organelles is the selective advantage of subcellular co-location of specific genes with their gene products. Co-location for Redox Regulation - CoRR - provides for a dialogue between chemical reduction-oxidation and the action of genes encoding its protein catalysts. These genes and their protein products are in intimate contact, and cannot be isolated from each other without loss of an essential mechanism of adaptation of electron transport to change in the external environment. Copyright © 2017 The Author. Published by Elsevier Ltd.. All rights reserved.

Data on changes in red wine phenolic compounds, headspace aroma compounds and sensory profile after treatment of red wines with activated carbons with different physicochemical characteristics.

PubMed

Filipe-Ribeiro, Luís; Milheiro, Juliana; Matos, Carlos C; Cosme, Fernanda; Nunes, Fernando M

2017-06-01

Data in this article presents the changes on phenolic compounds, headspace aroma composition and sensory profile of a red wine spiked with 4-ethylphenol and 4-ethylguaiacol and treated with seven activated carbons with different physicochemical characteristics, namely surface area, micropore volume and mesopore volume ("Reduction of 4-ethylphenol and 4-ethylguaiacol in red wine by activated carbons with different physicochemical characteristics: impact on wine quality" Filipe-Ribeiro et al. (2017) [1]). Data on the physicochemical characteristics of the activated carbons are shown. Statistical data on the sensory expert panel consistency by General Procrustes Analysis is shown. Statistical data is also shown, which correlates the changes in chemical composition of red wines with the physicochemical characteristics of activated carbons used.

A reduced adaptive observer for multivariable systems. [using reduced dynamic ordering

NASA Technical Reports Server (NTRS)

Carroll, R. L.; Lindorff, D. P.

1973-01-01

An adaptive observer for multivariable systems is presented for which the dynamic order of the observer is reduced, subject to mild restrictions. The observer structure depends directly upon the multivariable structure of the system rather than a transformation to a single-output system. The number of adaptive gains is at most the sum of the order of the system and the number of input parameters being adapted. Moreover, for the relatively frequent specific cases for which the number of required adaptive gains is less than the sum of system order and input parameters, the number of these gains is easily determined by inspection of the system structure. This adaptive observer possesses all the properties ascribed to the single-input single-output adpative observer. Like the other adaptive observers some restriction is required of the allowable system command input to guarantee convergence of the adaptive algorithm, but the restriction is more lenient than that required by the full-order multivariable observer. This reduced observer is not restricted to cycle systems.

Epidemics in adaptive networks with community structure

NASA Astrophysics Data System (ADS)

Shaw, Leah; Tunc, Ilker

2010-03-01

Models for epidemic spread on static social networks do not account for changes in individuals' social interactions. Recent studies of adaptive networks have modeled avoidance behavior, as non-infected individuals try to avoid contact with infectives. Such models have not generally included realistic social structure. Here we study epidemic spread on an adaptive network with community structure. We model the effect of heterogeneous communities on infection levels and epidemic extinction. We also show how an epidemic can alter the community structure.

An Adaptive Course Generation Framework

ERIC Educational Resources Information Center

Li, Frederick W. B.; Lau, Rynson W. H.; Dharmendran, Parthiban

2010-01-01

Existing adaptive e-learning methods are supported by student (user) profiling for capturing student characteristics, and course structuring for organizing learning materials according to topics and levels of difficulties. Adaptive courses are then generated by extracting materials from the course structure to match the criteria specified in the…

Physicochemical Characterization of Iron Carbohydrate Colloid Drug Products.

PubMed

Zou, Peng; Tyner, Katherine; Raw, Andre; Lee, Sau

2017-09-01

Iron carbohydrate colloid drug products are intravenously administered to patients with chronic kidney disease for the treatment of iron deficiency anemia. Physicochemical characterization of iron colloids is critical to establish pharmaceutical equivalence between an innovator iron colloid product and generic version. The purpose of this review is to summarize literature-reported techniques for physicochemical characterization of iron carbohydrate colloid drug products. The mechanisms, reported testing results, and common technical pitfalls for individual characterization test are discussed. A better understanding of the physicochemical characterization techniques will facilitate generic iron carbohydrate colloid product development, accelerate products to market, and ensure iron carbohydrate colloid product quality.

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

PubMed Central

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors. PMID:22701576

A mechanistic physicochemical model of carbon dioxide transport in blood.

PubMed

O'Neill, David P; Robbins, Peter A

2017-02-01

A number of mathematical models have been produced that, given the Pco 2 and Po 2 of blood, will calculate the total concentrations for CO 2 and O 2 in blood. However, all these models contain at least some empirical features, and thus do not represent all of the underlying physicochemical processes in an entirely mechanistic manner. The aim of this study was to develop a physicochemical model of CO 2 carriage by the blood to determine whether our understanding of the physical chemistry of the major chemical components of blood together with their interactions is sufficiently strong to predict the physiological properties of CO 2 carriage by whole blood. Standard values are used for the ionic composition of the blood, the plasma albumin concentration, and the hemoglobin concentration. All K m values required for the model are taken from the literature. The distribution of bicarbonate, chloride, and H + ions across the red blood cell membrane follows that of a Gibbs-Donnan equilibrium. The system of equations that results is solved numerically using constraints for mass balance and electroneutrality. The model reproduces the phenomena associated with CO 2 carriage, including the magnitude of the Haldane effect, very well. The structural nature of the model allows various hypothetical scenarios to be explored. Here we examine the effects of 1) removing the ability of hemoglobin to form carbamino compounds; 2) allowing a degree of Cl - binding to deoxygenated hemoglobin; and 3) removing the chloride (Hamburger) shift. The insights gained could not have been obtained from empirical models. This study is the first to incorporate a mechanistic model of chloride-bicarbonate exchange between the erythrocyte and plasma into a full physicochemical model of the carriage of carbon dioxide in blood. The mechanistic nature of the model allowed a theoretical study of the quantitative significance for carbon dioxide transport of carbamino compound formation; the putative binding of chloride to deoxygenated hemoglobin, and the chloride (Hamburger) shift. Copyright © 2017 the American Physiological Society.

A mechanistic physicochemical model of carbon dioxide transport in blood

PubMed Central

O’Neill, David P.

2017-01-01

A number of mathematical models have been produced that, given the Pco2 and Po2 of blood, will calculate the total concentrations for CO2 and O2 in blood. However, all these models contain at least some empirical features, and thus do not represent all of the underlying physicochemical processes in an entirely mechanistic manner. The aim of this study was to develop a physicochemical model of CO2 carriage by the blood to determine whether our understanding of the physical chemistry of the major chemical components of blood together with their interactions is sufficiently strong to predict the physiological properties of CO2 carriage by whole blood. Standard values are used for the ionic composition of the blood, the plasma albumin concentration, and the hemoglobin concentration. All Km values required for the model are taken from the literature. The distribution of bicarbonate, chloride, and H+ ions across the red blood cell membrane follows that of a Gibbs-Donnan equilibrium. The system of equations that results is solved numerically using constraints for mass balance and electroneutrality. The model reproduces the phenomena associated with CO2 carriage, including the magnitude of the Haldane effect, very well. The structural nature of the model allows various hypothetical scenarios to be explored. Here we examine the effects of 1) removing the ability of hemoglobin to form carbamino compounds; 2) allowing a degree of Cl− binding to deoxygenated hemoglobin; and 3) removing the chloride (Hamburger) shift. The insights gained could not have been obtained from empirical models. NEW & NOTEWORTHY This study is the first to incorporate a mechanistic model of chloride-bicarbonate exchange between the erythrocyte and plasma into a full physicochemical model of the carriage of carbon dioxide in blood. The mechanistic nature of the model allowed a theoretical study of the quantitative significance for carbon dioxide transport of carbamino compound formation; the putative binding of chloride to deoxygenated hemoglobin, and the chloride (Hamburger) shift. PMID:27881667

IDM-PhyChm-Ens: intelligent decision-making ensemble methodology for classification of human breast cancer using physicochemical properties of amino acids.

PubMed

Ali, Safdar; Majid, Abdul; Khan, Asifullah

2014-04-01

Development of an accurate and reliable intelligent decision-making method for the construction of cancer diagnosis system is one of the fast growing research areas of health sciences. Such decision-making system can provide adequate information for cancer diagnosis and drug discovery. Descriptors derived from physicochemical properties of protein sequences are very useful for classifying cancerous proteins. Recently, several interesting research studies have been reported on breast cancer classification. To this end, we propose the exploitation of the physicochemical properties of amino acids in protein primary sequences such as hydrophobicity (Hd) and hydrophilicity (Hb) for breast cancer classification. Hd and Hb properties of amino acids, in recent literature, are reported to be quite effective in characterizing the constituent amino acids and are used to study protein foldings, interactions, structures, and sequence-order effects. Especially, using these physicochemical properties, we observed that proline, serine, tyrosine, cysteine, arginine, and asparagine amino acids offer high discrimination between cancerous and healthy proteins. In addition, unlike traditional ensemble classification approaches, the proposed 'IDM-PhyChm-Ens' method was developed by combining the decision spaces of a specific classifier trained on different feature spaces. The different feature spaces used were amino acid composition, split amino acid composition, and pseudo amino acid composition. Consequently, we have exploited different feature spaces using Hd and Hb properties of amino acids to develop an accurate method for classification of cancerous protein sequences. We developed ensemble classifiers using diverse learning algorithms such as random forest (RF), support vector machines (SVM), and K-nearest neighbor (KNN) trained on different feature spaces. We observed that ensemble-RF, in case of cancer classification, performed better than ensemble-SVM and ensemble-KNN. Our analysis demonstrates that ensemble-RF, ensemble-SVM and ensemble-KNN are more effective than their individual counterparts. The proposed 'IDM-PhyChm-Ens' method has shown improved performance compared to existing techniques.

Influence of aminosilane precursor concentration on physicochemical properties of composite Nafion membranes for vanadium redox flow battery applications

NASA Astrophysics Data System (ADS)

Kondratenko, Mikhail S.; Karpushkin, Evgeny A.; Gvozdik, Nataliya A.; Gallyamov, Marat O.; Stevenson, Keith J.; Sergeyev, Vladimir G.

2017-02-01

A series of composite proton-exchange membranes have been prepared via sol-gel modification of commercial Nafion membranes with [N-(2-aminoethyl)-3-aminopropyl]trimethoxysilane. The structure and physico-chemical properties (water uptake, ion-exchange capacity, vanadyl ion permeability, and proton conductivity) of the prepared composite membranes have been studied as a function of the precursor loading (degree of the membrane modification). If the amount of the precursor is below 0.4/1 M ratio of the amino groups of the precursor to the sulfonic groups of Nafion, the composite membranes exhibit decreased vanadium ion permeability while having relatively high proton conductivity. With respect to the use of a non-modified Nafion membrane, the performance of the composite membrane with an optimum precursor loading in a single-cell vanadium redox flow battery demonstrates enhanced energy efficiency in 20-80 mA cm-2 current density range. The maximum efficiency increase of 8% is observed at low current densities.

Physicochemical of pillared clays prepared by several metal oxides

NASA Astrophysics Data System (ADS)

Rinaldi, Nino; Kristiani, Anis

2017-03-01

Natural clays could be modified by the pillarization method, called as Pillared Clays (PILCs). PILCs have been known as porous materials that can be used for many applications, one of the fields is catalysis. PILCs as two dimensional materials are interesting because their structures and textural properties can be controlled by using a metal oxide as the pillar. Different metal oxide used as the pillar causes different properties results of pillared clays. Usually, natural smectite clays/bentonites are used as a raw material. Therefore, a series of bentonite pillared by metal oxides was prepared through pillarization method. Variation of metals pillared into bentonite are aluminium, chromium, zirconium, and ferro. The physicochemical properties of catalysts were characterized by using X-ray Diffraction (XRD), Thermo Gravimetric Analysis (TGA), Brunauer-Emmett-Teller (BET) and Barret-Joyner-Halenda (BJH) analysis, and Fourier transform infrared spectroscopy (FTIR) measurement. Noteworthy characterization results showed that different metals pillared into bentonite affected physical and chemical properties, i.e. basal spacing, surface area, pore size distribution, thermal stability and acidity.

Formalized classification of moss litters in swampy spruce forests of intermontane depressions of Kuznetsk Alatau

NASA Astrophysics Data System (ADS)

Efremova, T. T.; Avrova, A. F.; Efremov, S. P.

2016-09-01

The approaches of multivariate statistics have been used for the numerical classification of morphogenetic types of moss litters in swampy spruce forests according to their physicochemical properties (the ash content, decomposition degree, bulk density, pH, mass, and thickness). Three clusters of moss litters— peat, peaty, and high-ash peaty—have been specified. The functions of classification for identification of new objects have been calculated and evaluated. The degree of decomposition and the ash content are the main classification parameters of litters, though all other characteristics are also statistically significant. The final prediction accuracy of the assignment of a litter to a particular cluster is 86%. Two leading factors participating in the clustering of litters have been determined. The first factor—the degree of transformation of plant remains (quality)—specifies 49% of the total variance, and the second factor—the accumulation rate (quantity)— specifies 26% of the total variance. The morphogenetic structure and physicochemical properties of the clusters of moss litters are characterized.

Cellular and Molecular Actions of Methylene Blue in the Nervous System

PubMed Central

Oz, Murat; Lorke, Dietrich E.; Hasan, Mohammed; Petroianu, George A.

2010-01-01

Methylene Blue (MB), following its introduction to biology in the 19th century by Ehrlich, has found uses in various areas of medicine and biology. At present, MB is the first line of treatment in methemoglobinemias, is used frequently in the treatment of ifosfamide-induced encephalopathy, and is routinely employed as a diagnostic tool in surgical procedures. Furthermore, recent studies suggest that MB has beneficial effects in Alzheimer's disease and memory improvement. Although the modulation of the cGMP pathway is considered the most significant effect of MB, mediating its pharmacological actions, recent studies indicate that it has multiple cellular and molecular targets. In the majority of cases, biological effects and clinical applications of MB are dictated by its unique physicochemical properties including its planar structure, redox chemistry, ionic charges, and light spectrum characteristics. In this review article, these physicochemical features and the actions of MB on multiple cellular and molecular targets are discussed with regard to their relevance to the nervous system. PMID:19760660

Bio-lubricants derived from waste cooking oil with improved oxidation stability and low-temperature properties.

PubMed

Li, Weimin; Wang, Xiaobo

2015-01-01

Waste cooking oil (WCO) was chemically modified via epoxidation using H2O2 followed by transesterification with methanol and branched alcohols (isooctanol, isotridecanol and isooctadecanol) to produce bio-lubricants with improved oxidative stability and low temperature properties. Physicochemical properties of synthesized bio-lubricants such as pour point (PP), cloud point (CP), viscosity, viscosity index (VI), oxidative stability, and corrosion resistant property were determined according to standard methods. The synthesized bio-lubricants showed improved low temperature flow performances compared with WCO, which can be attributing to the introduction of branched chains in their molecular structures. What's more, the oxidation stability of the WCO showed more than 10 folds improvement due to the elimination of -C=C-bonds in the WCO molecule. Tribological performances of these bio-lubricants were also investigated using four-ball friction and wear tester. Experimental results showed that derivatives of WCO exhibited favorable physicochemical properties and tribological performances which making them good candidates in formulating eco-friendly lubricants.

Physicochemical properties of nixtamalized corn flours with and without germ.

PubMed

Vega Rojas, Lineth J; Rojas Molina, Isela; Gutiérrez Cortez, Elsa; Rincón Londoño, Natalia; Acosta Osorio, Andrés A; Del Real López, Alicia; Rodríguez García, Mario E

2017-04-01

This research studied the influence of the germ components on the physicochemical properties of cooked corn and nixtamalized corn flours as a function of the calcium hydroxide content (from 0 to 2.1 w/w) and steeping time (between 0 and 9h). A linear relationship was found between calcium content in germ and steeping time used during nixtamalization process. X-ray diffraction analysis showed that calcium carbonate is formed into the germ structure to 2.1 w/w of calcium hydroxide and 9h steeping time. The presence of the germ improves the development of peak viscosity in flours, and it is related to the increases in calcium concentration in germ and the formation of amylose-lipid complexes. No significant changes were observed in palmitic, stearic, oleic and linoleic acids of corn oil. The levels of further corn oil deterioration were 2.1 w/w of calcium hydroxide concentration and 9h of steeping time. Copyright © 2016 Elsevier Ltd. All rights reserved.

Isolation, purification, toxicity and some physicochemical properties of mycotoxins produced by aspergillus quadrilineatus isolated from acha (Digitaria exilis stapf) in Plateau State of Nigeria.

PubMed

Gbodi, T A

1993-06-01

Some physico-chemical and toxicological studies were carried out on mycotoxins elaborated by Aspergillus quadrilineatus isolated from a grain foodstuff, acha (Digitaria exilis) in the Plateau State of Nigeria. The mycotoxins produced by A quadrilineatus were extractable from rice culture by chloroform. Column chromatographic separations of the crude extract in silica gel using different elution solvents and biological tests showed that the mycotoxins came off in the diethylether, chloroform and mostly in the ethyl acetate fractions. Use of different available mycotoxin standards on silica gel G coated chromatoplates revealed that 1 of the mycotoxins produced by A quadrilineatus was sterigmatocystin. Two other more toxic mycotoxins were isolated and purified from the crude chloroform extract; their column, preparative thin-layer chromatographic, infrared and UV-spectrophotometric characteristics were established. The infrared spectra of the 2 purified mycotoxins suggested that the carbonyl group of their structures were similar to that of aflatoxin.

Odor Impression Prediction from Mass Spectra.

PubMed

Nozaki, Yuji; Nakamoto, Takamichi

2016-01-01

The sense of smell arises from the perception of odors from chemicals. However, the relationship between the impression of odor and the numerous physicochemical parameters has yet to be understood owing to its complexity. As such, there is no established general method for predicting the impression of odor of a chemical only from its physicochemical properties. In this study, we designed a novel predictive model based on an artificial neural network with a deep structure for predicting odor impression utilizing the mass spectra of chemicals, and we conducted a series of computational analyses to evaluate its performance. Feature vectors extracted from the original high-dimensional space using two autoencoders equipped with both input and output layers in the model are used to build a mapping function from the feature space of mass spectra to the feature space of sensory data. The results of predictions obtained by the proposed new method have notable accuracy (R≅0.76) in comparison with a conventional method (R≅0.61).

Characterization of extracellular polymeric substances in the biofilms of typical bacteria by the sulfur K-edge XANES spectroscopy.

PubMed

Lin, Huirong; Ye, Chengsong; Lv, Lu; Zheng, Clark Renjun; Zhang, Shenghua; Zheng, Lei; Zhao, Yidong; Yu, Xin

2014-08-01

A combined approach of physicochemical extraction and sulfur K-edge X-ray absorption near-edge structure (XANES) spectroscopy was applied to characterize the extracellular polymeric substances (EPS) of typical bacterial biofilms in this study. Physicochemical analysis showed variation of the contents of DNA, polysaccharide and protein in different fractions of EPS in different mediums. The sulfur K-edge XANES analysis yielded a variety of spectra. Spectral fitting of the XANES spectra utilizing a large set of model compounds showed that there was more reduced sulfur in both LB-EPS (loosely bound EPS) and TB-EPS (tightly bound EPS) of all the biofilms in LB medium than in R2A medium. More oxidized sulfur was identified in LB-EPS than that in TB-EPS, suggesting different niches and physiological heterogeneity in the biofilms. Our results suggested that the sulfur K-edge XANES can be a useful tool to analyze the sulfur speciation in EPS of biofilms. Copyright © 2014. Published by Elsevier B.V.

Physicochemical properties and starch digestibility of whole grain sorghums, millet, quinoa and amaranth flours, as affected by starch and non-starch constituents.

PubMed

Srichuwong, Sathaporn; Curti, Delphine; Austin, Sean; King, Roberto; Lamothe, Lisa; Gloria-Hernandez, Hugo

2017-10-15

Minor grains such as sorghum, millet, quinoa and amaranth can be alternatives to wheat and corn as ingredients for whole grain and gluten-free products. In this study, influences of starch structures and other grain constituents on physicochemical properties and starch digestibility of whole flours made from these grains were investigated. Starches were classified into two groups according to their amylopectin branch chain-length: (i) quinoa, amaranth, wheat (shorter chains); and (ii) sorghum, millet, corn (longer chains). Such amylopectin features and amylose content contributed to the differences in thermal and pasting properties as well as starch digestibility of the flours. Non-starch constituents had additional impacts; proteins delayed starch gelatinization and pasting, especially in sorghum flours, and high levels of soluble fibre retarded starch retrogradation in wheat, quinoa and amaranth flours. Enzymatic hydrolysis of starch was restricted by the presence of associated protein matrix and enzyme inhibitors, but accelerated by endogenous amylolytic enzymes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Physicochemical properties and antioxidant activities of polysaccharides from Gynura procumbens leaves by fractional precipitation.

PubMed

Li, Jing-En; Wang, Wen-Jun; Zheng, Guo-Dong; Li, Lin-Yan

2017-02-01

Four new polysaccharides (GPP-20, GPP-40, GPP-60 and GPP-80) were fractionated from Gynura procumbens leaves by 20%, 40%, 60% and 80% (v/v) ethanol, successively. Their physicochemical properties including the contents of neutral sugar, uronic acid and protein, as well as the monosaccharide composition were determined. In addition, the antioxidant activities of them were investigated via the reducing power assay and scavenging capacities of 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radicals and hydroxyl free radicals, respectively. The results indicated that apart from neutral sugar, they all contained uronic acids and proteins in their structures, which were further proved by the UV-vis and FT-IR spectra. Monosaccharide composition analysis implied that they all belonged to heteropolysaccharides consisted of arabinose, galactose, glucose, xylose and galacturonic acid with different types and ratios. What's more, GPP-20, GPP-40 and GPP-80 always exhibited better antioxidant activities than GPP-60 among these three antioxidant assays in vitro. Copyright © 2016 Elsevier B.V. All rights reserved.