Synthetic biology for microbial heavy metal biosensors.

PubMed

Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

2018-02-01

Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

Hands-on-Entropy, Energy Balance with Biological Relevance

NASA Astrophysics Data System (ADS)

Reeves, Mark

2015-03-01

Entropy changes underlie the physics that dominates biological interactions. Indeed, introductory biology courses often begin with an exploration of the qualities of water that are important to living systems. However, one idea that is not explicitly addressed in most introductory physics or biology textbooks is important contribution of the entropy in driving fundamental biological processes towards equilibrium. From diffusion to cell-membrane formation, to electrostatic binding in protein folding, to the functioning of nerve cells, entropic effects often act to counterbalance deterministic forces such as electrostatic attraction and in so doing, allow for effective molecular signaling. A small group of biology, biophysics and computer science faculty have worked together for the past five years to develop curricular modules (based on SCALEUP pedagogy). This has enabled students to create models of stochastic and deterministic processes. Our students are first-year engineering and science students in the calculus-based physics course and they are not expected to know biology beyond the high-school level. In our class, they learn to reduce complex biological processes and structures in order model them mathematically to account for both deterministic and probabilistic processes. The students test these models in simulations and in laboratory experiments that are biologically relevant such as diffusion, ionic transport, and ligand-receptor binding. Moreover, the students confront random forces and traditional forces in problems, simulations, and in laboratory exploration throughout the year-long course as they move from traditional kinematics through thermodynamics to electrostatic interactions. This talk will present a number of these exercises, with particular focus on the hands-on experiments done by the students, and will give examples of the tangible material that our students work with throughout the two-semester sequence of their course on introductory

The Biological Relevance of Artificial Life: Lessons from Artificial Intelligence

NASA Technical Reports Server (NTRS)

Colombano, Silvano

2000-01-01

There is no fundamental reason why A-life couldn't simply be a branch of computer science that deals with algorithms that are inspired by, or emulate biological phenomena. However, if these are the limits we place on this field, we miss the opportunity to help advance Theoretical Biology and to contribute to a deeper understanding of the nature of life. The history of Artificial Intelligence provides a good example, in that early interest in the nature of cognition quickly was lost to the process of building tools, such as "expert systems" that, were certainly useful, but provided little insight in the nature of cognition. Based on this lesson, I will discuss criteria for increasing the biological relevance of A-life and the probability that this field may provide a theoretical foundation for Biology.

Systematically biological prioritizing remediation sites based on datasets of biological investigations and heavy metals in soil

NASA Astrophysics Data System (ADS)

Lin, Wei-Chih; Lin, Yu-Pin; Anthony, Johnathen

2015-04-01

Heavy metal pollution has adverse effects on not only the focal invertebrate species of this study, such as reduction in pupa weight and increased larval mortality, but also on the higher trophic level organisms which feed on them, either directly or indirectly, through the process of biomagnification. Despite this, few studies regarding remediation prioritization take species distribution or biological conservation priorities into consideration. This study develops a novel approach for delineating sites which are both contaminated by any of 5 readily bioaccumulated heavy metal soil contaminants and are of high ecological importance for the highly mobile, low trophic level focal species. The conservation priority of each site was based on the projected distributions of 6 moth species simulated via the presence-only maximum entropy species distribution model followed by the subsequent application of a systematic conservation tool. In order to increase the number of available samples, we also integrated crowd-sourced data with professionally-collected data via a novel optimization procedure based on a simulated annealing algorithm. This integration procedure was important since while crowd-sourced data can drastically increase the number of data samples available to ecologists, still the quality or reliability of crowd-sourced data can be called into question, adding yet another source of uncertainty in projecting species distributions. The optimization method screens crowd-sourced data in terms of the environmental variables which correspond to professionally-collected data. The sample distribution data was derived from two different sources, including the EnjoyMoths project in Taiwan (crowd-sourced data) and the Global Biodiversity Information Facility (GBIF) ?eld data (professional data). The distributions of heavy metal concentrations were generated via 1000 iterations of a geostatistical co-simulation approach. The uncertainties in distributions of the heavy

Mammalian lipoxygenases and their biological relevance.

PubMed

Kuhn, Hartmut; Banthiya, Swathi; van Leyen, Klaus

2015-04-01

Lipoxygenases (LOXs) form a heterogeneous class of lipid peroxidizing enzymes, which have been implicated not only in cell proliferation and differentiation but also in the pathogenesis of various diseases with major public health relevance. As other fatty acid dioxygenases LOXs oxidize polyunsaturated fatty acids to their corresponding hydroperoxy derivatives, which are further transformed to bioactive lipid mediators (eicosanoids and related substances). On the other hand, lipoxygenases are key players in the regulation of the cellular redox homeostasis, which is an important element in gene expression regulation. Although the first mammalian lipoxygenases were discovered 40 years ago and although the enzymes have been well characterized with respect to their structural and functional properties the biological roles of the different lipoxygenase isoforms are not completely understood. This review is aimed at summarizing the current knowledge on the physiological roles of different mammalian LOX-isoforms and their patho-physiological function in inflammatory, metabolic, hyperproliferative, neurodegenerative and infectious disorders. This article is part of a Special Issue entitled "Oxygenated metabolism of PUFA: analysis and biological relevance". Copyright © 2014 Elsevier B.V. All rights reserved.

Metal based biologically active compounds: design, synthesis, and antibacterial/antifungal/cytotoxic properties of triazole-derived Schiff bases and their oxovanadium(IV) complexes.

PubMed

Chohan, Zahid H; Sumrra, Sajjad H; Youssoufi, Moulay H; Hadda, Taibi B

2010-07-01

A new series of oxovanadium(IV) complexes have been designed and synthesized with a new class of triazole Schiff bases derived from the reaction of 3,5-diamino-1,2,4-triazole with 2-hydroxy-1-naphthaldehyde, pyrrole-2-carboxaldehyde, pyridine-2-carboxaldehyde and acetyl pyridine-2-carboxaldehyde, respectively. Physical (magnetic susceptibility, molar conductance), spectral (IR, (1)H NMR, (13)C NMR, mass and electronic) and analytical data have established the structures of these synthesized Schiff bases and their oxovanadium(IV) complexes. The Schiff bases, predominantly act as bidentate and coordinate with the vanadium(IV) metal to give a stoichiometric ratio of 1:2 [M:L], forming a general formulae, [M(L-H)(2)] and [M(L)(2)]SO(4) where L = (L(1))-(L(4)) and M = VO(IV) of these complexes in a square-pyramidal geometry. In order to evaluate the biological activity of Schiff bases and to assess the role of vanadium(IV) metal on biological activity, the triazole Schiff bases and their oxovanadium(IV) complexes have been studied for in vitro antibacterial activity against four Gram-negative (Escherichia coli, Shigella flexenari, Pseudomonas aeruginosa, Salmonella typhi) and two Gram-positive (Staphylococcus aureus, Bacillus subtilis) bacterial strains, in vitro antifungal activity against Trichophyton longifucus, Candida albican, Aspergillus flavus, Microscopum canis, Fusarium solani and Candida glaberata. The simple Schiff bases showed weaker to significant activity against one or more bacterial and fungal strains. In most of the cases higher activity was exhibited upon coordination with vanadium(IV) metal. Brine shrimp bioassay was also carried out for in vitro cytotoxic properties against Artemia salina. Copyright (c) 2010 Elsevier Masson SAS. All rights reserved.

biologically relevant effects of dipentyl phthalate

EPA Pesticide Factsheets

metadata sheet, data sheet for each table and figure in the published manuscriptThis dataset is associated with the following publication:Gray , E., J. Furr , K. Tatum-Gibbs, C. Lambright , H. Sampson, B. Hannas, V. Wilson , A. Hotchkiss , and P. Foster. Establishing the Biological Relevance of Dipentyl Phthalate Reductions in Fetal Rat Testosterone Production and Plasma and Testis Testosterone Levels. TOXICOLOGICAL SCIENCES. Society of Toxicology, 149(1): 178-91, (2016).

Design, spectral characterization and biological studies of transition metal(II) complexes with triazole Schiff bases

NASA Astrophysics Data System (ADS)

Hanif, Muhammad; Chohan, Zahid H.

2013-03-01

A new series of three biologically active triazole derived Schiff base ligands L1-L3 have been synthesized in equimolar reaction of 3-amino-1H-1,2,4-triazole with pyrrol-2-carboxaldehyde, 4-bromo-thiophene-2-carboxaldehyde, and 5-iodo-2-hydroxy benzaldehyde. The prepared Schiff bases were used for further complex formation reaction with different metal elements like Co(II), Ni(II), Cu(II) and Zn(II) as chlorides by using a molar ratio of ligand:metal as 2:1. The structure and bonding nature of all the compounds were identified by their physical, spectral and analytical data. All the metal(II) complexes possessed an octahedral geometry except the Cu(II) complexes which showed a distorted octahedral geometry. All the synthesized compounds, were studied for their in vitro antibacterial, and antifungal activities, against four Gram-negative (Escherichia coli, Shigella sonnei, Pseudomonas aeruginosa and Salmonella typhi) and two Gram-positive (Bacillus subtilis and Staphylococcus aureus) bacterial strains and against six fungal strains (Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glabrata) by using agar-well diffusion method. It has been shown that all the synthesized compounds showed moderate to significant antibacterial activity against one or more bacterial strains. In vitro Brine Shrimp bioassay was also carried out to investigate the cytotoxic properties of these compounds. The data also revealed that the metal complexes showed better activity than the ligands due to chelation/coordination.

Metal-mediated DNA base pairing: alternatives to hydrogen-bonded Watson-Crick base pairs.

PubMed

Takezawa, Yusuke; Shionoya, Mitsuhiko

2012-12-18

With its capacity to store and transfer the genetic information within a sequence of monomers, DNA forms its central role in chemical evolution through replication and amplification. This elegant behavior is largely based on highly specific molecular recognition between nucleobases through the specific hydrogen bonds in the Watson-Crick base pairing system. While the native base pairs have been amazingly sophisticated through the long history of evolution, synthetic chemists have devoted considerable efforts to create alternative base pairing systems in recent decades. Most of these new systems were designed based on the shape complementarity of the pairs or the rearrangement of hydrogen-bonding patterns. We wondered whether metal coordination could serve as an alternative driving force for DNA base pairing and why hydrogen bonding was selected on Earth in the course of molecular evolution. Therefore, we envisioned an alternative design strategy: we replaced hydrogen bonding with another important scheme in biological systems, metal-coordination bonding. In this Account, we provide an overview of the chemistry of metal-mediated base pairing including basic concepts, molecular design, characteristic structures and properties, and possible applications of DNA-based molecular systems. We describe several examples of artificial metal-mediated base pairs, such as Cu(2+)-mediated hydroxypyridone base pair, H-Cu(2+)-H (where H denotes a hydroxypyridone-bearing nucleoside), developed by us and other researchers. To design the metallo-base pairs we carefully chose appropriate combinations of ligand-bearing nucleosides and metal ions. As expected from their stronger bonding through metal coordination, DNA duplexes possessing metallo-base pairs exhibited higher thermal stability than natural hydrogen-bonded DNAs. Furthermore, we could also use metal-mediated base pairs to construct or induce other high-order structures. These features could lead to metal-responsive functional

Design, spectral characterization and biological studies of transition metal(II) complexes with triazole Schiff bases.

PubMed

Hanif, Muhammad; Chohan, Zahid H

2013-03-01

A new series of three biologically active triazole derived Schiff base ligands L(1)-L(3) have been synthesized in equimolar reaction of 3-amino-1H-1,2,4-triazole with pyrrol-2-carboxaldehyde, 4-bromo-thiophene-2-carboxaldehyde, and 5-iodo-2-hydroxy benzaldehyde. The prepared Schiff bases were used for further complex formation reaction with different metal elements like Co(II), Ni(II), Cu(II) and Zn(II) as chlorides by using a molar ratio of ligand:metal as 2:1. The structure and bonding nature of all the compounds were identified by their physical, spectral and analytical data. All the metal(II) complexes possessed an octahedral geometry except the Cu(II) complexes which showed a distorted octahedral geometry. All the synthesized compounds, were studied for their in vitro antibacterial, and antifungal activities, against four Gram-negative (Escherichia coli, Shigella sonnei, Pseudomonas aeruginosa and Salmonella typhi) and two Gram-positive (Bacillus subtilis and Staphylococcus aureus) bacterial strains and against six fungal strains (Trichophyton longifusus, Candida albicans, Aspergillus flavus, Microsporum canis, Fusarium solani and Candida glabrata) by using agar-well diffusion method. It has been shown that all the synthesized compounds showed moderate to significant antibacterial activity against one or more bacterial strains. In vitro Brine Shrimp bioassay was also carried out to investigate the cytotoxic properties of these compounds. The data also revealed that the metal complexes showed better activity than the ligands due to chelation/coordination. Copyright © 2012 Elsevier B.V. All rights reserved.

Nanoscale surface modifications of medically relevant metals: state-of-the art and perspectives.

PubMed

Variola, Fabio; Brunski, John B; Orsini, Giovanna; Tambasco de Oliveira, Paulo; Wazen, Rima; Nanci, Antonio

2011-02-01

Evidence that nanoscale surface properties stimulate and guide various molecular and biological processes at the implant/tissue interface is fostering a new trend in designing implantable metals. Cutting-edge expertise and techniques drawn from widely separated fields, such as nanotechnology, materials engineering and biology, have been advantageously exploited to nanoengineer surfaces in ways that control and direct these processes in predictable manners. In this review, we present and discuss the state-of-the-art of nanotechnology-based approaches currently adopted to modify the surface of metals used for orthopedic and dental applications, and also briefly consider their use in the cardiovascular field. The effects of nanoengineered surfaces on various in vitro molecular and cellular events are firstly discussed. This review also provides an overview of in vivo and clinical studies with nanostructured metallic implants, and addresses the potential influence of nanotopography on biomechanical events at interfaces. Ultimately, the objective of this work is to give the readership a comprehensive picture of the current advances, future developments and challenges in the application of the infinitesimally small to biomedical surface science. We believe that an integrated understanding of the in vitro and particularly of the in vivo behavior is mandatory for the proper exploitation of nanostructured implantable metals and, indeed, of all biomaterials.

In vitro element release and biological aspects of base–metal alloys for metal-ceramic applications

PubMed Central

Holm, Charlotta; Morisbak, Else; Kalfoss, Torill; Dahl, Jon E.

2015-01-01

Abstract Objective: The aims of this study were to investigate the release of element from, and the biological response in vitro to, cobalt–chromium alloys and other base–metal alloys used for the fabrication of metal-ceramic restorations. Material and methods: Eighteen different alloys were investigated. Nine cobalt–chromium alloys, three nickel–chromium alloys, two cobalt–chromium–iron alloys, one palladium–silver alloy, one high-noble gold alloy, titanium grade II and one type III copper–aluminium alloy. Pure copper served as positive control. The specimens were prepared according to the ISO standards for biological and corrosion testing. Passive leaching of elements was measured by using Inductively Coupled Plasma – Mass Spectrometry (ICP-MS) after incubation in cell culture media, MEM, for 3 days. Corrosion testing was carried out in 0.9% sodium chloride (NaCl) and 1% lactic acid for 7 days, and the element release was measured by Inductively Coupled Plasma – Optical Emission Spectroscopy (ICP-OES). The biological response from the extract solutions was measured though MTT cytotoxicity testing and the Hen's egg test-chorio-allantoic membrane (HET-CAM) technique for irritationt. Results: The corrosion test showed similar element release from base-metal alloys compared to noble alloys such as gold. Apart from the high-copper alloy, all alloys expressed low element release in the immersion test, no cytotoxic effect in the MTT test, and were rated non-irritant in the HET-CAM test. Conclusions: Minimal biological response was observed for all the alloys tested, with the exception of the high-copper alloy. PMID:28642904

Metal-catalyzed Decarboxylative Fluoroalkylation Reactions.

PubMed

Ambler, Brett R; Yang, Ming-Hsiu; Altman, Ryan A

2016-12-01

Metal-catalyzed decarboxylative fluoroalkylation reactions enable the conversion of simple O-based substrates into biologically relevant fluorinated analogs. Herein, we present decarboxylative methods that facilitate the synthesis of trifluoromethyl- and difluoroketone-containing products. We highlight key mechanistic aspects that are critical for efficient catalysis, and that inspired our thinking while developing the reactions.

Nanoscale surface modifications of medically-relevant metals: state-of-the art and perspectives

PubMed Central

Variola, Fabio; Brunski, John; Orsini, Giovanna; de Oliveira, Paulo Tambasco; Wazen, Rima; Nanci, Antonio

2011-01-01

Evidence that nanoscale surface properties stimulate and guide various molecular and biological processes at the implant/tissue interface is fostering a new trend in designing implantable metals. Cutting-edge expertise and techniques drawn from widely separated fields, such as nanotechnology, materials engineering and biology, have been advantageously exploited to nanoengineer surfaces in ways that control and direct these processes in predictable manners. In this review, we present and discuss the state-of-the-art of nanotechnology-based approaches currently used to modify the surface of metals used for orthopedic and dental applications, and also briefly consider their use in the cardiovascular field. The effects of nanoengineered surfaces on various in vitro molecular and cellular events are firstly discussed. Importantly, this review also provides an overview of in vivo and clinical studies with nanostructured metallic implants, and addresses the potential influence of nanotopography on biomechanical events at interfaces. Ultimately the objective of this work is to give the readership a comprehensive picture of the current advances, future developments and challenges in the application of the infinitesimally small to biomedical surface science. We believe that an integrated understanding of the in vitro and particularly of the in vivo behavior is mandatory for the proper exploitation of nanostructured implantable metals and, as a matter of fact, all biomaterials. PMID:20976359

Spectral characterization, cyclic voltammetry, morphology, biological activities and DNA cleaving studies of amino acid Schiff base metal(II) complexes

NASA Astrophysics Data System (ADS)

Neelakantan, M. A.; Rusalraj, F.; Dharmaraja, J.; Johnsonraja, S.; Jeyakumar, T.; Sankaranarayana Pillai, M.

2008-12-01

Metal complexes are synthesized with Schiff bases derived from o-phthalaldehyde (opa) and amino acids viz., glycine (gly) L-alanine (ala), L-phenylalanine (pal). Metal ions coordinate in a tetradentate or hexadentate manner with these N 2O 2 donor ligands, which are characterized by elemental analysis, molar conductance, magnetic moments, IR, electronic, 1H NMR and EPR spectral studies. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). Based on EPR studies, spin-Hamiltonian and bonding parameters have been calculated. The g-values calculated for copper complexes at 300 K and in frozen DMSO (77 K) indicate the presence of the unpaired electron in the d orbital. The evaluated metal-ligand bonding parameters showed strong in-plane σ- and π-bonding. X-ray diffraction (XRD) and scanning electron micrography (SEM) analysis provide the crystalline nature and the morphology of the metal complexes. The cyclic voltammograms of the Cu(II)/Mn(II)/VO(II) complexes investigated in DMSO solution exhibit metal centered electroactivity in the potential range -1.5 to +1.5 V. The electrochemical data obtained for Cu(II) complexes explains the change of structural arrangement of the ligand around Cu(II) ions. The biological activity of the complexes has been tested on eight bacteria and three fungi. Cu(II) and Ni(II) complexes show an increased activity in comparison to the controls. The metal complexes of opapal Schiff base were evaluated for their DNA cleaving activities with calf-thymus DNA (CT DNA) under aerobic conditions. Cu(II) and VO(II) complexes show more pronounced activity in presence of the oxidant.

Synthesis, spectroscopic characterization, DFT optimization and biological activities of Schiff bases and their metal (II) complexes

NASA Astrophysics Data System (ADS)

Rauf, Abdur; Shah, Afzal; Munawar, Khurram Shahzad; Khan, Abdul Aziz; Abbasi, Rashda; Yameen, Muhammad Arfat; Khan, Asad Muhammad; Khan, Abdur Rahman; Qureshi, Irfan Zia; Kraatz, Heinz-Bernhard; Zia-ur-Rehman

2017-10-01

A Novel Schiff base, 3-(((4-chlorophenyl)imino)methyl)benzene-1,2-diol (HL1) was successfully synthesized along with a structurally similar Schiff base 3-(((4-bromophenyl)imino)methyl)benzene-1,2-diol (HL2). Both the Schiff bases were used to synthesize their zinc (II) and cobalt (II) complexes. These compounds were characterized by FTIR, 1H NMR, 13C NMR and elemental analysis. Metal complexes were confirmed by TGA. Crystals of Schiff bases were also characterized by X-ray analysis and experimental parameters were found in line with the theoretical parameters. Quantum mechanical approach was also used to fine useful structural parameters and to ensure the geometry of metal complexes. The photometric behaviors of all the synthesized compounds were investigated in a wide pH range using BR buffers. The appearance of isosbestic points indicated the existence of Schiff bases in more than one isomeric form. Moreover, these compounds were screened for enzyme inhibition; antibacterial, cytotoxic and in vivo antidiabetic activities and compounds were found active against one or other activity. Results indicate that ZnL22 is a good inhibitor of alkaline phosphatase enzyme and possess highest potential against diabetes, blood cholesterol level and cancer cells. This effort just provides preliminary data for some biological properties. Further investigations are required to precisely determine mechanistic pathways of their use towards drug development.

Culturally relevant inquiry-based laboratory module implementations in upper-division genetics and cell biology teaching laboratories.

PubMed

Siritunga, Dimuth; Montero-Rojas, María; Carrero, Katherine; Toro, Gladys; Vélez, Ana; Carrero-Martínez, Franklin A

2011-01-01

Today, more minority students are entering undergraduate programs than ever before, but they earn only 6% of all science or engineering PhDs awarded in the United States. Many studies suggest that hands-on research activities enhance students' interest in pursuing a research career. In this paper, we present a model for the implementation of laboratory research in the undergraduate teaching laboratory using a culturally relevant approach to engage students. Laboratory modules were implemented in upper-division genetics and cell biology courses using cassava as the central theme. Students were asked to bring cassava samples from their respective towns, which allowed them to compare their field-collected samples against known lineages from agricultural stations at the end of the implementation. Assessment of content and learning perceptions revealed that our novel approach allowed students to learn while engaged in characterizing Puerto Rican cassava. In two semesters, based on the percentage of students who answered correctly in the premodule assessment for content knowledge, there was an overall improvement of 66% and 55% at the end in the genetics course and 24% and 15% in the cell biology course. Our proposed pedagogical model enhances students' professional competitiveness by providing students with valuable research skills as they work on a problem to which they can relate.

Culturally Relevant Inquiry-Based Laboratory Module Implementations in Upper-Division Genetics and Cell Biology Teaching Laboratories

PubMed Central

Siritunga, Dimuth; Montero-Rojas, María; Carrero, Katherine; Toro, Gladys; Vélez, Ana; Carrero-Martínez, Franklin A.

2011-01-01

Today, more minority students are entering undergraduate programs than ever before, but they earn only 6% of all science or engineering PhDs awarded in the United States. Many studies suggest that hands-on research activities enhance students’ interest in pursuing a research career. In this paper, we present a model for the implementation of laboratory research in the undergraduate teaching laboratory using a culturally relevant approach to engage students. Laboratory modules were implemented in upper-division genetics and cell biology courses using cassava as the central theme. Students were asked to bring cassava samples from their respective towns, which allowed them to compare their field-collected samples against known lineages from agricultural stations at the end of the implementation. Assessment of content and learning perceptions revealed that our novel approach allowed students to learn while engaged in characterizing Puerto Rican cassava. In two semesters, based on the percentage of students who answered correctly in the premodule assessment for content knowledge, there was an overall improvement of 66% and 55% at the end in the genetics course and 24% and 15% in the cell biology course. Our proposed pedagogical model enhances students’ professional competitiveness by providing students with valuable research skills as they work on a problem to which they can relate. PMID:21885825

Biological approaches to tackle heavy metal pollution: A survey of literature.

PubMed

Jacob, Jaya Mary; Karthik, Chinnannan; Saratale, Rijuta Ganesh; Kumar, Smita S; Prabakar, Desika; Kadirvelu, K; Pugazhendhi, Arivalagan

2018-07-01

Pollution by heavy metals has been identified as a global threat since the inception of industrial revolution. Heavy metal contamination induces serious health and environmental hazards due to its toxic nature. Remediation of heavy metals by conventional methods is uneconomical and generates a large quantity of secondary wastes. On the other hand, biological agents such as plants, microorganisms etc. offer easy and eco-friendly ways for metal removal; hence, considered as efficient and alternative tools for metal removal. Bioremediation involves adsorption, reduction or removal of contaminants from the environment through biological resources (both microorganisms and plants). The heavy metal remediation properties of microorganisms stem from their self defense mechanisms such as enzyme secretion, cellular morphological changes etc. These defence mechanisms comprise the active involvement of microbial enzymes such as oxidoreductases, oxygenases etc, which influence the rates of bioremediation. Further, immobilization techniques are improving the practice at industrial scales. This article summarizes the various strategies inherent in the biological sorption and remediation of heavy metals. Copyright © 2018 Elsevier Ltd. All rights reserved.

Predicting Metal Speciation & Bioavailability via Estimation of Metal-Organic Thermodynamic Properties

NASA Astrophysics Data System (ADS)

Prasad, A.; Howells, A. E.; Shock, E.

2017-12-01

The biological fate of any metal depends on its chemical form in the environment. Arsenic for example, is extremely toxic in the form of inorganic As+3 but completely benign in the organic form of arsenobetaine. Thus, given an exhaustive set of reactions and their equilibrium constants (logK), the bioavailability of any metal can be obtained for blood plasma, hydrothermal fluids or any system of interest. While many data exist for metal-inorganic ligands, logK data covering the temperature range of life for metal-organic complexes are sparse. Hence, we decided to estimate metal-organic logK values from correlations with the commonly available values of ligand pKa. Metal ion specific correlations were made with ligands classified according to their electron donor atoms, denticity and other chemical factors. While this approach has been employed before (Carbonaro et al. 2007, GCA 71, 3958-3968), new correlations were developed that provide estimates even when no metal-organic logK is available. In addition, we have used the same methods to make estimates of metal-organic entropy of association (ΔaS), which can provide logK for any temperature of biological relevance. Our current correlations employ logK and ΔaS data from 30 metal ions (like the biologically relevant Fe+3 & Zn+2) and 74 ligands (like formate and ethylenediamine), which can be expanded to estimate the metal-ligand reaction properties for these 30 metal ions with a possibly limitless number of ligands that may belong to our categories of ligands. With the help of such data, copper speciation was obtained for a defined growth medium for methanotrophs employed by Morton et al. (2000, AEM 66, 1730-1733) that agrees with experimental measurements showing that the free metal ion may not be the bioavailable form in all conditions. These results encourage us to keep filling the gaps in metal-organic logK data and continue finding relationships between biological responses (like metal-accumulation ratios

Understanding the biological responses of nanostructured metals and surfaces

NASA Astrophysics Data System (ADS)

Lowe, Terry C.; Reiss, Rebecca A.

2014-08-01

Metals produced by Severe Plastic Deformation (SPD) offer distinct advantages for medical applications such as orthopedic devices, in part because of their nanostructured surfaces. We examine the current theoretical foundations and state of knowledge for nanostructured biomaterials surface optimization within the contexts that apply to bulk nanostructured metals, differentiating how their microstructures impact osteogenesis, in particular, for Ultrafine Grained (UFG) titanium. Then we identify key gaps in the research to date, pointing out areas which merit additional focus within the scientific community. For example, we highlight the potential of next-generation DNA sequencing techniques (NGS) to reveal gene and non-coding RNA (ncRNA) expression changes induced by nanostructured metals. While our understanding of bio-nano interactions is in its infancy, nanostructured metals are already being marketed or developed for medical devices such as dental implants, spinal devices, and coronary stents. Our ability to characterize and optimize the biological response of cells to SPD metals will have synergistic effects on advances in materials, biological, and medical science.

Divergent biology of facultative heavy metal plants.

PubMed

Bothe, Hermann; Słomka, Aneta

2017-12-01

Among heavy metal plants (the metallophytes), facultative species can live both in soils contaminated by an excess of heavy metals and in non-affected sites. In contrast, obligate metallophytes are restricted to polluted areas. Metallophytes offer a fascinating biology, due to the fact that species have developed different strategies to cope with the adverse conditions of heavy metal soils. The literature distinguishes between hyperaccumulating, accumulating, tolerant and excluding metallophytes, but the borderline between these categories is blurred. Due to the fact that heavy metal soils are dry, nutrient limited and are not uniform but have a patchy distribution in many instances, drought-tolerant or low nutrient demanding species are often regarded as metallophytes in the literature. In only a few cases, the concentrations of heavy metals in soils are so toxic that only a few specifically adapted plants, the genuine metallophytes, can cope with these adverse soil conditions. Current molecular biological studies focus on the genetically amenable and hyperaccumulating Arabidopsis halleri and Noccaea (Thlaspi) caerulescens of the Brassicaceae. Armeria maritima ssp. halleri utilizes glands for the excretion of heavy metals and is, therefore, a heavy metal excluder. The two endemic zinc violets of Western Europe, Viola lutea ssp. calaminaria of the Aachen-Liège area and Viola lutea ssp. westfalica of the Pb-Cu-ditch of Blankenrode, Eastern Westphalia, as well as Viola tricolor ecotypes of Eastern Europe, keep their cells free of excess heavy metals by arbuscular mycorrhizal fungi which bind heavy metals. The Caryophyllaceae, Silene vulgaris f. humilis and Minuartia verna, apparently discard leaves when overloaded with heavy metals. All Central European metallophytes have close relatives that grow in areas outside of heavy metal soils, mainly in the Alps, and have, therefore, been considered as relicts of the glacial epoch in the past. However, the current

Perceived relevance of oral biology by dental students.

PubMed

Scheven, B A A

2012-02-01

This study investigated the perception that dental students have regarding the relevance of oral biology (OB) to dental education and dentistry in general. Moreover, this study analysed students' attitude towards OB learning approaches and resources. A questionnaire based on a Likert scale was used to survey pre-clinical/second (BDS2)- and final/fifth (BDS5)-year dental students at the School of Dentistry of the University of Birmingham (United Kingdom). In comparison, a small group of postgraduate specialist registrars were surveyed to evaluate the attitudes of practising dentists. The results show that all study groups expressed a high level of perceived relevance of OB to dentistry. Students' perception of OB for dental education, clinical training and practice also scored high. More than 40% of undergraduate students and about 55% of the postgraduates indicated a perceived change in their attitude towards OB with time characterised by increased appreciation of the subject. Lectures were considered as the most important teaching approach, whereas 'group poster projects' ranked lowest. Of the different study resources, lecture handouts received the overall highest importance score. The results indicate that dental students considered OB relevant for dental education and dentistry and suggest a positive attitude towards the subject. This study also suggested that dental students prefer teacher-centred/led teaching rather than student-directed learning of OB. The article addresses the role of OB and science-related research projects within the dental curriculum and discusses that close integration of basic sciences with dental education may enrich dental education and overall learning experience. © 2011 John Wiley & Sons A/S.

Sociability modifies dogs' sensitivity to biological motion of different social relevance.

PubMed

Ishikawa, Yuko; Mills, Daniel; Willmott, Alexander; Mullineaux, David; Guo, Kun

2018-03-01

Preferential attention to living creatures is believed to be an intrinsic capacity of the visual system of several species, with perception of biological motion often studied and, in humans, it correlates with social cognitive performance. Although domestic dogs are exceptionally attentive to human social cues, it is unknown whether their sociability is associated with sensitivity to conspecific and heterospecific biological motion cues of different social relevance. We recorded video clips of point-light displays depicting a human or dog walking in either frontal or lateral view. In a preferential looking paradigm, dogs spontaneously viewed 16 paired point-light displays showing combinations of normal/inverted (control condition), human/dog and frontal/lateral views. Overall, dogs looked significantly longer at frontal human point-light display versus the inverted control, probably due to its clearer social/biological relevance. Dogs' sociability, assessed through owner-completed questionnaires, further revealed that low-sociability dogs preferred the lateral point-light display view, whereas high-sociability dogs preferred the frontal view. Clearly, dogs can recognize biological motion, but their preference is influenced by their sociability and the stimulus salience, implying biological motion perception may reflect aspects of dogs' social cognition.

New applications in EPA’s ECOTOX Knowledge System: Assimilating relative potencies of metals across chemical and biological species from literature-based toxicity effects data.

EPA Science Inventory

Toxicity of metals in field settings can vary widely among ionic chemical species and across biological receptors. Thus, a challenge often found in developing TRVs for the risk assessment of metals is identifying the most appropriate metal and biological species combinations for...

Environmentally relevant metal and transition metal ions enhance Fc epsilon RI-mediated mast cell activation.

PubMed Central

Walczak-Drzewiecka, Aurelia; Wyczólkowska, Janina; Dastych, Jaroslaw

2003-01-01

Upon contact with allergen, sensitized mast cells release highly active proinflammatory mediators. Allergen-mediated mast cell activation is an important mechanism in the pathogenesis of atopic asthma. Asthmatic patients are especially susceptible to air pollution. Epidemiologic studies found a positive correlation between severity of symptoms among asthmatic patients and the level of particulate matter (PM) in the air. Among the constituents of PM are metals and transition metals, which could mediate some of its adverse effects on human health. We sought to determine the effect of metal and transition metal ions on allergen-mediated mast cell activation. We observed that several metal and transition metal ions activated mast cells and enhanced allergen-mediated mast cell activation. Thus, Al(3+), Cd(2+), and Sr(2+) induced release of granule-associated N-acetyl-ss-d-hexosaminidase, and Al(3+) and Ni(2+) enhanced antigen-mediated release. Metal and transition metal ions also induced significant secretion of interleukin (IL)-4 and increased antigen-mediated IL-4 secretion in mast cells. These effects of metal and transition metal ions on mast cells were observed at concentrations that do not result in direct cytotoxicity and might be relevant for environmental exposure. Thus, metals and transition metals could increase the level of allergen-mediated mast cell activation, which might be one of the mechanisms mediating exacerbation of allergen-driven asthma symptoms by air pollution. PMID:12727598

Mathematical biology modules based on modern molecular biology and modern discrete mathematics.

PubMed

Robeva, Raina; Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.

Mathematical Biology Modules Based on Modern Molecular Biology and Modern Discrete Mathematics

PubMed Central

Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network. PMID:20810955

Speciation in Metal Toxicity and Metal-Based Therapeutics

PubMed Central

Templeton, Douglas M.

2015-01-01

Metallic elements, ions and compounds produce varying degrees of toxicity in organisms with which they come into contact. Metal speciation is critical to understanding these adverse effects; the adjectives “heavy” and “toxic” are not helpful in describing the biological properties of individual elements, but detailed chemical structures are. As a broad generalization, the metallic form of an element is inert, and the ionic salts are the species that show more significant bioavailability. Yet the salts and other chelates of a metal ion can give rise to quite different toxicities, as exemplified by a range of carcinogenic potential for various nickel species. Another important distinction comes when a metallic element is organified, increasing its lipophilicity and hence its ability to penetrate the blood brain barrier, as is seen, for example, with organic mercury and tin species. Some metallic elements, such as gold and platinum, are themselves useful therapeutic agents in some forms, while other species of the same element can be toxic, thus focusing attention on species interconversions in evaluating metal-based drugs. The therapeutic use of metal-chelating agents introduces new species of the target metal in vivo, and this can affect not only its desired detoxification, but also introduce a potential for further mechanisms of toxicity. Examples of therapeutic iron chelator species are discussed in this context, as well as the more recent aspects of development of chelation therapy for uranium exposure. PMID:29056656

Biological and Environmental Transformations of Copper-Based Nanomaterials

PubMed Central

Wang, Zhongying; Von Dem Bussche, Annette; Kabadi, Pranita K.; Kane, Agnes B.; Hurt, Robert H.

2013-01-01

Copper-based nanoparticles are an important class of materials with applications as catalysts, conductive inks, and antimicrobial agents. Environmental and safety issues are particularly important for copper-based nanomaterials because of their potential large-scale use and their high redox activity and toxicity reported from in vitro studies. Elemental nanocopper oxidizes readily upon atmospheric exposure during storage and use, so copper oxides are highly relevant phases to consider in studies of environmental and health impacts. Here we show that copper oxide nanoparticles undergo profound chemical transformations under conditions relevant to living systems and the natural environment. Copper oxide nanoparticle (CuO-NP) dissolution occurs at lysosomal pH (4-5), but not at neutral pH in pure water. Despite the near-neutral pH of cell culture medium, CuO-NPs undergo significant dissolution in media over time scales relevant to toxicity testing due to ligand-assisted ion release, in which amino acid complexation is an important contributor. Electron paramagnetic resonance (EPR) spectroscopy shows that dissolved copper in association with CuO-NPs are the primary redox-active species. CuO-NPs also undergo sulfidation by a dissolution-reprecipitation mechanism, and the new sulfide surfaces act as catalysts for sulfide oxidation. Copper sulfide NPs are found to be much less cytotoxic than CuO NPs, which is consistent with the very low solubility of CuS. Despite this low solubility of CuS, EPR studies show that sulfidated CuO continues to generate some ROS activity due to the release of free copper by H2O2 oxidation during the Fenton-chemistry-based EPR assay. While sulfidation can serve as a natural detoxification process for nanosilver and other chalcophile metals, our results suggest that sulfidation may not fully and permanently detoxify copper in biological or environmental compartments that contain reactive oxygen species. PMID:24032665

HUMAN BIOMONITORING TO LINK ENVIRONMENTAL EXPOSURE TO BIOLOGICALLY RELEVANT DOSE

EPA Science Inventory

The abstract and presentation on Human Biomonitoring to Link Environmental Exposure to Biologically Relevant Dose describes the use of biomarkers of exposure, biomarkers of current health state, and biomarker measurements. The abstract and presentation focuses on how biomarkers ...

Biology of acute lymphoblastic leukemia (ALL): clinical and therapeutic relevance.

PubMed

Graux, Carlos

2011-04-01

Acute lymphoblastic leukemia is a heterogeneous disease comprising several clinico-biological entities. Karyotyping of leukemic cells identifies recurrent chromosome rearrangements. These are usually translocations that activate genes encoding transcription factor regulating B- or T-cell differentiation. Gene expression-array confirms the prognostic relevance of ALL subgroups identified by specific chromosomal rearrangements and isolates new subgroups. Analysis of genomic copy number changes and high throughput sequencing reveal new cryptic deletions. The challenge is now to understand how these cooperative genetic lesions interact in order to have the molecular rationales needed to select new therapeutic targets and to develop and combine inhibitors with high levels of anti-leukemic specificity. The aim of this paper is to provide some data on the biology of acute lymphoblastic leukemia which are relevant in clinical practice. Copyright © 2011 Elsevier Ltd. All rights reserved.

The Role of Reactive Oxygen Species (ROS) in the Biological Activities of Metallic Nanoparticles

PubMed Central

Abdal Dayem, Ahmed; Hossain, Mohammed Kawser; Lee, Soo Bin; Kim, Kyeongseok; Saha, Subbroto Kumar; Yang, Gwang-Mo; Choi, Hye Yeon; Cho, Ssang-Goo

2017-01-01

Nanoparticles (NPs) possess unique physical and chemical properties that make them appropriate for various applications. The structural alteration of metallic NPs leads to different biological functions, specifically resulting in different potentials for the generation of reactive oxygen species (ROS). The amount of ROS produced by metallic NPs correlates with particle size, shape, surface area, and chemistry. ROS possess multiple functions in cellular biology, with ROS generation a key factor in metallic NP-induced toxicity, as well as modulation of cellular signaling involved in cell death, proliferation, and differentiation. In this review, we briefly explained NP classes and their biomedical applications and describe the sources and roles of ROS in NP-related biological functions in vitro and in vivo. Furthermore, we also described the roles of metal NP-induced ROS generation in stem cell biology. Although the roles of ROS in metallic NP-related biological functions requires further investigation, modulation and characterization of metallic NP-induced ROS production are promising in the application of metallic NPs in the areas of regenerative medicine and medical devices. PMID:28075405

Chemical and biological extraction of metals present in E waste: A hybrid technology

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

Pant, Deepak, E-mail: deepakpant1@rediffmail.com; Joshi, Deepika; Upreti, Manoj K.

2012-05-15

Highlights: Black-Right-Pointing-Pointer Hybrid methodology for E waste management. Black-Right-Pointing-Pointer Efficient extraction of metals. Black-Right-Pointing-Pointer Trace metal extraction is possible. - Abstract: Management of metal pollution associated with E-waste is widespread across the globe. Currently used techniques for the extraction of metals from E-waste by using either chemical or biological leaching have their own limitations. Chemical leaching is much rapid and efficient but has its own environmental consequences, even the future prospects of associated nanoremediation are also uncertain. Biological leaching on the other hand is comparatively a cost effective technique but at the same moment it is time consuming and themore » complete recovery of the metal, alone by biological leaching is not possible in most of the cases. The current review addresses the individual issues related to chemical and biological extraction techniques and proposes a hybrid-methodology which incorporates both, along with safer chemicals and compatible microbes for better and efficient extraction of metals from the E-waste.« less

Urban Biomining: Biological Extraction of Metals and Materials from Electronics Waste Using a Synthetic Biology Approach

NASA Astrophysics Data System (ADS)

Urbina-Navarrete, J.; Rothschild, L.

2016-12-01

End-of-life electronics waste (e-waste) containing toxic and valuable materials is a rapidly progressing human health and environmental issue. Using synthetic biology tools, we have developed a recycling method for e-waste. Our innovation is to use a recombinant version of a naturally-occurring silica-degrading enzyme to depolymerize the silica in metal- and glass- containing e-waste components, and subsequently, to use engineered bacterial surfaces to bind and separate metals from a solution. The bacteria with bound metals can then be used as "bio-ink" to print new circuits using a novel plasma jet electronics printing technology. Here, we present the results from our initial studies that focus on the specificity of metal-binding motifs for a cognate metal. The candidate motifs that show high affinity and specificity will be engineered into bacterial surfaces for downstream applications in biologically-mediated metal recycling. Since the chemistry and role of Cu in metalloproteins is relatively well-characterized, we are using Cu as a proxy to elucidate metal and biological ligand interactions with various metals in e-waste. We assess the binding parameters of 3 representative classes of Cu-binding motifs using isothermal titration calorimetry; 1) natural motifs found in metalloproteins, 2) consensus motifs, and 3) rationally designed peptides that are predicted, in silico, to bind Cu. Our results indicate that naturally-occurring motifs have relative high affinity and specificity for Cu (association constant for Cu Ka 104 M-1, Zn Ka 103 M-1) when competing ions are present in the aqueous milieu. However, motifs developed through rational design by applying quantum mechanical methods that take into account complexation energies of the elemental binding partners and molecular geometry of the cognate metal, not only show high affinity for the cognate metal (Cu Ka 106 M-1), but they show specificity and discrimination against other metal ions that would be

Detection of heavy metal by paper-based microfluidics.

PubMed

Lin, Yang; Gritsenko, Dmitry; Feng, Shaolong; Teh, Yi Chen; Lu, Xiaonan; Xu, Jie

2016-09-15

Heavy metal pollution has shown great threat to the environment and public health worldwide. Current methods for the detection of heavy metals require expensive instrumentation and laborious operation, which can only be accomplished in centralized laboratories. Various microfluidic paper-based analytical devices have been developed recently as simple, cheap and disposable alternatives to conventional ones for on-site detection of heavy metals. In this review, we first summarize current development of paper-based analytical devices and discuss the selection of paper substrates, methods of device fabrication, and relevant theories in these devices. We then compare and categorize recent reports on detection of heavy metals using paper-based microfluidic devices on the basis of various detection mechanisms, such as colorimetric, fluorescent, and electrochemical methods. To finalize, the future development and trend in this field are discussed. Copyright © 2016 Elsevier B.V. All rights reserved.

Biological Relevance of Free Radicals and Nitroxides.

PubMed

Prescott, Christopher; Bottle, Steven E

2017-06-01

Nitroxides are stable, kinetically-persistent free radicals which have been successfully used in the study and intervention of oxidative stress, a critical issue pertaining to cellular health which results from an imbalance in the levels of damaging free radicals and redox-active species in the cellular environment. This review gives an overview of some of the biological processes that produce radicals and other reactive oxygen species with relevance to oxidative stress, and then discusses interactions of nitroxides with these species in terms of the use of nitroxides as redox-sensitive probes and redox-active therapeutic agents.

Design, Development, and Psychometric Analysis of a General, Organic, and Biological Chemistry Topic Inventory Based on the Identified Main Chemistry Topics Relevant to Nursing Clinical Practice

ERIC Educational Resources Information Center

Brown, Corina E.

2013-01-01

This two-stage study focused on the undergraduate nursing course that covers topics in general, organic, and biological (GOB) chemistry. In the first stage, the central objective was to identify the main concepts of GOB chemistry relevant to the clinical practice of nursing. The collection of data was based on open-ended interviews of both nursing…

DNA Hypomethylation Affects Cancer-Related Biological Functions and Genes Relevant in Neuroblastoma Pathogenesis

PubMed Central

Mayol, Gemma; Martín-Subero, José I.; Ríos, José; Queiros, Ana; Kulis, Marta; Suñol, Mariona; Esteller, Manel; Gómez, Soledad; Garcia, Idoia; de Torres, Carmen; Rodríguez, Eva; Galván, Patricia; Mora, Jaume; Lavarino, Cinzia

2012-01-01

Neuroblastoma (NB) pathogenesis has been reported to be closely associated with numerous genetic alterations. However, underlying DNA methylation patterns have not been extensively studied in this developmental malignancy. Here, we generated microarray-based DNA methylation profiles of primary neuroblastic tumors. Stringent supervised differential methylation analyses allowed us to identify epigenetic changes characteristic for NB tumors as well as for clinical and biological subtypes of NB. We observed that gene-specific loss of DNA methylation is more prevalent than promoter hypermethylation. Remarkably, such hypomethylation affected cancer-related biological functions and genes relevant to NB pathogenesis such as CCND1, SPRR3, BTC, EGF and FGF6. In particular, differential methylation in CCND1 affected mostly an evolutionary conserved functionally relevant 3′ untranslated region, suggesting that hypomethylation outside promoter regions may play a role in NB pathogenesis. Hypermethylation targeted genes involved in cell development and proliferation such as RASSF1A, POU2F2 or HOXD3, among others. The results derived from this study provide new candidate epigenetic biomarkers associated with NB as well as insights into the molecular pathogenesis of this tumor, which involves a marked gene-specific hypomethylation. PMID:23144874

Comparison of the perceived relevance of oral biology reported by students and interns of a Pakistani dental college.

PubMed

Farooq, I; Ali, S

2014-11-01

The purpose of this study was to analyse and compare the perceived relevance of oral biology with dentistry as reported by dental students and interns and to investigate the most popular teaching approach and learning resource. A questionnaire aiming to ask about the relevance of oral biology to dentistry, most popular teaching method and learning resource was utilised in this study. Study groups encompassed second-year dental students who had completed their course and dental interns. The data were obtained and analysed statistically. The overall response rate for both groups was 60%. Both groups reported high relevance of oral biology to dentistry. Perception of dental interns regarding the relevance of oral biology to dentistry was higher than that of students. Both groups identified student presentations as the most important teaching method. Amongst the most important learning resources, textbooks were considered most imperative by interns, whereas lecture handouts received the highest importance score by students. Dental students and interns considered oral biology to be relevant to dentistry, although greater relevance was reported by interns. Year-wise advancement in dental education and training improves the perception of the students about the relevance of oral biology to dentistry. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Structural and Biological Behaviour of Co(II), Cu(II) and Ni(II) Metal Complexes of Some Amino Acid Derived Schiff-Bases

PubMed Central

Chohan, Zahid H.; Praveen, M.; Ghaffar, A.

1997-01-01

Biologically active tridentate amino acid (Alanine, Glycine & Tyrosine) derived Schiff-bases and their Co(II), Cu(II) & Ni(II) complexes have been synthesised and characterised on the basis of their conductance and magnetic measurements, elemental analysis and 13C-NMR, 1H-NMR, IR and electronic spectral data. These Schiff-bases and their complexes have been evaluated for their antibacterial activity against bacterial species such as Staphylococcus aureus, Escherichia coli, Klebsiella pneumonae, Proteus vulgarus and Pseudomonas aeruginosa and this activity data show the metal complexes to be more antibacterial than the Schiff-bases against one or more bacterial species. PMID:18475798

Chemical and biological extraction of metals present in E waste: A hybrid technology.

PubMed

Pant, Deepak; Joshi, Deepika; Upreti, Manoj K; Kotnala, Ravindra K

2012-05-01

Management of metal pollution associated with E-waste is widespread across the globe. Currently used techniques for the extraction of metals from E-waste by using either chemical or biological leaching have their own limitations. Chemical leaching is much rapid and efficient but has its own environmental consequences, even the future prospects of associated nanoremediation are also uncertain. Biological leaching on the other hand is comparatively a cost effective technique but at the same moment it is time consuming and the complete recovery of the metal, alone by biological leaching is not possible in most of the cases. The current review addresses the individual issues related to chemical and biological extraction techniques and proposes a hybrid-methodology which incorporates both, along with safer chemicals and compatible microbes for better and efficient extraction of metals from the E-waste. Copyright © 2011 Elsevier Ltd. All rights reserved.

From pull-down data to protein interaction networks and complexes with biological relevance.

PubMed

Zhang, Bing; Park, Byung-Hoon; Karpinets, Tatiana; Samatova, Nagiza F

2008-04-01

Recent improvements in high-throughput Mass Spectrometry (MS) technology have expedited genome-wide discovery of protein-protein interactions by providing a capability of detecting protein complexes in a physiological setting. Computational inference of protein interaction networks and protein complexes from MS data are challenging. Advances are required in developing robust and seamlessly integrated procedures for assessment of protein-protein interaction affinities, mathematical representation of protein interaction networks, discovery of protein complexes and evaluation of their biological relevance. A multi-step but easy-to-follow framework for identifying protein complexes from MS pull-down data is introduced. It assesses interaction affinity between two proteins based on similarity of their co-purification patterns derived from MS data. It constructs a protein interaction network by adopting a knowledge-guided threshold selection method. Based on the network, it identifies protein complexes and infers their core components using a graph-theoretical approach. It deploys a statistical evaluation procedure to assess biological relevance of each found complex. On Saccharomyces cerevisiae pull-down data, the framework outperformed other more complicated schemes by at least 10% in F(1)-measure and identified 610 protein complexes with high-functional homogeneity based on the enrichment in Gene Ontology (GO) annotation. Manual examination of the complexes brought forward the hypotheses on cause of false identifications. Namely, co-purification of different protein complexes as mediated by a common non-protein molecule, such as DNA, might be a source of false positives. Protein identification bias in pull-down technology, such as the hydrophilic bias could result in false negatives.

Recognition- and reactivity-based fluorescent probes for studying transition metal signaling in living systems.

PubMed

Aron, Allegra T; Ramos-Torres, Karla M; Cotruvo, Joseph A; Chang, Christopher J

2015-08-18

Metals are essential for life, playing critical roles in all aspects of the central dogma of biology (e.g., the transcription and translation of nucleic acids and synthesis of proteins). Redox-inactive alkali, alkaline earth, and transition metals such as sodium, potassium, calcium, and zinc are widely recognized as dynamic signals, whereas redox-active transition metals such as copper and iron are traditionally thought of as sequestered by protein ligands, including as static enzyme cofactors, in part because of their potential to trigger oxidative stress and damage via Fenton chemistry. Metals in biology can be broadly categorized into two pools: static and labile. In the former, proteins and other macromolecules tightly bind metals; in the latter, metals are bound relatively weakly to cellular ligands, including proteins and low molecular weight ligands. Fluorescent probes can be useful tools for studying the roles of transition metals in their labile forms. Probes for imaging transition metal dynamics in living systems must meet several stringent criteria. In addition to exhibiting desirable photophysical properties and biocompatibility, they must be selective and show a fluorescence turn-on response to the metal of interest. To meet this challenge, we have pursued two general strategies for metal detection, termed "recognition" and "reactivity". Our design of transition metal probes makes use of a recognition-based approach for copper and nickel and a reactivity-based approach for cobalt and iron. This Account summarizes progress in our laboratory on both the development and application of fluorescent probes to identify and study the signaling roles of transition metals in biology. In conjunction with complementary methods for direct metal detection and genetic and/or pharmacological manipulations, fluorescent probes for transition metals have helped reveal a number of principles underlying transition metal dynamics. In this Account, we give three recent

Autonomous motion of metallic microrods propelled by ultrasound.

PubMed

Wang, Wei; Castro, Luz Angelica; Hoyos, Mauricio; Mallouk, Thomas E

2012-07-24

Autonomously moving micro-objects, or micromotors, have attracted the attention of the scientific community over the past decade, but the incompatibility of phoretic motors with solutions of high ionic strength and the use of toxic fuels have limited their applications in biologically relevant media. In this letter we demonstrate that ultrasonic standing waves in the MHz frequency range can levitate, propel, rotate, align, and assemble metallic microrods (2 μm long and 330 nm diameter) in water as well as in solutions of high ionic strength. Metallic rods levitated to the midpoint plane of a cylindrical cell when the ultrasonic frequency was tuned to create a vertical standing wave. Fast axial motion of metallic microrods at ~200 μm/s was observed at the resonant frequency using continuous or pulsed ultrasound. Segmented metal rods (AuRu or AuPt) were propelled unidirectionally with one end (Ru or Pt, respectively) consistently forward. A self-acoustophoresis mechanism based on the shape asymmetry of the metallic rods is proposed to explain this axial propulsion. Metallic rods also aligned and self-assembled into long spinning chains, which in the case of bimetallic rods had a head-to-tail alternating structure. These chains formed ring or streak patterns in the levitation plane. The diameter or distance between streaks was roughly half the wavelength of the ultrasonic excitation. The ultrasonically driven movement of metallic rods was insensitive to the addition of salt to the solution, opening the possibility of driving and controlling metallic micromotors in biologically relevant media using ultrasound.

MetalPDB in 2018: a database of metal sites in biological macromolecular structures.

PubMed

Putignano, Valeria; Rosato, Antonio; Banci, Lucia; Andreini, Claudia

2018-01-04

MetalPDB (http://metalweb.cerm.unifi.it/) is a database providing information on metal-binding sites detected in the three-dimensional (3D) structures of biological macromolecules. MetalPDB represents such sites as 3D templates, called Minimal Functional Sites (MFSs), which describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. The 2018 update of MetalPDB includes new contents and tools. A major extension is the inclusion of proteins whose structures do not contain metal ions although their sequences potentially contain a known MFS. In addition, MetalPDB now provides extensive statistical analyses addressing several aspects of general metal usage within the PDB, across protein families and in catalysis. Users can also query MetalPDB to extract statistical information on structural aspects associated with individual metals, such as preferred coordination geometries or aminoacidic environment. A further major improvement is the functional annotation of MFSs; the annotation is manually performed via a password-protected annotator interface. At present, ∼50% of all MFSs have such a functional annotation. Other noteworthy improvements are bulk query functionality, through the upload of a list of PDB identifiers, and ftp access to MetalPDB contents, allowing users to carry out in-depth analyses on their own computational infrastructure. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

A nanoscale Zr-based fluorescent metal-organic framework for selective and sensitive detection of hydrogen sulfide

NASA Astrophysics Data System (ADS)

Li, Yanping; Zhang, Xin; Zhang, Ling; Jiang, Ke; Cui, Yuanjing; Yang, Yu; Qian, Guodong

2017-11-01

Hydrogen sulfide (H2S) has been commonly viewed as a gas signaling molecule in various physiological and pathological processes. However, the highly efficient H2S detection still remains challenging. Herein, we designed a new robust nano metal-organic framework (MOF) UiO-66-CH=CH2 as a fluorescent probe for rapid, sensitive and selective detection of biological H2S. UiO-66-CH=CH2 was prepared by heating ZrCl4 and 2-vinylterephthalic acid via a simple method. UiO-66-CH=CH2 displayed fluorescence quenching to H2S and kept excellent selectivity in the presence of biological relevant analytes especially the cysteine and glutathione. This MOF-based probe also exhibited fast response (10 s) and high sensitivity with a detection limit of 6.46 μM which was within the concentration range of biological H2S in living system. Moreover, this constructed MOF featured water-stability, nanoscale (20-30 nm) and low toxicity, which made it a promising candidate for biological H2S sensing.

Single cell biology beyond the era of antibodies: relevance, challenges, and promises in biomedical research.

PubMed

Abraham, Parvin; Maliekal, Tessy Thomas

2017-04-01

Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems. Even though microfluidics and microraft array are newer techniques exploited for single cell biology, fluorescence-activated cell sorting (FACS) remains the gold standard technique for isolation of cells for many biomedical applications, like stem cell therapy. Here, we present a comprehensive and comparative account of some of the probes that are useful in FACS. Further, we illustrate how these techniques could be applied in biomedical research. It is postulated that intracellular molecular markers like nucleostemin (GNL3), alkaline phosphatase (ALPL) and HIRA can be used for improving the outcome of cardiac as well as bone regeneration. Another field that could utilize intracellular markers is diagnostics, and we propose the use of specific peptide nucleic acid probes (PNPs) against certain miRNAs for cancer surgical margin prediction. The newer techniques for single cell biology, based on intracellular molecules, will immensely enhance the repertoire of possible markers for the isolation of cell types useful in biomedical research.

Antibacterial and antifungal metal based triazole Schiff bases.

PubMed

Chohan, Zahid H; Hanif, Muhammad

2013-10-01

A new series of four biologically active triazole derived Schiff base ligands (L(1)-L(4)) and their cobalt(II), nickel(II), copper(II) and zinc(II) complexes (1-16) have been synthesized and characterized. The ligands were prepared by the condensation reaction of 3-amino-5-methylthio-1H-1,2,4-triazole with chloro-, bromo- and nitro-substituted 2-hydroxybenzaldehyde in an equimolar ratio. The antibacterial and antifungal bioactivity data showed the metal(II) complexes to be more potent antibacterial and antifungal than the parent Schiff bases against one or more bacterial and fungal species.

Recognition- and Reactivity-Based Fluorescent Probes for Studying Transition Metal Signaling in Living Systems

PubMed Central

2015-01-01

Conspectus Metals are essential for life, playing critical roles in all aspects of the central dogma of biology (e.g., the transcription and translation of nucleic acids and synthesis of proteins). Redox-inactive alkali, alkaline earth, and transition metals such as sodium, potassium, calcium, and zinc are widely recognized as dynamic signals, whereas redox-active transition metals such as copper and iron are traditionally thought of as sequestered by protein ligands, including as static enzyme cofactors, in part because of their potential to trigger oxidative stress and damage via Fenton chemistry. Metals in biology can be broadly categorized into two pools: static and labile. In the former, proteins and other macromolecules tightly bind metals; in the latter, metals are bound relatively weakly to cellular ligands, including proteins and low molecular weight ligands. Fluorescent probes can be useful tools for studying the roles of transition metals in their labile forms. Probes for imaging transition metal dynamics in living systems must meet several stringent criteria. In addition to exhibiting desirable photophysical properties and biocompatibility, they must be selective and show a fluorescence turn-on response to the metal of interest. To meet this challenge, we have pursued two general strategies for metal detection, termed “recognition” and “reactivity”. Our design of transition metal probes makes use of a recognition-based approach for copper and nickel and a reactivity-based approach for cobalt and iron. This Account summarizes progress in our laboratory on both the development and application of fluorescent probes to identify and study the signaling roles of transition metals in biology. In conjunction with complementary methods for direct metal detection and genetic and/or pharmacological manipulations, fluorescent probes for transition metals have helped reveal a number of principles underlying transition metal dynamics. In this Account, we give

Interactions of platinum metals and their complexes in biological systems.

PubMed Central

LeRoy, A F

1975-01-01

Platinum-metal oxidation catalysts are to be introduced in exhaust systems of many 1975 model-year automobiles in the U.S. to meet Clean Air Act standards. Small quantities of finely divided catalyst have been found issuing from prototype systems; platinum and palladium compounds may be found also. Although platinum exhibits a remarkable resistance to oxidation and chemical attack, it reacts chemically under some conditions producing coordination complex compounds. Palladium reacts more readily than platinum. Some platinum-metal complexes interact with biological systems as bacteriostatic, bacteriocidal, viricidal, and immunosuppressive agents. Workers chronically exposed to platinum complexes often develop asthma-like respiratory distress and skin reactions called platinosis. Platinum complexes used alone and in combination therapy with other drugs have recently emerged as effective agents in cancer chemotherapy. Understanding toxic and favorable interactions of metal species with living organisms requires basic information on quantities and chemical characteristics of complexes at trace concentrations in biological materials. Some basic chemical kinetic and thermodynamic data are presented to characterize the chemical behavior of the complex cis-[Pt(NH3)2Cl2] used therapeutically. A brief discussion of platinum at manogram levels in biological tissue is discussed. PMID:50943

Preparation, characterization and biological activity of novel metal-NNNN donor Schiff base complexes

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Omar, M. M.; Ibrahim, Amr A.

2010-02-01

Novel Schiff base (H 2L) ligand is prepared via condensation of benzil and triethylenetetraamine. The ligand is characterized based on elemental analysis, mass, IR and 1H NMR spectra. Metal complexes are reported and characterized based on elemental analyses, IR, 1H NMR, solid reflectance, magnetic moment, molar conductance, and thermal analyses (TG, DTG and DTA). 1:1 [M]:[H 2L] complexes are found from the elemental analyses data having the formulae [M(H 2L)Cl 2]· yH 2O (M = Mn(II), Co(II), Ni(II), Cu(II), Zn(II), Cd(II)), [Fe(H 2L)Cl 2]Cl·H 2O, [Th(H 2L)Cl 2]Cl 2·3H 2O and [UO 2(H 2L)](CH 3COO) 2·2H 2O. The metal chelates are found to be non-electrolytes except Fe(III), Th(IV) and UO 2(II) complexes are electrolytes. IR spectra show that H 2L is coordinated to the metal ions in a neutral tetradentate manner with 4Ns donor sites of the two azomethine N and two NH groups. The geometrical structures of these complexes are found to be octahedral. The thermal behaviour of these chelates is studied where the hydrated complexes lose water molecules of hydration in the first step followed immediately by decomposition of the anions and ligand molecules in the subsequent steps. The activation thermodynamic parameters are calculated using Coats-Redfern method. The ligand (H 2L), in comparison to its metal complexes, is screened for its antibacterial activity. The activity data show that the metal complexes have antibacterial activity more than the parent Schiff base ligand and cefepime standard against one or more bacterial species.

Acoustic fine structure may encode biologically relevant information for zebra finches.

PubMed

Prior, Nora H; Smith, Edward; Lawson, Shelby; Ball, Gregory F; Dooling, Robert J

2018-04-18

The ability to discriminate changes in the fine structure of complex sounds is well developed in birds. However, the precise limit of this discrimination ability and how it is used in the context of natural communication remains unclear. Here we describe natural variability in acoustic fine structure of male and female zebra finch calls. Results from psychoacoustic experiments demonstrate that zebra finches are able to discriminate extremely small differences in fine structure, which are on the order of the variation in acoustic fine structure that is present in their vocal signals. Results from signal analysis methods also suggest that acoustic fine structure may carry information that distinguishes between biologically relevant categories including sex, call type and individual identity. Combined, our results are consistent with the hypothesis that zebra finches can encode biologically relevant information within the fine structure of their calls. This study provides a foundation for our understanding of how acoustic fine structure may be involved in animal communication.

Clinical relevance and biology of circulating tumor cells

PubMed Central

2011-01-01

Most breast cancer patients die due to metastases, and the early onset of this multistep process is usually missed by current tumor staging modalities. Therefore, ultrasensitive techniques have been developed to enable the enrichment, detection, isolation and characterization of disseminated tumor cells in bone marrow and circulating tumor cells in the peripheral blood of cancer patients. There is increasing evidence that the presence of these cells is associated with an unfavorable prognosis related to metastatic progression in the bone and other organs. This review focuses on investigations regarding the biology and clinical relevance of circulating tumor cells in breast cancer. PMID:22114869

Ligand Exchange Kinetics of Environmentally Relevant Metals

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

Panasci, Adele Frances

2014-07-15

The interactions of ground water with minerals and contaminants are of broad interest for geochemists but are not well understood. Experiments on the molecular scale can determine reaction parameters (i.e. rates of ligand exchange, activation entropy, activation entropy, and activation volume) that can be used in computations to gain insight into reactions that occur in natural groundwaters. Experiments to determine the rate of isotopic ligand exchange for three environmentally relevant metals, rhodium (Rh), iron (Fe), and neptunium (Np), are described. Many environmental transformations of metals (e.g. reduction) in soil occur at trivalent centers, Fe(III) in particular. Contaminant ions absorb tomore » mineral surfaces via ligand exchange, and the reversal of this reaction can be dangerous, releasing contaminants into the environment. Ferric iron is difficult to study spectroscopically because most of its complexes are paramagnetic and are generally reactive toward ligand exchange; therefore, Rh(III), which is diamagnetic and less reactive, was used to study substitution reactions that are analogous to those that occur on mineral oxide surfaces. Studies on both Np(V) and Np(VI) are important in their own right, as 237Np is a radioactive transuranic element with a half-life of 2 million years.« less

Clinical usefulness of blood metal measurements to assess the failure of metal-on-metal hip implants

PubMed Central

Sampson, Barry; Hart, Alister

2012-01-01

In April 2010, a Medicines and Healthcare Products Regulatory Agency safety alert concerning all metal-on-metal (MOM) hip replacements recommended measuring chromium and cobalt concentrations when managing patients with painful prostheses. The need for this review is illustrated by the recent surge in requests for these blood tests from orthopaedic surgeons following this alert. The aim is to provide guidance to laboratories in assessing these requests and advising clinicians on interpretation. First, we summarize the basic terminology regarding the types of hip replacements, with emphasis on the MOM type. Second, we describe the clinical concerns over implant-derived wear debris in the local tissues and distant sites. Analytical aspects of the measurement of the relevant metal ions and what factors affect the levels measured are discussed. The application of inductively coupled plasma mass spectrometry techniques to the measurement of these metals is considered in detail. The biological effects of metal wear products are summarized with local toxicity and systemic biological effects considered, including carcinogenicity, genotoxicity and systemic toxicity. Clinical cases are used to illustrate pertinent points. PMID:22155921

[Relevance of long non-coding RNAs in tumour biology].

PubMed

Nagy, Zoltán; Szabó, Diána Rita; Zsippai, Adrienn; Falus, András; Rácz, Károly; Igaz, Péter

2012-09-23

The discovery of the biological relevance of non-coding RNA molecules represents one of the most significant advances in contemporary molecular biology. It has turned out that a major fraction of the non-coding part of the genome is transcribed. Beside small RNAs (including microRNAs) more and more data are disclosed concerning long non-coding RNAs of 200 nucleotides to 100 kb length that are implicated in the regulation of several basic molecular processes (cell proliferation, chromatin functioning, microRNA-mediated effects, etc.). Some of these long non-coding RNAs have been associated with human tumours, including H19, HOTAIR, MALAT1, etc., the different expression of which has been noted in various neoplasms relative to healthy tissues. Long non-coding RNAs may represent novel markers of molecular diagnostics and they might even turn out to be targets of therapeutic intervention.

Making developmental biology relevant to undergraduates in an era of economic rationalism in Australia.

PubMed

Key, Brian; Nurcombe, Victor

2003-01-01

This report describes the road map we followed at our university to accommodate three main factors: financial pressure within the university system; desire to enhance the learning experience of undergraduates; and motivation to increase the prominence of the discipline of developmental biology in our university. We engineered a novel, multi-year undergraduate developmental biology program which was "student-oriented," ensuring that students were continually exposed to the underlying principles and philosophy of this discipline throughout their undergraduate career. Among its key features are introductory lectures in core courses in the first year, which emphasize the relevance of developmental biology to tissue engineering, reproductive medicine, therapeutic approaches in medicine, agriculture and aquaculture. State-of-the-art animated computer graphics and images of high visual impact are also used. In addition, students are streamed into the developmental biology track in the second year, using courses like human embryology and courses shared with cell biology, which include practicals based on modern experimental approaches. Finally, fully dedicated third-year courses in developmental biology are undertaken in conjunction with stand-alone practical courses where students experiencefirst-hand work in a research laboratory. Our philosophy is a "cradle-to-grave" approach to the education of undergraduates so as to prepare highly motivated, enthusiastic and well-educated developmental biologists for entry into graduate programs and ultimately post-doctoral research.

Mammalian lipoxygenases and their biological relevance

PubMed Central

Kuhn, Hartmut; Banthiya, Swathi; van Leyen, Klaus

2015-01-01

Lipoxygenases (LOXs) form a heterogeneous class of lipid peroxidizing enzymes, which have been implicated in cell proliferation and differentiation but also in the pathogenesis of various diseases with major public health relevance. As other fatty acid dioxygenases LOX oxidize polyunsaturated fatty acids to their corresponding hydroperoxy derivatives, which are further transformed to bioactive lipid mediators (eicosanoids and related substances). On the other hand, lipoxygenases are key players in regulation of the cellular redox homeostasis, which is an important element in gene expression regulation. Although the first mammalian lipoxygenases were discovered 40 years ago and although the enzymes have been well characterized with respect to their structural and functional properties the biological roles of the different lipoxygenase isoforms are not completely understood. This review is aimed at summarizing the current knowledge on the physiological roles of different mammalian LOX-isoforms and their patho-physiological function in inflammatory, metabolic, hyperproliferative, neurodegenerative and infectious disorders. PMID:25316652

Biostable L-DNAzyme for Sensing of Metal Ions in Biological Systems

PubMed Central

2015-01-01

DNAzymes, an important type of metal ion-dependent functional nucleic acid, are widely applied in bioanalysis and biomedicine. However, the use of DNAzymes in practical applications has been impeded by the intrinsic drawbacks of natural nucleic acids, such as interferences from nuclease digestion and protein binding, as well as undesired intermolecular interactions with other nucleic acids. On the basis of reciprocal chiral substrate specificity, the enantiomer of D-DNAzyme, L-DNAzyme, could initiate catalytic cleavage activity with the same achiral metal ion as a cofactor. Meanwhile, by using the advantage of nonbiological L-DNAzyme, which is not subject to the interferences of biological matrixes, as recognition units, a facile and stable L-DNAzyme sensor was proposed for sensing metal ions in complex biological samples and live cells. PMID:26691677

Electrically induced reorganization phenomena of liquid metal film printed on biological skin

NASA Astrophysics Data System (ADS)

Guo, Cangran; Yi, Liting; Yu, Yang; Liu, Jing

2016-12-01

Liquid metal has been demonstrated to be directly printable on biological skin as physiological measurement elements. However, many fundamental issues remained unclear so far. Here, we disclosed an intriguing phenomenon of electrically induced reorganization of liquid metal film. According to the experiments, when applying an external electric field to liquid metal films which were spray printed on biological skin, it would induce unexpected transformations of the liquid metals among different morphologies and configurations. These include shape shift from a large liquid metal film into a tiny sphere and contraction of liquid metal pool into spherical one. For comprehensively understanding the issues, the impacts of the size, voltage, orientations of the liquid metal electrodes, etc., were clarified. Further, effects of various substrates such as in vitro skin and in vivo skin affecting the liquid metal transformations were experimentally investigated. Compared to the intact tissues, the contraction magnitude of the liquid metal electrode appears weaker on in vivo skin of nude mice under the same electric field. The mechanisms lying behind such phenomena were interpreted through theoretical modeling. Lastly, typical applications of applying the current effect into practical elements such as electrical gating devices were also illustrated as an example. The present findings have both fundamental and practical values, which would help design future technical strategies in fabricating electronically controlled liquid metal electronics on skin.

Current Understanding of the Binding Sites, Capacity, Affinity, and Biological Significance of Metals in Melanin

PubMed Central

Hong, Lian; Simon, John D.

2008-01-01

Metal chelation is often invoked as one of the main biological functions of melanin. In order to understand the interaction between metals and melanin, extensive studies have been carried out to determine the nature of the metal binding sites, binding capacity and affinity. These data are central to efforts aimed at elucidating the role metal binding plays in determining the physical, structural, biological, and photochemical properties of melanin. This article examines the current state of understanding of this field. PMID:17580858

Enhanced Bone Formation in Segmental Defects with BMP2 in a Biologically Relevant Molecular Context

DTIC Science & Technology

2016-10-16

gun shots . These do not heal on their own once a ‘critical size’ segment of bone is missing. One strategy to induce healing is to use bone-inducing...accelerate BMP2-induced bone formation by presenting the growth factor in a more biologically relevant context. This is based on our observation...that manganese increases the binding of BMP2 to COMP. The next steps are to validate these observations using BMP2:COMP on HA/PLG scaffolds in-vitro

Using novel descriptor accounting for ligand-receptor interactions to define and visually explore biologically relevant chemical space.

PubMed

Rabal, Obdulia; Oyarzabal, Julen

2012-05-25

The definition and pragmatic implementation of biologically relevant chemical space is critical in addressing navigation strategies in the overlapping regions where chemistry and therapeutically relevant targets reside and, therefore, also key to performing an efficient drug discovery project. Here, we describe the development and implementation of a simple and robust method for representing biologically relevant chemical space as a general reference according to current knowledge, independently of any reference space, and analyzing chemical structures accordingly. Underlying our method is the generation of a novel descriptor (LiRIf) that converts structural information into a one-dimensional string accounting for the plausible ligand-receptor interactions as well as for topological information. Capitalizing on ligand-receptor interactions as a descriptor enables the clustering, profiling, and comparison of libraries of compounds from a chemical biology and medicinal chemistry perspective. In addition, as a case study, R-groups analysis is performed to identify the most populated ligand-receptor interactions according to different target families (GPCR, kinases, etc.), as well as to evaluate the coverage of biologically relevant chemical space by structures annotated in different databases (ChEMBL, Glida, etc.).

Beyond arousal and valence: The importance of the biological versus social relevance of emotional stimuli

PubMed Central

Sakaki, Michiko; Niki, Kazuhisa; Mather, Mara

2012-01-01

The present study addressed the hypothesis that emotional stimuli relevant to survival or reproduction (biologically emotional stimuli) automatically affect cognitive processing (e.g., attention; memory), while those relevant to social life (socially emotional stimuli) require elaborative processing to modulate attention and memory. Results of our behavioral studies showed that: a) biologically emotional images hold attention more strongly than socially emotional images, b) memory for biologically emotional images was enhanced even with limited cognitive resources, but c) memory for socially emotional images was enhanced only when people had sufficient cognitive resources at encoding. Neither images’ subjective arousal nor their valence modulated these patterns. A subsequent functional magnetic resonance imaging study revealed that biologically emotional images induced stronger activity in visual cortex and greater functional connectivity between amygdala and visual cortex than did socially emotional images. These results suggest that the interconnection between the amygdala and visual cortex supports enhanced attention allocation to biological stimuli. In contrast, socially emotional images evoked greater activity in medial prefrontal cortex (MPFC) and yielded stronger functional connectivity between amygdala and MPFC than biological images. Thus, it appears that emotional processing of social stimuli involves elaborative processing requiring frontal lobe activity. PMID:21964552

Recent developments on ultrasound-assisted one-pot multicomponent synthesis of biologically relevant heterocycles.

PubMed

Banerjee, Bubun

2017-03-01

Heterocycles are the backbone of organic compounds. Specially, N- &O-containing heterocycles represent privileged structural subunits well distributed in naturally occurring compounds with immense biological activities. Multicomponent reactions (MCRs) are becoming valuable tool for synthesizing structurally diverse molecular entities. On the other hand, the last decade has seen a tremendous outburst in modifying chemical processes to make them sustainable for the betterment of our environment. The application of ultrasound in organic synthesis is fulfilling some of the goals of 'green and sustainable chemistry' as it has some advantages over the traditional thermal methods in terms of reaction rates, yields, purity of the products, product selectivity, etc. Therefore the synthesis of biologically relevant heterocycles using one-pot multi-component technique coupled with the application of ultrasound is one of the thrusting areas in the 21st Century among the organic chemists. The present review deals with the "up to date" developments on ultrasound assisted one-pot multi-component synthesis of biologically relevant heterocycles reported so far. Copyright © 2016 Elsevier B.V. All rights reserved.

Metal-like transport in proteins: A new paradigm for biological electron transfer

NASA Astrophysics Data System (ADS)

Malvankar, Nikhil; Vargas, Madeline; Tuominen, Mark; Lovley, Derek

2012-02-01

Electron flow in biologically proteins generally occurs via tunneling or hopping and the possibility of electron delocalization has long been discounted. Here we report metal-like transport in protein nanofilaments, pili, of bacteria Geobacter sulfurreducens that challenges this long-standing belief [1]. Pili exhibit conductivities comparable to synthetic organic metallic nanostructures. The temperature, magnetic field and gate-voltage dependence of pili conductivity is akin to that of quasi-1D disordered metals, suggesting a metal-insulator transition. Magnetoresistance (MR) data provide evidence for quantum interference and weak localization at room temperature, as well as a temperature and field-induced crossover from negative to positive MR. Furthermore, pili can be doped with protons. Structural studies suggest the possibility of molecular pi stacking in pili, causing electron delocalization. Reducing the disorder increases the metallic nature of pili. These electronically functional proteins are a new class of electrically conductive biological proteins that can be used to generate future generation of inexpensive and environmentally-sustainable nanomaterials and nanolectronic devices such as transistors and supercapacitors. [1] Malvankar et al. Nature Nanotechnology, 6, 573-579 (2011)

Spectroscopic characterization of metal complexes of novel Schiff base. Synthesis, thermal and biological activity studies

NASA Astrophysics Data System (ADS)

Omar, M. M.; Mohamed, Gehad G.; Ibrahim, Amr A.

2009-07-01

Novel Schiff base (HL) ligand is prepared via condensation of 4-aminoantipyrine and 2-aminobenzoic acid. The ligand is characterized based on elemental analysis, mass, IR and 1H NMR spectra. Metal complexes are reported and characterized based on elemental analyses, IR, 1H NMR, solid reflectance, magnetic moment, molar conductance and thermal analyses (TGA, DrTGA and DTA). The molar conductance data reveal that all the metal chelates are non-electrolytes. IR spectra show that HL is coordinated to the metal ions in a uninegatively tridentate manner with NNO donor sites of the azomethine N, amino N and deprotonated caroxylic-O. From the magnetic and solid reflectance spectra, it is found that the geometrical structures of these complexes are octahedral. The thermal behaviour of these chelates shows that the hydrated complexes losses water molecules of hydration in the first step followed immediately by decomposition of the anions and ligand molecules in the subsequent steps. The activation thermodynamic parameters, such as, E*, ΔH*, ΔS* and ΔG* are calculated from the DrTG curves using Coats-Redfern method. The synthesized ligands, in comparison to their metal complexes also were screened for their antibacterial activity against bacterial species, Escherichia Coli, Pseudomonas aeruginosa, Staphylococcus Pyogones and Fungi (Candida). The activity data show that the metal complexes to be more potent/antibacterial than the parent Shciff base ligand against one or more bacterial species.

Composition formulas of Fe-based transition metals-metalloid bulk metallic glasses derived from dual-cluster model of binary eutectics.

PubMed

Naz, Gul Jabeen; Dong, Dandan; Geng, Yaoxiang; Wang, Yingmin; Dong, Chuang

2017-08-22

It is known that bulk metallic glasses follow simple composition formulas [cluster](glue atom) 1 or 3 with 24 valence electrons within the framework of the cluster-plus-glue-atom model. Though the relevant nearest-neighbor cluster can be readily identified from a devitrification phase, the glue atoms remains poorly defined. The present work is devoted to understanding the composition rule of Fe-(B,P,C) based multi-component bulk metallic glasses, by introducing a cluster-based eutectic liquid model. This model regards a eutectic liquid to be composed of two stable liquids formulated respectively by cluster formulas for ideal metallic glasses from the two eutectic phases. The dual cluster formulas are first established for binary Fe-(B,C,P) eutectics: [Fe-Fe 14 ]B 2 Fe + [B-B 2 Fe 8 ]Fe ≈ Fe 83.3 B 16.7 for eutectic Fe 83 B 17 , [P-Fe 14 ]P + [P-Fe 9 ]P 2 Fe≈Fe 82.8 P 17.2 for Fe 83 P 17 , and [C-Fe 6 ]Fe 3  + [C-Fe 9 ]C 2 Fe ≈ Fe 82.6 C 17.4 for Fe 82.7 C 17.3 . The second formulas in these dual-cluster formulas, being respectively relevant to devitrification phases Fe 2 B, Fe 3 P, and Fe 3 C, well explain the compositions of existing Fe-based transition metals-metalloid bulk metallic glasses. These formulas also satisfy the 24-electron rule. The proposition of the composition formulas for good glass formers, directly from known eutectic points, constitutes a new route towards understanding and eventual designing metallic glasses of high glass forming abilities.

Accuracy of Small Base Metal Dental Castings,

DTIC Science & Technology

1980-07-10

onre r puf~ eece an dif bydo:k itse Base metal al oy, c s ii.ing c ucyicatin nesmncatn ecnqe an.DISRBTOTTMN in( sten te hiquestatetrdISoc20itifrntrmRpr...34alternatives" to conventional dental golds. Determination and evaluation of composition , structure, physical and chemical properties, biologic features...maxillary right first molar was made from an industrial grade silicone . Then the tooth was machined to receive a full crown cast restoration. The tapered

Beyond arousal and valence: the importance of the biological versus social relevance of emotional stimuli.

PubMed

Sakaki, Michiko; Niki, Kazuhisa; Mather, Mara

2012-03-01

The present study addressed the hypothesis that emotional stimuli relevant to survival or reproduction (biologically emotional stimuli) automatically affect cognitive processing (e.g., attention, memory), while those relevant to social life (socially emotional stimuli) require elaborative processing to modulate attention and memory. Results of our behavioral studies showed that (1) biologically emotional images hold attention more strongly than do socially emotional images, (2) memory for biologically emotional images was enhanced even with limited cognitive resources, but (3) memory for socially emotional images was enhanced only when people had sufficient cognitive resources at encoding. Neither images' subjective arousal nor their valence modulated these patterns. A subsequent functional magnetic resonance imaging study revealed that biologically emotional images induced stronger activity in the visual cortex and greater functional connectivity between the amygdala and visual cortex than did socially emotional images. These results suggest that the interconnection between the amygdala and visual cortex supports enhanced attention allocation to biological stimuli. In contrast, socially emotional images evoked greater activity in the medial prefrontal cortex (MPFC) and yielded stronger functional connectivity between the amygdala and MPFC than did biological images. Thus, it appears that emotional processing of social stimuli involves elaborative processing requiring frontal lobe activity.

Removal of toxic metals during biological treatment of landfill leachates.

PubMed

Robinson, T

2017-05-01

Progressive implementation of the European Water Framework Directive has resulted in substantial changes in limits for discharges of heavy metals both to watercourses, and to sewer. The objective of this paper is to provide original, real, full-scale data obtained for removal of metals during aerobic biological leachate treatment, and also to report on studies carried out to look at further trace metal removal. Polishing technologies examined and investigated include; the incorporation of ultrafiltration (UF) membranes into biological treatment systems, the use of ion exchange, and of activated carbon polishing processes. Ultrafiltration was able to provide a 60 percent reduction in COD values in treated leachates, compared with COD values found in settled/clarified effluents. Removal rates for COD varied from 30.5 to 79.8 percent. Additionally, ultrafiltration of treated leachates significantly reduced both chromium and nickel concentrations of effluents by 61.6% and 34.3% respectively (median values). Despite mean reductions of chromium (9.7%) and nickel (13.7%) noted during the ion exchange trials, these results would not justify use of this technology for metals removal at full-scale. Further preliminary studies used pulverized activated carbon (PAC) polishing of UF effluents to demonstrate that significant (up to 80 per cent) removal of COD, TOC and heavy metals could readily be achieved by doses of up to 10g/l of suitable activated carbons. Additional evidence is provided that many trace metals are present not in ionic form, but as organic complexes; this is likely to make their removal to low levels more difficult and expensive. Copyright © 2016 Elsevier Ltd. All rights reserved.

BIOLOGICAL MONITORING OF TOXIC TRACE METALS. VOLUME 2. TOXIC TRACE METALS IN PLANTS AND ANIMALS OF THE WORLD. PART II

EPA Science Inventory

The needs and priorities in using biological accumulator organisms for monitoring toxic trace metals in plants and animals are analyzed. The toxic trace metals selected for study are antimony, arsenic, beryllium, boron, cadmium, chromium, cobalt, copper, lead, mercury, nickel, se...

BIOLOGICAL MONITORING OF TOXIC TRACE METALS. VOLUME 2. TOXIC TRACE METALS IN PLANTS AND ANIMALS OF THE WORLD. PART I

EPA Science Inventory

The needs and priorities in using biological accumulator organisms for monitoring toxic trace metals in plants and animals are analyzed. The toxic trace metals selected for study are antimony, arsenic, beryllium, boron, cadmium, chromium, cobalt, copper, lead, mercury, nickel, se...

Toxicological importance of human biomonitoring of metallic and metalloid elements in different biological samples.

PubMed

Gil, F; Hernández, A F

2015-06-01

Human biomonitoring has become an important tool for the assessment of internal doses of metallic and metalloid elements. These elements are of great significance because of their toxic properties and wide distribution in environmental compartments. Although blood and urine are the most used and accepted matrices for human biomonitoring, other non-conventional samples (saliva, placenta, meconium, hair, nails, teeth, breast milk) may have practical advantages and would provide additional information on health risk. Nevertheless, the analysis of these compounds in biological matrices other than blood and urine has not yet been accepted as a useful tool for biomonitoring. The validation of analytical procedures is absolutely necessary for a proper implementation of non-conventional samples in biomonitoring programs. However, the lack of reliable and useful analytical methodologies to assess exposure to metallic elements, and the potential interference of external contamination and variation in biological features of non-conventional samples are important limitations for setting health-based reference values. The influence of potential confounding factors on metallic concentration should always be considered. More research is needed to ascertain whether or not non-conventional matrices offer definitive advantages over the traditional samples and to broaden the available database for establishing worldwide accepted reference values in non-exposed populations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Synthesis and Demonstration of the Biological Relevance of sp3 -rich Scaffolds Distantly Related to Natural Product Frameworks.

PubMed

Foley, Daniel J; Craven, Philip G E; Collins, Patrick M; Doveston, Richard G; Aimon, Anthony; Talon, Romain; Churcher, Ian; von Delft, Frank; Marsden, Stephen P; Nelson, Adam

2017-10-26

The productive exploration of chemical space is an enduring challenge in chemical biology and medicinal chemistry. Natural products are biologically relevant, and their frameworks have facilitated chemical tool and drug discovery. A "top-down" synthetic approach is described that enabled a range of complex bridged intermediates to be converted with high step efficiency into 26 diverse sp 3 -rich scaffolds. The scaffolds have local natural product-like features, but are only distantly related to specific natural product frameworks. To assess biological relevance, a set of 52 fragments was prepared, and screened by high-throughput crystallography against three targets from two protein families (ATAD2, BRD1 and JMJD2D). In each case, 3D fragment hits were identified that would serve as distinctive starting points for ligand discovery. This demonstrates that frameworks that are distantly related to natural products can facilitate discovery of new biologically relevant regions within chemical space. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dose addition models based on biologically-relevant reductions in fetal testosterone accurately predict postnatal reproductive tract alterations by a phthalate mixture in rats

EPA Science Inventory

Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the curren...

Evolving Concepts and Translational Relevance of Enteroendocrine Cell Biology.

PubMed

Drucker, Daniel J

2016-03-01

Classical enteroenteroendocrine cell (EEC) biology evolved historically from identification of scattered hormone-producing endocrine cells within the epithelial mucosa of the stomach, small and large intestine. Purification of functional EEC hormones from intestinal extracts, coupled with molecular cloning of cDNAs and genes expressed within EECs has greatly expanded the complexity of EEC endocrinology, with implications for understanding the contribution of EECs to disease pathophysiology. Pubmed searches identified manuscripts highlighting new concepts illuminating the molecular biology, classification and functional role(s) of EECs and their hormonal products. Molecular interrogation of EECs has been transformed over the past decade, raising multiple new questions that challenge historical concepts of EEC biology. Evidence for evolution of the EEC from a unihormonal cell type with classical endocrine actions, to a complex plurihormonal dynamic cell with pleiotropic interactive functional networks within the gastrointestinal mucosa is critically assessed. We discuss gaps in understanding how EECs sense and respond to nutrients, cytokines, toxins, pathogens, the microbiota, and the microbial metabolome, and highlight the expanding translational relevance of EECs in the pathophysiology and therapy of metabolic and inflammatory disorders. The EEC system represents the largest specialized endocrine network in human physiology, integrating environmental and nutrient cues, enabling neural and hormonal control of metabolic homeostasis. Updating EEC classification systems will enable more accurate comparative analyses of EEC subpopulations and endocrine networks in multiple regions of the gastrointestinal tract.

Biology and Clinical Relevance of Acute Myeloid Leukemia Stem Cells.

PubMed

Reinisch, Andreas; Chan, Steven M; Thomas, Daniel; Majeti, Ravindra

2015-07-01

Evidence for the cancer stem cell model was first demonstrated in xenotransplanted blood and bone marrow samples from patients with acute myeloid leukemia (AML) almost two decades ago, supporting the concept that a rare clonal and mutated leukemic stem cell (LSC) population is sufficient to drive leukemic growth. The inability to eliminate LSCs with conventional therapies is thought to be the primary cause of disease relapse in AML patients, and as such, novel therapies with the ability to target this population are required to improve patient outcomes. An important step towards this goal is the identification of common immunophenotypic surface markers and biological properties that distinguish LSCs from normal hematopoietic stem and progenitor cells (HSPCs) across AML patients. This work has resulted in the development of a large number of potential LSC-selective therapies that target cell surface molecules, intracellular signaling pathways, and the bone marrow microenvironment. Here, we will review the basic biology, immunophenotypic detection, and clinical relevance of LSCs, as well as emerging biological and small-molecule strategies that either directly target LSCs or indirectly target these cells through modulation of their microenvironment. Copyright © 2015 Elsevier Inc. All rights reserved.

Selective enrichment of metal-binding proteins based on magnetic core/shell microspheres functionalized with metal cations.

PubMed

Fang, Caiyun; Zhang, Lei; Zhang, Xiaoqin; Lu, Haojie

2015-06-21

Metal binding proteins play many important roles in a broad range of biological processes. Characterization of metal binding proteins is important for understanding their structure and biological functions, thus leading to a clear understanding of metal associated diseases. The present study is the first to investigate the effectiveness of magnetic microspheres functionalized with metal cations (Ca(2+), Cu(2+), Zn(2+) and Fe(3+)) as the absorbent matrix in IMAC technology to enrich metal containing/binding proteins. The putative metal binding proteins in rat liver were then globally characterized by using this strategy which is very easy to handle and can capture a number of metal binding proteins effectively. In total, 185 putative metal binding proteins were identified from rat liver including some known less abundant and membrane-bound metal binding proteins such as Plcg1, Acsl5, etc. The identified proteins are involved in many important processes including binding, catalytic activity, translation elongation factor activity, electron carrier activity, and so on.

Fast X-Ray Fluorescence Microtomography of Hydrated Biological Samples

PubMed Central

Lombi, Enzo; de Jonge, Martin D.; Donner, Erica; Kopittke, Peter M.; Howard, Daryl L.; Kirkham, Robin; Ryan, Chris G.; Paterson, David

2011-01-01

Metals and metalloids play a key role in plant and other biological systems as some of them are essential to living organisms and all can be toxic at high concentrations. It is therefore important to understand how they are accumulated, complexed and transported within plants. In situ imaging of metal distribution at physiological relevant concentrations in highly hydrated biological systems is technically challenging. In the case of roots, this is mainly due to the possibility of artifacts arising during sample preparation such as cross sectioning. Synchrotron x-ray fluorescence microtomography has been used to obtain virtual cross sections of elemental distributions. However, traditionally this technique requires long data acquisition times. This has prohibited its application to highly hydrated biological samples which suffer both radiation damage and dehydration during extended analysis. However, recent advances in fast detectors coupled with powerful data acquisition approaches and suitable sample preparation methods can circumvent this problem. We demonstrate the heightened potential of this technique by imaging the distribution of nickel and zinc in hydrated plant roots. Although 3D tomography was still impeded by radiation damage, we successfully collected 2D tomograms of hydrated plant roots exposed to environmentally relevant metal concentrations for short periods of time. To our knowledge, this is the first published example of the possibilities offered by a new generation of fast fluorescence detectors to investigate metal and metalloid distribution in radiation-sensitive, biological samples. PMID:21674049

Effects of aerobic and anaerobic biological processes on leaching of heavy metals from soil amended with sewage sludge compost.

PubMed

Fang, Wen; Wei, Yonghong; Liu, Jianguo; Kosson, David S; van der Sloot, Hans A; Zhang, Peng

2016-12-01

The risk from leaching of heavy metals is a major factor hindering land application of sewage sludge compost (SSC). Understanding the change in heavy metal leaching resulting from soil biological processes provides important information for assessing long-term behavior of heavy metals in the compost amended soil. In this paper, 180days aerobic incubation and 240days anaerobic incubation were conducted to investigate the effects of the aerobic and anaerobic biological processes on heavy metal leaching from soil amended with SSC, combined with chemical speciation modeling. Results showed that leaching concentrations of heavy metals at natural pH were similar before and after biological process. However, the major processes controlling heavy metals were influenced by the decrease of DOC with organic matter mineralization during biological processes. Mineralization of organic matter lowered the contribution of DOC-complexation to Ni and Zn leaching. Besides, the reducing condition produced by biological processes, particularly by the anaerobic biological process, resulted in the loss of sorption sites for As on Fe hydroxide, which increased the potential risk of As release at alkaline pH. Copyright © 2016 Elsevier Ltd. All rights reserved.

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions.

PubMed

Semenov, Sergey N; Kraft, Lewis J; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E; Kang, Kyungtae; Fox, Jerome M; Whitesides, George M

2016-09-29

Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving

Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions

NASA Astrophysics Data System (ADS)

Semenov, Sergey N.; Kraft, Lewis J.; Ainla, Alar; Zhao, Mengxia; Baghbanzadeh, Mostafa; Campbell, Victoria E.; Kang, Kyungtae; Fox, Jerome M.; Whitesides, George M.

2016-09-01

Networks of organic chemical reactions are important in life and probably played a central part in its origin. Network dynamics regulate cell division, circadian rhythms, nerve impulses and chemotaxis, and guide the development of organisms. Although out-of-equilibrium networks of chemical reactions have the potential to display emergent network dynamics such as spontaneous pattern formation, bistability and periodic oscillations, the principles that enable networks of organic reactions to develop complex behaviours are incompletely understood. Here we describe a network of biologically relevant organic reactions (amide formation, thiolate-thioester exchange, thiolate-disulfide interchange and conjugate addition) that displays bistability and oscillations in the concentrations of organic thiols and amides. Oscillations arise from the interaction between three subcomponents of the network: an autocatalytic cycle that generates thiols and amides from thioesters and dialkyl disulfides; a trigger that controls autocatalytic growth; and inhibitory processes that remove activating thiol species that are produced during the autocatalytic cycle. In contrast to previous studies that have demonstrated oscillations and bistability using highly evolved biomolecules (enzymes and DNA) or inorganic molecules of questionable biochemical relevance (for example, those used in Belousov-Zhabotinskii-type reactions), the organic molecules we use are relevant to metabolism and similar to those that might have existed on the early Earth. By using small organic molecules to build a network of organic reactions with autocatalytic, bistable and oscillatory behaviour, we identify principles that explain the ways in which dynamic networks relevant to life could have developed. Modifications of this network will clarify the influence of molecular structure on the dynamics of reaction networks, and may enable the design of biomimetic networks and of synthetic self-regulating and evolving

Discovery and Broad Relevance May Be Insignificant Components of Course-Based Undergraduate Research Experiences (CUREs) for Non-Biology Majors.

PubMed

Ballen, Cissy J; Thompson, Seth K; Blum, Jessamina E; Newstrom, Nicholas P; Cotner, Sehoya

2018-01-01

Course-based undergraduate research experiences (CUREs) are a type of laboratory learning environment associated with a science course, in which undergraduates participate in novel research. According to Auchincloss et al. (CBE Life Sci Educ 2104; 13:29-40), CUREs are distinct from other laboratory learning environments because they possess five core design components, and while national calls to improve STEM education have led to an increase in CURE programs nationally, less work has specifically focused on which core components are critical to achieving desired student outcomes. Here we use a backward elimination experimental design to test the importance of two CURE components for a population of non-biology majors: the experience of discovery and the production of data broadly relevant to the scientific or local community. We found nonsignificant impacts of either laboratory component on students' academic performance, science self-efficacy, sense of project ownership, and perceived value of the laboratory experience. Our results challenge the assumption that all core components of CUREs are essential to achieve positive student outcomes when applied at scale.

Identifying relevant data for a biological database: handcrafted rules versus machine learning.

PubMed

Sehgal, Aditya Kumar; Das, Sanmay; Noto, Keith; Saier, Milton H; Elkan, Charles

2011-01-01

With well over 1,000 specialized biological databases in use today, the task of automatically identifying novel, relevant data for such databases is increasingly important. In this paper, we describe practical machine learning approaches for identifying MEDLINE documents and Swiss-Prot/TrEMBL protein records, for incorporation into a specialized biological database of transport proteins named TCDB. We show that both learning approaches outperform rules created by hand by a human expert. As one of the first case studies involving two different approaches to updating a deployed database, both the methods compared and the results will be of interest to curators of many specialized databases.

Application of Biologically-Based Lumping To Investigate the ...

EPA Pesticide Factsheets

People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. However, investigators have often considered complex mixtures as one lumped entity. Valuable information can be obtained from these experiments, though this simplification provides little insight into the impact of a mixture's chemical composition on toxicologically-relevant metabolic interactions that may occur among its constituents. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically-based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate performance of our PBPK model. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course kinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for the 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 non-target chemicals. Application of this biologic

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA

PubMed Central

Wright, Imogen A.; Travers, Simon A.

2014-01-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. PMID:24861618

Influence of S. mutans on base-metal dental casting alloy toxicity.

PubMed

McGinley, E L; Dowling, A H; Moran, G P; Fleming, G J P

2013-01-01

We have highlighted that exposure of base-metal dental casting alloys to the acidogenic bacterium Streptococcus mutans significantly increases cellular toxicity following exposure to immortalized human TR146 oral keratinocytes. With Inductively Coupled Plasma-Mass Spectrometry (ICP-MS), S. mutans-treated nickel-based (Ni-based) and cobalt-chromium-based (Co-Cr-based) dental casting alloys were shown to leach elevated levels of metal ions compared with untreated dental casting alloys. We targeted several biological parameters: cell morphology, viable cell counts, cell metabolic activity, cell toxicity, and inflammatory cytokine expression. S. mutans-treated dental casting alloys disrupted cell morphology, elicited significantly decreased viable cell counts (p < 0.0001) and cell metabolic activity (p < 0.0001), and significantly increased cell toxicity (p < 0.0001) and inflammatory cytokine expression (p < 0.0001). S. mutans-treated Ni-based dental casting alloys induced elevated levels of cellular toxicity compared with S. mutans-treated Co-Cr-based dental casting alloys. While our findings indicated that the exacerbated release of metal ions from S. mutans-treated base-metal dental casting alloys was the likely result of the pH reduction during S. mutans growth, the exact nature of mechanisms leading to accelerated dissolution of alloy-discs is not yet fully understood. Given the predominance of S. mutans oral carriage and the exacerbated cytotoxicity observed in TR146 cells following exposure to S. mutans-treated base-metal dental casting alloys, the implications for the long-term stability of base-metal dental restorations in the oral cavity are a cause for concern.

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.

Synthesis and Demonstration of the Biological Relevance of sp3‐rich Scaffolds Distantly Related to Natural Product Frameworks

PubMed Central

Foley, Daniel J.; Craven, Philip G. E.; Collins, Patrick M.; Doveston, Richard G.; Aimon, Anthony; Talon, Romain; Churcher, Ian; von Delft, Frank

2017-01-01

Abstract The productive exploration of chemical space is an enduring challenge in chemical biology and medicinal chemistry. Natural products are biologically relevant, and their frameworks have facilitated chemical tool and drug discovery. A “top‐down” synthetic approach is described that enabled a range of complex bridged intermediates to be converted with high step efficiency into 26 diverse sp3‐rich scaffolds. The scaffolds have local natural product‐like features, but are only distantly related to specific natural product frameworks. To assess biological relevance, a set of 52 fragments was prepared, and screened by high‐throughput crystallography against three targets from two protein families (ATAD2, BRD1 and JMJD2D). In each case, 3D fragment hits were identified that would serve as distinctive starting points for ligand discovery. This demonstrates that frameworks that are distantly related to natural products can facilitate discovery of new biologically relevant regions within chemical space. PMID:28983993

Enhancement of COPD biological networks using a web-based collaboration interface

PubMed Central

Boue, Stephanie; Fields, Brett; Hoeng, Julia; Park, Jennifer; Peitsch, Manuel C.; Schlage, Walter K.; Talikka, Marja; Binenbaum, Ilona; Bondarenko, Vladimir; Bulgakov, Oleg V.; Cherkasova, Vera; Diaz-Diaz, Norberto; Fedorova, Larisa; Guryanova, Svetlana; Guzova, Julia; Igorevna Koroleva, Galina; Kozhemyakina, Elena; Kumar, Rahul; Lavid, Noa; Lu, Qingxian; Menon, Swapna; Ouliel, Yael; Peterson, Samantha C.; Prokhorov, Alexander; Sanders, Edward; Schrier, Sarah; Schwaitzer Neta, Golan; Shvydchenko, Irina; Tallam, Aravind; Villa-Fombuena, Gema; Wu, John; Yudkevich, Ilya; Zelikman, Mariya

2015-01-01

The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website ( https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be

Enhancement of COPD biological networks using a web-based collaboration interface.

PubMed

Boue, Stephanie; Fields, Brett; Hoeng, Julia; Park, Jennifer; Peitsch, Manuel C; Schlage, Walter K; Talikka, Marja; Binenbaum, Ilona; Bondarenko, Vladimir; Bulgakov, Oleg V; Cherkasova, Vera; Diaz-Diaz, Norberto; Fedorova, Larisa; Guryanova, Svetlana; Guzova, Julia; Igorevna Koroleva, Galina; Kozhemyakina, Elena; Kumar, Rahul; Lavid, Noa; Lu, Qingxian; Menon, Swapna; Ouliel, Yael; Peterson, Samantha C; Prokhorov, Alexander; Sanders, Edward; Schrier, Sarah; Schwaitzer Neta, Golan; Shvydchenko, Irina; Tallam, Aravind; Villa-Fombuena, Gema; Wu, John; Yudkevich, Ilya; Zelikman, Mariya

2015-01-01

The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website ( https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be

Biologics formulation factors affecting metal leachables from stainless steel.

PubMed

Zhou, Shuxia; Schöneich, Christian; Singh, Satish K

2011-03-01

An area of increasing concern and scientific scrutiny is the potential contamination of drug products by leachables entering the product during manufacturing and storage. These contaminants may either have a direct safety impact on the patients or act indirectly through the alteration of the physicochemical properties of the product. In the case of biotherapeutics, trace amounts of metal contaminants can arise from various sources, but mainly from contact with stainless steel (ss). The effect of the various factors, buffer species, solution fill volume per unit contact surface area, metal chelators, and pH, on metal leachables from contact with ss over time were investigated individually. Three major metal leachables, iron, chromium, and nickel, were monitored by inductively coupled plasma-mass spectrometry because they are the major components of 316L ss. Iron was primarily used to evaluate the effect of each factor since it is the most abundant. It was observed that each studied factor exhibited its own effect on metal leachables from contact with ss. The effect of buffer species and pH exhibited temperature dependence over the studied temperature range. The metal leachables decreased with the increased fill volume (mL) per unit contact ss surface area (cm(2)) but a plateau was achieved at approximately 3 mL/cm(2). Metal chelators produced the strongest effect in facilitating metal leaching. In order to minimize the metal leachables and optimize biological product stability, each formulation factor must be evaluated for its impact, to balance its risk and benefit in achieving the target drug product shelf life. © 2011 American Association of Pharmaceutical Scientists

Redox activation of metal-based prodrugs as a strategy for drug delivery

PubMed Central

Graf, Nora

2012-01-01

This review provides an overview of metal-based anticancer drugs and drug candidates. In particular, we focus on metal complexes that can be activated in the reducing environment of cancer cells, thus serving as prodrugs. There are many reports of Pt and Ru complexes as redox-activatable drug candidates, but other d-block elements with variable oxidation states have a similar potential to serve as prodrugs in this manner. In this context are compounds based on Fe, Co, or Cu chemistry, which are also covered. A trend in the field of medicinal inorganic chemistry has been toward molecularly targeted, metal-based drugs obtained by functionalizing complexes with biologically active ligands. Another recent activity is the use of nanomaterials for drug delivery, exploiting passive targeting of tumors with nanosized constructs made from Au, Fe, carbon, or organic polymers. Although complexes of all of the above mentioned metals will be described, this review focuses primarily on Pt compounds, including constructs containing nanomaterials. PMID:22289471

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

PubMed Central

Md Yusof, Enis Nadia; Ravoof, Thahira Begum S. A.; Tiekink, Edward R. T.; Veerakumarasivam, Abhimanyu; Crouse, Karen Anne; Mohamed Tahir, Mohamed Ibrahim; Ahmad, Haslina

2015-01-01

Two bidentate NS ligands were synthesized by the condensation reaction of S-2-methylbenzyldithiocarbazate (S2MBDTC) with 2-methoxybenzaldehyde (2MB) and 3-methoxybenzaldehyde (3MB). The ligands were reacted separately with acetates of Cu(II), Ni(II) and Zn(II) yielding 1:2 (metal:ligand) complexes. The metal complexes formed were expected to have a general formula of [M(NS)2] where M = Cu2+, Ni2+, and Zn2+. These compounds were characterized by elemental analysis, molar conductivity, magnetic susceptibility and various spectroscopic techniques. The magnetic susceptibility measurements and spectral results supported the predicted coordination geometry in which the Schiff bases behaved as bidentate NS donor ligands coordinating via the azomethine nitrogen and thiolate sulfur. The molecular structures of the isomeric S2M2MBH (1) and S2M3MBH (2) were established by X-ray crystallography to have very similar l-shaped structures. The Schiff bases and their metal complexes were evaluated for their biological activities against estrogen receptor-positive (MCF-7) and estrogen receptor-negative (MDA-MB-231) breast cancer cell lines. Only the Cu(II) complexes showed marked cytotoxicity against the cancer cell lines. Both Schiff bases and other metal complexes were found to be inactive. In concordance with the cytotoxicity studies, the DNA binding studies indicated that Cu(II) complexes have a strong DNA binding affinity. PMID:25988384

Functional characterisation of metal(loid) processes in planta through the integration of synchrotron techniques and plant molecular biology

PubMed Central

Donner, Erica; Punshon, Tracy; Guerinot, Mary Lou; Lombi, Enzo

2013-01-01

Functional characterisation of the genes regulating metal(loid) homeostasis in plants is a major focus of crop biofortification, phytoremediation, and food security research. This paper focuses on the potential for advancing plant metal(loid) research by combining molecular biology and synchrotron-based techniques. Recent advances in x-ray focussing optics and fluorescence detection have greatly improved the potential of synchrotron techniques for plant science research, allowing metal(loids) to be imaged in vivo in hydrated plant tissues at sub-micron resolution. Laterally resolved metal(loid) speciation can also be determined. By using molecular techniques to probe the location of gene expression and protein localisation and combining it with this synchrotron-derived data, functional information can be effectively and efficiently assigned to specific genes. This paper provides a review of the state of the art in this field, and provides examples as to how synchrotron-based methods can be combined with molecular techniques to facilitate functional characterisation of genes in planta. PMID:22200921

Biomedically relevant circuit-design strategies in mammalian synthetic biology

PubMed Central

Bacchus, William; Aubel, Dominique; Fussenegger, Martin

2013-01-01

The development and progress in synthetic biology has been remarkable. Although still in its infancy, synthetic biology has achieved much during the past decade. Improvements in genetic circuit design have increased the potential for clinical applicability of synthetic biology research. What began as simple transcriptional gene switches has rapidly developed into a variety of complex regulatory circuits based on the transcriptional, translational and post-translational regulation. Instead of compounds with potential pharmacologic side effects, the inducer molecules now used are metabolites of the human body and even members of native cell signaling pathways. In this review, we address recent progress in mammalian synthetic biology circuit design and focus on how novel designs push synthetic biology toward clinical implementation. Groundbreaking research on the implementation of optogenetics and intercellular communications is addressed, as particularly optogenetics provides unprecedented opportunities for clinical application. Along with an increase in synthetic network complexity, multicellular systems are now being used to provide a platform for next-generation circuit design. PMID:24061539

An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance.

PubMed

Casimiro, Ana C; Vinga, Susana; Freitas, Ana T; Oliveira, Arlindo L

2008-02-07

Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior classification of the output still suffers from some limitations, which makes it difficult to assess the biological significance of the motifs found. Previous work has highlighted the existence of positional bias of motifs in the DNA sequences, which might indicate not only that the pattern is important, but also provide hints of the positions where these patterns occur preferentially. We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery. We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.

Biology relevant to space radiation

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

Fry, R J.M.

There are only very limited data on the health effects to humans from the two major components of the radiations in space, namely protons and heavy ions. As a result, predictions of the accompanying effects must be based either on (1) data generated through studies of experimental systems exposed on earth at rates and fluences higher than those in space, or (2) extrapolations from studies of gamma and x rays. Better information is needed about the doses, dose rates, and the energy and LET spectra of the radiations at the organ level that are anticipated to be encountered during extendedmore » space missions. In particular, there is a need for better estimates of the relationship between radiation quality and biological effects. In the case of deterministic effects, it is the threshold that is important. The possibility of the occurrence of a large solar particle event (SPE) requires that such effects be considered during extended space missions. Analyses suggest, however, that it is feasible to provide sufficient shielding so as to reduce such effects to acceptable levels, particularly if the dose rates can be limited. If these analyses prove correct, the primary biological risks will be the stochastic effects (latent cancer induction). The contribution of one large SPE to the risk of stochastic effects while undesirable will not be large in comparison to the potential total dose on a mission of long duration.« less

Bioaccessibility, bioavailability and toxicity of commercially relevant iron- and chromium-based particles: in vitro studies with an inhalation perspective.

PubMed

Hedberg, Yolanda; Gustafsson, Johanna; Karlsson, Hanna L; Möller, Lennart; Odnevall Wallinder, Inger

2010-09-03

Production of ferrochromium alloys (FeCr), master alloys for stainless steel manufacture, involves casting and crushing processes where particles inevitably become airborne and potentially inhaled. The aim of this study was to assess potential health hazards induced by inhalation of different well-characterized iron- and chromium-based particles, i.e. ferrochromium (FeCr), ferrosiliconchromium (FeSiCr), stainless steel (316L), iron (Fe), chromium (Cr), and chromium(III)oxide (Cr2O3), in different size fractions using in vitro methods. This was done by assessing the extent and speciation of released metals in synthetic biological medium and by analyzing particle reactivity and toxicity towards cultured human lung cells (A549). The amount of released metals normalized to the particle surface area increased with decreasing particle size for all alloy particles, whereas the opposite situation was valid for particles of the pure metals. These effects were evident in artificial lysosomal fluid (ALF) of pH 4.5 containing complexing agents, but not in neutral or weakly alkaline biological media. Chromium, iron and nickel were released to very low extent from all alloy particles, and from particles of Cr due to the presence of a Cr(III)-rich protective surface oxide. Released elements were neither proportional to the bulk nor to the surface composition after the investigated 168 hours of exposure. Due to a surface oxide with less protective properties, significantly more iron was released from pure iron particles compared with the alloys. Cr was predominantly released as Cr(III) from all particles investigated and was strongly complexed by organic species of ALF. Cr2O3 particles showed hemolytic activity, but none of the alloy particles did. Fine-sized particles of stainless steel caused however DNA damage, measured with the comet assay after 4 h exposure. None of the particles revealed any significant cytotoxicity in terms of cell death after 24 h exposure. It is evident

Bioaccessibility, bioavailability and toxicity of commercially relevant iron- and chromium-based particles: in vitro studies with an inhalation perspective

PubMed Central

2010-01-01

Background Production of ferrochromium alloys (FeCr), master alloys for stainless steel manufacture, involves casting and crushing processes where particles inevitably become airborne and potentially inhaled. The aim of this study was to assess potential health hazards induced by inhalation of different well-characterized iron- and chromium-based particles, i.e. ferrochromium (FeCr), ferrosiliconchromium (FeSiCr), stainless steel (316L), iron (Fe), chromium (Cr), and chromium(III)oxide (Cr2O3), in different size fractions using in vitro methods. This was done by assessing the extent and speciation of released metals in synthetic biological medium and by analyzing particle reactivity and toxicity towards cultured human lung cells (A549). Results The amount of released metals normalized to the particle surface area increased with decreasing particle size for all alloy particles, whereas the opposite situation was valid for particles of the pure metals. These effects were evident in artificial lysosomal fluid (ALF) of pH 4.5 containing complexing agents, but not in neutral or weakly alkaline biological media. Chromium, iron and nickel were released to very low extent from all alloy particles, and from particles of Cr due to the presence of a Cr(III)-rich protective surface oxide. Released elements were neither proportional to the bulk nor to the surface composition after the investigated 168 hours of exposure. Due to a surface oxide with less protective properties, significantly more iron was released from pure iron particles compared with the alloys. Cr was predominantly released as Cr(III) from all particles investigated and was strongly complexed by organic species of ALF. Cr2O3 particles showed hemolytic activity, but none of the alloy particles did. Fine-sized particles of stainless steel caused however DNA damage, measured with the comet assay after 4 h exposure. None of the particles revealed any significant cytotoxicity in terms of cell death after 24 h

Human Metabolites of Cannabidiol: A Review on Their Formation, Biological Activity, and Relevance in Therapy

PubMed Central

Ujváry, István; Hanuš, Lumír

2016-01-01

Abstract Cannabidiol (CBD), the main nonpsychoactive constituent of Cannabis sativa, has shown a wide range of therapeutically promising pharmacological effects either as a sole drug or in combination with other drugs in adjunctive therapy. However, the targets involved in the therapeutic effects of CBD appear to be elusive. Furthermore, scarce information is available on the biological activity of its human metabolites which, when formed in pharmacologically relevant concentration, might contribute to or even account for the observed therapeutic effects. The present overview summarizes our current knowledge on the pharmacokinetics and metabolic fate of CBD in humans, reviews studies on the biological activity of CBD metabolites either in vitro or in vivo, and discusses relevant drug–drug interactions. To facilitate further research in the area, the reported syntheses of CBD metabolites are also catalogued. PMID:28861484

Human Metabolites of Cannabidiol: A Review on Their Formation, Biological Activity, and Relevance in Therapy.

PubMed

Ujváry, István; Hanuš, Lumír

2016-01-01

Cannabidiol (CBD), the main nonpsychoactive constituent of Cannabis sativa , has shown a wide range of therapeutically promising pharmacological effects either as a sole drug or in combination with other drugs in adjunctive therapy. However, the targets involved in the therapeutic effects of CBD appear to be elusive. Furthermore, scarce information is available on the biological activity of its human metabolites which, when formed in pharmacologically relevant concentration, might contribute to or even account for the observed therapeutic effects. The present overview summarizes our current knowledge on the pharmacokinetics and metabolic fate of CBD in humans, reviews studies on the biological activity of CBD metabolites either in vitro or in vivo , and discusses relevant drug-drug interactions. To facilitate further research in the area, the reported syntheses of CBD metabolites are also catalogued.

A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results

PubMed Central

Gallaher, Sean D.; Berk, Arnold J.

2013-01-01

Adenoviruses are employed in the study of cellular processes and as expression vectors used in gene therapy. The success and reproducibility of these studies is dependent in part on having accurate and meaningful titers of replication competent and helper-dependent adenovirus stocks, which is problematic due to the use of varied and divergent titration protocols. Physical titration methods, which quantify the total number of viral particles, are used by many, but are poor at estimating activity. Biological titration methods, such as plaque assays, are more biologically relevant, but are time consuming and not applicable to helper-dependent gene therapy vectors. To address this, a protocol was developed called “infectious genome titration” in which viral DNA is isolated from the nuclei of cells ~3 h post-infection, and then quantified by Q-PCR. This approach ensures that only biologically active virions are counted as part of the titer determination. This approach is rapid, robust, sensitive, reproducible, and applicable to all forms of adenovirus. Unlike other Q-PCR-based methods, titers determined by this protocol are well correlated with biological activity. PMID:23624118

Redox-activated MRI contrast agents based on lanthanide and transition metal ions.

PubMed

Tsitovich, Pavel B; Burns, Patrick J; McKay, Adam M; Morrow, Janet R

2014-04-01

The reduction/oxidation (redox) potential of tissue is tightly regulated in order to maintain normal physiological processes, but is disrupted in disease states. Thus, the development of new tools to map tissue redox potential may be clinically important for the diagnosis of diseases that lead to redox imbalances. One promising area of chemical research is the development of redox-activated probes for mapping tissue through magnetic resonance imaging (MRI). In this review, we summarize several strategies for the design of redox-responsive MRI contrast agents. Our emphasis is on both lanthanide(III) and transition metal(II/III) ion complexes that provide contrast either as T1 relaxivity MRI contrast agents or as paramagnetic chemical exchange saturation transfer (PARACEST) contrast agents. These agents are redox-triggered by a variety of chemical reactions or switches including redox-activated thiol groups, and heterocyclic groups that interact with the metal ion or influence properties of other ancillary ligands. Metal ion centered redox is an approach which is ripe for development by coordination chemists. Redox-triggered metal ion approaches have great potential for creating large differences in magnetic properties that lead to changes in contrast. An attractive feature of these agents is the ease of fine-tuning the metal ion redox potential over a biologically relevant range. Copyright © 2014 Elsevier Inc. All rights reserved.

Biological and chemical characterization of metal bioavailability in sediments from Lake Roosevelt, Columbia River, Washington, USA

USGS Publications Warehouse

Besser, J.M.; Brumbaugh, W.G.; Ivey, C.D.; Ingersoll, C.G.; Moran, P.W.

2008-01-01

We studied the bioavailability and toxicity of copper, zinc, arsenic, cadmium, and lead in sediments from Lake Roosevelt (LR), a reservoir on the Columbia River in Washington, USA that receives inputs of metals from an upstream smelter facility. We characterized chronic sediment toxicity, metal bioaccumulation, and metal concentrations in sediment and pore water from eight study sites: one site upstream in the Columbia River, six sites in the reservoir, and a reference site in an uncontaminated tributary. Total recoverable metal concentrations in LR sediments generally decreased from upstream to downstream in the study area, but sediments from two sites in the reservoir had metal concentrations much lower than adjacent reservoir sites and similar to the reference site, apparently due to erosion of uncontaminated bank soils. Concentrations of acid-volatile sulfide in LR sediments were too low to provide strong controls on metal bioavailability, and selective sediment extractions indicated that metals in most LR sediments were primarily associated with iron and manganese oxides. Oligochaetes (Lumbriculus variegatus) accumulated greatest concentrations of copper from the river sediment, and greatest concentrations of arsenic, cadmium, and lead from reservoir sediments. Chronic toxic effects on amphipods (Hyalella azteca; reduced survival) and midge larvae (Chironomus dilutus; reduced growth) in whole-sediment exposures were generally consistent with predictions of metal toxicity based on empirical and equilibrium partitioning-based sediment quality guidelines. Elevated metal concentrations in pore waters of some LR sediments suggested that metals released from iron and manganese oxides under anoxic conditions contributed to metal bioaccumulation and toxicity. Results of both chemical and biological assays indicate that metals in sediments from both riverine and reservoir habitats of Lake Roosevelt are available to benthic invertebrates. These findings will be used as

Fluorescent probes and bioimaging: alkali metals, alkaline earth metals and pH.

PubMed

Yin, Jun; Hu, Ying; Yoon, Juyoung

2015-07-21

All living species and life forms have an absolute requirement for bio-functional metals and acid-base equilibrium chemistry owing to the critical roles they play in biological processes. Hence, a great need exists for efficient methods to detect and monitor biometals and acids. In the last few years, great attention has been paid to the development of organic molecule based fluorescent chemosensors. The availability of new synthetic fluorescent probes has made fluorescence microscopy an indispensable tool for tracing biologically important molecules and in the area of clinical diagnostics. This review highlights the recent advances that have been made in the design and bioimaging applications of fluorescent probes for alkali metals and alkaline earth metal cations, including lithium, sodium and potassium, magnesium and calcium, and for pH determination within biological systems.

Spectral, biological screening of metal chelates of chalcone based Schiff bases of N-(3-aminopropyl) imidazole.

PubMed

Kalanithi, M; Rajarajan, M; Tharmaraj, P; Sheela, C D

2012-02-15

Tridentate chelate complexes of Co(II), Ni(II), Cu(II) and Zn(II) have been synthesized from the chalcone based ligands 2-[1-(3-(1H-imidazol-1-yl)propylimino)-3-(phenylallyl)]phenol(HL(1)), 2-[1-(3-(1H-imidazol-1-yl)propylimino)-3-p-tolylallyl]phenol(HL(2)), 2-[1-(3-(1H-imidazol-1-yl)propylimino)-3-4-nitrophenylallyl]phenol(HL(3)). Microanalytical data, UV-vis spectrophotometric method, magnetic susceptibility measurements, IR, 1H NMR, Mass, and EPR techniques were used to characterize the structure of chelates. The electronic absorption spectra and magnetic susceptibility measurements suggest a distorted square planar geometry for the copper(II) ion. The other metal complexes show distorted tetrahedral geometry. The coordination of the ligands with metal(II) ions was further confirmed by solution fluorescence spectrum. The antimicrobial activity of the ligands and metal(II) complexes against the species Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Bacillus subtilis, Candida albigans and Aspergillus niger has been carried out and compared. The electrochemical behavior of copper(II) complex is studied by cyclic voltammetry. Copyright © 2011 Elsevier B.V. All rights reserved.

Biological basis and pathological relevance of microvascular thrombosis.

PubMed

Pfeiler, Susanne; Massberg, Steffen; Engelmann, Bernd

2014-05-01

Microvascular thrombosis indicates a pathological occlusion of microvessels by fibrin- and/or platelet-rich thrombi. It is observed during systemic infections, cancer, myocardial infarction, stroke, neurodegenerative diseases and in thrombotic microangiopathies. Microvessel thrombosis can cause greatly differing symptoms that range from limited changes in plasma coagulation markers to severe multi-organ failure. Because microvessel thrombi are difficult to detect and often occur only transiently, their importance for disease development and host biology is likely markedly under-appreciated. Recently, clear indications for a biological basis of microvascular thrombosis have been obtained. During systemic infections microvessel thrombosis can mediate an intravascular innate immune response (immunothrombosis). This biological form of thrombosis is based on the generation of fibrin inside blood vessels and is critically triggered by neutrophils and their interactions with platelets which result in the release of neutrophil extracellular traps (extracellular nucleosomes). Immunothrombosis is critically supported by neutrophil elastase and the activator molecules of blood coagulation tissue factor and factor XII. Identification of the biological driving forces of microvascular thrombosis should help to elucidate the mechanisms promoting pathological vessel occlusions in both microvessels and large vessels. Copyright © 2014 Elsevier Ltd. All rights reserved.

Metal based biologically active compounds: Design, synthesis, DNA binding and antidiabetic activity of 6-methyl-3-formyl chromone derived hydrazones and their metal (II) complexes.

PubMed

Philip, Jessica Elizabeth; Shahid, Muhammad; Prathapachandra Kurup, M R; Velayudhan, Mohanan Puzhavoorparambil

2017-10-01

Two chromone hydrazone ligands HL 1 and HL 2 were synthesized and characterized by elemental analyses, IR, 1 H NMR & 13 C NMR, electronic absorption and mass spectra. The reactions of the chromone hydrazones with transition metals such as Ni, Cu, and Zn (II) salts of acetate afforded mononuclear metal complexes. Characterization and structure elucidation of the prepared chromone hydrazone metal (II) complexes were done by elemental, IR, electronic, EPR spectra and thermo gravimetric analyses as well as conductivity and magnetic susceptibility measurements. The spectroscopic data showed that the ligand acts as a mono basic bidentate with coordination sites are azomethine nitrogen and hydrazonic oxygen, and they exhibited distorted geometry. The biological studies involved antidiabetic activity i.e. enzyme inhibition of α-amylase and α-glucosidase, Calf Thymus - DNA (CT-DNA) interaction and molecular docking. Potential capacity of synthesized compounds to inhibit the α-amylase and α-glucosidase activity was assayed whereas DNA interaction studies were carried out with the help UV-Vis absorption titration and viscosity method. The docking studies of chromone hydrazones show that they are minor groove binders. Complexes were found to be good DNA - intercalates. Chromone hydrazones and its transition metal complexes have shown comparable antidiabetic activity with a standard drug acarbose. Copyright © 2017 Elsevier B.V. All rights reserved.

Classifying transcription factor targets and discovering relevant biological features

PubMed Central

Holloway, Dustin T; Kon, Mark; DeLisi, Charles

2008-01-01

Background An important goal in post-genomic research is discovering the network of interactions between transcription factors (TFs) and the genes they regulate. We have previously reported the development of a supervised-learning approach to TF target identification, and used it to predict targets of 104 transcription factors in yeast. We now include a new sequence conservation measure, expand our predictions to include 59 new TFs, introduce a web-server, and implement an improved ranking method to reveal the biological features contributing to regulation. The classifiers combine 8 genomic datasets covering a broad range of measurements including sequence conservation, sequence overrepresentation, gene expression, and DNA structural properties. Principal Findings (1) Application of the method yields an amplification of information about yeast regulators. The ratio of total targets to previously known targets is greater than 2 for 11 TFs, with several having larger gains: Ash1(4), Ino2(2.6), Yaf1(2.4), and Yap6(2.4). (2) Many predicted targets for TFs match well with the known biology of their regulators. As a case study we discuss the regulator Swi6, presenting evidence that it may be important in the DNA damage response, and that the previously uncharacterized gene YMR279C plays a role in DNA damage response and perhaps in cell-cycle progression. (3) A procedure based on recursive-feature-elimination is able to uncover from the large initial data sets those features that best distinguish targets for any TF, providing clues relevant to its biology. An analysis of Swi6 suggests a possible role in lipid metabolism, and more specifically in metabolism of ceramide, a bioactive lipid currently being investigated for anti-cancer properties. (4) An analysis of global network properties highlights the transcriptional network hubs; the factors which control the most genes and the genes which are bound by the largest set of regulators. Cell-cycle and growth related

Approximate geodesic distances reveal biologically relevant structures in microarray data.

PubMed

Nilsson, Jens; Fioretos, Thoas; Höglund, Mattias; Fontes, Magnus

2004-04-12

Genome-wide gene expression measurements, as currently determined by the microarray technology, can be represented mathematically as points in a high-dimensional gene expression space. Genes interact with each other in regulatory networks, restricting the cellular gene expression profiles to a certain manifold, or surface, in gene expression space. To obtain knowledge about this manifold, various dimensionality reduction methods and distance metrics are used. For data points distributed on curved manifolds, a sensible distance measure would be the geodesic distance along the manifold. In this work, we examine whether an approximate geodesic distance measure captures biological similarities better than the traditionally used Euclidean distance. We computed approximate geodesic distances, determined by the Isomap algorithm, for one set of lymphoma and one set of lung cancer microarray samples. Compared with the ordinary Euclidean distance metric, this distance measure produced more instructive, biologically relevant, visualizations when applying multidimensional scaling. This suggests the Isomap algorithm as a promising tool for the interpretation of microarray data. Furthermore, the results demonstrate the benefit and importance of taking nonlinearities in gene expression data into account.

RAMICS: trainable, high-speed and biologically relevant alignment of high-throughput sequencing reads to coding DNA.

PubMed

Wright, Imogen A; Travers, Simon A

2014-07-01

The challenge presented by high-throughput sequencing necessitates the development of novel tools for accurate alignment of reads to reference sequences. Current approaches focus on using heuristics to map reads quickly to large genomes, rather than generating highly accurate alignments in coding regions. Such approaches are, thus, unsuited for applications such as amplicon-based analysis and the realignment phase of exome sequencing and RNA-seq, where accurate and biologically relevant alignment of coding regions is critical. To facilitate such analyses, we have developed a novel tool, RAMICS, that is tailored to mapping large numbers of sequence reads to short lengths (<10 000 bp) of coding DNA. RAMICS utilizes profile hidden Markov models to discover the open reading frame of each sequence and aligns to the reference sequence in a biologically relevant manner, distinguishing between genuine codon-sized indels and frameshift mutations. This approach facilitates the generation of highly accurate alignments, accounting for the error biases of the sequencing machine used to generate reads, particularly at homopolymer regions. Performance improvements are gained through the use of graphics processing units, which increase the speed of mapping through parallelization. RAMICS substantially outperforms all other mapping approaches tested in terms of alignment quality while maintaining highly competitive speed performance. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

BIOLOGICAL RESPONSE TO VARIATION OF ACID-VOLATILE SULFIDES AND METALS IN FIELD-EXPOSED SPIKED SEDIMENTS

EPA Science Inventory

Vertical and temporal variations of acid-volatile sulfides (AVS) and simultaneously extracted metals (SEM) in sediment can control biological impacts of metals. To assess the significance of these variations in field sediments, sediments spiked with cadmium, copper, lead, nickel ...

FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal binding site prediction at the proteome level

PubMed Central

Brylinski, Michal; Skolnick, Jeffrey

2010-01-01

The rapid accumulation of gene sequences, many of which are hypothetical proteins with unknown function, has stimulated the development of accurate computational tools for protein function prediction with evolution/structure-based approaches showing considerable promise. In this paper, we present FINDSITE-metal, a new threading-based method designed specifically to detect metal binding sites in modeled protein structures. Comprehensive benchmarks using different quality protein structures show that weakly homologous protein models provide sufficient structural information for quite accurate annotation by FINDSITE-metal. Combining structure/evolutionary information with machine learning results in highly accurate metal binding annotations; for protein models constructed by TASSER, whose average Cα RMSD from the native structure is 8.9 Å, 59.5% (71.9%) of the best of top five predicted metal locations are within 4 Å (8 Å) from a bound metal in the crystal structure. For most of the targets, multiple metal binding sites are detected with the best predicted binding site at rank 1 and within the top 2 ranks in 65.6% and 83.1% of the cases, respectively. Furthermore, for iron, copper, zinc, calcium and magnesium ions, the binding metal can be predicted with high, typically 70-90%, accuracy. FINDSITE-metal also provides a set of confidence indexes that help assess the reliability of predictions. Finally, we describe the proteome-wide application of FINDSITE-metal that quantifies the metal binding complement of the human proteome. FINDSITE-metal is freely available to the academic community at http://cssb.biology.gatech.edu/findsite-metal/. PMID:21287609

Metal oxidation states in biological water splitting.

PubMed

Krewald, Vera; Retegan, Marius; Cox, Nicholas; Messinger, Johannes; Lubitz, Wolfgang; DeBeer, Serena; Neese, Frank; Pantazis, Dimitrios A

2015-03-01

A central question in biological water splitting concerns the oxidation states of the manganese ions that comprise the oxygen-evolving complex of photosystem II. Understanding the nature and order of oxidation events that occur during the catalytic cycle of five S i states ( i = 0-4) is of fundamental importance both for the natural system and for artificial water oxidation catalysts. Despite the widespread adoption of the so-called "high-valent scheme"-where, for example, the Mn oxidation states in the S 2 state are assigned as III, IV, IV, IV-the competing "low-valent scheme" that differs by a total of two metal unpaired electrons ( i.e. III, III, III, IV in the S 2 state) is favored by several recent studies for the biological catalyst. The question of the correct oxidation state assignment is addressed here by a detailed computational comparison of the two schemes using a common structural platform and theoretical approach. Models based on crystallographic constraints were constructed for all conceivable oxidation state assignments in the four (semi)stable S states of the oxygen evolving complex, sampling various protonation levels and patterns to ensure comprehensive coverage. The models are evaluated with respect to their geometric, energetic, electronic, and spectroscopic properties against available experimental EXAFS, XFEL-XRD, EPR, ENDOR and Mn K pre-edge XANES data. New 2.5 K 55 Mn ENDOR data of the S 2 state are also reported. Our results conclusively show that the entire S state phenomenology can only be accommodated within the high-valent scheme by adopting a single motif and protonation pattern that progresses smoothly from S 0 (III, III, III, IV) to S 3 (IV, IV, IV, IV), satisfying all experimental constraints and reproducing all observables. By contrast, it was impossible to construct a consistent cycle based on the low-valent scheme for all S states. Instead, the low-valent models developed here may provide new insight into the over-reduced S

Behavioral and Biological Effects of Housing Conditions and Stress in Male Rats - Relevance to Heart Disease

DTIC Science & Technology

2006-08-01

animals had higher corticosterone than Combined Enrichment/Not Stressed (CNS) animals (F [1, 22 ] = 6.78, p < 0.01). The greatest effects were in...biological effects of stress. In particular, plasma corticosterone levels have been reported to increase in response to stressors in different... effects of restraint stress on the biological and behavioral factors relevant to cardiovascular disease (e.g., plasma corticosterone levels

A biologically relevant method for considering patterns of oceanic retention in the Southern Ocean

NASA Astrophysics Data System (ADS)

Mori, Mao; Corney, Stuart P.; Melbourne-Thomas, Jessica; Klocker, Andreas; Sumner, Michael; Constable, Andrew

2017-12-01

Many marine species have planktonic forms - either during a larval stage or throughout their lifecycle - that move passively or are strongly influenced by ocean currents. Understanding these patterns of movement is important for informing marine ecosystem management and for understanding ecological processes generally. Retention of biological particles in a particular area due to ocean currents has received less attention than transport pathways, particularly for the Southern Ocean. We present a method for modelling retention time, based on the half-life for particles in a particular region, that is relevant for biological processes. This method uses geostrophic velocities at the ocean surface, derived from 23 years of satellite altimetry data (1993-2016), to simulate the advection of passive particles during the Southern Hemisphere summer season (from December to March). We assess spatial patterns in the retention time of passive particles and evaluate the processes affecting these patterns for the Indian sector of the Southern Ocean. Our results indicate that the distribution of retention time is related to bathymetric features and the resulting ocean dynamics. Our analysis also reveals a moderate level of consistency between spatial patterns of retention time and observations of Antarctic krill (Euphausia superba) distribution.

Metal-based NanoEnhancers for Future Radiotherapy: Radiosensitizing and Synergistic Effects on Tumor Cells

PubMed Central

Liu, Yan; Zhang, Pengcheng; Li, Feifei; Jin, Xiaodong; Li, Jin; Chen, Weiqiang; Li, Qiang

2018-01-01

Radiotherapy is one of the major therapeutic strategies for cancer treatment. In the past decade, there has been growing interest in using high Z (atomic number) elements (materials) as radiosensitizers. New strategies in nanomedicine could help to improve cancer diagnosis and therapy at cellular and molecular levels. Metal-based nanoparticles usually exhibit chemical inertness in cellular and subcellular systems and may play a role in radiosensitization and synergistic cell-killing effects for radiation therapy. This review summarizes the efficacy of metal-based NanoEnhancers against cancers in both in vitro and in vivo systems for a range of ionizing radiations including gamma-rays, X-rays, and charged particles. The potential of translating preclinical studies on metal-based nanoparticles-enhanced radiation therapy into clinical practice is also discussed using examples of several metal-based NanoEnhancers (such as CYT-6091, AGuIX, and NBTXR3). Also, a few general examples of theranostic multimetallic nanocomposites are presented, and the related biological mechanisms are discussed. PMID:29556359

Applicability of a high-throughput shotgun plasma protein screening approach in understanding maternal biological pathways relevant to infant birth weight outcome.

PubMed

Kumarathasan, P; Vincent, R; Das, D; Mohottalage, S; Blais, E; Blank, K; Karthikeyan, S; Vuong, N Q; Arbuckle, T E; Fraser, W D

2014-04-04

There are reports linking maternal nutritional status, smoking and environmental chemical exposures to adverse pregnancy outcomes. However, biological bases for association between some of these factors and birth outcomes are yet to be established. The objective of this preliminary work is to test the capability of a new high-throughput shotgun plasma proteomic screening in identifying maternal changes relevant to pregnancy outcome. A subset of third trimester plasma samples (N=12) associated with normal and low-birth weight infants were fractionated, tryptic-digested and analyzed for global proteomic changes using a MALDI-TOF-TOF-MS methodology. Mass spectral data were mined for candidate biomarkers using bioinformatic and statistical tools. Maternal plasma profiles of cytokines (e.g. IL8, TNF-α), chemokines (e.g. MCP-1) and cardiovascular endpoints (e.g. ET-1, MMP-9) were analyzed by a targeted approach using multiplex protein array and HPLC-Fluorescence methods. Target and global plasma proteomic markers were used to identify protein interaction networks and maternal biological pathways relevant to low infant birth weight. Our results exhibited the potential to discriminate specific maternal physiologies relevant to risk of adverse birth outcomes. This proteomic approach can be valuable in understanding the impacts of maternal factors such as environmental contaminant exposures and nutrition on birth outcomes in future work. We demonstrate here the fitness of mass spectrometry-based shot-gun proteomics for surveillance of biological changes in mothers, and for adverse pathway analysis in combination with target biomarker information. This approach has potential for enabling early detection of mothers at risk for low infant birth weight and preterm birth, and thus early intervention for mitigation and prevention of adverse pregnancy outcomes. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes? Copyright

Development of a paper-based carbon nanotube sensing microfluidic device for biological detection.

PubMed

Yang, Shih-I; Lei, Kin Fong; Tsai, Shiao-Wen; Hsu, Hsiao-Ting

2013-01-01

Carbon nanotube (CNT) has been utilized for the biological detection due to its extremely sensitive to biological molecules. A paper-based CNT sensing microfluidic device has been developed for the detection of protein, i.e., biotin-avidin, binding. We have developed a fabrication method that allows controlled deposition of bundled CNTs with well-defined dimensions to form sensors on paper. Then, polydimethyl siloxane (PDMS) was used to pattern the hydrophobic boundary on paper to form the reaction sites. The proposed fabrication method is based on vacuum filtration process with a metal mask covering on a filter paper for the definition of the dimension of sensor. The length, width, and thickness of the CNT-based sensors are readily controlled by the metal mask and the weight of the CNT powder used during the filtration process, respectively. Homogeneous deposition of CNTs with well-defined dimensions can be achieved. The CNT-based sensor on paper has been demonstrated on the detection of the protein binding. Biotin was first immobilized on the CNT's sidewall and avidin suspended solution was applied to the site. The result of the biotin-avidin binding was measured by the resistance change of the sensor, which is a label-free detection method. It showed the CNT is sensitive to the biological molecules and the proposed paper-based CNT sensing device is a possible candidate for point-of-care biosensors. Thus, electrical bio-assays on paper-based microfluidics can be realized to develop low cost, sensitive, and specific diagnostic devices.

Analytical strategies based on quantum dots for heavy metal ions detection.

PubMed

Vázquez-González, Margarita; Carrillo-Carrion, Carolina

2014-01-01

Heavy metal contamination is one of the major concerns to human health because these substances are toxic and retained by the ecological system. Therefore, in recent years, there has been a pressing need for fast and reliable methods for the analysis of heavy metal ions in environmental and biological samples. Quantum dots (QDs) have facilitated the development of sensitive sensors over the past decade, due to their unique photophysical properties, versatile surface chemistry and ligand binding ability, and the possibility of the encapsulation in different materials or attachment to different functional materials, while retaining their native luminescence property. This paper comments on different sensing strategies with QD for the most toxic heavy metal ions (i.e., cadmium, Cd2+; mercury, Hg2+; and lead, Pb2+). Finally, the challenges and outlook for the QD-based sensors for heavy metals ions are discussed.

Distinguishing Biologically Relevant Hexoses by Water Adduction to the Lithium-Cationized Molecule.

PubMed

Campbell, Matthew T; Chen, Dazhe; Wallbillich, Nicholas J; Glish, Gary L

2017-10-03

A method to distinguish the four most common biologically relevant underivatized hexoses, d-glucose, d-galactose, d-mannose, and d-fructose, using only mass spectrometry with no prior separation/derivatization step has been developed. Electrospray of a solution containing hexose and a lithium salt generates [Hexose+Li] + . The lithium-cationized hexoses adduct water in a quadrupole ion trap. The rate of this water adduction reaction can be used to distinguish the four hexoses. Additionally, for each hexose, multiple lithiation sites are possible, allowing for multiple structures of [Hexose+Li] + . Electrospray produces at least one structure that reacts with water and at least one that does not. The ratio of unreactive lithium-cationized hexose to total lithium-cationized hexose is unique for the four hexoses studied, providing a second method for distinguishing the isomers. Use of the water adduction reaction rate or the unreactive ratio provides two separate methods for confidently (p ≤ 0.02) distinguishing the most common biologically relevant hexoses using only femtomoles of hexose. Additionally, binary mixtures of glucose and fructose were studied. A calibration curve was created by measuring the reaction rate of various samples with different ratios of fructose and glucose. The calibration curve was used to accurately measure the percentage of fructose in three samples of high fructose corn syrup (<4% error).

Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery.

PubMed

Drawnel, Faye Marie; Zhang, Jitao David; Küng, Erich; Aoyama, Natsuyo; Benmansour, Fethallah; Araujo Del Rosario, Andrea; Jensen Zoffmann, Sannah; Delobel, Frédéric; Prummer, Michael; Weibel, Franziska; Carlson, Coby; Anson, Blake; Iacone, Roberto; Certa, Ulrich; Singer, Thomas; Ebeling, Martin; Prunotto, Marco

2017-05-18

Today, novel therapeutics are identified in an environment which is intrinsically different from the clinical context in which they are ultimately evaluated. Using molecular phenotyping and an in vitro model of diabetic cardiomyopathy, we show that by quantifying pathway reporter gene expression, molecular phenotyping can cluster compounds based on pathway profiles and dissect associations between pathway activities and disease phenotypes simultaneously. Molecular phenotyping was applicable to compounds with a range of binding specificities and triaged false positives derived from high-content screening assays. The technique identified a class of calcium-signaling modulators that can reverse disease-regulated pathways and phenotypes, which was validated by structurally distinct compounds of relevant classes. Our results advocate for application of molecular phenotyping in early drug discovery, promoting biological relevance as a key selection criterion early in the drug development cascade. Copyright © 2017 Elsevier Ltd. All rights reserved.

Acceptorless dehydrogenation of small molecules through cooperative base metal catalysis

PubMed Central

West, Julian G.; Huang, David; Sorensen, Erik J.

2015-01-01

The dehydrogenation of unactivated alkanes is an important transformation both in industrial and biological systems. Recent efforts towards this reaction have revolved around high temperature, organometallic C–H activation by noble metal catalysts that produce alkenes and hydrogen gas as the sole products. Conversely, natural desaturase systems proceed through stepwise hydrogen atom transfer at physiological temperature; however, these transformations require a terminal oxidant. Here we show combining tetra-n-butylammonium decatungstate (TBADT) and cobaloxime pyridine chloride (COPC) can catalytically dehydrogenate unactivated alkanes and alcohols under near-UV irradiation at room temperature with hydrogen as the sole by-product. This noble metal-free process follows a nature-inspired pathway of high- and low-energy hydrogen atom abstractions. The hydrogen evolution ability of cobaloximes is leveraged to render the system catalytic, with cooperative turnover numbers up to 48 and yields up to 83%. Our results demonstrate how cooperative base metal catalysis can achieve transformations previously restricted to precious metal catalysts. PMID:26656087

Biological, developmental, and neurobehavioral factors relevant to adolescent driving risks.

PubMed

Dahl, Ronald E

2008-09-01

This article reviews emerging knowledge about key aspects of neurobehavioral development, with an emphasis on the development of self-regulation over behavior and emotions and its relevance to driving risks among youth. It begins with a brief overview of recent advances in understanding adolescent brain maturation and presents a heuristic model focusing on brain-behavior-social-context interactions during adolescent development. The article considers the relatively slow neurobehavioral maturation of cognitive control and emphasizes the importance of affective influences on decision making. It points to several questions about programs and policies that may help to protect high-risk youth during this important maturational period. The heuristic model is then used to examine a specific neuroregulatory system during adolescence--the regulation of sleep and arousal. This focus on sleep illustrates key points about brain-behavior-social-context interactions by looking at both biological and social influences on sleep in teens. Moreover, sleep has direct relevance to understanding a specific dimension of driving risk in youth. Sleep deprivation is rampant among adolescents, and the consequences of insufficient sleep (sleepiness, lapses in attention, susceptibility to aggression, and negative synergy with alcohol) appear to contribute significantly to driving risks in teens.

Biological and Bioelectrochemical Recovery of Critical and Scarce Metals.

PubMed

Nancharaiah, Y V; Mohan, S Venkata; Lens, P N L

2016-02-01

Metal-bearing solid and liquid wastes are increasingly considered as secondary sources of critical and scarce metals. Undoubtedly, microorganisms are a cost-effective resource for extracting and concentrating diffuse elements from secondary sources. Microbial biotechnology for extracting base metals from ores and treatment of metal-laden wastewaters has already been applied at full scale. By contrast, microbe-metal interactions in the recovery of scarce metals and a few critical metals have received attention, whereas the recovery of many others has been barely explored. Therefore, this article explores and details the potential application of microbial biotechnologies in the recovery of critical and scarce metals. In the past decade bioelectrochemical systems have emerged as a new technology platform for metal recovery coupled to the removal of organic matter. Copyright © 2015 Elsevier Ltd. All rights reserved.

Development of a biologically based dose response (BBDR) model for arsenic induced cancer

EPA Science Inventory

We are developing a biologically based dose response (BBDR) model for arsenic carcinogenicity in order to reduce uncertainty in estimates of low dose risk by maximizing the use of relevant data on the mode of action. Expert consultation and literature review are being conducted t...

Vascular Biology of Glucagon Receptor Superfamily Peptides: Mechanistic and Clinical Relevance.

PubMed

Pujadas, Gemma; Drucker, Daniel J

2016-12-01

Regulatory peptides produced in islet and gut endocrine cells, including glucagon, glucagon-like peptide-1 (GLP-1), GLP-2, and glucose-dependent insulinotropic polypeptide, exert actions with considerable metabolic importance and translational relevance. Although the clinical development of GLP-1 receptor agonists and dipeptidyl peptidase-4 inhibitors has fostered research into how these hormones act on the normal and diseased heart, less is known about the actions of these peptides on blood vessels. Here we review the effects of these peptide hormones on normal blood vessels and highlight their vascular actions in the setting of experimental and clinical vascular injury. The cellular localization and signal transduction properties of the receptors for glucagon, GLP-1, GLP-2, and glucose-dependent insulinotropic polypeptide are discussed, with emphasis on endothelial cells and vascular smooth muscle cells. The actions of these peptides on the control of blood flow, blood pressure, angiogenesis, atherosclerosis, and vascular inflammation are reviewed with a focus on elucidating direct and indirect mechanisms of action. How these peptides traverse the blood-brain barrier is highlighted, with relevance to the use of GLP-1 receptor agonists to treat obesity and neurodegenerative disorders. Wherever possible, we compare actions identified in cell lines and primary cell culture with data from preclinical studies and, when available, results of human investigation, including studies in subjects with diabetes, obesity, and cardiovascular disease. Throughout the review, we discuss pitfalls, limitations, and challenges of the existing literature and highlight areas of controversy and uncertainty. The increasing use of peptide-based therapies for the treatment of diabetes and obesity underscores the importance of understanding the vascular biology of peptide hormone action.

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

PubMed

Muetze, Tanja; Goenawan, Ivan H; Wiencko, Heather L; Bernal-Llinares, Manuel; Bryan, Kenneth; Lynn, David J

2016-01-01

Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest. CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store ( http://apps.cytoscape.org/apps/chat).

Implantable liquid metal-based flexible neural microelectrode array and its application in recovering animal locomotion functions

NASA Astrophysics Data System (ADS)

Guo, Rui; Liu, Jing

2017-10-01

With significant advantages in rapidly restoring the nerve function, electrical stimulation of nervous tissue is a crucial treatment of peripheral nerve injuries leading to common movement disorder. However, the currently available stimulating electrodes generally based on rigid conductive materials would cause a potential mechanical mismatch with soft neural tissues which thus reduces long-term effects of electrical stimulation. Here, we proposed and fabricated a flexible neural microelectrode array system based on the liquid metal GaIn alloy (75.5% Ga and 24.5% In by weight) and via printing approach. Such an alloy with a unique low melting point (10.35 °C) owns excellent electrical conductivity and high compliance, which are beneficial to serve as implantable flexible neural electrodes. The flexible neural microelectrode array embeds four liquid metal electrodes and stretchable interconnects in a PDMS membrane (500 µm in thickness) that possess a lower elastic modulus (1.055 MPa), which is similar to neural tissues with elastic moduli in the 0.1-1.5 MPa range. The electrical experiments indicate that the liquid metal interconnects could sustain over 7000 mechanical stretch cycles with resistance approximately staying at 4 Ω. Over the conceptual experiments on animal sciatic nerve electrical stimulation, the dead bullfrog implanted with flexible neural microelectrode array could even rhythmically contract and move its lower limbs under the electrical stimulations from the implant. This demonstrates a highly efficient way for quickly recovering biological nerve functions. Further, the good biocompatibility of the liquid metal material was justified via a series of biological experiments. This liquid metal modality for neural stimulation is expected to play important roles as biologic electrodes to overcome the fundamental mismatch in mechanics between biological tissues and electronic devices in the coming time.

Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments (Final Report)

EPA Science Inventory

The Ecological Risk Assessment Support Center (ERASC) announced the release of the final report, Determination of the Biologically Relevant Sampling Depth for Terrestrial and Aquatic Ecological Risk Assessments. This technical paper provides defensible approximations fo...

Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

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

Elias, Dwayne; Schadt, Christopher; Miller, Lance

2010-05-17

One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophismmore » to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will

Biologically active and thermally stable polymeric Schiff base and its metal polychelates: Their synthesis and spectral aspects

NASA Astrophysics Data System (ADS)

Rasool, Raza; Hasnain, Sumaiya

2015-09-01

New metal polychelates of Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) obtained by the interaction of metal acetates with polymeric Schiff base containing formaldehyde and piperazine, have been investigated. Structural and spectroscopic properties have been evaluated by elemental analysis, FT-IR and 1H-NMR. Geometry of the chelated polymers was confirmed by magnetic susceptibility measurements, UV-Visible spectroscopy and Electron Spin Resonance. The molecular weight of the polymer was determined by gel permeation chromatography (GPC). Thermogravimetric analysis indicated that metal polychelates were more thermally stable than their corresponding ligand. All compounds were screened for their antimicrobial activities against Escherichia coli, Staphylococcus aureus, Bacillus subtilis, (bacteria) and Candida albicans, Microsporum canis, Cryptococcus neoformans (fungi) by agar well diffusion method. Interestingly, the polymeric Schiff base was found to be antimicrobial in nature but less effective as compared to the metal polychelates. On the basis of thermal and antimicrobial behavior, these polymers hold potential applications as thermally resistant antimicrobial and antifouling coating materials as well as antimicrobial packaging materials.

Statistical approach for selection of biologically informative genes.

PubMed

Das, Samarendra; Rai, Anil; Mishra, D C; Rai, Shesh N

2018-05-20

Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i.e. Boot-MRMR, was proposed based on a composite measure of maximum relevance and minimum redundancy, which is both statistically sound and biologically relevant for informative gene selection. For comparative evaluation of the proposed approach, we developed two biological sufficient criteria, i.e. Gene Set Enrichment with QTL (GSEQ) and biological similarity score based on Gene Ontology (GO). Further, a systematic and rigorous evaluation of the proposed technique with 12 existing gene selection techniques was carried out using five gene expression datasets. This evaluation was based on a broad spectrum of statistically sound (e.g. subject classification) and biological relevant (based on QTL and GO) criteria under a multiple criteria decision-making framework. The performance analysis showed that the proposed technique selects informative genes which are more biologically relevant. The proposed technique is also found to be quite competitive with the existing techniques with respect to subject classification and computational time. Our results also showed that under the multiple criteria decision-making setup, the proposed technique is best for informative gene selection over the available alternatives. Based on the proposed approach, an R Package, i.e. BootMRMR has been developed and available at https://cran.r-project.org/web/packages/BootMRMR. This study will provide a practical guide to select statistical techniques for selecting informative genes

Metal-containing and related polymers for biomedical applications.

PubMed

Yan, Yi; Zhang, Jiuyang; Ren, Lixia; Tang, Chuanbing

2016-10-07

A survey of the most recent progress in the biomedical applications of metal-containing polymers is given. Due to the unique optical, electrochemical, and magnetic properties, at least 30 different metal elements, most of them transition metals, are introduced into polymeric frameworks for interactions with biology-relevant substrates via various means. Inspired by the advance of metal-containing small molecular drugs and promoted by the great progress in polymer chemistry, metal-containing polymers have gained momentum during recent decades. According to their different applications, this review summarizes the following biomedical applications: (1) metal-containing polymers as drug delivery vehicles; (2) metal-containing polymeric drugs and biocides, including antimicrobial and antiviral agents, anticancer drugs, photodynamic therapy agents, radiotherapy agents and biocides; (3) metal-containing polymers as biosensors, and (4) metal-containing polymers in bioimaging.

Structures and physical properties of gaseous metal cationized biological ions.

PubMed

Burt, Michael B; Fridgen, Travis D

2012-01-01

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Rapid magnetic removal of aqueous heavy metals and their relevant mechanisms using nanoscale zero valent iron (nZVI) particles.

PubMed

Huang, Pengpeng; Ye, Zhengfang; Xie, Wuming; Chen, Qi; Li, Jing; Xu, Zhencheng; Yao, Maosheng

2013-08-01

Much work is devoted to heavy metal sorption, reduction and relevant mechanisms by nanoscale zero valent iron (nZVI) particle, but fewer studies utilize its magnetic properties in aqueous metal removals. Here, we have investigated the use of nZVI particles both electrosprayed (E-nZVI) and non-electrosprayed (NE-nZVI) with different concentration levels (0.186-1.86 mg/mL) in removing aqueous Cd(II), Cr(IV), and Pb(II) through the magnetic separation means. The effects of the reaction time (5-20 min) and magnetic treatment time (1-30 min) on relevant magnetic removal efficiencies were studied. Metal ion concentration was analyzed using inductively coupled plasma (ICP), and the magnetically obtained metal-nZVI mixtures were further analyzed using X-ray photoelectron spectroscopy (XPS). Results showed that the magnetic removal efficiencies of heavy metals varied with the metal species, nZVI loading, reaction and magnetic separation time. In most cases, use of 1.5 mg/mL E-nZVI or NE-nZVI resulted in removal efficiencies of more than 80% for Pb(II), Cd(II), and Cr(IV). Increasing the magnetic treatment time from 1 to 20 min was shown to lead to ≈ 20% increase in Pb(II) removal efficiency, but no improvements for Cd(II) and Cr(IV). In contrast, increasing the reaction time decreased the Pb(II) removal efficiency, yet no effects observed for Cd(II) and Cr(IV). In general, 1 min reaction and 5 min magnetic treatment were found sufficient to achieve considerable heavy metal removals. For comparable efficiencies, use of magnetic method could significantly reduce nZVI loading. XPS analysis results indicated that atomic percentages of O 1s, Fe 2p, Cd 3d, Pb 4f and Cr 2p varied with metal exposures. Different from Cd(II) and Cr(IV), aqueous iron ions might be possibly present when treating Pb(II). This study demonstrated a rapid heavy metal removal method using the magnetic property of nZVI particles, while contributing to understanding of the relevant removal mechanisms

Metal-Ion-Mediated Supramolecular Chirality of l-Phenylalanine Based Hydrogels.

PubMed

Wang, Fang; Feng, Chuan-Liang

2018-05-14

For chiral hydrogels and related applications, one of the critical issues is how to control the chirality of supramolecular systems in an efficient way, including easy operation, efficient transfer of chirality, and so on. Herein, supramolecular chirality of l-phenylalanine based hydrogels can be effectively controlled by using a broad range of metal ions. The degree of twisting (twist pitch) and the diameter of the chiral nanostructures can also be efficiently regulated. These are ascribed to the synergic effect of hydrogen bonding and metal ion coordination. This study may develop a method to design a new class of electronically, optically, and biologically active materials. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transition metal ions mediated tyrosine based short peptide amphiphile nanostructures inhibit bacterial growth.

PubMed

Joshi, Khashti Ballabh; Singh, Ramesh; Mishra, Narendra Kumar; Kumar, Vikas; Vinayak, Vandana

2018-05-17

We report the design and synthesis of biocompatible small peptide based molecule for the controlled and targeted delivery of the encapsulated bioactive metal ions via transforming their internal nanostructures. Tyrosine based short peptide amphiphile (sPA) was synthesized which self-assembled into β-sheet like secondary structures. The self assembly of the designed sPA was modulated by using different bioactive transition metal ions which is confirmed by spectroscopic and microscopic techniques. These bioactive metal ions conjugated sPA hybrid structures are further used to develop antibacterial materials. It is due to the excellent antibacterial activity of zinc ions that the growth of clinically relevant bacteria such as E. Coli was inhibited in the presence of zinc-sPA conjugate. The bacterial test demonstrated that owing to high biocompatibility with bacterial cell, the designed sPA worked as metal ions delivery agent and therefore it can show great potential in locally addressing bacterial infections. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

PubMed

Hastings, Janna; de Matos, Paula; Dekker, Adriano; Ennis, Marcus; Harsha, Bhavana; Kale, Namrata; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Williams, Mark; Steinbeck, Christoph

2013-01-01

ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

Scoring clustering solutions by their biological relevance.

PubMed

Gat-Viks, I; Sharan, R; Shamir, R

2003-12-12

A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them. We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data. The software is available from the authors upon request.

IDENTIFICATION OF BIOLOGICALLY RELEVANT GENES USING A DATABASE OF RAT LIVER AND KIDNEY BASELINE GENE EXPRESSION

EPA Science Inventory

Microarray data from independent labs and studies can be compared to potentially identify toxicologically and biologically relevant genes. The Baseline Animal Database working group of HESI was formed to assess baseline gene expression from microarray data derived from control or...

Research on metallic material defect detection based on bionic sensing of human visual properties

NASA Astrophysics Data System (ADS)

Zhang, Pei Jiang; Cheng, Tao

2018-05-01

Due to the fact that human visual system can quickly lock the areas of interest in complex natural environment and focus on it, this paper proposes an eye-based visual attention mechanism by simulating human visual imaging features based on human visual attention mechanism Bionic Sensing Visual Inspection Model Method to Detect Defects of Metallic Materials in the Mechanical Field. First of all, according to the biologically visually significant low-level features, the mark of defect experience marking is used as the intermediate feature of simulated visual perception. Afterwards, SVM method was used to train the advanced features of visual defects of metal material. According to the weight of each party, the biometrics detection model of metal material defect, which simulates human visual characteristics, is obtained.

Three-Dimensional Biologically Relevant Spectrum (BRS-3D): Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors.

PubMed

Hu, Ben; Kuang, Zheng-Kun; Feng, Shi-Yu; Wang, Dong; He, Song-Bing; Kong, De-Xin

2016-11-17

The crystallized ligands in the Protein Data Bank (PDB) can be treated as the inverse shapes of the active sites of corresponding proteins. Therefore, the shape similarity between a molecule and PDB ligands indicated the possibility of the molecule to bind with the targets. In this paper, we proposed a shape similarity profile that can be used as a molecular descriptor for ligand-based virtual screening. First, through three-dimensional (3D) structural clustering, 300 diverse ligands were extracted from the druggable protein-ligand database, sc-PDB. Then, each of the molecules under scrutiny was flexibly superimposed onto the 300 ligands. Superimpositions were scored by shape overlap and property similarity, producing a 300 dimensional similarity array termed the "Three-Dimensional Biologically Relevant Spectrum (BRS-3D)". Finally, quantitative or discriminant models were developed with the 300 dimensional descriptor using machine learning methods (support vector machine). The effectiveness of this approach was evaluated using 42 benchmark data sets from the G protein-coupled receptor (GPCR) ligand library and the GPCR decoy database (GLL/GDD). We compared the performance of BRS-3D with other 2D and 3D state-of-the-art molecular descriptors. The results showed that models built with BRS-3D performed best for most GLL/GDD data sets. We also applied BRS-3D in histone deacetylase 1 inhibitors screening and GPCR subtype selectivity prediction. The advantages and disadvantages of this approach are discussed.

Microstructure of a base metal thick film system. [Glass frit with base metal oxide addition

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

Mentley, D.E.

1976-06-01

A base metal thick film conductor system using glass frits with base metal oxide additions was investigated as metallization for hybrid microcircuits. Application of previous work on wetting and chemical bonding was made to this system. The observation of changes in the properties of the thick film was made by photomicrographs of screened samples and sheet resistivity measurements. In addition to the chemical and wetting properties, the effect of glass frit particle size on conductivity was also analyzed. The base metal oxide addition was found to produce a more consistent thick film conductor at low volume percentages of metal bymore » inhibiting the formation of low melting redox reaction products.« less

Behavior and Potential Impacts of Metal-Based Engineered Nanoparticles in Aquatic Environments

PubMed Central

Peng, Cheng; Zhang, Wen; Gao, Haiping; Li, Yang; Tong, Xin; Li, Kungang; Zhu, Xiaoshan; Wang, Yixiang; Chen, Yongsheng

2017-01-01

The specific properties of metal-based nanoparticles (NPs) have not only led to rapidly increasing applications in various industrial and commercial products, but also caused environmental concerns due to the inevitable release of NPs and their unpredictable biological/ecological impacts. This review discusses the environmental behavior of metal-based NPs with an in-depth analysis of the mechanisms and kinetics. The focus is on knowledge gaps in the interaction of NPs with aquatic organisms, which can influence the fate, transport and toxicity of NPs in the aquatic environment. Aggregation transforms NPs into micrometer-sized clusters in the aqueous environment, whereas dissolution also alters the size distribution and surface reactivity of metal-based NPs. A unique toxicity mechanism of metal-based NPs is related to the generation of reactive oxygen species (ROS) and the subsequent ROS-induced oxidative stress. Furthermore, aggregation, dissolution and ROS generation could influence each other and also be influenced by many factors, including the sizes, shapes and surface charge of NPs, as well as the pH, ionic strength, natural organic matter and experimental conditions. Bioaccumulation of NPs in single organism species, such as aquatic plants, zooplankton, fish and benthos, is summarized and compared. Moreover, the trophic transfer and/or biomagnification of metal-based NPs in an aquatic ecosystem are discussed. In addition, genetic effects could result from direct or indirect interactions between DNA and NPs. Finally, several challenges facing us are put forward in the review. PMID:28336855

Phytochelatins: peptides involved in heavy metal detoxification.

PubMed

Pal, Rama; Rai, J P N

2010-03-01

Phytochelatins (PCs) are enzymatically synthesized peptides known to involve in heavy metal detoxification and accumulation, which have been measured in plants grown at high heavy metal concentrations, but few studies have examined the response of plants even at lower environmentally relevant metal concentrations. Recently, genes encoding the enzyme PC synthase have been identified in plants and other species enabling molecular biological studies to untangle the mechanisms underlying PC synthesis and its regulation. The present paper embodies review on recent advances in structure of PCs, their biosynthetic regulation, roles in heavy metal detoxification and/or accumulation, and PC synthase gene expression for better understanding of mechanism involved and to improve phytoremediation efficiency of plants for wider application.

Biological Weapons -- Still a Relevant Threat

DTIC Science & Technology

2012-03-22

destruction in general, and biological weapons in particular. The IHS Janes: Defence and Security Intelligence & Analysis website notes that a number of...responder capabilities, and intelligence agency inputs. There needs, as well, to be continued research and development of sensor technologies, which...Mass Destruction – Radiological, Chemical and Biological,‖ 109 10 Mark, J. Carson; Taylor, Theodore; Eyster, Eugene; Maraman, William; Wechsler

Recent advances in transition-metal dichalcogenides based electrochemical biosensors: A review.

PubMed

Wang, Yi-Han; Huang, Ke-Jing; Wu, Xu

2017-11-15

Layered transition metal dichalcogenides (TMDCs) comprise a category of two-dimensional (2D) materials that offer exciting properties, including large surface area, metallic and semi-conducting electrical capabilities, and intercalatable morphologies. Biosensors employ biological molecules to recognize the target and utilize output elements which can translate the biorecognition event into electrical, optical or mass-sensitive signals to determine the quantities of the target. TMDCs nanomaterials have been widely applied in various electrochemical biosensors with high sensitivity and selectivity. The marriage of TMDCs and electrochemical biosensors has created many productive sensing strategies for applications in the areas of clinical diagnosis, environmental monitoring and food safety. In recent years, an increasing number of TMDCs-based electrochemical biosensors are reported, suggesting TMDCs offers new possibilities of improving the performance of electrochemical biosensors. This review summarizes recent advances in electrochemical biosensors based on TMDCs for detection of various inorganic and organic analytes in the last five years, including glucose, proteins, DNA, heavy metal, etc. In addition, we also point out the challenges and future perspectives related to the material design and development of TMDCs-based electrochemical biosensors. Copyright © 2017 Elsevier B.V. All rights reserved.

Mechanical homeostasis of a DOPA-enriched biological coating from mussels in response to metal variation

PubMed Central

Schmitt, Clemens N. Z.; Winter, Alette; Bertinetti, Luca; Masic, Admir; Strauch, Peter; Harrington, Matthew J.

2015-01-01

Protein–metal coordination interactions were recently found to function as crucial mechanical cross-links in certain biological materials. Mussels, for example, use Fe ions from the local environment coordinated to DOPA-rich proteins to stiffen the protective cuticle of their anchoring byssal attachment threads. Bioavailability of metal ions in ocean habitats varies significantly owing to natural and anthropogenic inputs on both short and geological spatio-temporal scales leading to large variations in byssal thread metal composition; however, it is not clear how or if this affects thread performance. Here, we demonstrate that in natural environments mussels can opportunistically replace Fe ions in the DOPA coordination complex with V and Al. In vitro removal of the native DOPA–metal complexes with ethylenediaminetetraacetic acid and replacement with either Fe or V does not lead to statistically significant changes in cuticle performance, indicating that each metal ion is equally sufficient as a DOPA cross-linking agent, able to account for nearly 85% of the stiffness and hardness of the material. Notably, replacement with Al ions also leads to full recovery of stiffness, but only 82% recovery of hardness. These findings have important implications for the adaptability of this biological material in a dynamically changing and unpredictable habitat. PMID:26311314

Characterization of Nanoparticle Aggregation in Biologically Relevant Fluids

NASA Astrophysics Data System (ADS)

McEnnis, Kathleen; Lahann, Joerg

Nanoparticles (NPs) are often studied as drug delivery vehicles, but little is known about their behavior in blood once injected into animal models. If the NPs aggregate in blood, they will be shunted to the liver or spleen instead of reaching the intended target. The use of animals for these experiments is costly and raises ethical questions. Typically dynamic light scattering (DLS) is used to analyze aggregation behavior, but DLS cannot be used because the components of blood also scatter light. As an alternative, a method of analyzing NPs in biologically relevant fluids such as blood plasma has been developed using nanoparticle tracking analysis (NTA) with fluorescent filters. In this work, NTA was used to analyze the aggregation behavior of fluorescent polystyrene NPs with different surface modifications in blood plasma. It was expected that different surface chemistries on the particles will change the aggregation behavior. The effect of the surface modifications was investigated by quantifying the percentage of NPs in aggregates after addition to blood plasma. The use of this characterization method will allow for better understanding of particle behavior in the body, and potential problems, specifically aggregation, can be addressed before investing in in vivo studies.

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

NASA Astrophysics Data System (ADS)

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

1985-07-01

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

21 CFR 872.3710 - Base metal alloy.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Base metal alloy. 872.3710 Section 872.3710 Food... DEVICES DENTAL DEVICES Prosthetic Devices § 872.3710 Base metal alloy. (a) Identification. A base metal alloy is a device composed primarily of base metals, such as nickel, chromium, or cobalt, that is...

21 CFR 872.3710 - Base metal alloy.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Base metal alloy. 872.3710 Section 872.3710 Food... DEVICES DENTAL DEVICES Prosthetic Devices § 872.3710 Base metal alloy. (a) Identification. A base metal alloy is a device composed primarily of base metals, such as nickel, chromium, or cobalt, that is...

21 CFR 872.3710 - Base metal alloy.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Base metal alloy. 872.3710 Section 872.3710 Food... DEVICES DENTAL DEVICES Prosthetic Devices § 872.3710 Base metal alloy. (a) Identification. A base metal alloy is a device composed primarily of base metals, such as nickel, chromium, or cobalt, that is...

21 CFR 872.3710 - Base metal alloy.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Base metal alloy. 872.3710 Section 872.3710 Food... DEVICES DENTAL DEVICES Prosthetic Devices § 872.3710 Base metal alloy. (a) Identification. A base metal alloy is a device composed primarily of base metals, such as nickel, chromium, or cobalt, that is...

Chemically Reversible Reactions of Hydrogen Sulfide with Metal Phthalocyanines

PubMed Central

2015-01-01

Hydrogen sulfide (H2S) is an important signaling molecule that exerts action on various bioinorganic targets. Despite this importance, few studies have investigated the differential reactivity of the physiologically relevant H2S and HS– protonation states with metal complexes. Here we report the distinct reactivity of H2S and HS– with zinc(II) and cobalt(II) phthalocyanine (Pc) complexes and highlight the chemical reversibility and cyclability of each metal. ZnPc reacts with HS–, but not H2S, to generate [ZnPc-SH]−, which can be converted back to ZnPc by protonation. CoPc reacts with HS–, but not H2S, to form [CoIPc]−, which can be reoxidized to CoPc by air. Taken together, these results demonstrate the chemically reversible reaction of HS– with metal phthalocyanine complexes and highlight the importance of H2S protonation state in understanding the reactivity profile of H2S with biologically relevant metal scaffolds. PMID:24785654

A multimodal imaging workflow to visualize metal mixtures in the human placenta and explore colocalization with biological response markers.

PubMed

Niedzwiecki, Megan M; Austin, Christine; Remark, Romain; Merad, Miriam; Gnjatic, Sacha; Estrada-Gutierrez, Guadalupe; Espejel-Nuñez, Aurora; Borboa-Olivares, Hector; Guzman-Huerta, Mario; Wright, Rosalind J; Wright, Robert O; Arora, Manish

2016-04-01

Fetal exposure to essential and toxic metals can influence life-long health trajectories. The placenta regulates chemical transmission from maternal circulation to the fetus and itself exhibits a complex response to environmental stressors. The placenta can thus be a useful matrix to monitor metal exposures and stress responses in utero, but strategies to explore the biologic effects of metal mixtures in this organ are not well-developed. In this proof-of-concept study, we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to measure the distributions of multiple metals in placental tissue from a low-birth-weight pregnancy, and we developed an approach to identify the components of metal mixtures that colocalized with biological response markers. Our novel workflow, which includes custom-developed software tools and algorithms for spatial outlier identification and background subtraction in multidimensional elemental image stacks, enables rapid image processing and seamless integration of data from elemental imaging and immunohistochemistry. Using quantitative spatial statistics, we identified distinct patterns of metal accumulation at sites of inflammation. Broadly, our multiplexed approach can be used to explore the mechanisms mediating complex metal exposures and biologic responses within placentae and other tissue types. Our LA-ICP-MS image processing workflow can be accessed through our interactive R Shiny application 'shinyImaging', which is available at or through our laboratory's website, .

'Fish matters': the relevance of fish skin biology to investigative dermatology.

PubMed

Rakers, Sebastian; Gebert, Marina; Uppalapati, Sai; Meyer, Wilfried; Maderson, Paul; Sell, Anne F; Kruse, Charli; Paus, Ralf

2010-04-01

Fish skin is a multi-purpose tissue that serves numerous vital functions including chemical and physical protection, sensory activity, behavioural purposes or hormone metabolism. Further, it is an important first-line defense system against pathogens, as fish are continuously exposed to multiple microbial challenges in their aquatic habitat. Fish skin excels in highly developed antimicrobial features, many of which have been preserved throughout evolution, and infection defense principles employed by piscine skin are still operative in human skin. This review argues that it is both rewarding and important for investigative dermatologists to revive their interest in fish skin biology, as it provides insights into numerous fundamental issues that are of major relevance to mammalian skin. The basic molecular insights provided by zebrafish in vivo-genomics for genetic, regeneration and melanoma research, the complex antimicrobial defense systems of fish skin and the molecular controls of melanocyte stem cells are just some of the fascinating examples that illustrate the multiple potential uses of fish skin models in investigative dermatology. We synthesize the essentials of fish skin biology and highlight selected aspects that are of particular comparative interest to basic and clinically applied human skin research.

Learning Systems Biology: Conceptual Considerations toward a Web-Based Learning Platform

ERIC Educational Resources Information Center

Emmert-Streib, Frank; Dehmer, Matthias; Lyardet, Fernando

2013-01-01

Within recent years, there is an increasing need to train students, from biology and beyond, in quantitative methods that are relevant to cope with data-driven biology. Systems Biology is such a field that places a particular focus on the functional aspect of biology and molecular interacting processes. This paper deals with the conceptual design…

Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems.

PubMed

Lê Cao, Kim-Anh; Boitard, Simon; Besse, Philippe

2011-06-22

Variable selection on high throughput biological data, such as gene expression or single nucleotide polymorphisms (SNPs), becomes inevitable to select relevant information and, therefore, to better characterize diseases or assess genetic structure. There are different ways to perform variable selection in large data sets. Statistical tests are commonly used to identify differentially expressed features for explanatory purposes, whereas Machine Learning wrapper approaches can be used for predictive purposes. In the case of multiple highly correlated variables, another option is to use multivariate exploratory approaches to give more insight into cell biology, biological pathways or complex traits. A simple extension of a sparse PLS exploratory approach is proposed to perform variable selection in a multiclass classification framework. sPLS-DA has a classification performance similar to other wrapper or sparse discriminant analysis approaches on public microarray and SNP data sets. More importantly, sPLS-DA is clearly competitive in terms of computational efficiency and superior in terms of interpretability of the results via valuable graphical outputs. sPLS-DA is available in the R package mixOmics, which is dedicated to the analysis of large biological data sets.

Bio-rescue of marine environments: On the track of microbially-based metal/metalloid remediation.

PubMed

Marques, Catarina R

2016-09-15

The recent awareness of the huge relevance of marine resources and ecological services is driving regulatory demands for their protection from overwhelming contaminants, such as metals/metalloids. These contaminants enter and accumulate in different marine niches, hence deeply compromising their quality and integrity. Bioremediation has been flourishing to counteract metal/metalloid impacts, since it provides cost-effective and sustainable options by relying on ecology-based technologies. The potential of marine microbes for metal/metalloid bioremediation is the core of many studies, due to their high plasticity to overcome successive environmental hurdles. However, any thorough review on the advances of metal/metalloid bioremediation in marine environments was so far unveiled. This review is designed to (i) outline the characteristics and potential of marine microbes for metal/metalloid bioremediation, (ii) describe the underlying pathways of resistance and detoxification, as well as useful methodologies for their characterization, (iii) identify major bottlenecks on metal/metalloid bioremediation with marine microbes, (iv) present alternative strategies based on microbial consortia and engineered microbes for enhanced bioremediation, and (v) propose key research avenues to keep pace with a changing society, science and economy in a sustainable manner. Copyright © 2016 Elsevier B.V. All rights reserved.

On the bioavailability of trace metals in surface sediments: a combined geochemical and biological approach.

PubMed

Roosa, Stéphanie; Prygiel, Emilie; Lesven, Ludovic; Wattiez, Ruddy; Gillan, David; Ferrari, Benoît J D; Criquet, Justine; Billon, Gabriel

2016-06-01

The bioavailability of metals was estimated in three river sediments (Sensée, Scarpe, and Deûle Rivers) impacted by different levels of Cu, Cd, Pb, and Zn (Northern France). For that, a combination of geochemistry and biological responses (bacteria and chironomids) was used. The results obtained illustrate the complexity of the notion of "bioavailability." Indeed, geochemical indexes suggested a low toxicity, even in surface sediments with high concentrations of total metals and a predicted severe effect levels for the organisms. This was also suggested by the abundance of total bacteria as determined by DAPI counts, with high bacterial cell numbers even in contaminated areas. However, a fraction of metals may be bioavailable as it was shown for chironomid larvae which were able to accumulate an important quantity of metals in surface sediments within just a few days.We concluded that (1) the best approach to estimate bioavailability in the selected sediments is a combination of geochemical and biological approaches and that (2) the sediments in the Deûle and Scarpe Rivers are highly contaminated and may impact bacterial populations but also benthic invertebrates.

Medulloblastoma: Tumor Biology and Relevance to Treatment and Prognosis Paradigm.

PubMed

Coluccia, Daniel; Figuereido, Carlyn; Isik, Semra; Smith, Christian; Rutka, James T

2016-05-01

Medulloblastoma is a malignant embryonic brain tumor arising in the posterior fossa and typically occurring in pediatric patients. Current multimodal treatment regimes have significantly improved the survival rates; however, a marked heterogeneity in therapy response is observed, and one third of all patients die within 5 years after diagnosis. Large-scale genetic and transcriptome analysis revealed four medulloblastoma subgroups (WNT, SHH, Group 3, and Group 4) associated with different demographic parameters, tumor manifestation, and clinical behavior. Future treatment protocols will integrate molecular classification schemes to evaluate subgroup-specific intensification or de-escalation of adjuvant therapies aimed to increase tumor control and reduce iatrogenic induced morbidity. Furthermore, the identification of genetic drivers allows assessing target therapies in order to increase the chemotherapeutic armamentarium. This review highlights the biology behind the current classification system and elucidates relevant aspects of the disease influencing forthcoming clinical trials.

Enhancing biological relevance of a weighted gene co-expression network for functional module identification.

PubMed

Prom-On, Santitham; Chanthaphan, Atthawut; Chan, Jonathan Hoyin; Meechai, Asawin

2011-02-01

Relationships among gene expression levels may be associated with the mechanisms of the disease. While identifying a direct association such as a difference in expression levels between case and control groups links genes to disease mechanisms, uncovering an indirect association in the form of a network structure may help reveal the underlying functional module associated with the disease under scrutiny. This paper presents a method to improve the biological relevance in functional module identification from the gene expression microarray data by enhancing the structure of a weighted gene co-expression network using minimum spanning tree. The enhanced network, which is called a backbone network, contains only the essential structural information to represent the gene co-expression network. The entire backbone network is decoupled into a number of coherent sub-networks, and then the functional modules are reconstructed from these sub-networks to ensure minimum redundancy. The method was tested with a simulated gene expression dataset and case-control expression datasets of autism spectrum disorder and colorectal cancer studies. The results indicate that the proposed method can accurately identify clusters in the simulated dataset, and the functional modules of the backbone network are more biologically relevant than those obtained from the original approach.

Metal (II) Complexes Derived from Naphthofuran-2-carbohydrazide and Diacetylmonoxime Schiff Base: Synthesis, Spectroscopic, Electrochemical, and Biological Investigation

PubMed Central

Sumathi, R. B.; Halli, M. B.

2014-01-01

A new Schiff base and a new series of Co(II), Ni(II), Cu(II), Cd(II), and Hg(II) complexes were synthesized by the condensation of naphthofuran-2-carbohydrazide and diacetylmonoxime. Metal complexes of the Schiff base were prepared from their chloride salts of Co(II), Ni(II), Cu(II), Cd(II), and Hg(II) in ethanol. The ligand along with its metal complexes have been characterized on the basis of analytical data, IR, electronic, mass, 1HNMR, ESR spectral data, thermal studies, magnetic susceptibility, and molar conductance measurements. The nonelectrolytic behaviour of the complexes was assessed from the measured low conductance data. The elemental analysis of the complexes confirm the stoichiometry of the type CuL2Cl2 and MLCl2 where M = Ni(II), Co(II), Cd(II), and Hg(II) and L = Schiff base. The redox property of the Cu(II) complex was investigated by electrochemical method using cyclic voltammetry. In the light of these results, Co(II), Ni(II), and Cu(II) complexes are assigned octahedral geometry, Cd(II), and Hg(II) complexes tetrahedral geometry. In order to evaluate the effect of metal ions upon chelation, both the ligand and its metal complexes were screened for their antibacterial and antifungal activities by minimum inhibitory concentration (MIC) method. The DNA cleaving capacity of all the complexes was analysed by agarose gel electrophoresis method. PMID:24592203

geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.

PubMed

Reboiro-Jato, Miguel; Arrais, Joel P; Oliveira, José Luis; Fdez-Riverola, Florentino

2014-01-30

The diagnosis and prognosis of several diseases can be shortened through the use of different large-scale genome experiments. In this context, microarrays can generate expression data for a huge set of genes. However, to obtain solid statistical evidence from the resulting data, it is necessary to train and to validate many classification techniques in order to find the best discriminative method. This is a time-consuming process that normally depends on intricate statistical tools. geneCommittee is a web-based interactive tool for routinely evaluating the discriminative classification power of custom hypothesis in the form of biologically relevant gene sets. While the user can work with different gene set collections and several microarray data files to configure specific classification experiments, the tool is able to run several tests in parallel. Provided with a straightforward and intuitive interface, geneCommittee is able to render valuable information for diagnostic analyses and clinical management decisions based on systematically evaluating custom hypothesis over different data sets using complementary classifiers, a key aspect in clinical research. geneCommittee allows the enrichment of microarrays raw data with gene functional annotations, producing integrated datasets that simplify the construction of better discriminative hypothesis, and allows the creation of a set of complementary classifiers. The trained committees can then be used for clinical research and diagnosis. Full documentation including common use cases and guided analysis workflows is freely available at http://sing.ei.uvigo.es/GC/.

Biological and functional relevance of CASP predictions

PubMed Central

Liu, Tianyun; Ish‐Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D.

2017-01-01

Abstract Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo‐sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo‐sites), and Ten sites containing important motifs, loops, or key residues with important disease‐associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best‐ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand‐binding sites, most prediction methods have higher performance on apo‐sites than holo‐sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein‐protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein‐protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. PMID:28975675

Biological and functional relevance of CASP predictions.

PubMed

Liu, Tianyun; Ish-Shalom, Shirbi; Torng, Wen; Lafita, Aleix; Bock, Christian; Mort, Matthew; Cooper, David N; Bliven, Spencer; Capitani, Guido; Mooney, Sean D; Altman, Russ B

2018-03-01

Our goal is to answer the question: compared with experimental structures, how useful are predicted models for functional annotation? We assessed the functional utility of predicted models by comparing the performances of a suite of methods for functional characterization on the predictions and the experimental structures. We identified 28 sites in 25 protein targets to perform functional assessment. These 28 sites included nine sites with known ligand binding (holo-sites), nine sites that are expected or suggested by experimental authors for small molecule binding (apo-sites), and Ten sites containing important motifs, loops, or key residues with important disease-associated mutations. We evaluated the utility of the predictions by comparing their microenvironments to the experimental structures. Overall structural quality correlates with functional utility. However, the best-ranked predictions (global) may not have the best functional quality (local). Our assessment provides an ability to discriminate between predictions with high structural quality. When assessing ligand-binding sites, most prediction methods have higher performance on apo-sites than holo-sites. Some servers show consistently high performance for certain types of functional sites. Finally, many functional sites are associated with protein-protein interaction. We also analyzed biologically relevant features from the protein assemblies of two targets where the active site spanned the protein-protein interface. For the assembly targets, we find that the features in the models are mainly determined by the choice of template. © 2017 The Authors Proteins: Structure, Function and Bioinformatics Published by Wiley Periodicals, Inc.

Relevance in the science classroom: A multidimensional analysis

NASA Astrophysics Data System (ADS)

Hartwell, Matthew F.

While perceived relevance is considered a fundamental component of adaptive learning, the experience of relevance and its conceptual definition have not been well described. The mixed-methods research presented in this dissertation aimed to clarify the conceptual meaning of relevance by focusing on its phenomenological experience from the students' perspective. Following a critical literature review, I propose an identity-based model of perceived relevance that includes three components: a contextual target, an identity target, and a connection type, or lens. An empirical investigation of this model that consisted of two general phases was implemented in four 9th grade-biology classrooms. Participants in Phase 1 (N = 118) completed a series of four open-ended writing activities focused on eliciting perceived personal connections to academic content. Exploratory qualitative content analysis of a 25% random sample of the student responses was used to identify the main meaning-units of the proposed model as well as different dimensions of student relevance perceptions. These meaning-units and dimensions provided the basis for the construction of a conceptual mapping sentence capturing students' perceived relevance, which was then applied in a confirmatory analysis to all other student responses. Participants in Phase 2 (N = 139) completed a closed survey designed based on the mapping sentence to assess their perceived relevance of a biology unit. The survey also included scales assessing other domain-level motivational processes. Exploratory factor analysis and non-metric multidimensional scaling indicated a coherent conceptual structure, which included a primary interpretive relevance dimension. Comparison of the conceptual structure across various groups (randomly-split sample, gender, academic level, domain-general motivational profiles) provided support for its ubiquity and insight into variation in the experience of perceived relevance among students of different

Disorders of metal metabolism

PubMed Central

Ferreira, Carlos R.; Gahl, William A.

2017-01-01

Trace elements are chemical elements needed in minute amounts for normal physiology. Some of the physiologically relevant trace elements include iodine, copper, iron, manganese, zinc, selenium, cobalt and molybdenum. Of these, some are metals, and in particular, transition metals. The different electron shells of an atom carry different energy levels, with those closest to the nucleus being lowest in energy. The number of electrons in the outermost shell determines the reactivity of such an atom. The electron shells are divided in sub-shells, and in particular the third shell has s, p and d sub-shells. Transition metals are strictly defined as elements whose atom has an incomplete d sub-shell. This incomplete d sub-shell makes them prone to chemical reactions, particularly redox reactions. Transition metals of biologic importance include copper, iron, manganese, cobalt and molybdenum. Zinc is not a transition metal, since it has a complete d sub-shell. Selenium, on the other hand, is strictly speaking a nonmetal, although given its chemical properties between those of metals and nonmetals, it is sometimes considered a metalloid. In this review, we summarize the current knowledge on the inborn errors of metal and metalloid metabolism. PMID:29354481

Biomedical application of hierarchically built structures based on metal oxides

NASA Astrophysics Data System (ADS)

Korovin, M. S.; Fomenko, A. N.

2017-12-01

Nowadays, the use of hierarchically built structures in biology and medicine arouses much interest. The aim of this work is to review and summarize the available literature data about hierarchically organized structures in biomedical application. Nanoparticles can serve as an example of such structures. Medicine holds a special place among various application methods of similar systems. Special attention is paid to inorganic nanoparticles based on different metal oxides and hydroxides, such as iron, zinc, copper, and aluminum. Our investigations show that low-dimensional nanostructures based on aluminum oxides and hydroxides have an inhibitory effect on tumor cells and possess an antimicrobial activity. At the same time, it is obvious that the large-scale use of nanoparticles by humans needs to thoroughly study their properties. Special attention should be paid to the study of nanoparticle interaction with living biological objects. The numerous data show that there is no clear understanding of interaction mechanisms between nanoparticles and various cell types.

Type-2 diabetes-associated variants with cross-trait relevance: Post-GWAs strategies for biological function interpretation.

PubMed

Frau, Francesca; Crowther, Daniel; Ruetten, Hartmut; Allebrandt, Karla V

2017-05-01

Genome-wide association studies (GWAs) for type 2 diabetes (T2D) have been successful in identifying many loci with robust association signals. Nevertheless, there is a clear need for post-GWAs strategies to understand mechanism of action and clinical relevance of these variants. The association of several comorbidities with T2D suggests a common etiology for these phenotypes and complicates the management of the disease. In this study, we focused on the genetics underlying these relationships, using systems genomics to identify genetic variation associated with T2D and 12 other traits. GWAs studies summary statistics for pairwise comparisons were obtained for glycemic traits, obesity, coronary artery disease, and lipids from large consortia GWAs meta-analyses. We used a network medicine approach to leverage experimental information about the identified genes and variants with cross traits effects for biological function interpretation. We identified a set of 38 genetic variants with cross traits effects that point to a main network of genes that should be relevant for T2D and its comorbidities. We prioritized the T2D associated genes based on the number of traits they showed association with and the experimental evidence showing their relation to the disease etiology. In this study, we demonstrated how systems genomics and network medicine approaches can shed light into GWAs discoveries, translating findings into a more therapeutically relevant context. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

The present status of biological effects of toxic metals in the environment: lead, cadmium, and manganese.

PubMed

Shukla, G S; Singhal, R L

1984-08-01

The number of reports concerning the chemical toxicology of metals which are released in the environment by natural as well as anthropogenic sources, have been increasing constantly. Lead, cadmium, and manganese have found a variety of uses in industry, craft, and agriculture owing to their physical and chemical properties. The environmental burden of heavy metals has been rising substantially by smelter emission in air and waste sewage in water. Further, organic compounds of lead and manganese used as antiknock substances in gasoline are emitted into the atmosphere by automobile exhaustion. Such environmental contamination of air, water, soil, and food is a serious threat to all living kinds. Although these metals are known to produce their toxic effects on a variety of body systems, much emphasis has been placed on their effects on the nervous system owing to apparent association of relatively low or "subclinical" levels of metallic exposure with behavioral and psychological disorders. Clinical and animal data on environmental exposure show that while lead and manganese are most toxic to the nervous system, cadmium exerts profound adverse effects on kidney and the male reproductive system. It appears that the consequences of exposure to lead in adults are less severe than the types of exposure associated with hyperactivity in neonates. Except for a few reports, hyperactivity has indeed been observed in animals exposed to either of these three metals. Experimental work has also shown that these metals produce behavioral changes by altering the metabolism of brain neurotransmitters, especially catecholamines. Recently, it is hypothesized that these metals exert their toxic effect by damaging biological defences which exist in the body to serve as protective mechanisms against exogenous toxins. A voluminous publication list with diverse opinions on the biological effects of metals is available and there is an urgent need to compile assessment of the existing

Bioactive components on immuno-enhancement effects in the traditional Chinese medicine Shenqi Fuzheng Injection based on relevance analysis between chemical HPLC fingerprints and in vivo biological effects.

PubMed

Wang, Jinxu; Tong, Xin; Li, Peibo; Liu, Menghua; Peng, Wei; Cao, Hui; Su, Weiwei

2014-08-08

Shenqi Fuzheng Injection (SFI) is an injectable traditional Chinese herbal formula comprised of two Chinese herbs, Radix codonopsis and Radix astragali, which were commonly used to improve immune functions against chronic diseases in an integrative and holistic way in China and other East Asian countries for thousands of years. This present study was designed to explore the bioactive components on immuno-enhancement effects in SFI using the relevance analysis between chemical fingerprints and biological effects in vivo. According to a four-factor, nine-level uniform design, SFI samples were prepared with different proportions of the four portions separated from SFI via high speed counter current chromatography (HSCCC). SFI samples were assessed with high performance liquid chromatography (HPLC) for 23 identified components. For the immunosuppressed murine experiments, biological effects in vivo were evaluated on spleen index (E1), peripheral white blood cell counts (E2), bone marrow cell counts (E3), splenic lymphocyte proliferation (E4), splenic natural killer cell activity (E5), peritoneal macrophage phagocytosis (E6) and the amount of interleukin-2 (E7). Based on the hypothesis that biological effects in vivo varied with differences in components, multivariate relevance analysis, including gray relational analysis (GRA), multi-linear regression analysis (MLRA) and principal component analysis (PCA), were performed to evaluate the contribution of each identified component. The results indicated that the bioactive components of SFI on immuno-enhancement activities were calycosin-7-O-β-d-glucopyranoside (P9), isomucronulatol-7,2'-di-O-glucoside (P11), biochanin-7-glucoside (P12), 9,10-dimethoxypterocarpan-3-O-xylosylglucoside (P15) and astragaloside IV (P20), which might have positive effects on spleen index (E1), splenic lymphocyte proliferation (E4), splenic natural killer cell activity (E5), peritoneal macrophage phagocytosis (E6) and the amount of interleukin

In vitro physical, chemical, and biological evaluation of commercially available metal orthodontic brackets.

PubMed

Kim, Joo Hyoung; Cha, Jung Yul; Hwang, Chung Ju

2012-12-01

This in vitro study was undertaken to evaluate the physical, chemical, and biological properties of commercially available metal orthodontic brackets in South Korea, because national standards for these products are lacking. FOUR BRACKET BRANDS WERE TESTED FOR DIMENSIONAL ACCURACY, (MANUFACTURING ERRORS IN ANGULATION AND TORQUE), CYTOTOXICITY, COMPOSITION, ELUTION, AND CORROSION: Archist (Daeseung Medical), Victory (3M Unitek), Kosaka (Tomy), and Confidence (Shinye Odontology Materials). The tested rackets showed no significant differences in manufacturing errors in angulation, but Confidence brackets showed a significant difference in manufacturing errors in torque. None of the brackets were cytotoxic to mouse fibroblasts. The metal ion components did not show a regular increasing or decreasing trend of elution over time, but the volume of the total eluted metal ions increased: Archist brackets had the maximal Cr elution and Confidence brackets appeared to have the largest volume of total eluted metal ions because of excessive Ni elution. Confidence brackets showed the lowest corrosion resistance during potentiodynamic polarization. The results of this study could potentially be applied in establishing national standards for metal orthodontic brackets and in evaluating commercially available products.

Inert anode containing base metal and noble metal useful for the electrolytic production of aluminum

DOEpatents

Ray, Siba P.; Liu, Xinghua

2000-01-01

An inert anode for production of metals such as aluminum is disclosed. The inert anode comprises a base metal selected from Cu and Ag, and at least one noble metal selected from Ag, Pd, Pt, Au, Rh, Ru, Ir and Os. The inert anode may optionally be formed of sintered particles having interior portions containing more base metal than noble metal and exterior portions containing more noble metal than base metal. In a preferred embodiment, the base metal comprises Cu, and the noble metal comprises Ag, Pd or a combination thereof.

Comparison of the cytotoxicity of clinically relevant cobalt-chromium and alumina ceramic wear particles in vitro.

PubMed

Germain, M A; Hatton, A; Williams, S; Matthews, J B; Stone, M H; Fisher, J; Ingham, E

2003-02-01

Concern over polyethylene wear particle induced aseptic loosening of metal-on-polyethylene hip prostheses has led to renewed interest in alternative materials such as metal-on-metal and alumina ceramic-on-alumina ceramic for total hip replacement. This study compared the effects of clinically relevant cobalt-chromium and alumina ceramic wear particles on the viability of U937 histiocytes and L929 fibroblasts in vitro. Clinically relevant cobalt-chromium wear particles were generated using a flat pin-on-plate tribometer. The mean size of the clinically relevant metal particles was 29.5+/-6.3 nm (range 5-200 nm). Clinically relevant alumina ceramic particles were generated in the Leeds MkII anatomical hip simulator from a Mittelmieier prosthesis using micro-separation motion. This produced particles with a bimodal size distribution. The majority (98%) of the clinically relevant alumina ceramic wear debris was 5-20 nm in size. The cytotoxicity of the clinically relevant wear particles was compared to commercially available cobalt-chromium (9.87 microm+/-5.67) and alumina ceramic (0.503+/-0.19 microm) particles. The effects of the particles on the cells over a 5 day period at different particle volume (microm(3)) to cell number ratios were tested and viability determined using ATP-Lite(TM). Clinically relevant cobalt-chromium particles 50 and 5 microm(3) per cell reduced the viability of U937 cells by 97% and 42% and reduced the viability of L929 cells by 95% and 73%, respectively. At 50 microm(3) per cell, the clinically relevant ceramic particles reduced U937 cell viability by 18%. None of the other concentrations of the clinically relevant particles were toxic. The commercial cobalt-chromium and alumina particles did not affect the viability of either the U937 histiocytes or the L929 fibroblasts.Thus at equivalent particle volumes the clinically relevant cobalt-chromium particles were more toxic then the alumina ceramic particles. This study has emphasised the fact

The Metals in the Biological Periodic System of the Elements: Concepts and Conjectures

PubMed Central

Maret, Wolfgang

2016-01-01

A significant number of chemical elements are either essential for life with known functions, or present in organisms with poorly defined functional outcomes. We do not know all the essential elements with certainty and we know even less about the functions of apparently non-essential elements. In this article, I discuss a basis for a biological periodic system of the elements and that biochemistry should include the elements that are traditionally part of inorganic chemistry and not only those that are in the purview of organic chemistry. A biological periodic system of the elements needs to specify what “essential” means and to which biological species it refers. It represents a snapshot of our present knowledge and is expected to undergo further modifications in the future. An integrated approach of biometal sciences called metallomics is required to understand the interactions of metal ions, the biological functions that their chemical structures acquire in the biological system, and how their usage is fine-tuned in biological species and in populations of species with genetic variations (the variome). PMID:26742035

Accounting for metal bioavailability in assessing water quality: A step change?

PubMed

Merrington, Graham; Peters, Adam; Schlekat, Christian E

2016-02-01

Bioavailability of metals to aquatic organisms can be considered to be a combination of the physicochemical factors governing metal behavior and the specific pathophysiological characteristics of the organism's biological receptor. Effectively this means that a measure of bioavailability will reflect the exposures that organisms in the water column actually "experience". This is important because it has long been established that measures of total metal in waters have limited relevance to potential environmental risk. The concept of accounting for bioavailability in regard to deriving and implementing environmental water quality standards is not new, but the regulatory reality has lagged behind the development of scientific evidence supporting the concept. Practical and technical reasons help to explain this situation. For example, concerns remain from regulators and the regulated that the efforts required to change existing systems of metal environmental protection that have been in place for over 35 yr are so great as not to be commensurate with likely benefits. However, more regulatory jurisdictions are now considering accounting for metal bioavailability in assessments of water quality as a means to support evidence-based decision-making. In the past decade, both the US Environmental Protection Agency and the European Commission have established bioavailability-based standards for metals, including Cu and Ni. These actions have shifted the debate toward identifying harmonized approaches for determining when knowledge is adequate to establish bioavailability-based approaches and how to implement them. © 2016 SETAC.

Metallic Nanostructures Based on DNA Nanoshapes

PubMed Central

Shen, Boxuan; Tapio, Kosti; Linko, Veikko; Kostiainen, Mauri A.; Toppari, Jari Jussi

2016-01-01

Metallic nanostructures have inspired extensive research over several decades, particularly within the field of nanoelectronics and increasingly in plasmonics. Due to the limitations of conventional lithography methods, the development of bottom-up fabricated metallic nanostructures has become more and more in demand. The remarkable development of DNA-based nanostructures has provided many successful methods and realizations for these needs, such as chemical DNA metallization via seeding or ionization, as well as DNA-guided lithography and casting of metallic nanoparticles by DNA molds. These methods offer high resolution, versatility and throughput and could enable the fabrication of arbitrarily-shaped structures with a 10-nm feature size, thus bringing novel applications into view. In this review, we cover the evolution of DNA-based metallic nanostructures, starting from the metallized double-stranded DNA for electronics and progress to sophisticated plasmonic structures based on DNA origami objects. PMID:28335274

Novel alanines bearing a heteroaromatic side chain: synthesis and studies on fluorescent chemosensing of metal cations with biological relevance.

PubMed

Ferreira, Rosa Cristina M; Raposo, Maria Manuela M; Costa, Susana P G

2018-06-01

A family of novel thienylbenzoxazol-5-yl-L-alanines, consisting of an alanine core bearing a benzoxazole at the side chain with a thiophene ring at position 2, substituted with different (hetero)aryl substituents, was synthesised to study the tuning of the photophysical and chemosensory properties of the resulting compounds. These novel heterocyclic alanines 3a-f and a series of structurally related bis-thienylbenzoxazolyl-alanines 3g-j were evaluated for the first time in the recognition of selected metal cations with environmental, medicinal and analytical interest such as Co 2+ , Cu 2+ , Zn 2+ and Ni 2+ , in acetonitrile solution, with the heterocycles at the side chain acting simultaneously as the coordinating and reporting units, via fluorescence changes. This behaviour can be explained by the involvement of the electron donor heteroatoms in the recognition event, through complexation of the metal cations. The spectrofluorimetric titrations showed that thienylbenzoxazolyl-alanines 3a-j and 4a,b were non-selective fluorimetric chemosensors for the above-mentioned cations, with the best results being obtained for the interaction of Cu 2+ with bis-alanine 3j and deprotected alanines 4a,b. The encouraging photophysical and metal ion sensing properties of these thienylbenzoxazolyl-alanines suggest that they can be used to obtain bioinspired fluorescent reporters for metal ion such as peptides/proteins with chemosensory/probing ability.

Qcritical as a Geomorphically and Biologically Relevant Flow Threshold for Stormwater Management and Catchment-scale Stream Restoration

NASA Astrophysics Data System (ADS)

Hawley, R. J.; Vietz, G. J.; Wooten, M. S.

2016-12-01

The threshold discharge that initiates streambed mobilization (Qcritical) is one of the most mechanistically-important flows for geomorphic function and biological integrity in stream ecosystems. Increased frequency and duration of flows that exceed Qcritical are a dominant driver of geomorphic instability and excess benthic disturbance in urban/suburban streams (i.e. the urban disturbance regime). Qcritical frequency also corresponds to measures of stream integrity in reference streams, with both geomorphic stability and biological indices significantly correlated to time since a Qcritical event in one 7-y study. Indeed, reference site macroinvertebrate communities during years with atypically frequent Qcritical events were more similar to sites draining watersheds with 30% imperviousness than to reference site communities of more typical rainfall years. Despite its biophysical relevance to stream ecosystems, Qcritical is one of the most overlooked and misunderstood flows in the stormwater management and stream restoration fields. Regional stormwater policies and stream restoration design guidance are often based on the misplaced assumption that streambed erosion does not occur at sub-bankfull events (often assumed to correspond to the 1-y recurrence discharge). Using an international database of nearly 200 sites we show that Qcritical varies by several orders of magnitude as a function of streambed particle size. Qcritical in sand-dominated streams is likely to be orders of magnitude less than the 1-yr discharge, whereas Qcritical in cobble/boulder dominated streams could be much larger than the 1-yr discharge, implying that stormwater/restoration policies focused on the 1-yr event could lack efficacy in many stream settings. Qcritical is a geomorphically- and biologically-relevant discharge threshold when developing stormwater management policies intended to protect streams from excess erosion, designing watershed-scale restoration efforts to restore a more

Biological nitric oxide signalling: chemistry and terminology

PubMed Central

Heinrich, Tassiele A; da Silva, Roberto S; Miranda, Katrina M; Switzer, Christopher H; Wink, David A; Fukuto, Jon M

2013-01-01

Biological nitrogen oxide signalling and stress is an area of extreme clinical, pharmacological, toxicological, biochemical and chemical research interest. The utility of nitric oxide and derived species as signalling agents is due to their novel and vast chemical interactions with a variety of biological targets. Herein, the chemistry associated with the interaction of the biologically relevant nitrogen oxide species with fundamental biochemical targets is discussed. Specifically, the chemical interactions of nitrogen oxides with nucleophiles (e.g. thiols), metals (e.g. hemeproteins) and paramagnetic species (e.g. dioxygen and superoxide) are addressed. Importantly, the terms associated with the mechanisms by which NO (and derived species) react with their respective biological targets have been defined by numerous past chemical studies. Thus, in order to assist researchers in referring to chemical processes associated with nitrogen oxide biology, the vernacular associated with these chemical interactions is addressed. PMID:23617570

[The common bed bug (Cimex lectularius) - biology, medical relevance, possibilities for the detection and control].

PubMed

Rupeš, V; Vlčková, J; Holý, O; Horáková, D; Azeem, K; Kollárová, H

2017-01-01

Bed bugs have become a major concern worldwide in the 21st century and are therefore intensively investigated. The new findings not only extend the knowledge of their biology, medical relevance, and causes of the resurgence, but also can be used in bed bug management. A brief overview is provided of some of the most important research results and opinions, published in the last few years in prestigious international journals.

Bio-recycling of metals: Recycling of technical products using biological applications.

PubMed

Pollmann, Katrin; Kutschke, Sabine; Matys, Sabine; Raff, Johannes; Hlawacek, Gregor; Lederer, Franziska L

2018-03-16

The increasing demand of different essential metals as a consequence of the development of new technologies, especially in the so called "low carbon technologies" require the development of innovative technologies that enable an economic and environmentally friendly metal recovery from primary and secondary resources. There is serious concern that the demand of some critical elements might exceed the present supply within a few years, thus necessitating the development of novel strategies and technologies to meet the requirements of industry and society. Besides an improvement of exploitation and processing of ores, the more urgent issue of recycling of strategic metals has to be enforced. However, current recycling rates are very low due to the increasing complexity of products and the low content of certain critical elements, thus hindering an economic metal recovery. On the other hand, increasing environmental consciousness as well as limitations of classical methods require innovative recycling methodologies in order to enable a circular economy. Modern biotechnologies can contribute to solve some of the problems related to metal recycling. These approaches use natural properties of organisms, bio-compounds, and biomolecules to interact with minerals, materials, metals, or metal ions such as surface attachment, mineral dissolution, transformation, and metal complexation. Further, modern genetic approaches, e.g. realized by synthetic biology, enable the smart design of new chemicals. The article presents some recent developments in the fields of bioleaching, biosorption, bioreduction, and bioflotation, and their use for metal recovery from different waste materials. Currently only few of these developments are commercialized. Major limitations are high costs in comparison to conventional methods and low element selectivity. The article discusses future trends to overcome these barriers. Especially interdisciplinary approaches, the combination of different

Prognostic relevance of biological subtype overrides that of TNM staging in breast cancer: discordance between stage and biology.

PubMed

Jung, Hyun Ae; Park, Yeon Hee; Kim, Moonjin; Kim, Sungmin; Chang, Won Jin; Choi, Moon Ki; Hong, Jung Yong; Kim, Seok Won; Kil, Won Ho; Lee, Jeong Eon; Nam, Seok Jin; Ahn, Jin Seok; Im, Young-Hyuck

2015-02-01

Recently, we faced difficult treatment decisions regarding appropriate adjuvant systemic treatment, especially for patients who show discordance between stage and tumor biology. The aim of this study was to compare the prognostic relevance of the TNM staging system with that of intrinsic subtype in breast cancer. We retrospectively identified women patients who received curative surgery for stage I-III breast cancer with available data on immunohistochemistry profiles including hormone receptor (HR) status, human epidermal growth factor receptor 2 (HER2) status, and Ki 67 staining at the Samsung Medical Center from January 2004 to September 2008. Primary outcomes were recurrence-free survival (RFS) and overall survival (OS). A total of 1145 patients were diagnosed with breast cancer and received curative surgery. Of these, 463 (40.4%) patients were stage I, and 682 (59.6%) were stage II or III. In addition, 701 (61.2%) patients were HR positive, 239 (20.9%) were HER2 positive, and 205 (20.9%) had triple-negative breast cancer. The 5-year RFS for the patients who were HR positive and HER2 negative with a low Ki 67 staining score (0-25%) was 99%. The 5-year RFS for patients who were HER2-positive or had triple-negative breast cancer were 89 and 83%, respectively (P value = <0.001). In multivariate analysis, advanced stage (II/III) and unfavorable biology (HER2 positive or triple negative) retained their statistical significance as predictors of decreased RFS and OS. Patients with advanced-stage disease (II or III) but favorable tumor biology (HR positive and HER2 negative and low Ki 67) had better clinical outcomes than those with stage I disease and unfavorable tumor biology in terms of RFS (99 versus 92%, P value = 0.011) and OS (99 versus 96%, P value = 0.03) at 5 years. The current results showed that intrinsic subtype has a greater prognostic impact in predicting clinical outcomes in subpopulations of patients with stage I-III breast cancer who show

Non-noble metal based metallization systems

NASA Technical Reports Server (NTRS)

Garcia, A., III

1983-01-01

The results of efforts to produce a nonsilver metallization system for silicon photovoltaic cells are given. The system uses a metallization system based on molybdenum, tin, and titanium hydride. The initial work in this system was done using the MIDFILM process. The MIDFILM process attains a line resolution comparable to photoresist methods with a process related to screen printing. The surface to be processed is first coated with a thin layer of photopolymer material. Upon exposure to ultraviolet light through a suitable mask, the polymer in the non-pattern area crosslinks and becomes hard. The unexposed pattern areas remain tacky. The conductor material is then applied in the form of a dry mixture of metal which adheres to the tacky pattern area. The assemblage is then fired to ash the photopolymer and sinter the conductor powder.

Chemical and biological methods to evaluate the availability of heavy metals in soils of the Siena urban area (Italy).

PubMed

Nannoni, Francesco; Protano, Giuseppe

2016-10-15

A biogeochemistry field study was conducted in the Siena urban area (Italy) with the main objective of establishing the relationship between available amounts of heavy metals in soil assessed by a chemical method (soil fractionation) and bioavailability assessed by a biological method (bioaccumulation in earthworm tissues). The total content of traffic-related (Cd, Cu, Pb, Sb, Zn) and geogenic (Co, Cr, Ni, U) heavy metals in uncontaminated and contaminated soils and their concentrations in soil fractions and earthworms were used for this purpose. The bioavailability of heavy metals assessed by earthworms did not always match the availability defined by soil fractionation. Earthworms were a good indicator to assess the bioavailability of Pb and Sb in soil, while due to physiological mechanisms of regulation and excretion, Cd, Cu and Zn tissue levels in these invertebrates gave misleading estimates of their bioavailable pool. No relationship was identified between chemical and biological availability for the geogenic heavy metals, characterized by a narrow range of total contents in soil. The study highlighted that chemical and biological methods should be combined to provide more complete information about heavy element bioavailability in soils. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthesis, characterization and biological approach of metal chelates of some first row transition metal ions with halogenated bidentate coumarin Schiff bases containing N and O donor atoms.

PubMed

Prabhakara, Chetan T; Patil, Sangamesh A; Toragalmath, Shivakumar S; Kinnal, Shivashankar M; Badami, Prema S

2016-04-01

The impregnation of halogen atoms in a molecule is an emerging trend in pharmaceutical chemistry. The presence of halogens (Cl, Br, I and F) increases the lipophilic nature of molecule and improves the penetration of lipid membrane. The presence of electronegative halogen atoms increases the bio- activity of core moiety. In the present study, Co(II), Ni(II) and Cu(II) complexes are synthesised using Schiff bases (HL(I) and HL(II)), derived from 8-formyl-7-hydroxy-4-methylcoumarin/3-chloro-8-formyl-7-hydroxy-4-methylcoumarin with 2,4-difluoroaniline/o-toluidine respectively. The synthesized compounds were characterized by spectral (IR, NMR, UV-visible, Mass, ESI-MS, ESR), thermal, fluorescence and molar conductivity studies. All the synthesized metal complexes are completely soluble in DMF and DMSO. The non-electrolytic nature of the metal complexes was confirmed by molar conductance studies. Elemental analysis study suggest [ML2(H2O)2] stoichiometry, here M=Co(II), Ni(II) and Cu(II), L=deprotonated ligand. The obtained IR data supports the binding of metal ion to Schiff base. Thermal study suggests the presence of coordinated water molecules. Electronic spectral results reveal six coordinated geometry for the synthesized metal complexes. The Schiff bases and their metal complexes were evaluated for antibacterial (Pseudomonas aureginosa and Proteus mirabilis), antifungal (Aspergillus niger and Rhizopus oryzae), anthelmintic (Pheretima posthuma) and DNA cleavage (Calf Thymus DNA) activities. Copyright © 2016 Elsevier B.V. All rights reserved.

New Fe-based superconductors: properties relevant for applications

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

Putti, M; Pallecchi, I; Bellingeri, E

2009-01-01

Less than two years after the discovery of high temperature superconductivity in oxypnictide LaFeAs(O, F) several families of superconductors based on Fe layers (1111, 122, 11, 111) are available. They share several characteristics with cuprate superconductors that compromise easy applications, such as the layered structure, the small coherence length and unconventional pairing. On the other hand, the Fe-based superconductors have metallic parent compounds and their electronic anisotropy is generally smaller and does not strongly depend on the level of doping, and the supposed order parameter symmetry is s-wave, thus in principle not so detrimental to current transmission across grain boundaries.more » From the application point of view, the main efforts are still devoted to investigate the superconducting properties, to distinguish intrinsic from extrinsic behaviors and to compare the different families in order to identify which one is the fittest for the quest for better and more practical superconductors. The 1111 family shows the highest T{sub c}, huge but also the most anisotropic upper critical field and in-field, fan-shaped resistive transitions reminiscent of those of cuprates. On the other hand, the 122 family is much less anisotropic with sharper resistive transitions as in low temperature superconductors, but with about half the T{sub c} of the 1111 compounds. An overview of the main superconducting properties relevant to applications will be presented. Upper critical field, electronic anisotropy parameter, and intragranular and intergranular critical current density will be discussed and compared, where possible, across the Fe-based superconductor families.« less

Peroxotitanates for Biodelivery of Metals

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

Hobbs, David; Elvington, M.

2009-02-11

Metal-based drugs are largely undeveloped in pharmacology. One limiting factor is the systemic toxicity of metal-based compounds. A solid-phase, sequestratable delivery agent for local delivery of metals could reduce systemic toxicity, facilitating new drug development in this nascent area. Amorphous peroxotitanates (APT) are ion exchange materials with high affinity for several heavy metal ions, and have been proposed to deliver or sequester metal ions in biological contexts. In the current study, we tested a hypothesis that APT are able to deliver metals or metal compounds to cells. We exposed fibroblasts (L929) or monocytes (THP1) to metal-APT materials for 72 hmore » in vitro, then measured cellular mitochondrial activity (SDH-MTT method) to assess the biological impact of the metal-APT materials vs. metals or APT alone. APT alone did not significantly affect cellular mitochondrial activity, but all metal-APT materials suppressed the mitochondrial activity of fibroblasts (by 30-65% of controls). The concentration of metal-APT materials required to suppress cellular mitochondrial activity was below that required for metals alone, suggesting that simple extracellular release of the metals from the metal-APT materials was not the primary mechanism of mitochondrial suppression. In contrast to fibroblasts, no metal-APT material had a measurable effect on THP1 monocyte mitochondrial activity, despite potent suppression by metals alone. This latter result suggested that 'biodelivery' by metal-APT materials may be cell type-specific. Therefore, it appears that APT are plausible solid phase delivery agents of metals or metal compounds to some types of cells for potential therapeutic effect.« less

Advanced nanoelectronic architectures for THz-based biological agent detection

NASA Astrophysics Data System (ADS)

Woolard, Dwight L.; Jensen, James O.

2009-02-01

The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

Graphical determination of metal bioavailability to soil invertebrates utilizing the Langmuir sorption model

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

Donkin, S.G.

1997-09-01

A new method of performing soil toxicity tests with free-living nematodes exposed to several metals and soil types has been adapted to the Langmuir sorption model in an attempt at bridging the gap between physico-chemical and biological data gathered in the complex soil matrix. Pseudo-Langmuir sorption isotherms have been developed using nematode toxic responses (lethality, in this case) in place of measured solvated metal, in order to more accurately model bioavailability. This method allows the graphical determination of Langmuir coefficients describing maximum sorption capacities and sorption affinities of various metal-soil combinations in the context of real biological responses of indigenousmore » organisms. Results from nematode mortality tests with zinc, cadmium, copper, and lead in four soil types and water were used for isotherm construction. The level of agreement between these results and available literature data on metal sorption behavior in soils suggests that biologically relevant data may be successfully fitted to sorption models such as the Langmuir. This would allow for accurate prediction of soil contaminant concentrations which have minimal effect on indigenous invertebrates.« less

Sensing of biologically relevant d-metal ions using a Eu(III)-cyclen based luminescent displacement assay in aqueous pH 7.4 buffered solution.

PubMed

Kotova, Oxana; Comby, Steve; Gunnlaugsson, Thorfinnur

2011-06-28

1·Eu·BPS was developed as a luminescent lanthanide sensor for use in displacement assays for detection of d-metal ions by monitoring the changes in the europium emission, which was quenched for iron(II), with a detection limit of ∼10 pM (0.002 μg L(-1)) for Fe(II) in buffered pH 7.4 solution. This journal is © The Royal Society of Chemistry 2011

Biologically relevant photoacoustic imaging phantoms with tunable optical and acoustic properties

PubMed Central

Vogt, William C.; Jia, Congxian; Wear, Keith A.; Garra, Brian S.; Joshua Pfefer, T.

2016-01-01

Abstract. Established medical imaging technologies such as magnetic resonance imaging and computed tomography rely on well-validated tissue-simulating phantoms for standardized testing of device image quality. The availability of high-quality phantoms for optical-acoustic diagnostics such as photoacoustic tomography (PAT) will facilitate standardization and clinical translation of these emerging approaches. Materials used in prior PAT phantoms do not provide a suitable combination of long-term stability and realistic acoustic and optical properties. Therefore, we have investigated the use of custom polyvinyl chloride plastisol (PVCP) formulations for imaging phantoms and identified a dual-plasticizer approach that provides biologically relevant ranges of relevant properties. Speed of sound and acoustic attenuation were determined over a frequency range of 4 to 9 MHz and optical absorption and scattering over a wavelength range of 400 to 1100 nm. We present characterization of several PVCP formulations, including one designed to mimic breast tissue. This material is used to construct a phantom comprised of an array of cylindrical, hemoglobin-filled inclusions for evaluation of penetration depth. Measurements with a custom near-infrared PAT imager provide quantitative and qualitative comparisons of phantom and tissue images. Results indicate that our PVCP material is uniquely suitable for PAT system image quality evaluation and may provide a practical tool for device validation and intercomparison. PMID:26886681

Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species

PubMed Central

André, Nicole M.

2018-01-01

ABSTRACT The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses, we argue that consideration of biological properties in addition to sequence-based demarcations is critical for generating useful taxonomy that recapitulates complex evolutionary histories. Within the Alphacoronavirus genus, the Alphacoronavirus 1 species encompasses several biologically distinct viruses. We carried out functionally based phylogenetic analysis, centered on the spike gene, which encodes the main surface antigen and primary driver of tropism and pathogenesis. Within the Alphacoronavirus 1 species, we identify clade A (encompassing serotype I feline coronavirus [FCoV] and canine coronavirus [CCoV]) and clade B (grouping serotype II FCoV and CCoV and transmissible gastroenteritis virus [TGEV]-like viruses). We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the Alphacoronavirus genus. IMPORTANCE Our work focuses on improving the classification of the Alphacoronavirus genus. The Alphacoronavirus 1 species groups viruses of veterinary importance that infect distinct mammalian hosts and includes canine and feline coronaviruses and transmissible gastroenteritis virus. It is the prototype species of the Alphacoronavirus genus; however, it encompasses biologically distinct viruses. To better characterize this prototypical species, we performed phylogenetic analyses based on the sequences of the spike protein, one of the main determinants of tropism and pathogenesis, and reveal the existence of two subgroups or clades that fit with previously established serotype demarcations. We propose a new clade designation to better classify Alphacoronavirus 1 members. PMID:29299531

Improving Virus Taxonomy by Recontextualizing Sequence-Based Classification with Biologically Relevant Data: the Case of the Alphacoronavirus 1 Species.

PubMed

Whittaker, Gary R; André, Nicole M; Millet, Jean Kaoru

2018-01-01

The difficulties related to virus taxonomy have been amplified by recent advances in next-generation sequencing and metagenomics, prompting the field to revisit the question of what constitutes a useful viral classification. Here, taking a challenging classification found in coronaviruses, we argue that consideration of biological properties in addition to sequence-based demarcations is critical for generating useful taxonomy that recapitulates complex evolutionary histories. Within the Alphacoronavirus genus, the Alphacoronavirus 1 species encompasses several biologically distinct viruses. We carried out functionally based phylogenetic analysis, centered on the spike gene, which encodes the main surface antigen and primary driver of tropism and pathogenesis. Within the Alphacoronavirus 1 species, we identify clade A (encompassing serotype I feline coronavirus [FCoV] and canine coronavirus [CCoV]) and clade B (grouping serotype II FCoV and CCoV and transmissible gastroenteritis virus [TGEV]-like viruses). We propose this clade designation, along with the newly proposed Alphacoronavirus 2 species, as an improved way to classify the Alphacoronavirus genus. IMPORTANCE Our work focuses on improving the classification of the Alphacoronavirus genus. The Alphacoronavirus 1 species groups viruses of veterinary importance that infect distinct mammalian hosts and includes canine and feline coronaviruses and transmissible gastroenteritis virus. It is the prototype species of the Alphacoronavirus genus; however, it encompasses biologically distinct viruses. To better characterize this prototypical species, we performed phylogenetic analyses based on the sequences of the spike protein, one of the main determinants of tropism and pathogenesis, and reveal the existence of two subgroups or clades that fit with previously established serotype demarcations. We propose a new clade designation to better classify Alphacoronavirus 1 members.

Nutrient enrichment and fish nutrient tolerance: Assessing biologically relevant nutrient criteria

USGS Publications Warehouse

Meador, Michael R.

2013-01-01

Relationships between nutrient concentrations and fish nutrient tolerance were assessed relative to established nutrient criteria. Fish community, nitrate plus nitrite (nitrate), and total phosphorus (TP) data were collected during summer low-flow periods in 2003 and 2004 at stream sites along a nutrient-enrichment gradient in an agricultural basin in Indiana and Ohio and an urban basin in the Atlanta, Georgia, area. Tolerance indicator values for nitrate and TP were assigned for each species and averaged separately for fish communities at each site (TIVo). Models were used to predict fish species expected to occur at a site under minimally disturbed conditions and average tolerance indicator values were determined for nitrate and TP separately for expected communities (TIVe). In both areas, tolerance scores (TIVo/TIVe) for nitrate increased significantly with increased nitrate concentrations whereas no significant relationships were detected between TP tolerance scores and TP concentrations. A 0% increase in the tolerance score (TIVo/TIVe = 1) for nitrate corresponded to a nitrate concentration of 0.19 mg/l (compared with a USEPA summer nitrate criterion of 0.17 mg/l) in the urban area and 0.31 mg/l (compared with a USEPA summer nitrate criterion of 0.86 mg/l) in the agricultural area. Fish nutrient tolerance values offer the ability to evaluate nutrient enrichment based on a quantitative approach that can provide insights into biologically relevant nutrient criteria.

Teaching Cell Biology to Dental Students with a Project-Based Learning Approach.

PubMed

Costa-Silva, Daniela; Côrtes, Juliana A; Bachinski, Rober F; Spiegel, Carolina N; Alves, Gutemberg G

2018-03-01

Although the discipline of cell biology (CB) is part of the curricula of predoctoral dental schools, students often fail to recognize its practical relevance. The aim of this study was to assess the effectiveness of a practical-theoretical project-based course in closing the gaps among CB, scientific research, and dentistry for dental students. A project-based learning course was developed with nine sequential lessons to evaluate 108 undergraduate dental students enrolled in CB classes of a Brazilian school of dentistry during 2013-16. To highlight the relevance of in vitro studies in the preclinical evaluation of dental materials at the cellular level, the students were challenged to complete the process of drafting a protocol and performing a cytocompatibility assay for a bone substitute used in dentistry. Class activities included small group discussions, scientific database search and article presentations, protocol development, lab experimentation, and writing of a final scientific report. A control group of 31 students attended only one laboratory class on the same theme, and the final reports were compared between the two groups. The results showed that the project-based learning students had superior outcomes in acknowledging the relevance of in vitro methods during biocompatibility testing. Moreover, they produced scientifically sound reports with more content on methodological issues, the relationship with dentistry, and the scientific literature than the control group (p<0.05). The project-based learning students also recognized a higher relevance of scientific research and CB to dental practice. These results suggest that a project-based approach can help contextualize scientific research in dental curricula.

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense.

PubMed

Yu, Agnès; Lepère, Gersende; Jay, Florence; Wang, Jingyu; Bapaume, Laure; Wang, Yu; Abraham, Anne-Laure; Penterman, Jon; Fischer, Robert L; Voinnet, Olivier; Navarro, Lionel

2013-02-05

DNA methylation is an epigenetic mark that silences transposable elements (TEs) and repeats. Whereas the establishment and maintenance of DNA methylation are relatively well understood, little is known about their dynamics and biological relevance in plant and animal innate immunity. Here, we show that some TEs are demethylated and transcriptionally reactivated during antibacterial defense in Arabidopsis. This effect is correlated with the down-regulation of key transcriptional gene silencing factors and is partly dependent on an active demethylation process. DNA demethylation restricts multiplication and vascular propagation of the bacterial pathogen Pseudomonas syringae in leaves and, accordingly, some immune-response genes, containing repeats in their promoter regions, are negatively regulated by DNA methylation. This study provides evidence that DNA demethylation is part of a plant-induced immune response, potentially acting to prime transcriptional activation of some defense genes linked to TEs/repeats.

Development of peptoid-based ligands for the removal of cadmium from biological media

DOE PAGES

Knight, Abigail S.; Zhou, Effie Y.; Francis, Matthew B.

2015-05-14

Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate themore » significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.« less

Development of peptoid-based ligands for the removal of cadmium from biological media

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

Knight, Abigail S.; Zhou, Effie Y.; Francis, Matthew B.

Cadmium poisoning poses a serious health concern due to cadmium's increasing industrial use, yet there is currently no recommended treatment. The selective coordination of cadmium in a biological environment—i.e. in the presence of serum ions, small molecules, and proteins—is a difficult task. To address this challenge, a combinatorial library of peptoid-based ligands has been evaluated to identify structures that selectively bind to cadmium in human serum with minimal chelation of essential metal ions. Eighteen unique ligands were identified in this screening procedure, and the binding affinity of each was measured using metal titrations monitored by UV-vis spectroscopy. To evaluate themore » significance of each chelating moiety, sequence rearrangements and substitutions were examined. Analysis of a metal–ligand complex by NMR spectroscopy highlighted the importance of particular residues. Depletion experiments were performed in serum mimetics and human serum with exogenously added cadmium. These depletion experiments were used to compare and demonstrate the ability of these peptoids to remove cadmium from blood-like mixtures. In one of these depletion experiments, the peptoid sequence was able to deplete the cadmium to a level comparable to the reported acute toxicity limit. Evaluation of the metal selectivity in buffered solution and in human serum was performed to verify minimal off-target binding. These studies highlight a screening platform for the identification of metal–ligands that are capable of binding in a complex environment. They additionally demonstrate the potential utility of biologically-compatible ligands for the treatment of heavy metal poisoning.« less

BicPAMS: software for biological data analysis with pattern-based biclustering.

PubMed

Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

2017-02-02

Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the

Chemical Foundations of Hydrogen Sulfide Biology

PubMed Central

Li, Qian; Lancaster, Jack R.

2013-01-01

Following nitric oxide (nitrogen monoxide) and carbon monoxide, hydrogen sulfide (or its newer systematic name sulfane, H2S) became the third small molecule that can be both toxic and beneficial depending on the concentration. In spite of its impressive therapeutic potential, the underlying mechanisms for its beneficial effects remain unclear. Any novel mechanism has to obey fundamental chemical principles. H2S chemistry was studied long before its biological relevance was discovered, however, with a few exceptions, these past works have received relatively little attention in the path of exploring the mechanistic conundrum of H2S biological functions. This review calls attention to the basic physical and chemical properties of H2S, focuses on the chemistry between H2S and its three potential biological targets: oxidants, metals and thiol derivatives, discusses the applications of these basics into H2S biology and methodology, and introduces the standard terminology to this youthful field. PMID:23850631

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Blood metal levels and third trimester maternal plasma matrix metalloproteinases (MMPs).

PubMed

Au, Felicia; Bielecki, Agnieszka; Blais, Erica; Fisher, Mandy; Cakmak, Sabit; Basak, Ajoy; Gomes, James; Arbuckle, Tye E; Fraser, William D; Vincent, Renaud; Kumarathasan, Prem

2016-09-01

While it is known that in utero exposure to environmental toxicants, namely heavy metals, can adversely affect the neonate, there remains a significant paucity of information on maternal biological changes specific to metal exposures during pregnancy. This study aims at identifying associations between maternal metal exposures and matrix metalloproteinases (MMPs) that are known to be engaged in pregnancy process. Third trimester maternal plasma (n = 1533) from a pregnancy cohort (Maternal-Infant Research on Environmental Chemicals Study, MIREC) were analyzed for MMP-1,-2,-7,-9 and -10 by affinity-based multiplex protein array analyses. Maternal metal concentrations (mercury, cadmium, lead, arsenic and manganese) in 1st and 3rd trimesters exhibited strong correlations (p < 0.05). Multivariate regression models were used to estimate odds ratio (OR) for the association between metal concentrations in quartiles and high (90%) and low (10%) maternal MMP levels. Significant (p < 0.05) metal exposure-related effects were observed with the different MMP isoform responses. MMP profiles were specific to the trimester at which the maternal blood metals were analyzed. Our findings suggest that the profiles of these MMP isoforms vary with the type of metal exposure, blood metal concentrations and the trimester at which metal levels were determined. These new findings on maternal metal-MMP relationships can guide future explorations on toxicity mechanisms relevant to metal exposure-mediated adverse birth outcomes. Copyright © 2016. Published by Elsevier Ltd.

Biological-based and physical-based optimization for biological evaluation of prostate patient's plans

NASA Astrophysics Data System (ADS)

Sukhikh, E.; Sheino, I.; Vertinsky, A.

2017-09-01

Modern modalities of radiation treatment therapy allow irradiation of the tumor to high dose values and irradiation of organs at risk (OARs) to low dose values at the same time. In this paper we study optimal radiation treatment plans made in Monaco system. The first aim of this study was to evaluate dosimetric features of Monaco treatment planning system using biological versus dose-based cost functions for the OARs and irradiation targets (namely tumors) when the full potential of built-in biological cost functions is utilized. The second aim was to develop criteria for the evaluation of radiation dosimetry plans for patients based on the macroscopic radiobiological criteria - TCP/NTCP. In the framework of the study four dosimetric plans were created utilizing the full extent of biological and physical cost functions using dose calculation-based treatment planning for IMRT Step-and-Shoot delivery of stereotactic body radiation therapy (SBRT) in prostate case (5 fractions per 7 Gy).

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

PubMed Central

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

2013-01-01

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

Simple Biological Systems for Assessing the Activity of Superoxide Dismutase Mimics

PubMed Central

Tovmasyan, Artak; Reboucas, Julio S.

2014-01-01

Abstract Significance: Half a century of research provided unambiguous proof that superoxide and species derived from it—reactive oxygen species (ROS)—play a central role in many diseases and degenerative processes. This stimulated the search for pharmaceutical agents that are capable of preventing oxidative damage, and methods of assessing their therapeutic potential. Recent Advances: The limitations of superoxide dismutase (SOD) as a therapeutic tool directed attention to small molecules, SOD mimics, that are capable of catalytically scavenging superoxide. Several groups of compounds, based on either metal complexes, including metalloporphyrins, metallocorroles, Mn(II) cyclic polyamines, and Mn(III) salen derivatives, or non-metal based compounds, such as fullerenes, nitrones, and nitroxides, have been developed and studied in vitro and in vivo. Very few entered clinical trials. Critical Issues and Future Directions: Development of SOD mimics requires in-depth understanding of their mechanisms of biological action. Elucidation of both molecular features, essential for efficient ROS-scavenging in vivo, and factors limiting the potential side effects requires biologically relevant and, at the same time, relatively simple testing systems. This review discuses the advantages and limitations of genetically engineered SOD-deficient unicellular organisms, Escherichia coli and Saccharomyces cerevisiae as tools for investigating the efficacy and mechanisms of biological actions of SOD mimics. These simple systems allow the scrutiny of the minimal requirements for a functional SOD mimic: the association of a high catalytic activity for superoxide dismutation, low toxicity, and an efficient cellular uptake/biodistribution. Antioxid. Redox Signal. 20, 2416–2436. PMID:23964890

Lateral Hypothalamus GABAergic Neurons Modulate Consummatory Behaviors Regardless of the Caloric Content or Biological Relevance of the Consumed Stimuli.

PubMed

Navarro, Montserrat; Olney, Jeffrey J; Burnham, Nathan W; Mazzone, Christopher M; Lowery-Gionta, Emily G; Pleil, Kristen E; Kash, Thomas L; Thiele, Todd E

2016-05-01

It was recently reported that activation of a subset of lateral hypothalamus (LH) GABAergic neurons induced both appetitive (food-seeking) and consummatory (eating) behaviors in vGat-ires-cre mice, while inhibition or deletion of GABAergic neurons blunted these behaviors. As food and caloric-dense liquid solutions were used, the data reported suggest that these LH GABAergic neurons may modulate behaviors that function to maintain homeostatic caloric balance. Here we report that chemogenetic activation of this GABAergic population in vGat-ires-cre mice increased consummatory behavior directed at any available stimulus, including those entailing calories (food, sucrose, and ethanol), those that do not (saccharin and water), and those lacking biological relevance (wood). Chemogenetic inhibition of these neurons attenuated consummatory behaviors. These data indicate that LH GABAergic neurons modulate consummatory behaviors regardless of the caloric content or biological relevance of the consumed stimuli.

Self-adaptive relevance feedback based on multilevel image content analysis

NASA Astrophysics Data System (ADS)

Gao, Yongying; Zhang, Yujin; Fu, Yu

2001-01-01

In current content-based image retrieval systems, it is generally accepted that obtaining high-level image features is a key to improve the querying. Among the related techniques, relevance feedback has become a hot research aspect because it combines the information from the user to refine the querying results. In practice, many methods have been proposed to achieve the goal of relevance feedback. In this paper, a new scheme for relevance feedback is proposed. Unlike previous methods for relevance feedback, our scheme provides a self-adaptive operation. First, based on multi- level image content analysis, the relevant images from the user could be automatically analyzed in different levels and the querying could be modified in terms of different analysis results. Secondly, to make it more convenient to the user, the procedure of relevance feedback could be led with memory or without memory. To test the performance of the proposed method, a practical semantic-based image retrieval system has been established, and the querying results gained by our self-adaptive relevance feedback are given.

Self-adaptive relevance feedback based on multilevel image content analysis

NASA Astrophysics Data System (ADS)

Gao, Yongying; Zhang, Yujin; Fu, Yu

2000-12-01

In current content-based image retrieval systems, it is generally accepted that obtaining high-level image features is a key to improve the querying. Among the related techniques, relevance feedback has become a hot research aspect because it combines the information from the user to refine the querying results. In practice, many methods have been proposed to achieve the goal of relevance feedback. In this paper, a new scheme for relevance feedback is proposed. Unlike previous methods for relevance feedback, our scheme provides a self-adaptive operation. First, based on multi- level image content analysis, the relevant images from the user could be automatically analyzed in different levels and the querying could be modified in terms of different analysis results. Secondly, to make it more convenient to the user, the procedure of relevance feedback could be led with memory or without memory. To test the performance of the proposed method, a practical semantic-based image retrieval system has been established, and the querying results gained by our self-adaptive relevance feedback are given.

Structural, chemical and biological aspects of antioxidants for strategies against metal and metalloid exposure

PubMed Central

2009-01-01

Oxidative stress contributes to the pathophysiology of exposure to heavy metals/metalloid. Beneficial renal effects of some medications, such as chelation therapy depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in the prevention and attenuation of metal induced biochemical alterations. These include vitamins, N-acetylcysteine, α-lipoic acid, melatonin, dietary flavonoids and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen metal induced toxic damage. To date, the evidence is insufficient to recommend antioxidant supplements in subject with exposure to metals. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies either individually or in combination with chelating agent are indispensable. The present review focuses on structural, chemical and biological aspects of antioxidants particularly related to their chelating properties. PMID:20716905

Dual-energy-based metal segmentation for metal artifact reduction in dental computed tomography.

PubMed

Hegazy, Mohamed A A; Eldib, Mohamed Elsayed; Hernandez, Daniel; Cho, Myung Hye; Cho, Min Hyoung; Lee, Soo Yeol

2018-02-01

In a dental CT scan, the presence of dental fillings or dental implants generates severe metal artifacts that often compromise readability of the CT images. Many metal artifact reduction (MAR) techniques have been introduced, but dental CT scans still suffer from severe metal artifacts particularly when multiple dental fillings or implants exist around the region of interest. The high attenuation coefficient of teeth often causes erroneous metal segmentation, compromising the MAR performance. We propose a metal segmentation method for a dental CT that is based on dual-energy imaging with a narrow energy gap. Unlike a conventional dual-energy CT, we acquire two projection data sets at two close tube voltages (80 and 90 kV p ), and then, we compute the difference image between the two projection images with an optimized weighting factor so as to maximize the contrast of the metal regions. We reconstruct CT images from the weighted difference image to identify the metal region with global thresholding. We forward project the identified metal region to designate metal trace on the projection image. We substitute the pixel values on the metal trace with the ones computed by the region filling method. The region filling in the metal trace removes high-intensity data made by the metallic objects from the projection image. We reconstruct final CT images from the region-filled projection image with the fusion-based approach. We have done imaging experiments on a dental phantom and a human skull phantom using a lab-built micro-CT and a commercial dental CT system. We have corrected the projection images of a dental phantom and a human skull phantom using the single-energy and dual-energy-based metal segmentation methods. The single-energy-based method often failed in correcting the metal artifacts on the slices on which tooth enamel exists. The dual-energy-based method showed better MAR performances in all cases regardless of the presence of tooth enamel on the slice of

Reputation-based collaborative network biology.

PubMed

Binder, Jean; Boue, Stephanie; Di Fabio, Anselmo; Fields, R Brett; Hayes, William; Hoeng, Julia; Park, Jennifer S; Peitsch, Manuel C

2015-01-01

A pilot reputation-based collaborative network biology platform, Bionet, was developed for use in the sbv IMPROVER Network Verification Challenge to verify and enhance previously developed networks describing key aspects of lung biology. Bionet was successful in capturing a more comprehensive view of the biology associated with each network using the collective intelligence and knowledge of the crowd. One key learning point from the pilot was that using a standardized biological knowledge representation language such as BEL is critical to the success of a collaborative network biology platform. Overall, Bionet demonstrated that this approach to collaborative network biology is highly viable. Improving this platform for de novo creation of biological networks and network curation with the suggested enhancements for scalability will serve both academic and industry systems biology communities.

Total petroleum hydrocarbons and heavy metals in the surface sediments of Bohai Bay, China: long-term variations in pollution status and adverse biological risk.

PubMed

Zhou, Ran; Qin, Xuebo; Peng, Shitao; Deng, Shihuai

2014-06-15

Surface sediments collected from 2001 to 2011 were analyzed for total petroleum hydrocarbons (TPH) and five heavy metals. The sediment concentration ranges of TPH, Zn, Cu, Pb, Cd and Hg were 6.3-535 μg/g, 58-332 μg/g, 7.2-63 μg/g, 4.3-138 μg/g, 0-0.98μg/g, and 0.10-0.68 μg/g, respectively. These results met the highest marine sediment quality standards in China, indicating that the sediment was fairly clean. However, based on the effects range-median (ERM) quotient method, the calculated values for all of the sampling sites were higher than 0.10, suggesting that there was a potential adverse biological risk in Bohai Bay. According to the calculated results, the biological risk decreased from 2001 to 2007 and increased afterwards. High-risk sites were mainly distributed along the coast. This study suggests that anthropogenic influences might be responsible for the potential risk of adverse biological effects from TPH and heavy metals in Bohai Bay. Copyright © 2014 Elsevier Ltd. All rights reserved.

6,7-dimethoxy-coumarin as a probe of hydration dynamics in biologically relevant systems

NASA Astrophysics Data System (ADS)

Ghose, Avisek; Amaro, Mariana; Kovaricek, Petr; Hof, Martin; Sykora, Jan

2018-04-01

Coumarin derivatives are well known fluorescence reporters for investigating biological systems due to their strong micro-environment sensitivity. Despite having wide range of environment sensitive fluorescence probes, the potential of 6,7-dimethoxy-coumarin has not been studied extensively so far. With a perspective of its use in protein studies, namely using the unnatural amino acid technology or as a substrate for hydrolase enzymes, we study acetyloxymethyl-6,7-dimethoxycoumarin (Ac-DMC). We investigate the photophysics and hydration dynamics of this dye in aerosol-OT (AOT) reverse micelles at various water contents using the time dependent fluorescence shift (TDFS) method. The TDFS response in AOT reverse micelles from water/surfactant ratio of 0 to 20 confirms its sensitivity towards the hydration and mobility of its microenvironment. Moreover, we show that the fluorophore can be efficiently quenched by halide ions. Hence, we conclude that the 6,7-dimethoxy-methylcoumarin fluorophore is useful for studying hydration parameters in biologically relevant systems.

Green Synthesis of Metallic Nanoparticles via Biological Entities

PubMed Central

Shah, Monaliben; Fawcett, Derek; Sharma, Shashi; Tripathy, Suraj Kumar; Poinern, Gérrard Eddy Jai

2015-01-01

Nanotechnology is the creation, manipulation and use of materials at the nanometre size scale (1 to 100 nm). At this size scale there are significant differences in many material properties that are normally not seen in the same materials at larger scales. Although nanoscale materials can be produced using a variety of traditional physical and chemical processes, it is now possible to biologically synthesize materials via environment-friendly green chemistry based techniques. In recent years, the convergence between nanotechnology and biology has created the new field of nanobiotechnology that incorporates the use of biological entities such as actinomycetes algae, bacteria, fungi, viruses, yeasts, and plants in a number of biochemical and biophysical processes. The biological synthesis via nanobiotechnology processes have a significant potential to boost nanoparticles production without the use of harsh, toxic, and expensive chemicals commonly used in conventional physical and chemical processes. The aim of this review is to provide an overview of recent trends in synthesizing nanoparticles via biological entities and their potential applications. PMID:28793638

Do two machine-learning based prognostic signatures for breast cancer capture the same biological processes?

PubMed

Drier, Yotam; Domany, Eytan

2011-03-14

The fact that there is very little if any overlap between the genes of different prognostic signatures for early-discovery breast cancer is well documented. The reasons for this apparent discrepancy have been explained by the limits of simple machine-learning identification and ranking techniques, and the biological relevance and meaning of the prognostic gene lists was questioned. Subsequently, proponents of the prognostic gene lists claimed that different lists do capture similar underlying biological processes and pathways. The present study places under scrutiny the validity of this claim, for two important gene lists that are at the focus of current large-scale validation efforts. We performed careful enrichment analysis, controlling the effects of multiple testing in a manner which takes into account the nested dependent structure of gene ontologies. In contradiction to several previous publications, we find that the only biological process or pathway for which statistically significant concordance can be claimed is cell proliferation, a process whose relevance and prognostic value was well known long before gene expression profiling. We found that the claims reported by others, of wider concordance between the biological processes captured by the two prognostic signatures studied, were found either to be lacking statistical rigor or were in fact based on addressing some other question.

Preliminary Results on the Surface of a New Fe-Based Metallic Material after “In Vivo” Maintaining

NASA Astrophysics Data System (ADS)

Săndulache, F.; Stanciu, S.; Cimpoeşu, N.; Stanciu, T.; Cimpoeșu, R.; Enache, A.; Baciu, R.

2017-06-01

Abstract A new Fe-based alloy was obtained using UltraCast melting equipment. The alloy, after mechanical processing, was implanted in five rabbit specimens (with respect for the “in-bone” procedure). After 30 days of implantation the samples were recovered and analyzed by weight and surface state meanings. Scanning electron microscopy technique was used to determine the new compounds morphology from the metallic surface and X-ray dispersive energy spectroscopy for chemical analyze results. A bond between the metallic material and biological material of the bone was observed through increasing of sample weight and by SEM images. After the first set of tests, as the samples were extracted and biologically cleaned, the samples were ultrasonically cleaned and re-analyzed in order to establish the stability of the chemical compounds.

Mass fractionation processes of transition metal isotopes

NASA Astrophysics Data System (ADS)

Zhu, X. K.; Guo, Y.; Williams, R. J. P.; O'Nions, R. K.; Matthews, A.; Belshaw, N. S.; Canters, G. W.; de Waal, E. C.; Weser, U.; Burgess, B. K.; Salvato, B.

2002-06-01

Recent advances in mass spectrometry make it possible to utilise isotope variations of transition metals to address some important issues in solar system and biological sciences. Realisation of the potential offered by these new isotope systems however requires an adequate understanding of the factors controlling their isotope fractionation. Here we show the results of a broadly based study on copper and iron isotope fractionation during various inorganic and biological processes. These results demonstrate that: (1) naturally occurring inorganic processes can fractionate Fe isotope to a detectable level even at temperature ˜1000°C, which challenges the previous view that Fe isotope variations in natural system are unique biosignatures; (2) multiple-step equilibrium processes at low temperatures may cause large mass fractionation of transition metal isotopes even when the fractionation per single step is small; (3) oxidation-reduction is an importation controlling factor of isotope fractionation of transition metal elements with multiple valences, which opens a wide range of applications of these new isotope systems, ranging from metal-silicate fractionation in the solar system to uptake pathways of these elements in biological systems; (4) organisms incorporate lighter isotopes of transition metals preferentially, and transition metal isotope fractionation occurs stepwise along their pathways within biological systems during their uptake.

Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes

NASA Astrophysics Data System (ADS)

Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

2015-02-01

Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, 1H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand.

Tag-Based Social Image Search: Toward Relevant and Diverse Results

NASA Astrophysics Data System (ADS)

Yang, Kuiyuan; Wang, Meng; Hua, Xian-Sheng; Zhang, Hong-Jiang

Recent years have witnessed a great success of social media websites. Tag-based image search is an important approach to access the image content of interest on these websites. However, the existing ranking methods for tag-based image search frequently return results that are irrelevant or lack of diversity. This chapter presents a diverse relevance ranking scheme which simultaneously takes relevance and diversity into account by exploring the content of images and their associated tags. First, it estimates the relevance scores of images with respect to the query term based on both visual information of images and semantic information of associated tags. Then semantic similarities of social images are estimated based on their tags. Based on the relevance scores and the similarities, the ranking list is generated by a greedy ordering algorithm which optimizes Average Diverse Precision (ADP), a novel measure that is extended from the conventional Average Precision (AP). Comprehensive experiments and user studies demonstrate the effectiveness of the approach.

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.

Implementation of biological tissue Mueller matrix for polarization-sensitive optical coherence tomography based on LabVIEW

NASA Astrophysics Data System (ADS)

Lin, Yongping; Zhang, Xiyang; He, Youwu; Cai, Jianyong; Li, Hui

2018-02-01

The Jones matrix and the Mueller matrix are main tools to study polarization devices. The Mueller matrix can also be used for biological tissue research to get complete tissue properties, while the commercial optical coherence tomography system does not give relevant analysis function. Based on the LabVIEW, a near real time display method of Mueller matrix image of biological tissue is developed and it gives the corresponding phase retardant image simultaneously. A quarter-wave plate was placed at 45 in the sample arm. Experimental results of the two orthogonal channels show that the phase retardance based on incident light vector fixed mode and the Mueller matrix based on incident light vector dynamic mode can provide an effective analysis method of the existing system.

Transition metal coordination chemistry ofN,N-bis(2-{pyrid-2-ylethyl})hydroxylamine.

PubMed

Belock, Christopher W; Cetin, Anil; Barone, Natalie V; Ziegler, Christopher J

2008-08-18

Although directly relevant to metal mediated biological nitrification as well as the coordination chemistry of peroxide, the metal complexes of hydroxylamines and their functionalized variants remain largely unexplored. The chelating hydroxylamine ligand N,N-bis(2-{pyrid-2-ylethyl})hydroxylamine can be readily generated via a solvent free reaction in high purity; however, the ligand is prone to decomposition which can hamper metal reaction. N,N-bis(2-{pyrid-2-ylethyl})hydroxylamine forms stable complexes with chromium(III), manganese(II), nickel(II), and cadmium(II) ions, coordinating in a side-on mode in the case of chromium and via the nitrogen in the case of the latter three metal ions. The hydroxylamine ligand can also be reduced to form N,N-bis(2-{pyrid-2-ylethyl})amine upon exposure to a stoichiometric amount of the metal salts cobalt(II) nitrate, vanadium(III) chloride, and iron(II) chloride. In the reaction with cobalt nitrate, the reduced ligand then chelates to the metal to form [N,N-bis(2-{pyrid-2-ylethyl})amine]dinitrocobalt(II). Upon reaction with vanadium(III) chloride and iron(III) chloride, the reduced ligand is isolated as the protonated free base, resulting from a metal-mediated decomposition reaction.

Microfluidic platforms for gallium-based liquid metal alloy

NASA Astrophysics Data System (ADS)

Kim, Daeyoung

As an alternative to toxic mercury, non-toxic gallium-based liquid metal alloy has been gaining popularity due to its higher thermal and electrical conductivities, and low toxicity along with liquid property. However, it is difficult to handle as the alloy becomes readily oxidized in atmospheric air environment. This instant oxidation causes the gallium-based liquid metal alloy to wet almost any solid surface. Therefore, it has been primarily limited to applications which rely only on its deformability, not on its mobility. In this research, various approaches to mobilize gallium-based liquid metal alloy were investigated. Multi-scale surface patterned with polydimethylsiloxane (PDMS) micro pillar array showed super-lyophobic property against gallium-based liquid metal alloy by minimizing the contact area between the solid surface and the liquid metal, and it was expanded to a three-dimensional tunnel shaped microfluidic channel. Vertically-aligned carbon nanotube forest leads to another promising super-lyophobic surface due to its hierarchical micro/nano scale combined structures and chemical inertness. When the carbon nanotubes were transferred onto flexible PDMS by imprinting, the super-lyophobic property was still maintained even under the mechanical deformation such as stretching and bending. Alternatively, the gallium-based liquid metal can be manipulated by modifying the surface of liquid metal itself. With chemical reaction with HCl 'vapor', the oxidized surface (mainly Ga2O3/Ga2O) of gallium-based liquid metal was converted to GaCl3/InCl 3 resulting in the recovery of non-wetting characteristics. Paper which is intrinsically porous is attractive as a super-lyophobic surface and it was found that hydrochloric acid (HCl) impregnation enhanced the anti-wetting property by the chemical reaction. As another alternative method, by coating the viscoelastic oxidized surface of liquid metal with ferromagnetic materials (CoNiMnP or Fe), it showed non

METHOD OF JOINING CARBIDES TO BASE METALS

DOEpatents

Krikorian, N.H.; Farr, J.D.; Witteman, W.G.

1962-02-13

A method is described for joining a refractory metal carbide such as UC or ZrC to a refractory metal base such as Ta or Nb. The method comprises carburizing the surface of the metal base and then sintering the base and carbide at temperatures of about 2000 deg C in a non-oxidizing atmosphere, the base and carbide being held in contact during the sintering step. To reduce the sintering temperature and time, a sintering aid such as iron, nickel, or cobait is added to the carbide, not to exceed 5 wt%. (AEC)

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule.

PubMed

Zheng, Peng; Arantes, Guilherme M; Field, Martin J; Li, Hongbin

2015-06-25

Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions.

Force-induced chemical reactions on the metal centre in a single metalloprotein molecule

PubMed Central

Zheng, Peng; Arantes, Guilherme M.; Field, Martin J.; Li, Hongbin

2015-01-01

Metalloproteins play indispensable roles in biology owing to the versatile chemical reactivity of metal centres. However, studying their reactivity in many metalloproteins is challenging, as protein three-dimensional structure encloses labile metal centres, thus limiting their access to reactants and impeding direct measurements. Here we demonstrate the use of single-molecule atomic force microscopy to induce partial unfolding to expose metal centres in metalloproteins to aqueous solution, thus allowing for studying their chemical reactivity in aqueous solution for the first time. As a proof-of-principle, we demonstrate two chemical reactions for the FeS4 centre in rubredoxin: electrophilic protonation and nucleophilic ligand substitution. Our results show that protonation and ligand substitution result in mechanical destabilization of the FeS4 centre. Quantum chemical calculations corroborated experimental results and revealed detailed reaction mechanisms. We anticipate that this novel approach will provide insights into chemical reactivity of metal centres in metalloproteins under biologically more relevant conditions. PMID:26108369

A survey of chemicals inducing lipid peroxidation in biological systems.

PubMed

Kappus, H

1987-01-01

A great number of drugs and chemicals are reviewed which have been shown to stimulate lipid peroxidation in any biological system. The underlying mechanisms, as far as known, are also dealt with. Lipid peroxidation induced by iron ions, organic hydroperoxides, halogenated hydrocarbons, redox cycling drugs, glutathione depleting chemicals, ethanol, heavy metals, ozone, nitrogen dioxide and a number of miscellaneous compounds, e.g. hydrazines, pesticides, antibiotics, are mentioned. It is shown that lipid peroxidation is stimulated by many of these compounds. However, quantitative estimates cannot be given yet and it is still impossible to judge the biological relevance of chemical-induced lipid peroxidation.

Biology of sepsis: its relevance to pediatric nephrology.

PubMed

Blatt, Neal B; Srinivasan, Sushant; Mottes, Theresa; Shanley, Maureen M; Shanley, Thomas P

2014-12-01

Because of its multi-organ involvement, the syndrome of sepsis provides clinical challenges to a wide variety of health care providers. While multi-organ dysfunction triggered by sepsis requires general supportive critical care provided by intensivists, the impact of sepsis on renal function and the ability of renal replacement therapies to modulate its biologic consequences provide a significant opportunity for pediatric nephrologists and related care providers to impact outcomes. In this review, we aim to highlight newer areas of understanding of the pathobiology of sepsis with special emphasis on those aspects of particular interest to pediatric nephrology. As such, we aim to: (1) review the definition of sepsis and discuss advances in our mechanistic understanding of sepsis; (2) review current hypotheses regarding sepsis-induced acute kidney injury (AKI) and describe its epidemiology based on evolving definitions of AKI; (3) review the impact of renal failure on the immune system, highlighting the sepsis risk in this cohort and strategies that might minimize this risk; (4) review how renal replacement therapeutic strategies may impact sepsis-induced AKI outcomes. By focusing the review on these specific areas, we have omitted other important areas of the biology of sepsis and additional interactions with renal function from this discussion; however, we have aimed to provide a comprehensive list of references that provide contemporary reviews of these additional areas.

The biological response to laser-aided direct metal-coated Titanium alloy (Ti6Al4V)

PubMed Central

Shin, T.; Lim, D.; Kim, Y. S.; Kim, S. C.; Jo, W. L.

2018-01-01

Objectives Laser-engineered net shaping (LENS) of coated surfaces can overcome the limitations of conventional coating technologies. We compared the in vitro biological response with a titanium plasma spray (TPS)-coated titanium alloy (Ti6Al4V) surface with that of a Ti6Al4V surface coated with titanium using direct metal fabrication (DMF) with 3D printing technologies. Methods The in vitro ability of human osteoblasts to adhere to TPS-coated Ti6Al4V was compared with DMF-coating. Scanning electron microscopy (SEM) was used to assess the structure and morphology of the surfaces. Biological and morphological responses to human osteoblast cell lines were then examined by measuring cell proliferation, alkaline phosphatase activity, actin filaments, and RUNX2 gene expression. Results Morphological assessment of the cells after six hours of incubation using SEM showed that the TPS- and DMF-coated surfaces were largely covered with lamellipodia from the osteoblasts. Cell adhesion appeared similar in both groups. The differences in the rates of cell proliferation and alkaline phosphatase activities were not statistically significant. Conclusions The DMF coating applied using metal 3D printing is similar to the TPS coating, which is the most common coating process used for bone ingrowth. The DMF method provided an acceptable surface structure and a viable biological surface. Moreover, this method is automatable and less complex than plasma spraying. Cite this article: T. Shin, D. Lim, Y. S. Kim, S. C. Kim, W. L. Jo, Y. W. Lim. The biological response to laser-aided direct metal-coated Titanium alloy (Ti6Al4V). Bone Joint Res 2018;7:357–361. DOI: 10.1302/2046-3758.75.BJR-2017-0222.R1. PMID:29922456

Copper(II)-based metal affinity chromatography for the isolation of the anticancer agent bleomycin from Streptomyces verticillus culture.

PubMed

Gu, Jiesi; Codd, Rachel

2012-10-01

The glycopeptide-based bleomycins are structurally complex natural products produced by Streptomyces verticillus used in combination therapy against testicular and other cancers. Bleomycin has a high affinity towards a range of transition metal ions with the 1:1 Fe(II) complex relevant to its mechanism of action in vivo and the 1:1 Cu(II) complex relevant to its production from culture. The affinity between Cu(II) and bleomycin was the underlying principle for using Cu(II)-based metal affinity chromatography in this work to selectively capture bleomycin from crude S. verticillus culture. A solution of standard bleomycin was retained at a binding capacity of 300 nmol mL(-1) on a 1-mL bed volume of Cu(II)-loaded iminodiacetate (IDA) resin at pH 9 via the formation of the heteroleptic immobilized complex [Cu(IDA)(bleomycin)]. Bleomycin was eluted from the resin at pH 5 as the metal-free ligand under conditions where pK(a) (IDA)based metal affinity chromatography as a green chemistry platform for streamlined access to this high-value therapeutic agent. Copyright © 2012 Elsevier Inc. All rights reserved.

Fundamental Principles of Cancer Biology: Does it have relevance to the perioperative period?

PubMed

Jiang, Li; Nick, Alpa M; Sood, Anil K

2015-09-01

Malignant tumors are characterized by their ability to metastasize, which is the main cause of cancer-related mortality. Besides intrinsic alternations in cancer cells, the tumor microenvironment plays a pivotal role in tumor growth and metastasis. Ample evidence suggests that the perioperative period and the excision of the primary tumor can promote the development of metastases and can influence long-term cancer patient outcomes. The role of cancer biology and its impact on the perioperative period are of increasing interest. This review will present evidence regarding fundamental principles of cancer biology, especially tumor microenvironment, and discuss new therapeutic opportunities in the perioperative timeframe. We will also discuss the regulatory signaling that could be relevant to various aspects of surgery and surgical responses, which could facilitate the metastatic process by directly or indirectly affecting malignant tissues and the tumor microenvironment. We address the influences of surgery-related stress, anesthetic and analgesic agents, blood transfusion, hypothermia, and β-adrenergic blockade administration on tumor growth and metastasis. Through an improved understanding of these processes, we will provide suggestions for potential new perioperative approaches aimed at improving treatment outcomes of cancer patients.

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; preparation procedure for aquatic biological material determined for trace metals

USGS Publications Warehouse

Hoffman, Gerald L.

1996-01-01

A method for the chemical preparation of tissue samples that are subsequently analyzed for 22 trace metals is described. The tissue-preparation procedure was tested with three National Institute of Standards and Technology biological standard reference materials and two National Water Quality Laboratory homogenized biological materials. A low-temperature (85 degrees Celsius) nitric acid digestion followed by the careful addition of hydrogen peroxide (30-percent solution) is used to decompose the biological material. The solutions are evaporated to incipient dryness, reconstituted with 5 percent nitric acid, and filtered. After filtration the solutions were diluted to a known volume and analyzed by inductively coupled plasma-mass spectrometry (ICP-MS), inductively coupled plasma-atomic emission spectrometry (ICP-AES), and cold vapor-atomic absorption spectrophotometry (CV-AAS). Many of the metals were determined by both ICP-MS and ICP-AES. This report does not provide a detailed description of the instrumental procedures and conditions used with the three types of instrumentation for the quantitation of trace metals determined in this study. Statistical data regarding recovery, accuracy, and precision for individual trace metals determined in the biological material tested are summarized.

Service-based analysis of biological pathways

PubMed Central

Zheng, George; Bouguettaya, Athman

2009-01-01

Background Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at achieving either objective, but not both. Such limitations can be effectively tackled leveraging a Web service-based modeling and mining approach. Results Inspired by molecular recognitions and drug discovery processes, we developed a Web service mining tool, named PathExplorer, to discover potentially interesting biological pathways linking service models of biological processes. The tool uses an innovative approach to identify useful pathways based on graph-based hints and service-based simulation verifying user's hypotheses. Conclusion Web service modeling of biological processes allows the easy access and invocation of these processes on the Web. Web service mining techniques described in this paper enable the discovery of biological pathways linking these process service models. Algorithms presented in this paper for automatically highlighting interesting subgraph within an identified pathway network enable the user to formulate hypothesis, which can be tested out using our simulation algorithm that are also described in this paper. PMID:19796403

The analytical calibration in (bio)imaging/mapping of the metallic elements in biological samples--definitions, nomenclature and strategies: state of the art.

PubMed

Jurowski, Kamil; Buszewski, Bogusław; Piekoszewski, Wojciech

2015-01-01

Nowadays, studies related to the distribution of metallic elements in biological samples are one of the most important issues. There are many articles dedicated to specific analytical atomic spectrometry techniques used for mapping/(bio)imaging the metallic elements in various kinds of biological samples. However, in such literature, there is a lack of articles dedicated to reviewing calibration strategies, and their problems, nomenclature, definitions, ways and methods used to obtain quantitative distribution maps. The aim of this article was to characterize the analytical calibration in the (bio)imaging/mapping of the metallic elements in biological samples including (1) nomenclature; (2) definitions, and (3) selected and sophisticated, examples of calibration strategies with analytical calibration procedures applied in the different analytical methods currently used to study an element's distribution in biological samples/materials such as LA ICP-MS, SIMS, EDS, XRF and others. The main emphasis was placed on the procedures and methodology of the analytical calibration strategy. Additionally, the aim of this work is to systematize the nomenclature for the calibration terms: analytical calibration, analytical calibration method, analytical calibration procedure and analytical calibration strategy. The authors also want to popularize the division of calibration methods that are different than those hitherto used. This article is the first work in literature that refers to and emphasizes many different and complex aspects of analytical calibration problems in studies related to (bio)imaging/mapping metallic elements in different kinds of biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

Enhanced stability and local structure in biologically relevant amorphous materials containing pyrophosphate

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

Slater, Colin; Laurencin, Danielle; Burnell, Victoria

2012-10-25

There is increasing evidence that amorphous inorganic materials play a key role in biomineralisation in many organisms, however the inherent instability of synthetic analogues in the absence of the complex in vivo matrix limits their study and clinical exploitation. To address this, we report here an approach that enhances long-term stability to >1 year of biologically relevant amorphous metal phosphates, in the absence of any complex stabilizers, by utilizing pyrophosphates (P{sub 2}O{sub 7}{sup 4-}); species themselves ubiquitous in vivo. Ambient temperature precipitation reactions were employed to synthesise amorphous Ca{sub 2}P{sub 2}O{sub 7}.nH{sub 2}O and Sr{sub 2}P{sub 2}O{sub 7}.nH{sub 2}O (3.8more » < n < 4.2) and their stability and structure were investigated. Pair distribution functions (PDF) derived from synchrotron X-ray data indicated a lack of structural order beyond 8 {angstrom} in both phases, with this local order found to resemble crystalline analogues. Further studies, including {sup 1}H and {sup 31}P solid state NMR, suggest the unusually high stability of these purely inorganic amorphous phases is partly due to disorder in the P-O-P bond angles within the P{sub 2}O{sub 7} units, which impede crystallization, and to water molecules, which are involved in H-bonds of various strengths within the structures and hamper the formation of an ordered network. In situ high temperature powder X-ray diffraction data indicated that the amorphous nature of both phases surprisingly persisted to 450 C. Further NMR and TGA studies found that above ambient temperature some water molecules reacted with P{sub 2}O{sub 7} anions, leading to the hydrolysis of some P-O-P linkages and the formation of HPO{sub 4}{sup 2-} anions within the amorphous matrix. The latter anions then recombined into P{sub 2}O{sub 7} ions at higher temperatures prior to crystallization. Together, these findings provide important new materials with unexplored potential for enzyme

Seven-day human biological rhythms: An expedition in search of their origin, synchronization, functional advantage, adaptive value and clinical relevance.

PubMed

Reinberg, Alain E; Dejardin, Laurence; Smolensky, Michael H; Touitou, Yvan

2017-01-01

This fact-finding expedition explores the perspectives and knowledge of the origin and functional relevance of the 7 d domain of the biological time structure, with special reference to human beings. These biological rhythms are displayed at various levels of organization in diverse species - from the unicellular sea algae of Acetabularia and Goniaulax to plants, insects, fish, birds and mammals, including man - under natural as well as artificial, i.e. constant, environmental conditions. Nonetheless, very little is known about their derivation, functional advantage, adaptive value, synchronization and potential clinical relevance. About 7 d cosmic cycles are seemingly too weak, and the 6 d work/1 d rest week commanded from G-d through the Laws of Mosses to the Hebrews is too recent an event to be the origin in humans. Moreover, human and insect studies conducted under controlled constant conditions devoid of environmental, social and other time cues report the persistence of 7 d rhythms, but with a slightly different (free-running) period (τ), indicating their source is endogenous. Yet, a series of human and laboratory rodent studies reveal certain mainly non-cyclic exogenous events can trigger 7 d rhythm-like phenomena. However, it is unknown whether such triggers unmask, amplify and/or synchronize previous non-overtly expressed oscillations. Circadian (~24 h), circa-monthly (~30 d) and circannual (~1 y) rhythms are viewed as genetically based features of life forms that during evolution conferred significant functional advantage to individual organisms and survival value to species. No such advantages are apparent for endogenous 7 d rhythms, raising several questions: What is the significance of the 7 d activity/rest cycle, i.e. week, storied in the Book of Genesis and adopted by the Hebrews and thereafter the residents of nearby Mediterranean countries and ultimately the world? Why do humans require 1 d off per 7 d span? Do 7 d rhythms bestow functional

Versatile nature of hetero-chitosan based derivatives as biodegradable adsorbent for heavy metal ions; a review.

PubMed

Ahmad, Mudasir; Manzoor, Kaiser; Ikram, Saiqa

2017-12-01

The polyfunctional chitosan can act as the biological macromolecule ligand not only for the adsorption and the recovery of metal ions from an aqueous media, but also for the fabrication of novel adsorbents which shows selectivity and better adsorption properties. The unmodified chitosan itself, a single cationic polysaccharide, has hydroxyl and amine groups carrying complex properties with the metal ions. In addition, the selectivity of metal ions, the adsorption efficiency and adsorption capacity of the adsorbent can be modified chemically. This review covers the synthetic strategies of chitosan towards the synthesis of hetero-chitosan based adsorbents via chemical modifications in past two decades. It also includes how chemical modification influences the metal adsorption with N, O, S and P containing chitosan derivatives. Hope this review article provides an opportunity for researchers in the future to explore the potential of chitosan as an adsorbent for removal of metal ions from wastewater. Copyright © 2017 Elsevier B.V. All rights reserved.

Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease.

PubMed

Azuaje, Francisco; Zheng, Huiru; Camargo, Anyela; Wang, Haiying

2011-08-01

The discovery of novel disease biomarkers is a crucial challenge for translational bioinformatics. Demonstration of both their classification power and reproducibility across independent datasets are essential requirements to assess their potential clinical relevance. Small datasets and multiplicity of putative biomarker sets may explain lack of predictive reproducibility. Studies based on pathway-driven discovery approaches have suggested that, despite such discrepancies, the resulting putative biomarkers tend to be implicated in common biological processes. Investigations of this problem have been mainly focused on datasets derived from cancer research. We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain. A diversity of biosignatures was identified by the different methods. However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis. With a few exceptions, we observed lack of classification reproducibility using independent datasets. Partial overlaps between our putative sets of biomarkers and the primary studies exist. Despite the observed limitations, pathway-driven or gene set analysis can predict potentially novel biomarkers and can jointly point to biomedically-relevant underlying molecular mechanisms. Copyright © 2011 Elsevier Inc. All rights reserved.

Subcellular compartmentalization of Cd and Zn in two bivalves. I. Significance of metal-sensitive fractions (MSF) and biologically detoxified metal (BDM)

USGS Publications Warehouse

Wallace, W.G.; Lee, B.-G.; Luoma, S.N.

2003-01-01

Many aspects of metal accumulation in aquatic invertebrates (i.e. toxicity, tolerance and trophic transfer) can be understood by examining the subcellular partitioning of accumulated metal. In this paper, we use a compartmentalization approach to interpret the significance of metal, species and size dependence in the subcellular partitioning of Cd and Zn in the bivalves Macoma balthica and Potamocorbula amurensis. Of special interest is the compartmentalization of metal as metal-sensitive fractions (MSF) (i.e. organelles and heat-sensitive proteins, termed 'enzymes' hereafter) and biologically detoxified metal (BDM) (i.e. metallothioneins [MT] and metal-rich granules [MRG]). Clams from San Francisco Bay, CA, were exposed for 14 d to seawater (20??? salinity) containing 3.5 ??g l-1 Cd and 20.5 ??g l-1 Zn, including 109Cd and 65Zn as radiotracers. Uptake was followed by 21 d of depuration. The subcellular partitioning of metal within clams was examined following exposure and loss. P. amurensis accumulated ???22x more Cd and ???2x more Zn than M. balthica. MT played an important role in the storage of Cd in P. amurensis, while organelles were the major site of Zn accumulation. In M. balthica, Cd and Zn partitioned similarly, although the pathway of detoxification was metal-specific (MRG for Cd; MRG and MT for Zn). Upon loss, M. balthica depurated ???40% of Cd with Zn being retained; P. amurensis retained Cd and depurated Zn (???40%). During efflux, Cd and Zn concentrations in the MSF compartment of both clams declined with metal either being lost from the animal or being transferred to the BDM compartment. Subcellular compartmentalization was also size-dependent, with the importance of BDM increasing with clam size; MSF decreased accordingly. We hypothesized that progressive retention of metal as BDM (i.e. MRG) with age may lead to size dependency of metal concentrations often observed in some populations of M. balthica.

A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

NASA Astrophysics Data System (ADS)

van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

2011-10-01

Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of such a situated learning approach. What content knowledge do biology teachers need for teaching genetics in the personal health context of genetic testing? This study describes the required content knowledge by exploring the educational practice and clinical genetic practices. Nine experienced teachers and 12 respondents representing the clinical genetic practices (clients, medical professionals, and medical ethicists) were interviewed about the biological concepts and ethical, legal, and social aspects (ELSA) of testing they considered relevant to empowering students as future health care clients. The ELSA suggested by the respondents were complemented by suggestions found in the literature on genetic counselling. The findings revealed that the required teacher knowledge consists of multiple layers that are embedded in specific genetic test situations: on the one hand, the knowledge of concepts represented by the curricular framework and some additional concepts (e.g. multifactorial and polygenic disorder) and, on the other hand, more knowledge of ELSA and generic characteristics of genetic test practice (uncertainty, complexity, probability, and morality). Suggestions regarding how to translate these characteristics, concepts, and ELSA into context-based genetics education are discussed.

Do biological-based strategies hold promise to biofouling control in MBRs?

PubMed

Malaeb, Lilian; Le-Clech, Pierre; Vrouwenvelder, Johannes S; Ayoub, George M; Saikaly, Pascal E

2013-10-01

implications as well as knowledge gaps, warranting future targeted research. Systematic and representative microbiological studies, complementary utilization of molecular and biofilm characterization tools, standardized experimental methods and validation of successful biological-based antifouling strategies for MBR applications are needed. Specifically, in addition, linking these studies to relevant operational conditions in MBRs is an essential step to ultimately develop a better understanding and more effective and directed control strategy for biofouling. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetically-Based Biologic Technologies. Biology and Human Welfare.

ERIC Educational Resources Information Center

Mayer, William V.; McInerney, Joseph D.

The purpose of this six-part booklet is to review the current status of genetically-based biologic technologies and to suggest how information about these technologies can be inserted into existing educational programs. Topic areas included in the six parts are: (1) genetically-based technologies in the curriculum; (2) genetic technologies…

Nucleic Acid-Based Nanodevices in Biological Imaging.

PubMed

Chakraborty, Kasturi; Veetil, Aneesh T; Jaffrey, Samie R; Krishnan, Yamuna

2016-06-02

The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.

Tox21 Enricher: Web-based Chemical/Biological Functional Annotation Analysis Tool Based on Tox21 Toxicity Screening Platform.

PubMed

Hur, Junguk; Danes, Larson; Hsieh, Jui-Hua; McGregor, Brett; Krout, Dakota; Auerbach, Scott

2018-05-01

The US Toxicology Testing in the 21st Century (Tox21) program was established to develop more efficient and human-relevant toxicity assessment methods. The Tox21 program screens >10,000 chemicals using quantitative high-throughput screening (qHTS) of assays that measure effects on toxicity pathways. To date, more than 70 assays have yielded >12 million concentration-response curves. The patterns of activity across assays can be used to define similarity between chemicals. Assuming chemicals with similar activity profiles have similar toxicological properties, we may infer toxicological properties based on its neighbourhood. One approach to inference is chemical/biological annotation enrichment analysis. Here, we present Tox21 Enricher, a web-based chemical annotation enrichment tool for the Tox21 toxicity screening platform. Tox21 Enricher identifies over-represented chemical/biological annotations among lists of chemicals (neighbourhoods), facilitating the identification of the toxicological properties and mechanisms in the chemical set. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bioavailability of biologically sequestered cadmium and the implications of metal detoxification

USGS Publications Warehouse

Wallace, W.G.; Lopez, G.R.

1997-01-01

The deposit-feeding oligochaete Limnodrilus hoffmeisteri possesses metallothionein-like proteins and metal-rich granules for storing and detoxifying cadmium (Cd). In this study we investigated the bioavailability of Cd sequestered within this oligochaete by conducting feeding experiments with 109Cd-labeled oligochaetes and the omnivorous grass shrimp Palaemonetes pugio. We also make predictions on Cd trophic transfer based on oligochaete subcellular Cd distributions and absorption efficiencies of Cd by shrimp Cytosol [including metallothionein-like proteins and other proteins) and a debris fraction (including metal-rich granules and tissue fragments) isolated from homogenized 109Cd-labeled oligochaetes were embedded in gelatin and fed to shrimp. The 109Cd absorption efficiencies of shrimp fed these subcellular fractions were 84.8 and 48.6%, respectively, and were significantly different (p < 0.001), indicating that 109Cd bound in these fractions was not equally available to a predator. Mass balance equations demonstrate that shrimp fed whole worms absorb 61.5% of the ingested 109Cd, an absorption efficiency similar to that obtained experimentally (57.1%). Furthermore, the majority of the absorbed 109Cd comes from the fraction containing metallothionein-like proteins (i.e. cytosol). 109Cd absorbed from the debris fraction probably comes from the digestion of tissue fragments, rather than metal-rich granules. The ecological significance of these findings is that prey detoxification mechanisms may mediate the bioreduction or bioaccumulation of toxic metals along fond chains by altering metal bioavailability. Another important finding is that trophic transfer of metal can be predicted based on the subcellular metal distribution of prey.

Lab-based x-ray tomography of a cochlear implant using energy discriminating detectors for metal artefact reduction

NASA Astrophysics Data System (ADS)

Yokhana, Viona S. K.; Arhatari, Benedicta D.; Gureyev, Timur E.; Abbey, Brian

2018-01-01

X-ray computed tomography (XCT) is an important clinical diagnostic tool which is also used in a range of biological imaging applications in research. The increasing prevalence of metallic implants in medical and dental radiography and tomography has driven the demand for new approaches to solving the issue of metal artefacts in XCT. Metal artefacts occur when a highly absorbing material is imaged which is in boundary contact with one or more weakly absorbing components, such as soft-tissue. The resulting `streaking' in the reconstructed images creates significant challenges for X-ray analysis due to the non-linear dependence on the absorption properties of the sample. In this paper we introduce a new approach to removing metal artefacts which exploits the capabilities of the recently available, photon-counting PiXirad detector. Our approach works for standard lab-based polychromatic X-ray tubes and does not rely on any postprocessing of the data. The method is demonstrated using both simulated data from a test phantom and experimental data collected from a cochlear implant. The results show that by combining the individual images, which are simultaneously generated for each different energy threshold, artefact -free segmentation of the implant from the surrounding biological tissue is achieved.

Sub-0.5 V Highly Stable Aqueous Salt Gated Metal Oxide Electronics

PubMed Central

Park, Sungjun; Lee, SeYeong; Kim, Chang-Hyun; Lee, Ilseop; Lee, Won-June; Kim, Sohee; Lee, Byung-Geun; Jang, Jae-Hyung; Yoon, Myung-Han

2015-01-01

Recently, growing interest in implantable bionics and biochemical sensors spurred the research for developing non-conventional electronics with excellent device characteristics at low operation voltages and prolonged device stability under physiological conditions. Herein, we report high-performance aqueous electrolyte-gated thin-film transistors using a sol-gel amorphous metal oxide semiconductor and aqueous electrolyte dielectrics based on small ionic salts. The proper selection of channel material (i.e., indium-gallium-zinc-oxide) and precautious passivation of non-channel areas enabled the development of simple but highly stable metal oxide transistors manifested by low operation voltages within 0.5 V, high transconductance of ~1.0 mS, large current on-off ratios over 107, and fast inverter responses up to several hundred hertz without device degradation even in physiologically-relevant ionic solutions. In conjunction with excellent transistor characteristics, investigation of the electrochemical nature of the metal oxide-electrolyte interface may contribute to the development of a viable bio-electronic platform directly interfacing with biological entities in vivo. PMID:26271456

Metal-organic frameworks as biosensors for luminescence-based detection and imaging

PubMed Central

Miller, Sophie E.; Teplensky, Michelle H.; Moghadam, Peyman Z.; Fairen-Jimenez, David

2016-01-01

Metal-organic frameworks (MOFs), formed by the self-assembly of metal centres or clusters and organic linkers, possess many key structural and chemical features that have enabled them to be used in sensing platforms for a variety of environmentally, chemically and biomedically relevant compounds. In particular, their high porosity, large surface area, tuneable chemical composition, high degree of crystallinity, and potential for post-synthetic modification for molecular recognition make MOFs promising candidates for biosensing applications. In this review, we separate our discussion of MOF biosensors into two categories: quantitative sensing, focusing specifically on luminescence-based sensors for the direct measurement of a specific analyte, and qualitative sensing, where we describe MOFs used for fluorescence microscopy and as magnetic resonance imaging contrast agents. We highlight several key publications in each of these areas, concluding that MOFs present an exciting, versatile new platform for biosensing applications and imaging, and we expect to see their usage grow as the field progresses. PMID:27499847

Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities.

PubMed

Vergucht, Eva; Brans, Toon; Beunis, Filip; Garrevoet, Jan; Bauters, Stephen; De Rijcke, Maarten; Deruytter, David; Janssen, Colin; Riekel, Christian; Burghammer, Manfred; Vincze, Laszlo

2015-07-01

Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their natural in vivo state was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitive in vivo multi-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.

Sex Differences in Panic-Relevant Responding to a 10% Carbon Dioxide-Enriched Air Biological Challenge

PubMed Central

Nillni, Yael I.; Berenz, Erin C.; Rohan, Kelly J.; Zvolensky, Michael J.

2011-01-01

The current study examined sex differences in psychological (i.e., self-reported anxiety, panic symptoms, and avoidance) and physiological (i.e., heart rate and skin conductance level) response to, and recovery from, a laboratory biological challenge. Participants were a community-recruited sample of 128 adults (63.3% women; Mage = 23.2 years, SD = 8.9) who underwent a 4-minute 10% CO2-enriched air biological challenge. As predicted, women reported more severe physical panic symptoms and avoidance (i.e., less willingness to participate in another challenge) and demonstrated increased heart rate as compared to men above and beyond the variance accounted for by other theoretically-relevant variables (recent panic attack history, neuroticism, and anxiety sensitivity). Additionally, women demonstrated a faster rate of recovery with respect to heart rate compared to men. These results are in line with literature documenting sex-specific differences in panic psychopathology, and results are discussed in the context of possible mechanisms underlying sex differences in panic vulnerability. PMID:22115836

Syntheses, spectroscopic characterization, thermal study, molecular modeling, and biological evaluation of novel Schiff's base benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) with Ni(II), and Cu(II) metal complexes.

PubMed

Chandra, Sulekh; Gautam, Seema; Rajor, Hament Kumar; Bhatia, Rohit

2015-02-25

Novel Schiff's base ligand, benzil bis(5-amino-1,3,4-thiadiazole-2-thiol) was synthesized by the condensation of benzil and 5-amino-1,3,4-thiadiazole-2-thiol in 1:2 ratio. The structure of ligand was determined on the basis of elemental analyses, IR, (1)H NMR, mass, and molecular modeling studies. Synthesized ligand behaved as tetradentate and coordinated to metal ion through sulfur atoms of thiol ring and nitrogen atoms of imine group. Ni(II), and Cu(II) complexes were synthesized with this nitrogen-sulfur donor (N2S2) ligand. Metal complexes were characterized by elemental analyses, molar conductance, magnetic susceptibility measurements, IR, electronic spectra, EPR, thermal, and molecular modeling studies. All the complexes showed molar conductance corresponding to non-electrolytic nature, expect [Ni(L)](NO3)2 complex, which was 1:2 electrolyte in nature. [Cu(L)(SO4)] complex may possessed square pyramidal geometry, [Ni(L)](NO3)2 complex tetrahedral and rest of the complexes six coordinated octahedral/tetragonal geometry. Newly synthesized ligand and its metal complexes were examined against the opportunistic pathogens. Results suggested that metal complexes were more biological sensitive than free ligand. Copyright © 2014 Elsevier B.V. All rights reserved.

Metallic nanoislands on graphene: A metamaterial for chemical, mechanical, optical, and biological applications.

PubMed

Marin, Brandon C; Ramirez, Julian; Root, Samuel E; Aklile, Eden; Lipomi, Darren J

2017-01-01

Graphene decorated with metallic nanoparticles exhibits electronic, optical, and mechanical properties that neither the graphene nor the metal possess alone. These composite films have electrical conductivity and optical properties that can be modulated by a range of physical, chemical, and biological signals. Such properties are controlled by the morphology of the nanoisland films, which can be deposited on graphene using a variety of techniques, including in situ chemical synthesis and physical vapor deposition. These techniques produce non-random (though loosely defined) morphologies, but can be combined with lithography to generate deterministic patterns. Applications of these composite films include chemical sensing and catalysis, energy storage and transport (including photoconductivity), mechanical sensing (using a highly sensitive piezroresistive effect), optical sensing (including so-called "piezoplasmonic" effects), and cellular biophysics (i.e sensing the contractions of cardiomyocytes and myoblasts).

Heavy Metals in ToxCast: Relevance to Food Safety (SOT)

EPA Science Inventory

Human exposure to heavy metals occurs through food contamination due to industrial processes, vehicle emissions and farming methods. Specific toxicity endpoints have been associated with metal exposures, e.g. lead and neurotoxicity; however, numerous varieties of heavy metals hav...

Discovery of Anti-inflammatory Ingredients in Chinese Herbal Formula Kouyanqing Granule based on Relevance Analysis between Chemical Characters and Biological Effects

PubMed Central

Liu, Hong; Zheng, Yan-fang; Li, Chu-yuan; Zheng, Yu-ying; Wang, De-qin; Wu, Zhong; Huang, Lin; Wang, Yong-gang; Li, Pei-bo; Peng, Wei; Su, Wei-wei

2015-01-01

Kouyanqing Granule (KYQG) is a traditional Chinese herbal formula composed of Flos lonicerae (FL), Radix scrophulariae (RS), Radix ophiopogonis (RO), Radix asparagi (RA), and Radix et rhizoma glycyrrhizae (RG). In contrast with the typical method of separating and then biologicalily testing the components individually, this study was designed to establish an approach in order to define the core bioactive ingredients of the anti-inflammatory effects of KYQG based on the relevance analysis between chemical characters and biological effects. Eleven KYQG samples with different ingredients were prepared by changing the ratios of the 5 herbs. Thirty-eight ingredients in KYQG were identified using Ultra-fast liquid chromatography-Diode array detector-Quadrupole-Time-of-flight-Tandem mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) technology. Human oral keratinocytes (HOK) were cultured for 24 hours with 5% of Cigarette smoke extract (CSE) to induce inflammation stress. Interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and tumour necrosis factor-α (TNF-α) were evaluated after treatment with the eleven KYQG samples. Grey relational analysis(GRA), Pearson’s correlations (PCC), and partial least-squares (PLS) were utilized to evaluate the contribution of each ingredient. The results indicated that KYQG significantly reduced interleukin-1β, interleukin-6, interleukin-8, and tumour necrosis factor-α levels, in which lysine, γ-aminobutyric acid, chelidonic acid, tyrosine, harpagide, neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, isoquercitrin, luteolin-7-o-glucoside, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, angoroside C, harpagoside, cinnamic acid, and ruscogenin play a vital role. PMID:26657159

Discovery of Anti-inflammatory Ingredients in Chinese Herbal Formula Kouyanqing Granule based on Relevance Analysis between Chemical Characters and Biological Effects.

PubMed

Liu, Hong; Zheng, Yan-fang; Li, Chu-yuan; Zheng, Yu-ying; Wang, De-qin; Wu, Zhong; Huang, Lin; Wang, Yong-gang; Li, Pei-bo; Peng, Wei; Su, Wei-wei

2015-12-10

Kouyanqing Granule (KYQG) is a traditional Chinese herbal formula composed of Flos lonicerae (FL), Radix scrophulariae (RS), Radix ophiopogonis (RO), Radix asparagi (RA), and Radix et rhizoma glycyrrhizae (RG). In contrast with the typical method of separating and then biologicalily testing the components individually, this study was designed to establish an approach in order to define the core bioactive ingredients of the anti-inflammatory effects of KYQG based on the relevance analysis between chemical characters and biological effects. Eleven KYQG samples with different ingredients were prepared by changing the ratios of the 5 herbs. Thirty-eight ingredients in KYQG were identified using Ultra-fast liquid chromatography-Diode array detector-Quadrupole-Time-of-flight-Tandem mass spectrometry (UFLC-DAD-Q-TOF-MS/MS) technology. Human oral keratinocytes (HOK) were cultured for 24 hours with 5% of Cigarette smoke extract (CSE) to induce inflammation stress. Interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and tumour necrosis factor-α (TNF-α) were evaluated after treatment with the eleven KYQG samples. Grey relational analysis(GRA), Pearson's correlations (PCC), and partial least-squares (PLS) were utilized to evaluate the contribution of each ingredient. The results indicated that KYQG significantly reduced interleukin-1β, interleukin-6, interleukin-8, and tumour necrosis factor-α levels, in which lysine, γ-aminobutyric acid, chelidonic acid, tyrosine, harpagide, neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, isoquercitrin, luteolin-7-o-glucoside, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid, angoroside C, harpagoside, cinnamic acid, and ruscogenin play a vital role.

A handy liquid metal based electroosmotic flow pump.

PubMed

Gao, Meng; Gui, Lin

2014-06-07

A room temperature liquid metal based electroosmotic flow (EOF) pump has been proposed in this work. This low-cost EOF pump is convenient for both fabrication and integration. It utilizes polydimethylsiloxane (PDMS) microchannels filled with the liquid-metal as non-contact pump electrodes. The electrode channels are fabricated symmetrically to both sides of the pumping channel, having no contact with the pumping channel. To test the pumping performance of the EOF pump, the mean flow velocities of the fluid (DI water) in the EOF pumps were experimentally measured by tracing the fluorescent microparticles in the flow. To provide guidance for designing a low voltage EOF pump, parametric studies on dimensions of the electrode and pumping channels were performed in this work. According to the experimental results, the pumping speed can reach 5.93 μm s(-1) at a driving voltage of only 1.6 V, when the gap between the electrode and the pumping channel is 20 μm. Injecting a room temperature liquid metal into microchannels can provide a simple, rapid, low-cost but accurately self-aligned way to fabricate microelectrodes for EOF pumps, which is a promising method to achieve the miniaturization and integration of the EOF pump in microfluidic systems. The non-contact liquid electrodes have no influence on the fluid in the pumping channel when pumping, reducing Joule heat generation and preventing gas bubble formation at the surface of electrodes. The pump has great potential to drive a wide range of fluids, such as drug reagents, cell suspensions and biological macromolecule solutions.

General and programmable synthesis of hybrid liposome/metal nanoparticles

PubMed Central

Lee, Jin-Ho; Shin, Yonghee; Lee, Wooju; Whang, Keumrai; Kim, Dongchoul; Lee, Luke P.; Choi, Jeong-Woo; Kang, Taewook

2016-01-01

Hybrid liposome/metal nanoparticles are promising candidate materials for biomedical applications. However, the poor selectivity and low yield of the desired hybrid during synthesis pose a challenge. We designed a programmable liposome by selective encoding of a reducing agent, which allows self-crystallization of metal nanoparticles within the liposome to produce stable liposome/metal nanoparticles alone. We synthesized seven types of liposome/monometallic and more complex liposome/bimetallic hybrids. The resulting nanoparticles are tunable in size and metal composition, and their surface plasmon resonance bands are controllable in visible and near infrared. Owing to outer lipid bilayer, our liposome/Au nanoparticle shows better colloidal stability in biologically relevant solutions as well as higher endocytosis efficiency than gold nanoparticles without the liposome. We used this hybrid in intracellular imaging of living cells via surface-enhanced Raman spectroscopy, taking advantage of its improved physicochemical properties. We believe that our method greatly increases the utility of metal nanoparticles in in vivo applications. PMID:28028544

General and programmable synthesis of hybrid liposome/metal nanoparticles.

PubMed

Lee, Jin-Ho; Shin, Yonghee; Lee, Wooju; Whang, Keumrai; Kim, Dongchoul; Lee, Luke P; Choi, Jeong-Woo; Kang, Taewook

2016-12-01

Hybrid liposome/metal nanoparticles are promising candidate materials for biomedical applications. However, the poor selectivity and low yield of the desired hybrid during synthesis pose a challenge. We designed a programmable liposome by selective encoding of a reducing agent, which allows self-crystallization of metal nanoparticles within the liposome to produce stable liposome/metal nanoparticles alone. We synthesized seven types of liposome/monometallic and more complex liposome/bimetallic hybrids. The resulting nanoparticles are tunable in size and metal composition, and their surface plasmon resonance bands are controllable in visible and near infrared. Owing to outer lipid bilayer, our liposome/Au nanoparticle shows better colloidal stability in biologically relevant solutions as well as higher endocytosis efficiency than gold nanoparticles without the liposome. We used this hybrid in intracellular imaging of living cells via surface-enhanced Raman spectroscopy, taking advantage of its improved physicochemical properties. We believe that our method greatly increases the utility of metal nanoparticles in in vivo applications.

Stability of silver nanoparticles: agglomeration and oxidation in biological relevant conditions

NASA Astrophysics Data System (ADS)

Valenti, Laura E.; Giacomelli, Carla E.

2017-05-01

Silver nanoparticles (Ag-NP) are the most used nanomaterial in consumer products due to the intrinsic antimicrobial capacity of silver. However, Ag-NP may be also harmful to algae, aquatic species, mammalian cells, and higher plants because both Ag+ and nanoparticles are responsible of cell damages. The oxidative dissolution of Ag-NP would proceed to completion under oxic conditions, but the rate and extent of the dissolution depend on several factors. This work correlates the effect of the capping agent (albumin and citrate) with the stability of Ag-NP towards agglomeration in simulated body fluid (SBF) and oxidation in the presence of ROS species (H2O2). Capping provides colloidal stability only through electrostatic means, whereas albumin acts as bulky ligands giving steric and electrostatic repulsion, inhibiting the agglomeration in SBF. However, citrate capping protects Ag-NP from dissolution to a major extent than albumin does because of its reducing power. Moreover, citrate in solution minimizes the oxidation of albumin-coated Ag-NP even after long incubation times. H2O2-induced dissolution proceeds to completion with Ag-NP incubated in SBF, while incubation in citrate leads to an incomplete oxidation. In short, albumin is an excellent capping agent to minimize Ag-NP agglomeration whereas citrate provides a mild-reductive medium that prevents dissolution in biological relevant media as well as in the presence of ROS species. These results provide insight into how the surface properties and media composition affect the release of Ag+ from Ag-NP, related to the cell toxicity and relevant to the storage and lifetime of silver-containing nanomaterials.

Synthesis, spectroscopic, coordination and biological activities of some organometallic complexes derived from thio-Schiff base ligands

NASA Astrophysics Data System (ADS)

Abou-Hussein, Azza A.; Linert, Wolfgang

2014-01-01

Two series of mono- and binuclear complexes cyclic or acyclic thio-ferocine Schiff base ligands, derived from the condensation of 2-aminobenzenthiol (L) with monoacetyl ferrocene in the molar ratio 1:1 or in the molar ratio 1:2 for diacetyl ferocine have been prepared. The condensation reactions yield the corresponding Schiff Base ligands, HLa-Maf and H2Lb-Daf. The chelation of the ligands to metal ions occurs through the sulfur of the thiol group as well as the nitrogen atoms of the azomethine group of the ligands. HLa-Maf acts as monobasic bidentate or dibasic tetradentate, while H2Lb-Daf behaves as twice negatively cargend tetradentate ligand. The structures of these ligands were elucidated by elemental analysis, infrared, ultraviolet-visible spectra, as well as 1H NMR spectra. Reactions of the Schiff bases ligands with ruthenium(III), oxovanadium(IV) and dioxouranium(VI) afforded the corresponding transition metal complexes. The properties of the newly prepared complexes were analyse by elemental analyses, infrared, electronic spectra, 1H NMR as well as the magnetic susceptibility and conductivity measurement. The metal complexes exhibits different geometrical arrangements such as octahedral and square pyramidal coordination. Schiff base ligands and their metal complexes were tested against two pathogenic bacteria as Gram-positive and Gram-negative bacteria as well as one kind of fungi to study their biological activity. All the complexes exhibit antibacterial and antifungal activities against these organisms.

Metal hydride-based thermal energy storage systems

DOEpatents

Vajo, John J.; Fang, Zhigang

2017-10-03

The invention provides a thermal energy storage system comprising a metal-containing first material with a thermal energy storage density of about 1300 kJ/kg to about 2200 kJ/kg based on hydrogenation; a metal-containing second material with a thermal energy storage density of about 200 kJ/kg to about 1000 kJ/kg based on hydrogenation; and a hydrogen conduit for reversibly transporting hydrogen between the first material and the second material. At a temperature of 20.degree. C. and in 1 hour, at least 90% of the metal is converted to the hydride. At a temperature of 0.degree. C. and in 1 hour, at least 90% of the metal hydride is converted to the metal and hydrogen. The disclosed metal hydride materials have a combination of thermodynamic energy storage densities and kinetic power capabilities that previously have not been demonstrated. This performance enables practical use of thermal energy storage systems for electric vehicle heating and cooling.

Fundamentals and applications of SERS-based bioanalytical sensing

NASA Astrophysics Data System (ADS)

Kahraman, Mehmet; Mullen, Emma R.; Korkmaz, Aysun; Wachsmann-Hogiu, Sebastian

2017-03-01

Plasmonics is an emerging field that examines the interaction between light and metallic nanostructures at the metal-dielectric interface. Surface-enhanced Raman scattering (SERS) is a powerful analytical technique that uses plasmonics to obtain detailed chemical information of molecules or molecular assemblies adsorbed or attached to nanostructured metallic surfaces. For bioanalytical applications, these surfaces are engineered to optimize for high enhancement factors and molecular specificity. In this review we focus on the fabrication of SERS substrates and their use for bioanalytical applications. We review the fundamental mechanisms of SERS and parameters governing SERS enhancement. We also discuss developments in the field of novel SERS substrates. This includes the use of different materials, sizes, shapes, and architectures to achieve high sensitivity and specificity as well as tunability or flexibility. Different fundamental approaches are discussed, such as label-free and functional assays. In addition, we highlight recent relevant advances for bioanalytical SERS applied to small molecules, proteins, DNA, and biologically relevant nanoparticles. Subsequently, we discuss the importance of data analysis and signal detection schemes to achieve smaller instruments with low cost for SERS-based point-of-care technology developments. Finally, we review the main advantages and challenges of SERS-based biosensing and provide a brief outlook.

Schiff bases in medicinal chemistry: a patent review (2010-2015).

PubMed

Hameed, Abdul; Al-Rashida, Mariya; Uroos, Maliha; Abid Ali, Syed; Khan, Khalid Mohammed

2017-01-01

Schiff bases are synthetically accessible and structurally diverse compounds, typically obtained by facile condensation between an aldehyde, or a ketone with primary amines. Schiff bases contain an azomethine (-C = N-) linkage that stitches together two or more biologically active aromatic/heterocyclic scaffolds to form various molecular hybrids with interesting biological properties. Schiff bases are versatile metal complexing agents and have been known to coordinate all metals to form stable metal complexes with vast therapeutic applications. Areas covered: This review aims to provide a comprehensive overview of the various patented therapeutic applications of Schiff bases and their metal complexes from 2010 to 2015. Expert opinion: Schiff bases are a popular class of compounds with interesting biological properties. Schiff bases are also versatile metal complexing ligands and have been used to coordinate almost all d-block metals as well as lanthanides. Therapeutically, Schiff bases and their metal complexes have been reported to exhibit a wide range of biological activities such as antibacterial including antimycobacterial, antifungal, antiviral, antimalarial, antiinflammatory, antioxidant, pesticidal, cytotoxic, enzyme inhibitory, and anticancer including DNA damage.

Agent-based modelling in synthetic biology.

PubMed

Gorochowski, Thomas E

2016-11-30

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

Metal species involved in long distance metal transport in plants

PubMed Central

Álvarez-Fernández, Ana; Díaz-Benito, Pablo; Abadía, Anunciación; López-Millán, Ana-Flor; Abadía, Javier

2014-01-01

The mechanisms plants use to transport metals from roots to shoots are not completely understood. It has long been proposed that organic molecules participate in metal translocation within the plant. However, until recently the identity of the complexes involved in the long-distance transport of metals could only be inferred by using indirect methods, such as analyzing separately the concentrations of metals and putative ligands and then using in silico chemical speciation software to predict metal species. Molecular biology approaches also have provided a breadth of information about putative metal ligands and metal complexes occurring in plant fluids. The new advances in analytical techniques based on mass spectrometry and the increased use of synchrotron X-ray spectroscopy have allowed for the identification of some metal-ligand species in plant fluids such as the xylem and phloem saps. Also, some proteins present in plant fluids can bind metals and a few studies have explored this possibility. This study reviews the analytical challenges researchers have to face to understand long-distance metal transport in plants as well as the recent advances in the identification of the ligand and metal-ligand complexes in plant fluids. PMID:24723928

Applications of Microfluidics in Quantitative Biology.

PubMed

Bai, Yang; Gao, Meng; Wen, Lingling; He, Caiyun; Chen, Yuan; Liu, Chenli; Fu, Xiongfei; Huang, Shuqiang

2018-05-01

Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future. © 2017 Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Synthesis, characterization and biological activity of some transition metals with Schiff base derived from 2-thiophene carboxaldehyde and aminobenzoic acid.

PubMed

Mohamed, Gehad G; Omar, M M; Hindy, Ahmed M M

2005-12-01

Metal complexes of Schiff base derived from 2-thiophene carboxaldehyde and 2-aminobenzoic acid (HL) are reported and characterized based on elemental analyses, IR, 1H NMR, solid reflectance, magnetic moment, molar conductance and thermal analysis (TGA). The ligand dissociation as well as the metal-ligand stability constants were calculated pH metrically at 25 degrees C and ionic strength mu=0.1 (1M NaCl). The complexes are found to have the formulae [M(HL)2](X)n.yH2O (where M=Fe(III) (X=Cl, n=3, y=3), Co(II) (X=Cl, n=2, y=1.5), Ni(II) (X=Cl, n=2, y=1) and UO2(II) (X=NO3, n=2, y=0)) and [M(L)2] (where M=Cu(II) (X=Cl) and Zn(II) (X=AcO)). The molar conductance data reveal that Fe(III) and Co(II), Ni(II) and UO2(II) chelates are ionic in nature and are of the type 3:1 and 2:1 electrolytes, respectively, while Cu(II) and Zn(II) complexes are non-electrolytes. IR spectra show that HL is coordinated to the metal ions in a terdentate manner with ONS donor sites of the carboxylate O, azomethine N and thiophene S. From the magnetic and solid reflectance spectra, it is found that the geometrical structure of these complexes are octahedral. The thermal behaviour of these chelates shows that the hydrated complexes losses water molecules of hydration in the first step followed immediately by decomposition of the anions and ligand molecules in the subsequent steps. The activation thermodynamic parameters, such as, E*, DeltaH*, DeltaS* and DeltaG* are calculated from the DrTG curves using Coats-Redfern method. The synthesized ligands, in comparison to their metal complexes also were screened for their antibacterial activity against bacterial species, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus pyogones and Fungi (Candida). The activity data show that the metal complexes to be more potent/antibacterial than the parent Schiff base ligand against one or more bacterial species.

Synthesis, characterization and biological activity of some transition metals with Schiff base derived from 2-thiophene carboxaldehyde and aminobenzoic acid

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Omar, M. M.; Hindy, Ahmed M. M.

2005-12-01

Metal complexes of Schiff base derived from 2-thiophene carboxaldehyde and 2-aminobenzoic acid (HL) are reported and characterized based on elemental analyses, IR, 1H NMR, solid reflectance, magnetic moment, molar conductance and thermal analysis (TGA). The ligand dissociation as well as the metal-ligand stability constants were calculated pH metrically at 25 °C and ionic strength μ = 0.1 (1 M NaCl). The complexes are found to have the formulae [M(HL) 2](X) n· yH 2O (where M = Fe(III) (X = Cl, n = 3, y = 3), Co(II) (X = Cl, n = 2, y = 1.5), Ni(II) (X = Cl, n = 2, y = 1) and UO 2(II) (X = NO 3, n = 2, y = 0)) and [M(L) 2] (where M = Cu(II) (X = Cl) and Zn(II) (X = AcO)). The molar conductance data reveal that Fe(III) and Co(II), Ni(II) and UO 2(II) chelates are ionic in nature and are of the type 3:1 and 2:1 electrolytes, respectively, while Cu(II) and Zn(II) complexes are non-electrolytes. IR spectra show that HL is coordinated to the metal ions in a terdentate manner with ONS donor sites of the carboxylate O, azomethine N and thiophene S. From the magnetic and solid reflectance spectra, it is found that the geometrical structure of these complexes are octahedral. The thermal behaviour of these chelates shows that the hydrated complexes losses water molecules of hydration in the first step followed immediately by decomposition of the anions and ligand molecules in the subsequent steps. The activation thermodynamic parameters, such as, E*, Δ H*, Δ S* and Δ G* are calculated from the DrTG curves using Coats-Redfern method. The synthesized ligands, in comparison to their metal complexes also were screened for their antibacterial activity against bacterial species, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus pyogones and Fungi (Candida). The activity data show that the metal complexes to be more potent/antibacterial than the parent Schiff base ligand against one or more bacterial species.

Pulmonary toxicity after exposure to military-relevant heavy metal tungsten alloy particles

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

Roedel, Erik Q., E-mail: Erik.Roedel@amedd.army.mil; Cafasso, Danielle E., E-mail: Danielle.Cafasso@amedd.army.mil; Lee, Karen W.M., E-mail: Karen.W.Lee@amedd.army.mil

2012-02-15

Significant controversy over the environmental and public health impact of depleted uranium use in the Gulf War and the war in the Balkans has prompted the investigation and use of other materials including heavy metal tungsten alloys (HMTAs) as nontoxic alternatives. Interest in the health effects of HMTAs has peaked since the recent discovery that rats intramuscularly implanted with pellets containing 91.1% tungsten/6% nickel/2.9% cobalt rapidly developed aggressive metastatic tumors at the implantation site. Very little is known, however, regarding the cellular and molecular mechanisms associated with the effects of inhalation exposure to HMTAs despite the recognized risk of thismore » route of exposure to military personnel. In the current study military-relevant metal powder mixtures consisting of 92% tungsten/5% nickel/3% cobalt (WNiCo) and 92% tungsten/5% nickel/3% iron (WNiFe), pure metals, or vehicle (saline) were instilled intratracheally in rats. Pulmonary toxicity was assessed by cytologic analysis, lactate dehydrogenase activity, albumin content, and inflammatory cytokine levels in bronchoalveolar lavage fluid 24 h after instillation. The expression of 84 stress and toxicity-related genes was profiled in lung tissue and bronchoalveolar lavage cells using real-time quantitative PCR arrays, and in vitro assays were performed to measure the oxidative burst response and phagocytosis by lung macrophages. Results from this study determined that exposure to WNiCo and WNiFe induces pulmonary inflammation and altered expression of genes associated with oxidative and metabolic stress and toxicity. Inhalation exposure to both HMTAs likely causes lung injury by inducing macrophage activation, neutrophilia, and the generation of toxic oxygen radicals. -- Highlights: ► Intratracheal instillation of W–Ni–Co and W–Ni–Fe induces lung inflammation in rats. ► W–Ni–Co and W–Ni–Fe alter expression of oxidative stress and toxicity genes. ► W�

A general framework to learn surrogate relevance criterion for atlas based image segmentation

NASA Astrophysics Data System (ADS)

Zhao, Tingting; Ruan, Dan

2016-09-01

Multi-atlas based image segmentation sees great opportunities in the big data era but also faces unprecedented challenges in identifying positive contributors from extensive heterogeneous data. To assess data relevance, image similarity criteria based on various image features widely serve as surrogates for the inaccessible geometric agreement criteria. This paper proposes a general framework to learn image based surrogate relevance criteria to better mimic the behaviors of segmentation based oracle geometric relevance. The validity of its general rationale is verified in the specific context of fusion set selection for image segmentation. More specifically, we first present a unified formulation for surrogate relevance criteria and model the neighborhood relationship among atlases based on the oracle relevance knowledge. Surrogates are then trained to be small for geometrically relevant neighbors and large for irrelevant remotes to the given targets. The proposed surrogate learning framework is verified in corpus callosum segmentation. The learned surrogates demonstrate superiority in inferring the underlying oracle value and selecting relevant fusion set, compared to benchmark surrogates.

Biomachining: metal etching via microorganisms.

PubMed

Díaz-Tena, Estíbaliz; Barona, Astrid; Gallastegui, Gorka; Rodríguez, Adrián; López de Lacalle, L Norberto; Elías, Ana

2017-05-01

The use of microorganisms to remove metal from a workpiece is known as biological machining or biomachining, and it has gained in both importance and scientific relevance over the past decade. Conversely to mechanical methods, the use of readily available microorganisms is low-energy consuming, and no thermal damage is caused during biomachining. The performance of this sustainable process is assessed by the material removal rate, and certain parameters have to be controlled for manufacturing the machined part with the desired surface finish. Although the variety of microorganisms is scarce, cell concentration or density plays an important role in the process. There is a need to control the temperature to maintain microorganism activity at its optimum, and a suitable shaking rate provides an efficient contact between the workpiece and the biological medium. The system's tolerance to the sharp changes in pH is quite limited, and in many cases, an acid medium has to be maintained for effective performance. This process is highly dependent on the type of metal being removed. Consequently, the operating parameters need to be determined on a case-by-case basis. The biomachining time is another variable with a direct impact on the removal rate. This biological technique can be used for machining simple and complex shapes, such as series of linear, circular, and square micropatterns on different metal surfaces. The optimal biomachining process should be fast enough to ensure high production, a smooth and homogenous surface finish and, in sum, a high-quality piece. As a result of the high global demand for micro-components, biomachining provides an effective and sustainable alternative. However, its industrial-scale implementation is still pending.

Metals, minerals and microbes: geomicrobiology and bioremediation.

PubMed

Gadd, Geoffrey Michael

2010-03-01

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social

Studies on DNA binding behaviour of biologically active transition metal complexes of new tetradentate N2O2 donor Schiff bases: inhibitory activity against bacteria.

PubMed

Sobha, S; Mahalakshmi, R; Raman, N

2012-06-15

A series of Cu(II), Ni(II) and Zn(II) complexes of the type ML have been synthesized with Schiff bases derived from o-acetoacetotoluidide, 2-hydroxybenzaldehyde and o-phenylenediamine/1,4-diaminobutane. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the six metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff bases are found to act as tetradentate ligands using N(2)O(2) donor set of atoms leading to a square-planar geometry for the complexes around all the metal ions. The binding properties of metal complexes with DNA were investigated by absorption spectra, viscosity measurements and cyclic voltammetry. Detailed analysis reveals that the metal complexes intercalate into the DNA base stack as intercalators. All the metal complexes cleave the pUC19 DNA in presence of H(2)O(2.) The Schiff bases and their complexes have been screened for their antibacterial activity against five bacterial strains (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae) by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligands. Copyright © 2012 Elsevier B.V. All rights reserved.

A critical review of approaches and limitations of inhalation bioavailability and bioaccessibility of metal(loid)s from ambient particulate matter or dust.

PubMed

Kastury, Farzana; Smith, Euan; Juhasz, Albert L

2017-01-01

Inhalation of metal(loid)s in ambient particulate matter (APM) represents a significant exposure pathway to humans. Although exposure assessment associated with this pathway is currently based on total metal(loid) content, a bioavailability (i.e. absorption in the systemic circulation) and/or bioaccessibility (i.e. solubility in simulated lung fluid) based approach may more accurately quantify exposure. Metal(loid) bioavailability-bioaccessibility assessment from APM is inherently complex and lacks consensus. This paper reviews the discrepancies that impede the adoption of a universal protocol for the assessment of inhalation bioaccessibility. Exposure assessment approaches for in-vivo bioavailability, in-vitro cell culture and in-vitro bioaccessibility (composition of simulated lungs fluid, physico-chemical and methodological considerations) are critiqued in the context of inhalation exposure refinement. An important limitation of bioavailability and bioaccessibility studies is the use of considerably higher than environmental metal(loid) concentration, which diminishing their relevance to human exposure scenarios. Similarly, individual metal(loid) studies have been criticised due to complexities of APM metal(loid) mixtures which may impart synergistic or antagonistic effects compared to single metal(loid) exposure. Although a number of different simulated lung fluid (SLF) compositions have been used in metal(loid) bioaccessibility studies, information regarding the comparative leaching efficiency among these different SLF and comparisons to in-vivo bioavailability data is lacking. In addition, the particle size utilised is often not representative of what is deposited in the lungs while assay parameters (extraction time, solid to liquid ratio, temperature and agitation) are often not biologically relevant. Research needs are identified in order to develop robust in-vitro bioaccessibility protocols for the assessment or prediction of metal(loid) bioavailability in

Current biochemistry, molecular biology, and clinical relevance of natriuretic peptides.

PubMed

Nishikimi, Toshio; Kuwahara, Koichiro; Nakao, Kazuwa

2011-03-01

The mammalian natriuretic peptide family consists of atrial (ANP), brain [B-type; BNP] and C-type natriuretic peptide (CNP) and three receptors, natriuretic receptors-A (NPR-A), -B (NPR-B) and -C (NPR-C). Both ANP and BNP are abundantly expressed in the heart and are secreted mainly from the atria and ventricles, respectively. By contrast, CNP is mainly expressed in the central nervous system, bone and vasculature. Plasma concentrations of both ANP and BNP are elevated in patients with cardiovascular disease, though the magnitude of the increase in BNP is usually greater than the increase in ANP. This makes BNP is a clinically useful diagnostic marker for several pathophysiological conditions, including heart failure, ventricular remodeling and pulmonary hypertension, among others. Recent studies have shown that in addition to BNP-32, proBNP-108 also circulates in human plasma and that levels of both forms are increased in heart failure. Furthermore, proBNP-108 is O-glycosylated and circulates at higher levels in patients with severe heart failure. In this review we discuss recent progress in our understanding of the biochemistry, molecular biology and clinical relevance of the natriuretic peptide system. Copyright © 2011 Japanese College of Cardiology. Published by Elsevier Ltd. All rights reserved.

Categorization of biologically relevant chemical signals in the medial amygdala

PubMed Central

Samuelsen, Chad L.; Meredith, Michael

2009-01-01

Many species employ chemical signals to convey messages between members of the same species (conspecific), but chemosignals may also provide information to another species (heterospecific). Here, we found that conspecific chemosignals (male, female mouse urine) increased immediate early gene-protein (IEG) expression in both anterior and posterior medial amygdala of male mice, whereas most heterospecific chemosignals (e.g.: hamster vaginal fluid, steer urine) increased expression only in anterior medial amygdala. This categorization of responses in medial amygdala conforms to our previously reported findings in male hamsters. The same characteristic pattern of IEG expression appears in the medial amygdala of each species in response to conspecific stimuli for that species. These results suggest that the amygdala categorizes stimuli according to the biological relevance for the tested species. Thus, a heterospecific predator (cat collar) stimulus, which elicited behavioral avoidance in mice, increased IEG expression in mouse posterior medial amygdala (like conspecific stimuli). Further analysis suggests reproduction related and potentially threatening stimuli produce increased IEG expression in different sub-regions of posterior medial amygdala (dorsal and ventral, respectively). These patterns of IEG expression in medial amygdala may provide glimpses of a tertiary sorting of chemosensory signals beyond the primary-level selectivity of chemosensory neurons and the secondary sorting in main and accessory olfactory bulbs. PMID:19368822

Biological relevance of decamethylcyclopentasiloxane (D5) induced rat uterine endometrial adenocarcinoma tumorigenesis: Mode of action and relevance to humans.

PubMed

Klaunig, James E; Dekant, Wolfgang; Plotzke, Kathy; Scialli, Anthony R

2016-02-01

Decamethylcyclopentasiloxane (D5) is a cyclic siloxane used in the production and formulation of consumer products with potential exposure to manufacturing workers, consumer, and the general public. Following a combined 2-year inhalation chronic bioassay performed in Fischer 344 (F344) rats, an increase in uterine endometrial adenocarcinomas was noted at the highest concentration to which animals were exposed. No other neoplasms were detected. In this study, a dose of 160 ppm produced an incidence of 8% endometrial adenocarcinomas. Based on a number of experimental studies with D5, the current manuscript examines the biological relevance and possible modes of action for the uterine endometrial adenocarcinomas observed in the rat following chronic exposure to D5. Variable rates of spontaneous uterine endometrial adenocarcinomas have been reported for untreated F344 CrlBr rats. As such, we concluded that the slight increase in uterine endometrial adenocarcinomas observed in the D5 chronic bioassay might not be the result of D5 exposure but may be related to variability of the spontaneous tumor incidence in this strain of rat. However, if the uterine endometrial adenocarcinomas are related to D5-exposure, alteration in the estrous cycle in the aging F344 rat is the most likely mode of action. D5 is not genotoxic or estrogenic. The alteration in the estrous cycle is caused by a decrease in progesterone with an increase in the estrogen:progesterone ratio most likely induced by a decrease in prolactin concentration. Available data support that exposure to D5 influences prolactin concentration. Although the effects on prolactin concentrations in a number of experiments were not always consistent, the available data support the conclusion that D5 is acting via a dopamine receptor agonist-like mechanism to alter the pituitary control of the estrous cycle. In further support of this mode of action, studies in F344 aged animals showed that the effects of D5 on estrous

Heavy Metals in ToxCast: Relevance to Food Safety (SOT) ...

EPA Pesticide Factsheets

Human exposure to heavy metals occurs through food contamination due to industrial processes, vehicle emissions and farming methods. Specific toxicity endpoints have been associated with metal exposures, e.g. lead and neurotoxicity; however, numerous varieties of heavy metals have not been systematically examined for potential toxicities. We describe results from testing a large set of heavy metal-containing compounds in extensive suites of in vitro assays to suggest possible molecular initiating events in toxicity pathways. A broad definition of heavy metals that includes As, Se and organometallics or inorganic salts containing metals in Group III or higher (MW > 40) was used to identify 75 different compounds tested in the EPA’s ToxCast assays encompassing biochemical, cellular and model organism assays. These 75, plus an additional 100 metal-containing compounds, were tested in Tox21 quantitative high-throughput screening (qHTS) assays covering nuclear receptor and stress pathways. Known activities were confirmed such as activation of stress pathways and nuclear receptors (RXR, PPARg) as well as overt cytotoxicity. Specifically, organotin and organomercury were among the most potent of over 8K chemicals tested. The HTS results support known toxicities, including promiscuous GPCR activity for mercury compounds consistent with the neuropsychiatric effects seen in mercury poisoning (Mad Hatter’s Syndrome). As such, HTS approaches provide an efficient method

Singlet molecular oxygen generated by biological hydroperoxides.

PubMed

Miyamoto, Sayuri; Martinez, Glaucia R; Medeiros, Marisa H G; Di Mascio, Paolo

2014-10-05

The chemistry behind the phenomenon of ultra-weak photon emission has been subject of considerable interest for decades. Great progress has been made on the understanding of the chemical generation of electronically excited states that are involved in these processes. Proposed mechanisms implicated the production of excited carbonyl species and singlet molecular oxygen in the mechanism of generation of chemiluminescence in biological system. In particular, attention has been focused on the potential generation of singlet molecular oxygen in the recombination reaction of peroxyl radicals by the Russell mechanism. In the last ten years, our group has demonstrated the generation of singlet molecular oxygen from reactions involving the decomposition of biologically relevant hydroperoxides, especially from lipid hydroperoxides in the presence of metal ions, peroxynitrite, HOCl and cytochrome c. In this review we will discuss details on the chemical aspects related to the mechanism of singlet molecular oxygen generation from different biological hydroperoxides. Copyright © 2014 Elsevier B.V. All rights reserved.

Biological synthesis of nanosized sulfide semiconductors: current status and future prospects.

PubMed

da Costa, João Pinto; Girão, Ana Violeta; Trindade, Tito; Costa, Maria Clara; Duarte, Armando; Rocha-Santos, Teresa

2016-10-01

There have been extensive and comprehensive reviews in the field of metal sulfide precipitation in the context of environmental remediation. However, these works have focused mainly on the removal of metals from aqueous solutions-usually, metal-contaminated effluents-with less emphasis on the precipitation process and on the end-products, frequently centering on metal removal efficiencies. Recently, there has been an increasing interest not only in the possible beneficial effects of these bioremediation strategies for metal-rich effluents but also on the formed precipitates. These metal sulfide materials are of special relevance in industry, due to their optical, electronic, and mechanical properties. Hence, identifying new routes for synthesizing these materials, as well as developing methodologies allowing for the control of the shape and size of particulates, is of environmental, economic, and practical importance. Multiple studies have shown proof-of-concept for the biological synthesis of inorganic metallic sulfide nanoparticles (NPs), resorting to varied organisms or cell components, though this information has scarcely been structured and compiled in a systematic manner. In this review, we overview the biological synthesis methodologies of nanosized metal sulfides and the advantages of these strategies when compared to more conventional chemical routes. Furthermore, we highlight the possibility of the use of numerous organisms for the synthesis of different metal sulfide NPs, with emphasis on sulfate-reducing bacteria (SRB). Finally, we put in perspective the potential of these methodologies in the emerging research areas of biohydrometallurgy and nanobiotechnology for the uptake of metals in the form of metal sulfide nanoparticles. A more complete understanding of the principles underlying the (bio)chemistry of formation of solids in these conditions may lead to the large-scale production of such metal sulfides, while simultaneously allowing an enhanced

Heavy Metal Contaminated Soil Imitation Biological Treatment Overview

NASA Astrophysics Data System (ADS)

Pan, Chang; Chen, Jun; Wu, Ke; Zhou, Zhongkai; Cheng, Tingting

2018-01-01

In this paper, the treatment methods of heavy metal pollution in soils were analyzed, the existence and transformation of heavy metals in soil were explored, and the mechanism of heavy metal absorption by plants was studied. It was concluded that the main form of plants absorb heavy metals in the soil is exchangeable. The main mechanism was that the plant cell wall can form complex with heavy metals, so that heavy metals fixed on the cell wall, and through the selective absorption of plasma membrane into the plant body. In addition, the adsorption mechanism of the adsorbed material was analyzed. According to the results of some researchers, it was found that the mechanism of adsorption of heavy metals was similar to that of plants. According to this, using adsorbent material as the main material, Imitate the principle of plant absorption of heavy metals in the soil to removing heavy metals in the soil at one-time and can be separated from the soil after adsorption to achieve permanent removal of heavy metals in the soil was feasibility.

Biologics in pediatric psoriasis - efficacy and safety.

PubMed

Dogra, Sunil; Mahajan, Rahul

2018-01-01

Childhood psoriasis is a special situation that is a management challenge for the treating dermatologist. As is the situation with traditional systemic agents, which are commonly used in managing severe psoriasis in children, the biologics are being increasingly used in the recalcitrant disease despite limited data on long term safety. Areas covered: We performed an extensive literature search to collect evidence-based data on the use of biologics in pediatric psoriasis. The relevant literature published from 2000 to September 2017 was obtained from PubMed, using the MeSH words 'biologics', 'biologic response modifiers' and 'treatment of pediatric/childhood psoriasis'. All clinical trials, randomized double-blind or single-blind controlled trials, open-label studies, retrospective studies, reviews, case reports and letters concerning the use of biologics in pediatric psoriasis were screened. Articles covering the use of biologics in pediatric psoriasis were screened and reference lists in the selected articles were scrutinized to identify other relevant articles that had not been found in the initial search. Articles without relevant information about biologics in general (e.g. its mechanism of action, pharmacokinetics and adverse effects) and its use in psoriasis in particular were excluded. We screened 427 articles and finally selected 41 relevant articles. Expert opinion: The available literature on the use of biologics such as anti-tumor necrosis factor (TNF)-α agents, and anti-IL-12/23 agents like ustekinumab suggests that these are effective and safe in managing severe pediatric psoriasis although there is an urgent need to generate more safety data. Dermatologists must be careful about the potential adverse effects of the biologics before administering them to children with psoriasis. It is likely that with rapidly evolving scenario of biologics in psoriasis, these will prove to be very useful molecules particularly in managing severe and recalcitrant

Approaches to chemical synthetic biology.

PubMed

Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

2012-07-16

Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Sex differences in panic-relevant responding to a 10% carbon dioxide-enriched air biological challenge.

PubMed

Nillni, Yael I; Berenz, Erin C; Rohan, Kelly J; Zvolensky, Michael J

2012-01-01

The current study examined sex differences in psychological (i.e., self-reported anxiety, panic symptoms, and avoidance) and physiological (i.e., heart rate and skin conductance level) response to, and recovery from, a laboratory biological challenge. Participants were a community-recruited sample of 128 adults (63.3% women; M(age)=23.2 years, SD=8.9) who underwent a 4-min 10% CO(2)-enriched air biological challenge. As predicted, women reported more severe physical panic symptoms and avoidance (i.e., less willingness to participate in another challenge) and demonstrated increased heart rate as compared to men above and beyond the variance accounted for by other theoretically relevant variables (recent panic attack history, neuroticism, and anxiety sensitivity). Additionally, women demonstrated a faster rate of recovery with respect to heart rate compared to men. These results are in line with literature documenting sex-specific differences in panic psychopathology, and results are discussed in the context of possible mechanisms underlying sex differences in panic vulnerability. Copyright © 2011 Elsevier Ltd. All rights reserved.

Affinity to bovine serum albumin and anticancer activity of some new water-soluble metal Schiff base complexes

NASA Astrophysics Data System (ADS)

Asadi, Mozaffar; Asadi, Zahra; Zarei, Leila; Sadi, Somaye Barzegar; Amirghofran, Zahra

2014-12-01

Metal Schiff-base complexes show biological activity but they are usually insoluble in water so four new water-soluble metal Schiff base complexes of Na2[M(5-SO3-1,2-salben]; (5-SO3-1,2-salben denoted N,N";-bis(5-sulphosalicyliden)-1,2-diaminobenzylamine and M = Mg, Mn, Cu, Zn) were synthesized and characterized. The formation constants of the metal complexes were determined by UV-Vis absorption spectroscopy. The interaction of these complexes with bovine serum albumin (BSA) was studied by fluorescence spectroscopy. Type of quenching, binding constants, number of binding sites and binding stoichiometries were determined by fluorescence quenching method. The results showed that the mentioned complexes strongly bound to BSA. Thermodynamic parameters indicated that hydrophobic association was the major binding force and that the interaction was entropy driven and enthalpically disfavoured. The displacement experiment showed that these complexes could bind to the subdomain IIA (site I) of albumin. Furthermore the synchronous fluorescence spectra showed that the microenvironment of the tryptophan residues was not apparently changed. Based on the Förster theory of non-radiation energy transfer, the distance between the donor (Trp residues) and the acceptor metal complexes was obtained. The growth inhibitory effect of complexes toward the K562 cancer cell line was measured.

Heavy metal toxicity to bacteria - are the existing growth media accurate enough to determine heavy metal toxicity?

PubMed

Rathnayake, I V N; Megharaj, Mallavarapu; Krishnamurti, G S R; Bolan, Nanthi S; Naidu, Ravi

2013-01-01

A new minimal medium was formulated considering the limitations of the existing media for testing heavy metal sensitivity to bacteria. Toxicity of cadmium and copper to three bacteria was investigated in the new medium and compared with three other media commonly used to study the effect of the toxic metals. Based on speciation data arrived at using ion-selective electrodes, the available free-metal concentration in solution was highest in the MES-buffered medium. This finding was strongly supported by the estimated EC(50) values for the metals tested based on the toxicity bioassays. The free-ionic cadmium and copper concentrations in the medium provide more accurate determination of metal concentrations that affects the bacteria, than with most of other existing media. This will avoid doubts on other media and misleading conclusions relevant to the toxicity of heavy metals to bacteria and provides a better option for the study of metal-bacteria interactions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Spatial release from masking improves sound pattern discrimination along a biologically relevant pulse-rate continuum in gray treefrogs

PubMed Central

Ward, Jessica L.; Buerkle, Nathan P.; Bee, Mark A.

2013-01-01

Frogs form large choruses during the mating season in which males produce loud advertisement calls to attract females and repel rival males. High background noise levels in these social aggregations can impair vocal perception. In humans, spatial release from masking contributes to our ability to understand speech in noisy social groups. Here, we tested the hypothesis that spatial separation between target signals and ‘chorus-shaped noise’ improves the ability of female gray treefrogs (Hyla chrysoscelis) to perform a behavioral discrimination task based on perceiving differences in the pulsatile structure of advertisement calls. We used two-stimulus choice tests to measure phonotaxis (approach toward sound) in response to calls differing in pulse rate along a biologically relevant continuum between conspecific (50 pulses s−1) and heterospecific (20 pulses s−1) calls. Signals were presented in quiet, in colocated noise, and in spatially separated noise. In quiet conditions, females exhibited robust preferences for calls with relatively faster pulse rates more typical of conspecific calls. Behavioral discrimination between calls differing in pulse rate was impaired in the presence of colocated noise but similar between quiet and spatially separated noise conditions. Our results indicate that spatial release from energetic masking facilitates a biologically important temporal discrimination task in frogs. We discuss these results in light of previous work on spatial release from masking in frogs and other animals. PMID:24055623

Biomimetic cellular metals-using hierarchical structuring for energy absorption.

PubMed

Bührig-Polaczek, A; Fleck, C; Speck, T; Schüler, P; Fischer, S F; Caliaro, M; Thielen, M

2016-07-19

Fruit walls as well as nut and seed shells typically perform a multitude of functions. One of the biologically most important functions consists in the direct or indirect protection of the seeds from mechanical damage or other negative environmental influences. This qualifies such biological structures as role models for the development of new materials and components that protect commodities and/or persons from damage caused for example by impacts due to rough handling or crashes. We were able to show how the mechanical properties of metal foam based components can be improved by altering their structure on various hierarchical levels inspired by features and principles important for the impact and/or puncture resistance of the biological role models, rather than by tuning the properties of the bulk material. For this various investigation methods have been established which combine mechanical testing with different imaging methods, as well as with in situ and ex situ mechanical testing methods. Different structural hierarchies especially important for the mechanical deformation and failure behaviour of the biological role models, pomelo fruit (Citrus maxima) and Macadamia integrifolia, were identified. They were abstracted and transferred into corresponding structural principles and thus hierarchically structured bio-inspired metal foams have been designed. A production route for metal based bio-inspired structures by investment casting was successfully established. This allows the production of complex and reliable structures, by implementing and combining different hierarchical structural elements found in the biological concept generators, such as strut design and integration of fibres, as well as by minimising casting defects. To evaluate the structural effects, similar investigation methods and mechanical tests were applied to both the biological role models and the metallic foams. As a result an even deeper quantitative understanding of the form

Highly sensitive DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization

PubMed Central

Yu, Xu; Zhang, Zhi-Ling; Zheng, Si-Yang

2014-01-01

A novel highly sensitive colorimetric assay for DNA detection using cascade amplification strategy based on hybridization chain reaction and enzyme-induced metallization was established. The DNA modified superparamagnetic beads were demonstrated to capture and enrich the target DNA in the hybridization buffer or human plasma. The hybridization chain reaction and enzyme-induced silver metallization on the gold nanoparticles were used as cascade signal amplification for the detection of target DNA. The metalization of silver on the gold nanoparticles induced a significant colour change from red to yellow until black depending on the concentration of the target DNA, which could be recognized by naked eyes. This method showed a good specificity for the target DNA detection, with the capabilty to discriminate single-base-pair mismatched DNA mutation (single nucleotide polymorphism). Meanwhile, this approach exhibited an excellent anti-interference capability with the convenience of the magentic seperation and washing, which enabled its usage in complex biological systems such as human blood plasma. As an added benefit, the utilization of hybridization chain reaction and enzyme-induced metallization improved detection sensitivity down to 10 pM, which is about 100-fold lower than that of traditional unamplified homogeneous assays. PMID:25500528

Preparation of non-metals properties for data base

NASA Technical Reports Server (NTRS)

1988-01-01

The development of non-metallic material properties data bases is discussed. The data bases consist of the non-metallic material classes of adhesives, adhesive/sealants, plastics, and elastomers. A specifications data base was also developed to incorporate material specifications data as a supplement to the Elastomers Data Base. Examples of the forms used are provided to show the properties of the materials which appear in the data base.

Chemical biology-based approaches on fluorescent labeling of proteins in live cells.

PubMed

Jung, Deokho; Min, Kyoungmi; Jung, Juyeon; Jang, Wonhee; Kwon, Youngeun

2013-05-01

Recently, significant advances have been made in live cell imaging owing to the rapid development of selective labeling of proteins in vivo. Green fluorescent protein (GFP) was the first example of fluorescent reporters genetically introduced to protein of interest (POI). While GFP and various types of engineered fluorescent proteins (FPs) have been actively used for live cell imaging for many years, the size and the limited windows of fluorescent spectra of GFP and its variants set limits on possible applications. In order to complement FP-based labeling methods, alternative approaches that allow incorporation of synthetic fluorescent probes to target POIs were developed. Synthetic fluorescent probes are smaller than fluorescent proteins, often have improved photochemical properties, and offer a larger variety of colors. These synthetic probes can be introduced to POIs selectively by numerous approaches that can be largely categorized into chemical recognition-based labeling, which utilizes metal-chelating peptide tags and fluorophore-carrying metal complexes, and biological recognition-based labeling, such as (1) specific non-covalent binding between an enzyme tag and its fluorophore-carrying substrate, (2) self-modification of protein tags using substrate variants conjugated to fluorophores, (3) enzymatic reaction to generate a covalent binding between a small molecule substrate and a peptide tag, and (4) split-intein-based C-terminal labeling of target proteins. The chemical recognition-based labeling reaction often suffers from compromised selectivity of metal-ligand interaction in the cytosolic environment, consequently producing high background signals. Use of protein-substrate interactions or enzyme-mediated reactions generally shows improved specificity but each method has its limitations. Some examples are the presence of large linker protein, restriction on the choice of introducible probes due to the substrate specificity of enzymes, and competitive

Prebiotic synthesis of carboxylic acids, amino acids and nucleic acid bases from formamide under photochemical conditions⋆

NASA Astrophysics Data System (ADS)

Botta, Lorenzo; Mattia Bizzarri, Bruno; Piccinino, Davide; Fornaro, Teresa; Robert Brucato, John; Saladino, Raffaele

2017-07-01

The photochemical transformation of formamide in the presence of a mixture of TiO2 and ZnO metal oxides as catalysts afforded a large panel of molecules of biological relevance, including carboxylic acids, amino acids and nucleic acid bases. The reaction was less effective when performed in the presence of only one mineral, highlighting the role of synergic effects between the photoactive catalysts. Taken together, these results suggest that the synthesis of chemical precursors for both the genetic and the metabolic apparatuses might have occurred in a simple environment, consisting of formamide, photoactive metal oxides and UV-radiation.

Linking School Biology and Community in Developing Countries.

ERIC Educational Resources Information Center

Knamiller, Gary W.

1984-01-01

Explores the role of biological education in placing the school in its own local community and the real social-economic environment that surrounds it. Particular reference is made to issue-based biological education in schools as an attempt to bridge the gap between purely academic schooling and education for relevance. (Author)

Identifying biologically relevant putative mechanisms in a given phenotype comparison

PubMed Central

Hanoudi, Samer; Donato, Michele; Draghici, Sorin

2017-01-01

A major challenge in life science research is understanding the mechanism involved in a given phenotype. The ability to identify the correct mechanisms is needed in order to understand fundamental and very important phenomena such as mechanisms of disease, immune systems responses to various challenges, and mechanisms of drug action. The current data analysis methods focus on the identification of the differentially expressed (DE) genes using their fold change and/or p-values. Major shortcomings of this approach are that: i) it does not consider the interactions between genes; ii) its results are sensitive to the selection of the threshold(s) used, and iii) the set of genes produced by this approach is not always conducive to formulating mechanistic hypotheses. Here we present a method that can construct networks of genes that can be considered putative mechanisms. The putative mechanisms constructed by this approach are not limited to the set of DE genes, but also considers all known and relevant gene-gene interactions. We analyzed three real datasets for which both the causes of the phenotype, as well as the true mechanisms were known. We show that the method identified the correct mechanisms when applied on microarray datasets from mouse. We compared the results of our method with the results of the classical approach, showing that our method produces more meaningful biological insights. PMID:28486531

Interpreting the biological relevance of bioinformatic analyses with T-DNA sequence for protein allergenicity.

PubMed

Harper, B; McClain, S; Ganko, E W

2012-08-01

Global regulatory agencies require bioinformatic sequence analysis as part of their safety evaluation for transgenic crops. Analysis typically focuses on encoded proteins and adjacent endogenous flanking sequences. Recently, regulatory expectations have expanded to include all reading frames of the inserted DNA. The intent is to provide biologically relevant results that can be used in the overall assessment of safety. This paper evaluates the relevance of assessing the allergenic potential of all DNA reading frames found in common food genes using methods considered for the analysis of T-DNA sequences used in transgenic crops. FASTA and BLASTX algorithms were used to compare genes from maize, rice, soybean, cucumber, melon, watermelon, and tomato using international regulatory guidance. Results show that BLASTX for maize yielded 7254 alignments that exceeded allergen similarity thresholds and 210,772 alignments that matched eight or more consecutive amino acids with an allergen; other crops produced similar results. This analysis suggests that each nontransgenic crop has a much greater potential for allergenic risk than what has been observed clinically. We demonstrate that a meaningful safety assessment is unlikely to be provided by using methods with inherently high frequencies of false positive alignments when broadly applied to all reading frames of DNA sequence. Copyright © 2012 Elsevier Inc. All rights reserved.

Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students.

PubMed

Beach, Dale L; Alvarez, Consuelo J

2015-12-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic "parts," students construct a "reporter plasmid" expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a "sensor plasmid," the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.

Engineered metal based nanomaterials in aqueous environments: Interactions, transformations and implications

NASA Astrophysics Data System (ADS)

Mudunkotuwa, Imali Ama

Nanoscience and nanotechnology offer potential routes towards addressing critical issues such as clean and sustainable energy, environmental protection and human health. Specifically, metal and metal oxide nanomaterials are found in a wide range of applications and therefore hold a greater potential of possible release into the environment or for the human to be exposed. Understanding the aqueous phase behavior of metal and metal oxide nanomaterials is a key factor in the safe design of these materials because their interactions with living systems are always mediated through the aqueous phase. Broadly the transformations in the aqueous phase can be classified as dissolution, aggregation and adsorption which are dependent and linked processes to one another. The complexity of these processes at the liquid-solid interface has therefore been one of the grand challenges that has persisted since the beginning of nanotechnology. Although classical models provide guidance for understanding dissolution and aggregation of nanoparticles in water, there are many uncertainties associated with the recent findings. This is often due to a lack of fundamental knowledge of the surface structure and surface energetics for very small particles. Therefore currently the environmental health and safety studies related to nanomaterials are more focused on understanding the surface chemistry that governs the overall processes in the liquid-solid interfacial region at the molecular level. The metal based nanomaterials focused on in this dissertation include TiO2, ZnO, Cu and CuO. These are among the most heavily used in a number of applications ranging from uses in the construction industry to cosmetic formulation. Therefore they are produced in large scale and have been detected in the environment. There is debate within the scientific community related to their safety as a result of the lack of understanding on the surface interactions that arise from the detailed nature of the surfaces

Biologically Relevant Heterogeneity: Metrics and Practical Insights

PubMed Central

Gough, A; Stern, AM; Maier, J; Lezon, T; Shun, T-Y; Chennubhotla, C; Schurdak, ME; Haney, SA; Taylor, DL

2017-01-01

Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications including basic biomedical research, drug discovery, diagnostics and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell level data, as well as the need for standard metrics of the spatial, temporal and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics and the design of optimal therapeutic strategies for individual patients. PMID:28231035

Biologically Relevant Heterogeneity: Metrics and Practical Insights.

PubMed

Gough, Albert; Stern, Andrew M; Maier, John; Lezon, Timothy; Shun, Tong-Ying; Chennubhotla, Chakra; Schurdak, Mark E; Haney, Steven A; Taylor, D Lansing

2017-03-01

Heterogeneity is a fundamental property of biological systems at all scales that must be addressed in a wide range of biomedical applications, including basic biomedical research, drug discovery, diagnostics, and the implementation of precision medicine. There are a number of published approaches to characterizing heterogeneity in cells in vitro and in tissue sections. However, there are no generally accepted approaches for the detection and quantitation of heterogeneity that can be applied in a relatively high-throughput workflow. This review and perspective emphasizes the experimental methods that capture multiplexed cell-level data, as well as the need for standard metrics of the spatial, temporal, and population components of heterogeneity. A recommendation is made for the adoption of a set of three heterogeneity indices that can be implemented in any high-throughput workflow to optimize the decision-making process. In addition, a pairwise mutual information method is suggested as an approach to characterizing the spatial features of heterogeneity, especially in tissue-based imaging. Furthermore, metrics for temporal heterogeneity are in the early stages of development. Example studies indicate that the analysis of functional phenotypic heterogeneity can be exploited to guide decisions in the interpretation of biomedical experiments, drug discovery, diagnostics, and the design of optimal therapeutic strategies for individual patients.

Relevance between SV and components based on water quality inspection by gas plumes

NASA Astrophysics Data System (ADS)

Nakanishi, A.; Aoyama, C.; Fukuoka, H.; Tajima, H.; Kumagai, H.; Takahashi, A.

2017-12-01

Gas and hydrate seeping from the seafloor into ocean water can be monitored on board, as images on echogram (acoustic equipment display inboard) by utilizing acoustic measurement equipment such as multi-beam sonars. Colors and shades of these images displayed on the monitor vary depending on the acoustic impedance. Backscattering strength (hereinafter referred as SV) depends on the type and density of plume components. Therefore, plume components should not be determined only by examining volume scattering density. By standardizing the relevance between gas plume SV and the components, types of plume components can be presumed just by calculating plume SV based on multi-beam data.Data from the following explorations will be utilized to perform the analysis of metal sensor, CTD measurement, and sampling. July, 2017 KAIYO-MARU2 (KAIYO ENGINEERING CO., LTD) @ Sea of Japan July, 2017 SIHNYO MARU (Tokyo University of Marine Science and Technology) @ Sea of Japan. And Chemical data obtained through YK16-07 cruise is also to be discussed.

The relevance of nanoscale biological fragments for ice nucleation in clouds

NASA Astrophysics Data System (ADS)

O‧Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

2015-01-01

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

The relevance of nanoscale biological fragments for ice nucleation in clouds.

PubMed

O'Sullivan, D; Murray, B J; Ross, J F; Whale, T F; Price, H C; Atkinson, J D; Umo, N S; Webb, M E

2015-01-28

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

The relevance of nanoscale biological fragments for ice nucleation in clouds

PubMed Central

O′Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

2015-01-01

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles. PMID:25626414

The Importance of Biological Databases in Biological Discovery.

PubMed

Baxevanis, Andreas D; Bateman, Alex

2015-06-19

Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. Copyright © 2015 John Wiley & Sons, Inc.

Quantifying restoration success and recovery in a metal-polluted stream: A 17-year assessment of physicochemical and biological responses

USGS Publications Warehouse

Clements, W.H.; Vieira, N.K.M.; Church, S.E.

2010-01-01

Evaluating the effectiveness of stream restoration is often challenging because of the lack of pre-treatment data, narrow focus on physicochemical measures and insufficient post-restoration monitoring. Even when these fundamental elements are present, quantifying restoration success is difficult because of the challenges associated with distinguishing treatment effects from seasonal variation, episodic events and long-term climatic changes.2. We report results of one of the most comprehensive and continuous records of physical, chemical and biological data available to assess restoration success for a stream ecosystem in North America. Over a 17 year period we measured seasonal and annual changes in metal concentrations, physicochemical characteristics, macroinvertebrate communities, and brown trout Salmo trutta populations in the Arkansas River, a metal-contaminated stream in Colorado, USA.3. Although we observed significant improvements in water quality after treatment, the effectiveness of restoration varied temporally, spatially and among biological response variables. The fastest recovery was observed at stations where restoration eliminated point sources of metal contamination. Recovery of macroinvertebrates was significantly delayed at some stations because of residual sediment contamination and because extreme seasonal and episodic variation in metal concentrations prevented recolonization by sensitive species. Synthesis and applications. Because recovery trajectories after the removal of a stressor are often complex or nonlinear, long-term studies are necessary to assess restoration success within the context of episodic events and changes in regional climate. The observed variation in recovery among chemical and biological endpoints highlights the importance of developing objective criteria to assess restoration success. Although the rapid response of macroinvertebrates to reduced metal concentrations is encouraging, we have previously demonstrated that

Learning Biological Networks via Bootstrapping with Optimized GO-based Gene Similarity

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

Taylor, Ronald C.; Sanfilippo, Antonio P.; McDermott, Jason E.

2010-08-02

Microarray gene expression data provide a unique information resource for learning biological networks using "reverse engineering" methods. However, there are a variety of cases in which we know which genes are involved in a given pathology of interest, but we do not have enough experimental evidence to support the use of fully-supervised/reverse-engineering learning methods. In this paper, we explore a novel semi-supervised approach in which biological networks are learned from a reference list of genes and a partial set of links for these genes extracted automatically from PubMed abstracts, using a knowledge-driven bootstrapping algorithm. We show how new relevant linksmore » across genes can be iteratively derived using a gene similarity measure based on the Gene Ontology that is optimized on the input network at each iteration. We describe an application of this approach to the TGFB pathway as a case study and show how the ensuing results prove the feasibility of the approach as an alternate or complementary technique to fully supervised methods.« less

Patterns of metal composition and biological condition and their association in male common carp across an environmental contaminant gradient in Lake Mead National Recreation Area, Nevada and Arizona, USA

USGS Publications Warehouse

Patino, R.; Rosen, Michael R.; Orsak, E.L.; Goodbred, S.L.; May, T.W.; Alvarez, David; Echols, K.R.; Wieser, C.M.; Ruessler, S.; Torres, L.

2012-01-01

There is a contaminant gradient in Lake Mead National Recreation Area (LMNRA) that is partly driven by municipal and industrial runoff and wastewater inputs via Las Vegas Wash (LVW). Adult male common carp (Cyprinus carpio; 10 fish/site) were collected from LVW, Las Vegas Bay (receiving LVW flow), Overton Arm (OA, upstream reference), and Willow Beach (WB, downstream) in March 2008. Discriminant function analysis was used to describe differences in metal concentrations and biological condition of fish collected from the four study sites, and canonical correlation analysis was used to evaluate the association between metal and biological traits. Metal concentrations were determined in whole-body extracts. Of 63 metals screened, those initially used in the statistical analysis were Ag, As, Ba, Cd, Co, Fe, Hg, Pb, Se, Zn. Biological variables analyzed included total length (TL), Fulton's condition factor, gonadosomatic index (GSI), hematocrit (Hct), and plasma estradiol-17?? and 11-ketotestosterone (11kt) concentrations. Analysis of metal composition and biological condition both yielded strong discrimination of fish by site (respective canonical model, p< 0.0001). Compared to OA, pairwise Mahalanobis distances between group means were WB < LVB < LVW for metal concentrations and LVB < WB < LVW for biological traits. Respective primary drivers for these separations were Ag, As, Ba, Hg, Pb, Se and Zn; and TL, GSI, 11kt, and Hct. Canonical correlation analysis using the latter variable sets showed they are significantly associated (p<0.0003); with As, Ba, Hg, and Zn, and TL, 11kt, and Hct being the primary contributors to the association. In conclusion, male carp collected along a contaminant gradient in LMNRA have distinct, collection site-dependent metal and morpho-physiological profiles that are significantly associated with each other. These associations suggest that fish health and reproductive condition (as measured by the biological variables evaluated in this

Chemoelectronic circuits based on metal nanoparticles

NASA Astrophysics Data System (ADS)

Yan, Yong; Warren, Scott C.; Fuller, Patrick; Grzybowski, Bartosz A.

2016-07-01

To develop electronic devices with novel functionalities and applications, various non-silicon-based materials are currently being explored. Nanoparticles have unique characteristics due to their small size, which can impart functions that are distinct from those of their bulk counterparts. The use of semiconductor nanoparticles has already led to improvements in the efficiency of solar cells, the processability of transistors and the sensitivity of photodetectors, and the optical and catalytic properties of metal nanoparticles have led to similar advances in plasmonics and energy conversion. However, metals screen electric fields and this has, so far, prevented their use in the design of all-metal nanoparticle circuitry. Here, we show that simple electronic circuits can be made exclusively from metal nanoparticles functionalized with charged organic ligands. In these materials, electronic currents are controlled by the ionic gradients of mobile counterions surrounding the ‘jammed’ nanoparticles. The nanoparticle-based electronic elements of the circuitry can be interfaced with metal nanoparticles capable of sensing various environmental changes (humidity, gas, the presence of various cations), creating electronic devices in which metal nanoparticles sense, process and ultimately report chemical signals. Because the constituent nanoparticles combine electronic and chemical sensing functions, we term these systems ‘chemoelectronic’. The circuits have switching times comparable to those of polymer electronics, selectively transduce parts-per-trillion chemical changes into electrical signals, perform logic operations, consume little power (on the scale of microwatts), and are mechanically flexible. They are also ‘green’, in the sense that they comprise non-toxic nanoparticles cast at room temperature from alcohol solutions.

Chemoelectronic circuits based on metal nanoparticles.

PubMed

Yan, Yong; Warren, Scott C; Fuller, Patrick; Grzybowski, Bartosz A

2016-07-01

To develop electronic devices with novel functionalities and applications, various non-silicon-based materials are currently being explored. Nanoparticles have unique characteristics due to their small size, which can impart functions that are distinct from those of their bulk counterparts. The use of semiconductor nanoparticles has already led to improvements in the efficiency of solar cells, the processability of transistors and the sensitivity of photodetectors, and the optical and catalytic properties of metal nanoparticles have led to similar advances in plasmonics and energy conversion. However, metals screen electric fields and this has, so far, prevented their use in the design of all-metal nanoparticle circuitry. Here, we show that simple electronic circuits can be made exclusively from metal nanoparticles functionalized with charged organic ligands. In these materials, electronic currents are controlled by the ionic gradients of mobile counterions surrounding the 'jammed' nanoparticles. The nanoparticle-based electronic elements of the circuitry can be interfaced with metal nanoparticles capable of sensing various environmental changes (humidity, gas, the presence of various cations), creating electronic devices in which metal nanoparticles sense, process and ultimately report chemical signals. Because the constituent nanoparticles combine electronic and chemical sensing functions, we term these systems 'chemoelectronic'. The circuits have switching times comparable to those of polymer electronics, selectively transduce parts-per-trillion chemical changes into electrical signals, perform logic operations, consume little power (on the scale of microwatts), and are mechanically flexible. They are also 'green', in the sense that they comprise non-toxic nanoparticles cast at room temperature from alcohol solutions.

Metallic ions as therapeutic agents in tissue engineering scaffolds: an overview of their biological applications and strategies for new developments

PubMed Central

Mouriño, Viviana; Cattalini, Juan Pablo; Boccaccini, Aldo R.

2012-01-01

This article provides an overview on the application of metallic ions in the fields of regenerative medicine and tissue engineering, focusing on their therapeutic applications and the need to design strategies for controlling the release of loaded ions from biomaterial scaffolds. A detailed summary of relevant metallic ions with potential use in tissue engineering approaches is presented. Remaining challenges in the field and directions for future research efforts with focus on the key variables needed to be taken into account when considering the controlled release of metallic ions in tissue engineering therapeutics are also highlighted. PMID:22158843

Molecular crowding has no effect on the dilution thermodynamics of the biologically relevant cation mixtures.

PubMed

Głogocka, Daria; Przybyło, Magdalena; Langner, Marek

2017-04-01

The ionic composition of intracellular space is rigorously maintained in the expense of high-energy expenditure. It has been recently postulated that the cytoplasmic ionic composition is optimized so the energy cost of the fluctuations of calcium ion concentration is minimized. Specifically, thermodynamic arguments have been produced to show that the presence of potassium ions at concentrations higher than 100 mM reduce extend of the energy dissipation required for the dilution of calcium cations. No such effect has been measured when sodium ions were present in the solution or when the other divalent cation magnesium was diluted. The experimental observation has been interpreted as the indication of the formation of ionic clusters composed of calcium, chloride and potassium. In order to test the possibility that such clusters may be preserved in biological space, the thermodynamics of ionic mixtures dilution in solutions containing albumins and model lipid bilayers have been measured. Obtained thermograms clearly demonstrate that the energetics of calcium/potassium mixture is qualitatively different from calcium/sodium mixture indicating that the presence of the biologically relevant quantities of proteins and membrane hydrophilic surfaces do not interfere with the properties of the intracellular aqueous phase.

The road not taken: Applications of fluorescence spectroscopy and electronic structure theory to systems of materials and biological relevance

NASA Astrophysics Data System (ADS)

Carlson, Philip Joseph

Applications of Fluorescence Spectroscopy and Electronic Structure Theory to Systems of Materials and Biological Relevance. The photophysics of curcumin was studied in micelles and the solvation dynamics were probed. The high-energy ionic liquid HEATN was also studied using the fragment molecular orbital method. The solvation dynamics of the HEATN system were determined. This marks the first study of the solvation dynamics in a triazolium ionic liquid system.

Optical Antenna-Based Fluorescence Correlation Spectroscopy to Probe the Nanoscale Dynamics of Biological Membranes.

PubMed

Winkler, Pamina M; Regmi, Raju; Flauraud, Valentin; Brugger, Jürgen; Rigneault, Hervé; Wenger, Jérôme; García-Parajo, María F

2018-01-04

The plasma membrane of living cells is compartmentalized at multiple spatial scales ranging from the nano- to the mesoscale. This nonrandom organization is crucial for a large number of cellular functions. At the nanoscale, cell membranes organize into dynamic nanoassemblies enriched by cholesterol, sphingolipids, and certain types of proteins. Investigating these nanoassemblies known as lipid rafts is of paramount interest in fundamental cell biology. However, this goal requires simultaneous nanometer spatial precision and microsecond temporal resolution, which is beyond the reach of common microscopes. Optical antennas based on metallic nanostructures efficiently enhance and confine light into nanometer dimensions, breaching the diffraction limit of light. In this Perspective, we discuss recent progress combining optical antennas with fluorescence correlation spectroscopy (FCS) to monitor microsecond dynamics at nanoscale spatial dimensions. These new developments offer numerous opportunities to investigate lipid and protein dynamics in both mimetic and native biological membranes.

[The bonding mechanisms of base metals for metal-ceramic crown microstructure analysis of bonding agent and gold bond between porcelain and base metals].

PubMed

Wang, C C; Hsu, C S

1996-06-01

The use of base metal alloys for porcelain fused to a metal crown and bridges has increased recently because of lower price, high hardness, high tensile strength and high elastic modulus. The addition of beryllium to base metal alloys increased fluidity and improved casting fitness. Beryllium also controlled surface oxidation and bonding strength. The bonding agent and gold bonding agent also affected the bonding strength between porcelain and metal alloys. Four commercially available ceramic base alloys were studied (two alloys contained beryllium element, another two did not). The purpose of this investigation was to study the microstructure between porcelain matrix, bonding agent and alloy matrix interfaces. A scanning electron micro-probe analyzer and energy dispersive X-ray spectroscopy (EDXS) were used to study the distribution of elements (Ni, Cr, Mo, Cu, O, Si, Sn, Al) in four base alloys. The following results were obtained: 1. The thickness of the oxidized layer of Rexillium III alloy and Unitbond alloy (contained beryllium) was thinner than Unibond alloy and Wiron 88 alloy (no beryllium). 2. The thickness of the oxidized layer of alloys in air (10 minutes and 30 minutes) was thinner in Unitbond (2.45 microns and 3.80 microns) and thicker in Wiron 88 (4.39 microns and 5.96 microns). 3. The thickness of the oxidized layer occurring for a duration of ten minutes (in vaccum) showed that the Rexillium III alloy was the thinnest (1.93 microns), and Wiron 88 alloy was the thickest (2.30 microns). But in thirty minutes (vacuum), Unitbond alloy was the thinnest (3.37 microns), and Wiron 88 alloy was the thickest (5.51 microns). 4. The intensity of Cr elements was increased obviously near the interface between Unitbond alloy, Wiron 88 alloy (no beryllium) and oxidized layer, but the intensity of Ni and Mo elements was slightly increased. The intensity of Cr element was not increased markedly between Rexillium III alloy, Unitbond alloy (beryllium) and oxidized

Invited Review Article: Advanced light microscopy for biological space research

NASA Astrophysics Data System (ADS)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; van Loon, Jack J. W. A.; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Invited review article: Advanced light microscopy for biological space research.

PubMed

De Vos, Winnok H; Beghuin, Didier; Schwarz, Christian J; Jones, David B; van Loon, Jack J W A; Bereiter-Hahn, Juergen; Stelzer, Ernst H K

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Metallomics of two microorganisms relevant to heavy metal bioremediation reveal fundamental differences in metal assimilation and utilization

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

Lancaster, Andrew; Menon, Angeli; Scott, Israel

2014-03-26

Although as many as half of all proteins are thought to require a metal cofactor, the metalloproteomes of microorganisms remain relatively unexplored. Microorganisms from different environments are likely to vary greatly in the metals that they assimilate, not just among the metals with well-characterized roles but also those lacking any known function. Herein we investigated the metal utilization of two microorganisms that were isolated from very similar environments and are of interest because of potential roles in the immobilization of heavy metals, such as uranium and chromium. The metals assimilated and their concentrations in the cytoplasm of Desulfovibrio vulgaris strainmore » Hildenborough (DvH) and Enterobacter cloacae strain Hanford (EcH) varied dramatically, with a larger number of metals present in Enterobacter. For example, a total of 9 and 19 metals were assimilated into their cytoplasmic fractions, respectively, and DvH did not assimilate significant amounts of zinc or copper whereas EcH assimilated both. However, bioinformatic analysis of their genome sequences revealed a comparable number of predicted metalloproteins, 813 in DvH and 953 in EcH. These allowed some rationalization of the types of metal assimilated in some cases (Fe, Cu, Mo, W, V) but not in others (Zn, Nd, Ce, Pr, Dy, Hf and Th). It was also shown that U binds an unknown soluble protein in EcH but this incorporation was the result of extracellular U binding to cytoplasmic components after cell lysis.« less

Synthesis of metal complexes involving Schiff base ligand with methylenedioxy moiety: spectral, thermal, XRD and antimicrobial studies.

PubMed

Sundararajan, M L; Jeyakumar, T; Anandakumaran, J; Karpanai Selvan, B

2014-10-15

Metal complexes of Zn(II), Cd(II), Ni(II), Cu(II), Fe(III), Co(II), Mn(II) Hg(II), and Ag(I) have been synthesized from Schiff base ligand, prepared by the condensation of 3,4-(methylenedioxy)aniline and 5-bromo salicylaldehyde. All the compounds have been characterized by using elemental analysis, molar conductance, FT-IR, UV-Vis, (1)H NMR, (13)C NMR, mass spectra, powder XRD and thermal analysis (TG/DTA) technique. The elemental analysis suggests the stoichiometry to be 1:1 (metal:ligand). The FT-IR, (1)H NMR, (13)C NMR and UV-Vis spectral data suggest that the ligand coordinate to the metal atom by imino nitrogen and phenolic oxygen as bidentate manner. Mass spectral data further support the molecular mass of the compounds and their structure. Powder XRD indicates the crystalline state and morphology of the ligand and its metal complexes. The thermal behaviors of the complexes prove the presence of lattice as well as coordinated water molecules in the complexes. Melting point supports the thermal stability of all the compounds. The in vitro antimicrobial effects of the synthesized compounds were tested against five bacterial and three fungal species by well diffusion method. Antioxidant activities have also been performed for all the compounds. Metal complexes show more biological activity than the Schiff base. Copyright © 2014 Elsevier B.V. All rights reserved.

Charge transport in metal oxide nanocrystal-based materials

NASA Astrophysics Data System (ADS)

Runnerstrom, Evan Lars

There is probably no class of materials more varied, more widely used, or more ubiquitous than metal oxides. Depending on their composition, metal oxides can exhibit almost any number of properties. Of particular interest are the ways in which charge is transported in metal oxides: devices such as displays, touch screens, and smart windows rely on the ability of certain metal oxides to conduct electricity while maintaining visible transparency. Smart windows, fuel cells, and other electrochemical devices additionally rely on efficient transport of ionic charge in and around metal oxides. Colloidal synthesis has enabled metal oxide nanocrystals to emerge as a relatively new but highly tunable class of materials. Certain metal oxide nanocrystals, particularly highly doped metal oxides, have been enjoying rapid development in the last decade. As in myriad other materials systems, structure dictates the properties of metal oxide nanocrystals, but a full understanding of how nanocrystal synthesis, the processing of nanocrystal-based materials, and the structure of nanocrystals relate to the resulting properties of nanocrystal-based materials is still nascent. Gaining a fundamental understanding of and control over these structure-property relationships is crucial to developing a holistic understanding of metal oxide nanocrystals. The unique ability to tune metal oxide nanocrystals by changing composition through the introduction of dopants or by changing size and shape affords a way to study the interplay between structure, processing, and properties. This overall goal of this work is to chemically synthesize colloidal metal oxide nanocrystals, process them into useful materials, characterize charge transport in materials based on colloidal metal oxide nanocrystals, and develop ways to manipulate charge transport. In particular, this dissertation characterizes how the charge transport properties of metal oxide nanocrystal-based materials depend on their processing and

Metal shadowing for electron microscopy.

PubMed

Hendricks, Gregory M

2014-01-01

Metal shadowing of bacteria, viruses, isolated molecules, and macromolecular assemblies is another high-resolution method for observing the ultrastructure of biological specimens. The actual procedure for producing a metal shadow is relatively simple; a heavy metal is evaporated from a source at an oblique angle to the specimen. The metal atoms pile up on the surfaces that face the source, but the surfaces away from the source are shielded and receive little metal deposit, creating a "shadow." However, the process of producing biological specimens that are suitable for metal shadowing can be very complex. There are a whole host of specimen preparation techniques that can precede metal shadowing, and all provide superior preservation in comparison to air drying, a required step in negative staining procedures. The physical forces present during air drying (i.e., surface tension of the water-air interface) will literally crush most biological specimens as they dry. In this chapter I explain the development of and procedures for the production of biological specimens from macromolecular assemblies (e.g., DNA and RNA), purified isolated molecules (e.g., proteins), and isolated viruses and bacteria preparations suitable for metal shadowing. A variation on this basic technique is to rotate the specimen during the metal deposition to produce a high-resolution three-dimensional rendering of the specimen.

On making nursing undergraduate human reproductive physiology content meaningful and relevant: discussion of human pleasure in its biological context.

PubMed

McClusky, Leon Mendel

2012-01-01

The traditional presentation of the Reproductive Physiology component in an Anatomy and Physiology course to nursing undergraduates focuses on the broad aspects of hormonal regulation of reproduction and gonadal anatomy, with the role of the higher centres of the brain omitted. An introductory discussion is proposed which could precede the lectures on the reproductive organs. The discussion gives an overview of the biological significance of human pleasure, the involvement of the neurotransmitter dopamine, and the role of pleasure in the survival of the individual and even species. Pleasure stimuli (positive and negative) and the biological significance of naturally-induced pleasurable experiences are briefly discussed in the context of reproduction and the preservation of genetic material with an aim to foster relevancy between subject material and human behaviour in any type of society. The tenderness of this aspect of the human existence is well-understood because of its invariable association with soul-revealing human expressions such as love, infatuation, sexual flirtations, all of which are underpinned by arousal, desire and/or pleasure. Assuming that increased knowledge correlates with increased confidence, the proposed approach may provide the nurse with an adequate knowledge base to overcome well-known barriers in communicating with their patients about matters of sexual health and intimacy. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bioaccessibility of micron-sized powder particles of molybdenum metal, iron metal, molybdenum oxides and ferromolybdenum--Importance of surface oxides.

PubMed

Mörsdorf, Alexander; Odnevall Wallinder, Inger; Hedberg, Yolanda

2015-08-01

The European chemical framework REACH requires that hazards and risks posed by chemicals, including alloys and metals, that are manufactured, imported or used in different products (substances or articles) are identified and proven safe for humans and the environment. Metals and alloys need hence to be investigated on their extent of released metals (bioaccessibility) in biologically relevant environments. Read-across from available studies may be used for similar materials. This study investigates the release of molybdenum and iron from powder particles of molybdenum metal (Mo), a ferromolybdenum alloy (FeMo), an iron metal powder (Fe), MoO2, and MoO3 in different synthetic body fluids of pH ranging from 1.5 to 7.4 and of different composition. Spectroscopic tools and cyclic voltammetry have been employed to characterize surface oxides, microscopy, light scattering and nitrogen absorption for particle characterization, and atomic absorption spectroscopy to quantify released amounts of metals. The release of molybdenum from the Mo powder generally increased with pH and was influenced by the fluid composition. The mixed iron and molybdenum surface oxide of the FeMo powder acted as a barrier both at acidic and weakly alkaline conditions. These findings underline the importance of the surface oxide characteristics for the bioaccessibility of metal alloys. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Biological Low-pH Mn(II) Oxidation in a Manganese Deposit Influenced by Metal-Rich Groundwater

PubMed Central

Bohu, Tsing; Akob, Denise M.; Abratis, Michael; Lazar, Cassandre S.

2016-01-01

ABSTRACT The mechanisms, key organisms, and geochemical significance of biological low-pH Mn(II) oxidation are largely unexplored. Here, we investigated the structure of indigenous Mn(II)-oxidizing microbial communities in a secondary subsurface Mn oxide deposit influenced by acidic (pH 4.8) metal-rich groundwater in a former uranium mining area. Microbial diversity was highest in the Mn deposit compared to the adjacent soil layers and included the majority of known Mn(II)-oxidizing bacteria (MOB) and two genera of known Mn(II)-oxidizing fungi (MOF). Electron X-ray microanalysis showed that romanechite [(Ba,H2O)2(Mn4+,Mn3+)5O10] was conspicuously enriched in the deposit. Canonical correspondence analysis revealed that certain fungal, bacterial, and archaeal groups were firmly associated with the autochthonous Mn oxides. Eight MOB within the Proteobacteria, Actinobacteria, and Bacteroidetes and one MOF strain belonging to Ascomycota were isolated at pH 5.5 or 7.2 from the acidic Mn deposit. Soil-groundwater microcosms demonstrated 2.5-fold-faster Mn(II) depletion in the Mn deposit than adjacent soil layers. No depletion was observed in the abiotic controls, suggesting that biological contribution is the main driver for Mn(II) oxidation at low pH. The composition and species specificity of the native low-pH Mn(II) oxidizers were highly adapted to in situ conditions, and these organisms may play a central role in the fundamental biogeochemical processes (e.g., metal natural attenuation) occurring in the acidic, oligotrophic, and metalliferous subsoil ecosystems. IMPORTANCE This study provides multiple lines of evidence to show that microbes are the main drivers of Mn(II) oxidation even at acidic pH, offering new insights into Mn biogeochemical cycling. A distinct, highly adapted microbial community inhabits acidic, oligotrophic Mn deposits and mediates biological Mn oxidation. These data highlight the importance of biological processes for Mn biogeochemical cycling

Mechanics of metal-catecholate complexes: The roles of coordination state and metal types

PubMed Central

Xu, Zhiping

2013-01-01

There have been growing evidences for the critical roles of metal-coordination complexes in defining structural and mechanical properties of unmineralized biological materials, including hardness, toughness, and abrasion resistance. Their dynamic (e.g. pH-responsive, self-healable, reversible) properties inspire promising applications of synthetic materials following this concept. However, mechanics of these coordination crosslinks, which lays the ground for predictive and rational material design, has not yet been well addressed. Here we present a first-principles study of representative coordination complexes between metals and catechols. The results show that these crosslinks offer stiffness and strength near a covalent bond, which strongly depend on the coordination state and type of metals. This dependence is discussed by analyzing the nature of bonding between metals and catechols. The responsive mechanics of metal-coordination is further mapped from the single-molecule level to a networked material. The results presented here provide fundamental understanding and principles for material selection in metal-coordination-based applications. PMID:24107799

Automatic medical image annotation and keyword-based image retrieval using relevance feedback.

PubMed

Ko, Byoung Chul; Lee, JiHyeon; Nam, Jae-Yeal

2012-08-01

This paper presents novel multiple keywords annotation for medical images, keyword-based medical image retrieval, and relevance feedback method for image retrieval for enhancing image retrieval performance. For semantic keyword annotation, this study proposes a novel medical image classification method combining local wavelet-based center symmetric-local binary patterns with random forests. For keyword-based image retrieval, our retrieval system use the confidence score that is assigned to each annotated keyword by combining probabilities of random forests with predefined body relation graph. To overcome the limitation of keyword-based image retrieval, we combine our image retrieval system with relevance feedback mechanism based on visual feature and pattern classifier. Compared with other annotation and relevance feedback algorithms, the proposed method shows both improved annotation performance and accurate retrieval results.

Discovery and biological relevance of 3,4-didehydroretinol (vitamin A2) in small indigenous fish species and its potential as a dietary source for addressing vitamin A deficiency.

PubMed

La Frano, Michael R; Cai, Yimeng; Burri, Betty J; Thilsted, Shakuntala H

2018-05-01

Discovered in the late 1920s, 3,4-didehydroretinol (DROL, vitamin A 2 ) plays a significant biological role in freshwater fish. The functions of this vitamin have been investigated but to a far lesser extent than those of retinol (ROL, vitamin A 1 ). A recent study indicating all-trans DROL has 119-127% vitamin A biological activity compared to that of all-trans ROL suggests the significance of DROL for addressing vitamin A deficiency (VAD) in comparison to ROL may be currently overlooked. Freshwater fish such as small indigenous fish species (SIS), with high DROL content can be a promising dietary source for reducing VAD in areas where SIS are readily available and consumed. In this paper, the discovery and biological relevance of DROL are reviewed and furthermore, the vast potential of production and consumption of DROL-rich SIS in food-based strategies to combat VAD in Bangladesh and other developing countries with high prevalence of VAD is highlighted.

Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students†

PubMed Central

Beach, Dale L.; Alvarez, Consuelo J.

2015-01-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic “parts,” students construct a “reporter plasmid” expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a “sensor plasmid,” the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses. PMID:26753032

Bivalent metal-based MIL-53 analogues: Synthesis, properties and application

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

Liu, Yongxin; University of the Chinese Academy of Science, Beijing 100049; Liu, Dan, E-mail: liudan2007@ciac.ac.cn

Trivalent metal-based MIL-53 (Al{sup 3+}, Cr{sup 3+}, Fe{sup 3+}, In{sup 3+}) compounds are interesting metal–organic frameworks (MOFs) with breathing effect and are promising gas sorption materials. Replacing bridging μ{sub 2}-OH group by neutral ligands such as pyridine N-oxide and its derivatives (PNOs), the trivalent metal-based MIL-53 analogous structures could be extended to bivalent metal systems. The introduction of PNOs and bivalent metal elements endows the frameworks with new structural features and physical and chemical properties. This minireview summarizes the recent development of bivalent metal-based MIL-53 analogues (Mn{sup 2+}, Co{sup 2+}, Ni{sup 2+}), typically, focusing on the synthetic strategies and potentialmore » applications based on our own works and literatures. We present the synthetic strategy to achieve structures evolution from single-ligand-walled to double-ligand-walled channel. Properties and application of these new materials in a wide range of potential areas are discussed including thermal stability, gas adsorption, magnetism and liquid-phase separation. Promising directions of this research field are also highlighted. - Graphical abstract: The recent development of bivalent metal-based MIL-53 analogues (Mn{sup 2+}, Co{sup 2+}, Ni{sup 2+}) on their synthetic strategies, properties and potential applications was reviewed. - Highlights: • Structure features of bivalent metal-based MIL-53 analogues are illustrated. • Important properties and application are presented. • Host–guest interactions are main impetus for liquid-phase separation. • Promising directions of bivalent metal-based MIL-53 analogues are highlighted.« less

Influence of Nano-Crystal Metals on Texture and Biological Properties of Water Soluble Polysaccharides of Medicinal Plants

NASA Astrophysics Data System (ADS)

Churilov, G.; Ivanycheva, J.; Kiryshin, V.

2015-11-01

When treating the plants seeds with nano-materials there are some quality and quantity changes of polysaccharides, the molecular mass increase and monosaccharides change that leads to the increase of physiological and pharmacological activity of carbohydrates got from medicinal plants. We have got water soluble polysaccharides and nano-metals combinations containing 0.000165-0.000017 mg/dm3 of the metal. In a case of induced anemia the blood composition has practically restored on the 10th day of the treatment with nanocomposites. The use of pectin polysaccharides (that are attributed to modifiers of biological respond) to get nano-structured materials seems to be actual relative to their physiological activity (radio nuclides persorption, heavy metals ions, bacteria cells and their toxins; lipids metabolism normalization; bowels secreting and motor functions activation and modulation of the endocrine system.

Comparison of sediments and organisms in identifying sources of biologically available trace metal contamination

USGS Publications Warehouse

Thomson, E.A.; Luoma, S.N.; Johansson, C.E.; Cain, D.J.

1984-01-01

Sediments and an indicator organism (Macoma balthica, a deposit-feeding bivalve) were used to assess the relative importance of secondary sewage, urban runoff, a landfill containing metal-enriched ash wastes and a yacht harbor in contributing to Ag, Cu and Zn enrichment in South San Francisco Bay. Spatial gradients in sediments and organisms showed Cu and Ag enrichment originated from sewage discharge, whereas Zn enrichment originated from both sewage and urban runoff. Elevated concentrations of Cu in the sediments of the yacht harbor resulted from a high abundance of fine particles. The biological availability of Cu, Ag and Zn did not coincide with metal enrichment in sediments. The availability of Cu and Ag was greatest nearest the sewage outfall and greater in winter and spring than in summer. The availability of Zn in urban runoff appeared to be lower than the availability of Zn associated with sewage.

Dose Enhancement near Metal Interfaces in Synthetic Diamond Based X-ray Dosimeters

NASA Astrophysics Data System (ADS)

Alamoudi, Dalal

Diamond is an attractive material for medical dosimetry due to its radiation hardness, fast response, chemical resilience, small sensitive volume, high spatial resolution, near-tissue equivalence, and energy and dose rate independence. These properties make diamond a promising material for medical dosimetry compared to other semiconductor detector materials and wider radiation detection applications. This study is focused on one of the important factors to consider in the radiation detector; the influence of dose enhancement on the photocurrent performance at metallic interfaces in synthetic diamond radiation dosimeters with carbon based electrodes as a function of bias voltages. Monte Carlo (MC) simulations with BEAMnrc code were carried out to simulate the dose enhancement factor (DEF) and compared against the equivalent photocurrent ratio from experimental investigation. MC simulations show that the sensitive region for the absorbed dose distribution covers a few micrometers distances from the interface. Experimentally, two single crystal (SC) and one polycrystalline (PC) samples with carbon based electrodes were used. The samples were each mounted inside a tissue equivalent encapsulation design in order to minimize fluence perturbations. Copper, Gold and Lead have been investigated experimentally as generators of photoelectrons using 50 kVp and 100 kVp X-rays relevant for medical dosimetry. The results show enhancement in the detectors' photocurrent performance when different metals are butted up to the diamond detector. The variation in the photocurrent ratio measurements depends on the type of diamond samples, their electrode fabrication and the applied bias voltages indicating that the dose enhancement from diamond-metal interface modifies the electronic performance of the detector.

Using a biology-based model (DEBtox) to analyze bioassays in ecotoxicology: opportunities and recommendations.

PubMed

Péry, Alexandre R R; Flammarion, Patrick; Vollat, Bernard; Bedaux, Jacques J M; Kooijman, Sebastiaan A L M; Garric, Jeanne

2002-02-01

The conventional analysis of bioassays does not account for biological significance. However, mathematical models do exist that are realistic from a biological point of view and describe toxicokinetics and effects on test organisms of chemical compounds. Here we studied a biology-based model (DEBtox) that provides an estimate of a no-effect concentration, and we demonstrated the ability of such a model to adapt to different situations. We showed that the basic model can be extended to deal with problems usually faced during bioassays like time-varying concentrations or unsuitable choices of initial concentrations. To reach this goal, we report experimental data from Daphnia magna exposed to zinc. These data also showed the potential benefit of the model in understanding the influence of food on toxicity. We finally make some recommendations about the choice of initial concentrations, and we propose a test with a depuration period to check the relevance and the predictive capacity of the DEBtox model. In our experiments, the model performed well and proved its usefulness as a tool in risk assessment.

In silico epigenetics of metal exposure and subclinical atherosclerosis in middle aged men: pilot results from the Aragon Workers Health Study.

PubMed

Riffo-Campos, Angela L; Fuentes-Trillo, Azahara; Tang, Wan Y; Soriano, Zoraida; De Marco, Griselda; Rentero-Garrido, Pilar; Adam-Felici, Victoria; Lendinez-Tortajada, Veronica; Francesconi, Kevin; Goessler, Walter; Ladd-Acosta, Christine; Leon-Latre, Montse; Casasnovas, Jose A; Chaves, F Javier; Navas-Acien, Ana; Guallar, Eliseo; Tellez-Plaza, Maria

2018-06-05

We explored the association of metal levels with subclinical atherosclerosis and epigenetic changes in relevant biological pathways. Whole blood DNA Infinium Methylation 450 K data were obtained from 23 of 73 middle age men without clinically evident cardiovascular disease (CVD) who participated in the Aragon Workers Health Study in 2009 (baseline visit) and had available baseline urinary metals and subclinical atherosclerosis measures obtained in 2010-2013 (follow-up visit). The median metal levels were 7.36 µg g -1 , 0.33 µg g -1 , 0.11 µg g -1 and 0.07 µg g -1 , for arsenic (sum of inorganic and methylated species), cadmium, antimony and tungsten, respectively. Urine cadmium and tungsten were associated with femoral and carotid intima-media thickness, respectively (Pearson's r = 0.27; p = 0.03 in both cases). Among nearest genes to identified differentially methylated regions (DMRs), 46% of metal-DMR genes overlapped with atherosclerosis-DMR genes ( p < 0.001). Pathway enrichment analysis of atherosclerosis-DMR genes showed a role in inflammatory, metabolic and transport pathways. In in silico protein-to-protein interaction networks among proteins encoded by 162 and 108 genes attributed to atherosclerosis- and metal-DMRs, respectively, with proteins known to have a role in atherosclerosis pathways, we observed hub proteins in the network associated with both atherosclerosis and metal-DMRs (e.g. SMAD3 and NOP56 ), and also hub proteins associated with metal-DMRs only but with relevant connections with atherosclerosis effectors (e.g. SSTR5 , HDAC4 , AP2A2 , CXCL12 and SSTR4 ). Our integrative in silico analysis demonstrates the feasibility of identifying epigenomic regions linked to environmental exposures and potentially involved in relevant pathways for human diseases. While our results support the hypothesis that metal exposures can influence health due to epigenetic changes, larger studies are needed to confirm our pilot results.This article is part of a

Antimicrobial resistance challenged with metal-based antimicrobial macromolecules.

PubMed

Abd-El-Aziz, Alaa S; Agatemor, Christian; Etkin, Nola

2017-02-01

Antimicrobial resistance threatens the achievements of science and medicine, as it deactivates conventional antimicrobial therapeutics. Scientists respond to the threat by developing new antimicrobial platforms to prevent and treat infections from these resistant strains. Metal-based antimicrobial macromolecules are emerging as an alternative to conventional platforms because they combine multiple mechanisms of action into one platform due to the distinctive properties of metals. For example, metals interact with intracellular proteins and enzymes, and catalyse various intracellular processes. The macromolecular architecture offers a means to enhance antimicrobial activity since several antimicrobial moieties can be conjugated to the scaffold. Further, these macromolecules can be fabricated into antimicrobial materials for contact-killing medical implants, fabrics, and devices. As volatilization or leaching out of the antimicrobial moieties from the macromolecular scaffold is reduced, these medical implants, fabrics, and devices can retain their antimicrobial activity over an extended period. Recent advances demonstrate the potential of metal-based antimicrobial macromolecules as effective platforms that prevent and treat infections from resistant strains. In this review these advances are thoroughly discussed within the context of examples of metal-based antimicrobial macromolecules, their mechanisms of action and biocompatibility. Copyright © 2016 Elsevier Ltd. All rights reserved.

The effectiveness of spent coffee grounds and its biochar on the amelioration of heavy metals-contaminated water and soil using chemical and biological assessments.

PubMed

Kim, Min-Suk; Min, Hyun-Gi; Koo, Namin; Park, Jeongsik; Lee, Sang-Hwan; Bak, Gwan-In; Kim, Jeong-Gyu

2014-12-15

Spent coffee grounds (SCG) and charred spent coffee grounds (SCG-char) have been widely used to adsorb or to amend heavy metals that contaminate water or soil and their success is usually assessed by chemical analysis. In this work, the effects of SCG and SCG-char on metal-contaminated water and soil were evaluated using chemical and biological assessments; a phytotoxicity test using bok choy (Brassica campestris L. ssp. chinensis Jusl.) was conducted for the biological assessment. When SCG and SCG-char were applied to acid mine drainage, the heavy metal concentrations were decreased and the pH was increased. However, for SCG, the phytotoxicity increased because a massive amount of dissolved organic carbon was released from SCG. In contrast, SCG-char did not exhibit this phenomenon because any easily released organic matter was removed during pyrolysis. While the bioavailable heavy metal content decreased in soils treated with SCG or SCG-char, the phytotoxicity only rose after SCG treatment. According to our statistical methodology, bioavailable Pb, Cu and As, as well as the electrical conductivity representing an increase in organic content, affected the phytotoxicity of soil. Therefore, applying SCG during environment remediation requires careful biological assessments and evaluations of the efficiency of this remediation technology. Copyright © 2014 Elsevier Ltd. All rights reserved.

Characterizing the Diversity and Biological Relevance of the MLPCN Assay Manifold and Screening Set

PubMed Central

Zhang, Jintao; Lushington, Gerald H.; Huan, Jun

2011-01-01

The NIH Molecular Libraries Initiative (MLI), launched in 2004 with initial goals of identifying chemical probes for characterizing gene function and druggability, has produced PubChem, a chemical genomics knowledgebase for fostering translation of basic research into new therapeutic strategies. This paper assesses progress toward these goals by evaluating MLI target novelty and propensity for undergoing biochemically or therapeutically relevant modulations and the degree of chemical diversity and biogenic bias inherent in the MLI screening set. Our analyses suggest that while MLI target selection has not yet been fully optimized for biochemical diversity, it covers biologically interesting pathway space that complements established drug targets. We find the MLI screening set to be chemically diverse and to have greater biogenic bias than comparable collections of commercially available compounds. Biogenic enhancements such as incorporation of more metabolite-like chemotypes are suggested. PMID:21568288

Long-wavelength TCF-based fluorescence probes for the detection and intracellular imaging of biological thiols.

PubMed

Sedgwick, Adam C; Gardiner, Jordan E; Kim, Gyoungmi; Yevglevskis, Maksims; Lloyd, Matthew D; Jenkins, A Toby A; Bull, Steven D; Yoon, Juyoung; James, Tony D

2018-05-08

Two 'turn on' TCF-based fluorescence probes were developed for the detection of biological thiols (TCF-GSH and TCFCl-GSH). TCF-GSH was shown to have a high sensitivity towards glutathione (GSH) with a 0.28 μM limit of detection. Unfortunately, at higher GSH concentrations the fluorescence intensity of TCF-GSH decreased and toxicity was observed for TCF-GSH in live cells. However, TCFCl-GSH was shown to be able to detect GSH at biologically relevant concentrations with a 0.45 μM limit of detection. No toxicity was found for TCFCl-GSH and a clear 'turn on' with good photostability was observed for the exogenous addition of GSH, Cys and HCys. Furthermore, TCFCl-GSH was used to evaluate the effects of drug treatment on the levels of GSH in live cells.

Developmental Testing of Liquid and Gaseous/Vaporous Decontamination on Bacterial Spores and Other Biological Warfare Agents on Military Relevant Surfaces

DTIC Science & Technology

2016-02-11

process ( gas /vapor or liquid ), sampling will be conducted as soon as possible. Samples will be incubated for 12 to 48 hours (depending on the...Final 3. DATES COVERED (From - To) 4. TITLE AND SUBTITLE Test Operations Procedure (TOP) 08-2-065 Developmental Testing of Liquid and Gaseous...biological decontamination protocol to analyze the efficacy of liquid and gaseous/vaporous decontaminants on military-relevant surfaces. The

Evaluation of Surface Roughness and Tensile Strength of Base Metal Alloys Used for Crown and Bridge on Recasting (Recycling).

PubMed

Agrawal, Amit; Hashmi, Syed W; Rao, Yogesh; Garg, Akanksha

2015-07-01

Dental casting alloys play a prominent role in the restoration of the partial dentition. Casting alloys have to survive long term in the mouth and also have the combination of structure, molecules, wear resistance and biologic compatibility. According to ADA system casting alloys were divided into three groups (wt%); high noble, Noble and predominantly base metal alloys. To evaluate the mechanical properties such as tensile strength and surface roughness of the new and recast base metal (nickel-chromium) alloys. Recasting of the base metal alloys derived from sprue and button, to make it reusable has been done. A total of 200 test specimens were fabricated using specially fabricated jig of metal and divided into two groups- 100 specimens of new alloy and 100 specimens of recast alloys, which were tested for tensile strength on universal testing machine and surface roughness on surface roughness tester. Tensile strength of new alloy showed no statistically significant difference (p-value>0.05) from recast alloy whereas new alloy had statistically significant surface roughness (Maximum and Average surface roughness) difference (p-value<0.01) as compared to recast alloy. Within the limitations of the study it is concluded that the tensile strength will not be affected by recasting of nickel-chromium alloy whereas surface roughness increases markedly.

Acoustic wave-driven oxidized liquid metal-based energy harvester

NASA Astrophysics Data System (ADS)

Jeon, Jinpyo; Chung, Sang Kug; Lee, Jeong-Bong; Doo, Seok Joo; Kim, Daeyoung

2018-06-01

We report an oxidized liquid metal droplet-based energy harvester that converts acoustic energy into electrical energy by modulating an electrical double layer that originates from the deformation of the oxidized liquid metal droplet. Gallium-based liquid metal alloy has been developed for various applications owing to the outstanding material properties, such as its high electrical conductivity (metallic property) and unlimited deformability (liquid property). In this study, we demonstrated energy harvesting using an electrical double layer between the acoustic wave-modulated liquid metal droplet and two electrodes. The proposed energy harvester consisted of top and bottom electrodes covered with the dielectric layer and a Gallium-based liquid metal droplet placed between the electrodes. When we applied an external bias voltage and acoustic wave to the proposed device, the contact area between the liquid metal droplet and the electrodes changed, leading to the variation of the capacitance in the electrical double layer and the generation of electrical output current. Using the proposed energy harvester, the maximum output current of 41.2 nA was generated with an applied acoustic wave of 30 Hz. In addition, we studied the relationships between the maximum output current and a variety of factors, such as the size of the liquid metal droplet, the thickness of the hydrophobic layer, and the distance between the top and bottom electrode plates.

Metal-coordination: Using one of nature’s tricks to control soft material mechanics

PubMed Central

Holten-Andersen, Niels; Jaishankar, Aditya; Harrington, Matthew; Fullenkamp, Dominic E.; DiMarco, Genevieve; He, Lihong; McKinley, Gareth H.; Messersmith, Phillip B.; Lee, Ka Yee C.

2015-01-01

Growing evidence supports a critical role of dynamic metal-coordination crosslinking in soft biological material properties such as self-healing and underwater adhesion1. Using bio-inspired metal-coordinating polymers, initial efforts to mimic these properties have shown promise2. Here we demonstrate how bio-inspired aqueous polymer network mechanics can be easily controlled via metal-coordination crosslink dynamics; metal ion-based crosslink stability control allows aqueous polymer network relaxation times to be finely tuned over several orders of magnitude. In addition to further biological material insights, our demonstration of this compositional scaling mechanism should provide inspiration for new polymer material property-control designs. PMID:26413297

Anion binding in biological systems

NASA Astrophysics Data System (ADS)

Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

2009-11-01

We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

Gene expression profiling to identify the toxicities and potentially relevant human disease outcomes associated with environmental heavy metal exposure.

PubMed

Korashy, Hesham M; Attafi, Ibraheem M; Famulski, Konrad S; Bakheet, Saleh A; Hafez, Mohammed M; Alsaad, Abdulaziz M S; Al-Ghadeer, Abdul Rahman M

2017-02-01

Heavy metals are the most commonly encountered toxic substances that increase susceptibility to various diseases after prolonged exposure. We have previously shown that healthy volunteers living near a mining area had significant contamination with heavy metals associated with significant changes in the expression of some detoxifying genes, xenobiotic metabolizing enzymes, and DNA repair genes. However, alterations of most of the molecular target genes associated with diseases are still unknown. Thus, the aims of this study were to (a) evaluate the gene expression profile and (b) identify the toxicities and potentially relevant human disease outcomes associated with long-term human exposure to environmental heavy metals in mining area using microarray analysis. For this purpose, 40 healthy male volunteers who were residents of a heavy metal-polluted area (Mahd Al-Dhahab city, Saudi Arabia) and 20 healthy male volunteers who were residents of a non-heavy metal-polluted area were included in the study. Total RNA was isolated from whole blood using PAXgene Blood RNA tubes and then reversed transcribed and hybridized to the gene array using the Affymetrix U219 GeneChip. Microarray analysis showed about 2129 genes were identified and differentially altered, among which a shared set of 425 genes was differentially expressed in the heavy metal-exposed groups. Ingenuity pathway analysis revealed that the most altered gene-regulated diseases in heavy metal-exposed groups included hematological and developmental disorders and mostly renal and urological diseases. Quantitative real-time polymerase chain reaction closely matched the microarray data for some genes tested. Importantly, changes in gene-related diseases were attributed to alterations in the genes encoded for protein synthesis. Renal and urological diseases were the diseases that were most frequently associated with the heavy metal-exposed group. Therefore, there is a need for further studies to validate these

Spectroscopic studies and biological evaluation of some transition metal complexes of azo Schiff-base ligand derived from (1-phenyl-2,3-dimethyl-4-aminopyrazol-5-one) and 5-((4-chlorophenyl)diazenyl)-2-hydroxybenzaldehyde

NASA Astrophysics Data System (ADS)

Anitha, C.; Sheela, C. D.; Tharmaraj, P.; Sumathi, S.

2012-10-01

A series of metal(II) complexes of VO(II), Co(II), Ni(II), Cu(II) and Zn(II) have been synthesized from the azo Schiff base ligand 4-((E)-4-((E)-(4-chlorophenyl)diazenyl)-2-hydroxybenzylideneamino)-1,5-dimethyl-2-phenyl-1H-pyrazol-3(2H)-one (CDHBAP) and characterized by elemental analysis, spectral (IR, UV-Vis, 1H NMR, ESR and EI-mass), magnetic moment measurements, molar conductance, DNA, SEM, X-ray crystallography and fluorescence studies. The electronic absorption spectra and magnetic susceptibility measurements of the complexes indicate square pyramidal geometry for VO(II) and octahedral geometry for all the other complexes. The important infrared (IR) spectral bands corresponding to the active groups in the ligand and the solid complexes under investigation were studied and implies that CDHBAP is coordinated to the metal ions in a neutral tridentate manner. The redox behavior of copper(II) and vanadyl(II) complexes have been studied by cyclic voltammetry. The nuclease activity of the above metal(II) complexes shows that the complexes cleave DNA. All the synthesized complexes can serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The antibacterial and antifungal activities of the synthesized ligand and its metal complexes were screened against bacterial species (Staphylococcus aureus, Salmonella typhi, Escherichia coli, Bacillus subtilis, Shigella sonnie) and fungi (Candida albicans, Aspergillus niger, Rhizoctonia bataicola). Amikacin and Ketoconozole were used as references for antibacterial and antifungal studies. The activity data show that the metal complexes have a promising biological activity comparable with the parent Schiff base ligand against bacterial and fungal species. The second harmonic generation (SHG) efficiency of the ligand was measured and the NLO (non-linear optical) properties of the ligand are expected to result in the realization of advanced optical devices in optical fiber

Conservation biology in Asia: the major policy challenges.

PubMed

McNeely, Jeffrey A; Kapoor-Vijay, Promila; Zhi, Lu; Olsvig-Whittaker, Linda; Sheikh, Kashif M; Smith, Andrew T

2009-08-01

With about half the world's human population and booming economies, Asia faces numerous challenges to its biodiversity. The Asia Section of the Society for Conservation Biology has identified some key policy issues in which significant progress can be made. These include developing new sources of funding for forest conservation; identifying potential impacts of energy alternatives on the conservation of biodiversity; curbing the trade in endangered species of plants and animals; a special focus on the conservation of mountain biodiversity; enhancing relevant research; ensuring that conservation biology contributes to major international conventions and funding mechanisms; using conservation biology to build a better understanding of zoonotic diseases; more effectively addressing human-animal conflicts; enhancing community-based conservation; and using conservation biology to help address the pervasive water-deficit problems in much of Asia. These challenges can be met through improved regional cooperation among the relevant stakeholders.

Making Biology Learning Relevant to Students: Integrating People, History, and Context into College Biology Teaching

ERIC Educational Resources Information Center

Chamany, Katayoun; Allen, Deborah; Tanner, Kimberly

2008-01-01

Teaching students to make connections between what they learn in the classroom and what they see in everyday life is imperative. As biology instructors, they may choose to teach biology devoid of social context, believing that students can make these connections on their own. However, students model their instructors' behaviors, and follow their…

Relevant role of dissolved humic matter in phosphorus bioavailability in natural and agronomical ecosystems through the formation of Humic-(Metal)-Phosphate complexes

NASA Astrophysics Data System (ADS)

Baigorri, Roberto; Urrutia, Óscar; Erro, Javier; Pazos-Pérez, Nicolás; María García-Mina, José

2016-04-01

Natural Organic Matter (NOM) and the NOM fraction present in soil solution (dissolved organic matter: DOM) are currently considered as fundamental actors in soil fertility and crop mineral nutrition. Indeed, decreases in crop yields as well as soil erosion are closely related to low values of NOM and, in fact, the use of organic amendments as both soil improvers and plant growth enhancers is very usual in countries with soils poor in NOM. This role of NOM (and DOM) seems to be associated with the presence of bio-transformed organic molecules (humic substances) with high cation chelating-complexing ability. In fact, bioavailable micronutrients with metallic character in soil solutions of alkaline and calcareous soils are forming stable complexes with DOM. This beneficial action of DOM also concerns other plant nutrients such as inorganic phosphate (Pi). Among the different mechanisms involved in the beneficial action of DOM on P bioavailability, the possible formation of poly-nuclear complexes including stable chemical bonds between negative binding sites in humic substances and Pi through metal bridges in soil solution might be relevant, especially in acidic soils. In fact, several studies have proven that these complexes can be obtained in the laboratory and are very efficient in prevent Pi soil fixation and improve Pi root uptake. However, clear experimental evidence about their presence in soil solutions of natural and agronomical soil ecosystems has not published yet. We present here experimental results supporting the real presence of stable Pi-metal-Humic (PMH) complexes in the soil solution of several acidic soils. The study is based on the physico-chemical characterization (31P-NMR, FTIR, TEM-EDAX, ICP-OES) of the DOM fraction isolated by ultrafiltration from the soil solution of several representative acidic soils. In average, more than 60 % of Pi was found in the soil solution humic fraction forming stable humic-metal (Fe, Al) complexes.

[Bioaccumulation and Biomagnification of Heavy Metals in Three Gorges Reservoir and Effect of Biological Factors].

PubMed

Wei, Li-li; Zhou, Qiong; Xie, Cong-xin; Wang, Jun; Li, Jun

2016-01-15

Three Gorges Reservoir (TGR) reached the maximum water level (175 m) of impoundment in Oct. 2010. In order to reveal the potential influence of the greatest water-level impoundment on the heavy metal pollution in the typical waters of TGR, the content level of trace metals ( Hg, Cd and Pb) in biota and potential biomagnification along the aquatic food chain were investigated in the main stem of TGR from July 2011 to August 2012, as well as the relationship between the trace metal concentrations of aquatic consumers (fish and aquatic invertebrate) and biological factors. Our study showed that no individual data of the three trace metals in biota exceeded the edible safety criteria of aquatic products in China and FAO. In contrast with those before the impoundment of TGR, Hg showed a little higher, while Cd and Pb exhibited a little lower level after the impoundment. Trace metals in TGR exhibited relatively lower concentrations compared with those in reservoirs in other countries. Significant correlations were found between the Cd concentration and body size (body length and body weight) of Cyprinus carpio, as well as the Hg concentration and body size (body length and body weight) of Erythroculter ilishaeformis. As for feeding habits, there was statistically significant difference between trace metal concentrations in herbivorous, planktonic, omnivorous and carnivorous fish. However, no significant difference was found between the metal concentrations in fish with different habitats (pelagic, mesopelagic and benthic). Even so, the overall trend was that fish living in benthic layer had higher heavy metal concentrations than those in pelagic and mesopelagic zones. The regression slopes of log-Hg concentration versus delta(15)N, served as an indicator of trophic magnification factor (TMF). Significant correlations (P < 0.05) were observed for Hg in the food web of TGR. TMF of Hg in TGR indicated lower level (0.046-0.066) in contrast with those in the reservoirs of

Synthesis, spectroscopic and biological activities studies of acyclic and macrocyclic mono and binuclear metal complexes containing a hard-soft Schiff base

NASA Astrophysics Data System (ADS)

Abou-Hussein, Azza A. A.; Linert, Wolfgang

Mono- and bi-nuclear acyclic and macrocyclic complexes with hard-soft Schiff base, H2L, ligand derived from the reaction of 4,6-diacetylresorcinol and thiocabohydrazide, in the molar ratio 1:2 have been prepared. The H2L ligand reacts with Co(II), Ni(II), Cu(II), Zn(II), Mn(II) and UO2(VI) nitrates, VO(IV) sulfate and Ru(III) chloride to get acyclic binuclear complexes except for VO(IV) and Ru(III) which gave acyclic mono-nuclear complexes. Reaction of the acyclic mono-nuclear VO(IV) and Ru(III) complexes with 4,6-diacetylresorcinol afforded the corresponding macrocyclic mono-nuclear VO(IV) and Ru(IIII) complexes. Template reactions of the 4,6-diacetylresorcinol and thiocarbohydrazide with either VO(IV) or Ru(III) salts afforded the macrocyclic binuclear VO(IV) and Ru(III) complexes. The Schiff base, H2L, ligand acts as dibasic with two NSO-tridentate sites and can coordinate with two metal ions to form binuclear complexes after the deprotonation of the hydrogen atoms of the phenolic groups in all the complexes, except in the case of the acyclic mononuclear Ru(III) and VO(IV) complexes, where the Schiff base behaves as neutral tetradentate chelate with N2S2 donor atoms. The ligands and the metal complexes were characterized by elemental analysis, IR, UV-vis 1H-NMR, thermal gravimetric analysis (TGA) and ESR, as well as the measurements of conductivity and magnetic moments at room temperature. Electronic spectra and magnetic moments of the complexes indicate the geometries of the metal centers are either tetrahedral, square planar or octahedral. Kinetic and thermodynamic parameters were calculated using Coats-Redfern equation, for the different thermal decomposition steps of the complexes. The ligands and the metal complexes were screened for their antimicrobial activity against Staphylococcus aureus as Gram-positive bacteria, and Pseudomonas fluorescens as Gram-negative bacteria in addition to Fusarium oxysporum fungus. Most of the complexes exhibit mild

Synthesis, spectroscopic and biological activities studies of acyclic and macrocyclic mono and binuclear metal complexes containing a hard-soft Schiff base.

PubMed

Abou-Hussein, Azza A A; Linert, Wolfgang

2012-09-01

Mono- and bi-nuclear acyclic and macrocyclic complexes with hard-soft Schiff base, H(2)L, ligand derived from the reaction of 4,6-diacetylresorcinol and thiocabohydrazide, in the molar ratio 1:2 have been prepared. The H(2)L ligand reacts with Co(II), Ni(II), Cu(II), Zn(II), Mn(II) and UO(2)(VI) nitrates, VO(IV) sulfate and Ru(III) chloride to get acyclic binuclear complexes except for VO(IV) and Ru(III) which gave acyclic mono-nuclear complexes. Reaction of the acyclic mono-nuclear VO(IV) and Ru(III) complexes with 4,6-diacetylresorcinol afforded the corresponding macrocyclic mono-nuclear VO(IV) and Ru(IIII) complexes. Template reactions of the 4,6-diacetylresorcinol and thiocarbohydrazide with either VO(IV) or Ru(III) salts afforded the macrocyclic binuclear VO(IV) and Ru(III) complexes. The Schiff base, H(2)L, ligand acts as dibasic with two NSO-tridentate sites and can coordinate with two metal ions to form binuclear complexes after the deprotonation of the hydrogen atoms of the phenolic groups in all the complexes, except in the case of the acyclic mononuclear Ru(III) and VO(IV) complexes, where the Schiff base behaves as neutral tetradentate chelate with N(2)S(2) donor atoms. The ligands and the metal complexes were characterized by elemental analysis, IR, UV-vis (1)H-NMR, thermal gravimetric analysis (TGA) and ESR, as well as the measurements of conductivity and magnetic moments at room temperature. Electronic spectra and magnetic moments of the complexes indicate the geometries of the metal centers are either tetrahedral, square planar or octahedral. Kinetic and thermodynamic parameters were calculated using Coats-Redfern equation, for the different thermal decomposition steps of the complexes. The ligands and the metal complexes were screened for their antimicrobial activity against Staphylococcus aureus as Gram-positive bacteria, and Pseudomonas fluorescens as Gram-negative bacteria in addition to Fusarium oxysporum fungus. Most of the complexes exhibit

Clinical and biological relevance of genomic heterogeneity in chronic lymphocytic leukemia.

PubMed

Friedman, Daphne R; Lucas, Joseph E; Weinberg, J Brice

2013-01-01

Chronic lymphocytic leukemia (CLL) is typically regarded as an indolent B-cell malignancy. However, there is wide variability with regards to need for therapy, time to progressive disease, and treatment response. This clinical variability is due, in part, to biological heterogeneity between individual patients' leukemias. While much has been learned about this biological variation using genomic approaches, it is unclear whether such efforts have sufficiently evaluated biological and clinical heterogeneity in CLL. To study the extent of genomic variability in CLL and the biological and clinical attributes of genomic classification in CLL, we evaluated 893 unique CLL samples from fifteen publicly available gene expression profiling datasets. We used unsupervised approaches to divide the data into subgroups, evaluated the biological pathways and genetic aberrations that were associated with the subgroups, and compared prognostic and clinical outcome data between the subgroups. Using an unsupervised approach, we determined that approximately 600 CLL samples are needed to define the spectrum of diversity in CLL genomic expression. We identified seven genomically-defined CLL subgroups that have distinct biological properties, are associated with specific chromosomal deletions and amplifications, and have marked differences in molecular prognostic markers and clinical outcomes. Our results indicate that investigations focusing on small numbers of patient samples likely provide a biased outlook on CLL biology. These findings may have important implications in identifying patients who should be treated with specific targeted therapies, which could have efficacy against CLL cells that rely on specific biological pathways.

Biological regeneration of manganese (IV) and iron (III) for anaerobic metal oxide-mediated removal of pharmaceuticals from water.

PubMed

Liu, Wenbo; Langenhoff, Alette A M; Sutton, Nora B; Rijnaarts, Huub H M

2018-05-18

Applying manganese(IV)- or iron(III)-(hydr)oxides to remove pharmaceuticals from water could be attractive, due to the capacity of these metal oxides to remove pharmaceuticals and be regenerated. As pharmaceutical removal under anaerobic conditions is foreseen, Mn(IV) or Fe(III) regeneration under anaerobic conditions, or with minimum oxygen dosage, is preferred. In this study, batch experiments are performed to investigate (1) Mn(IV) and Fe(III) regeneration from Mn(II) and Fe(II); (2) the pharmaceutical removal during biological Mn(IV) and Fe(III) regeneration; and (3) anaerobic abiotic pharmaceutical removal with different Mn(IV) or Fe(III) species. Results show that biological re-oxidation of reduced Mn(II) to Mn(IV) occurs under oxygen-limiting conditions. Biological re-oxidation of Fe(II) to Fe(III) is obtained with nitrate under anaerobic conditions. Both bio-regenerated Mn(IV)-oxides and Fe(III)-hydroxides are amorphous. The pharmaceutical removal is insignificant by Mn(II)- or Fe(II)-oxidizing bacteria during regeneration. Finally, pharmaceutical removal is investigated with various Mn(IV) and Fe(III) sources. Anaerobic abiotic removal using Mn(IV) produced from drinking water treatment plants results in 23% metoprolol and 44% propranolol removal, similar to chemically synthesized Mn(IV). In contrast, Fe(III) from drinking water treatment plants outperformed chemically or biologically synthesized Fe(III); Fe (III) from drinking water treatment can remove 31-43% of propranolol via anaerobic abiotic process. In addition, one of the Fe(III)-based sorbents tested, FerroSorp ® RW, can also remove propranolol (20-25%). Biological regeneration of Mn(IV) and Fe(III) from the reduced species Mn(II) and Fe(II) could be more effective in terms of cost and treatment efficiency. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Foamed-metal-based catalytic afterburners in automotive exhaust systems

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

Pestryakov, A.N.; Ametov, V.A.

1994-08-10

Properties of exhaust afterburning catalysts based on porous cellular materials (foamed metals) have been investigated. Catalysts containing oxides of base metals provide a two-to-threefold reduction of CO emission. Platinum-containing foamed catalysts lower the toxicity of exhaust by 85-90%. A favorable effect is demonstrated by the combined use of afterburners and a motor oil additive based on ultradispersed copper.

Agent-based models in translational systems biology

PubMed Central

An, Gary; Mi, Qi; Dutta-Moscato, Joyeeta; Vodovotz, Yoram

2013-01-01

Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent-based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing. PMID:20835989

Metal-based nanoparticle interactions with the nervous system: the challenge of brain entry and the risk of retention in the organism.

PubMed

Yokel, Robert; Grulke, Eric; MacPhail, Robert

2013-01-01

This review of metal-based nanoparticles focuses on factors influencing their distribution into the nervous system, evidence they enter brain parenchyma, and nervous system responses. Gold is emphasized as a model metal-based nanoparticle and for risk assessment in the companion review. The anatomy and physiology of the nervous system, basics of colloid chemistry, and environmental factors that influence what cells see are reviewed to provide background on the biological, physical-chemical, and internal milieu factors that influence nervous system nanoparticle uptake. The results of literature searches reveal little nanoparticle research included the nervous system, which about equally involved in vitro and in vivo methods, and very few human studies. The routes of uptake into the nervous system and mechanisms of nanoparticle uptake by cells are presented with examples. Brain nanoparticle uptake inversely correlates with size. The influence of shape has not been reported. Surface charge has not been clearly shown to affect flux across the blood-brain barrier. There is very little evidence for metal-based nanoparticle distribution into brain parenchyma. Metal-based nanoparticle disruption of the blood-brain barrier and adverse brain changes have been shown, and are more pronounced for spheres than rods. Study concentrations need to be put in exposure contexts. Work with dorsal root ganglion cells and brain cells in vitro show the potential for metal-based nanoparticles to produce toxicity. Interpretation of these results must consider the ability of nanoparticles to distribute across the barriers protecting the nervous system. Effects of the persistence of poorly soluble metal-based nanoparticles are of particular concern. Copyright © 2013 Wiley Periodicals, Inc.

Gonioreflectometric properties of metal surfaces

NASA Astrophysics Data System (ADS)

Jaanson, P.; Manoocheri, F.; Mäntynen, H.; Gergely, M.; Widlowski, J.-L.; Ikonen, E.

2014-12-01

Angularly resolved measurements of scattered light from surfaces can provide useful information in various fields of research and industry, such as computer graphics, satellite based Earth observation etc. In practice, empirical or physics-based models are needed to interpolate the measurement results, because a thorough characterization of the surfaces under all relevant conditions may not be feasible. In this work, plain and anodized metal samples were prepared and measured optically for bidirectional reflectance distribution function (BRDF) and mechanically for surface roughness. Two models for BRDF (Torrance-Sparrow model and a polarimetric BRDF model) were fitted to the measured values. A better fit was obtained for plain metal surfaces than for anodized surfaces.

A Versatile Method for Nanostructuring Metals, Alloys and Metal Based Composites

NASA Astrophysics Data System (ADS)

Gurau, G.; Gurau, C.; Bujoreanu, L. G.; Sampath, V.

2017-06-01

A new severe plastic deformation method based on High Pressure Torsion is described. The method patented as High Speed High Pressure Torsion (HSHPT) shows a wide scope and excellent adaptability assuring large plastic deformation degree on metals, alloys even on hard to deform or brittle alloys. The paper present results obtained on aluminium, magnesium, titan, iron and coper alloys. In addition capability of HSHPT to process metallic composites is described. OM SEM, TEM, DSC, RDX and HV investigation methods were employed to confirm fine and ultrafine structure.

Understanding photoluminescence of metal nanostructures based on an oscillator model.

PubMed

Cheng, Yuqing; Zhang, Weidong; Zhao, Jingyi; Wen, Te; Hu, Aiqin; Gong, Qihuang; Lu, Guowei

2018-08-03

Scattering and absorption properties of metal nanostructures have been well understood based on the classic oscillator theory. Here, we demonstrate that photoluminescence of metal nanostructures can also be explained based on a classic model. The model shows that inelastic radiation of an oscillator resembles its resonance band after external excitation, and is related to the photoluminescence from metallic nanostructures. The understanding based on the classic oscillator model is in agreement with that predicted by a quantum electromagnetic cavity model. Moreover, by correlating a two-temperature model and the electron distributions, we demonstrate that both one-photon and two-photon luminescence of the metal nanostructures undergo the same mechanism. Furthermore, the model explains most of the emission characteristics of the metallic nanostructures, such as quantum yield, spectral shape, excitation polarization and power dependence. The model based on an oscillator provides an intuitive description of the photoluminescence process and may enable rapid optimization and exploration of the plasmonic properties.

A Comparison of the Outcomes for Cartilage Defects of the Knee Treated With Biologic Resurfacing Versus Focal Metallic Implants.

PubMed

Pascual-Garrido, Cecilia; Daley, Erika; Verma, Nikhil N; Cole, Brian J

2017-02-01

To compare the results of focal metallic resurfacing with biologic procedures in patients more than 35 years of age with isolated, full thickness defects of the femoral condyle. A total of 61 patients met the selection criteria resulting in 30 patients treated with biological procedures, including debridement, microfracture, osteochondral autograft transplantation, osteochondral allograft, and autologous chondrocyte implantation (BIO group), and 32 patients treated with focal metallic resurfacing (CAP group). The BIO and CAP groups were matched according to treatment location, defect grade and size, and age profile. Outcomes included Western Ontario and McMaster Osteoarthritis Index (WOMAC), Short Form-12, and satisfaction. The primary combination endpoint was determined as a 20% improvement (minimum clinically important difference-20) on WOMAC pain and function at 2 years and no additional index lesion-related surgical intervention. Safety and effectiveness were also reported. Thirty patients in the BIO group (mean age of 44.6, range 35-64) had an average follow-up of 2.6 years and 32 patients in the CAP group (mean age 47.9, range 37-68) were followed for 2.0 years. Fifty-three percent in the BIO group and 75% in the CAP group achieved success per the endpoint definition. The mean total WOMAC score improved significantly for both groups (BIO: 57-78; P < .001) (CAP: 41-86; P < .001). The physical component score (Short Form-12 PCS) improved significantly in the CAP group only (30-36.4; P < .001). Good to excellent patient satisfaction was achieved by 80% in BIO and 91% in CAP. There were 4 secondary procedures on the index lesion in the BIO group and 2 in the CAP group. Careful patient selection can achieve high satisfaction rates with both biological and focal metal resurfacing procedures for the treatment of isolated focal chondral lesions of the femoral condyle in the knee. Focal metallic resurfacing results in similar clinical outcomes and provides

Simultaneous fluorescent detection of multiple metal ions based on the DNAzymes and graphene oxide.

PubMed

Yun, Wen; Wu, Hong; Liu, Xingyan; Fu, Min; Jiang, Jiaolai; Du, Yunfeng; Yang, Lizhu; Huang, Yu

2017-09-15

A novel fluorescent detection strategy for simultaneous detection of Cu 2+ , Pb 2+ and Mg 2+ based on DNAzyme branched junction structure with three kinds of DNAzymes and graphene oxide (GO) was presented. Three fluorophores labeled DNA sequences consisted with enzyme-strand (E-DNA) and substrate strand (S-DNA) were annealed to form DNAzyme branched junction structure. In the presence of target metal ion, the DNAzyme was activated to cleave the fluorophore labeled S-DNA. The S-DNA fragments were released and adsorbed onto GO surface to quench the fluorescent signal. The detection limit was calculated to be 1 nM for Cu 2+ , 200 nM for Mg 2+ , and 0.3 nM for Pb 2+ , respectively. This strategy was successfully used for simultaneous detection of Cu 2+ , Mg 2+ and Pb 2+ in human serum. Moreover, it had potential application for simultaneous detection of multiple metal ions in environmental and biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Identifying Epigenetic Biomarkers using Maximal Relevance and Minimal Redundancy Based Feature Selection for Multi-Omics Data.

PubMed

Mallik, Saurav; Bhadra, Tapas; Maulik, Ujjwal

2017-01-01

Epigenetic Biomarker discovery is an important task in bioinformatics. In this article, we develop a new framework of identifying statistically significant epigenetic biomarkers using maximal-relevance and minimal-redundancy criterion based feature (gene) selection for multi-omics dataset. Firstly, we determine the genes that have both expression as well as methylation values, and follow normal distribution. Similarly, we identify the genes which consist of both expression and methylation values, but do not follow normal distribution. For each case, we utilize a gene-selection method that provides maximal-relevant, but variable-weighted minimum-redundant genes as top ranked genes. For statistical validation, we apply t-test on both the expression and methylation data consisting of only the normally distributed top ranked genes to determine how many of them are both differentially expressed andmethylated. Similarly, we utilize Limma package for performing non-parametric Empirical Bayes test on both expression and methylation data comprising only the non-normally distributed top ranked genes to identify how many of them are both differentially expressed and methylated. We finally report the top-ranking significant gene-markerswith biological validation. Moreover, our framework improves positive predictive rate and reduces false positive rate in marker identification. In addition, we provide a comparative analysis of our gene-selection method as well as othermethods based on classificationperformances obtained using several well-known classifiers.

Metal solubilization from metal-containing solid materials by cyanogenic Chromobacterium violaceum.

PubMed

Faramarzi, Mohammad A; Stagars, Marion; Pensini, Enrico; Krebs, Walter; Brandl, Helmut

2004-09-30

Different cyanogenic bacterial strains (Chromobacterium violaceum, Pseudomonas fluorescens, Bacillus megaterium) were cultivated under cyanide-forming conditions in the presence of metal-containing solids such as nickel powder or electronic scrap. All microorganisms were able to form water-soluble metal cyanides, however, with different efficiencies. C. violaceum was able to mobilize nickel as tetracyanonickelate [Ni(CN)4(2-)] from fine-grained nickel powder. Gold was microbially solubilized as dicyanaoaurate [Au(CN)2-] from electronic waste. Additionally, cyanide-complexed copper was detected during biological treatment of shredded printed circuit boards scrap. Regarding the formation of tetracyanonickelate, C. violaceum was more effective than P. fluorescens or B. megaterium. Besides a few previous reports on gold solubilization from gold-containing ores or native gold by C. violaceum, the findings demonstrate for the first time the microbial mobilization of metals other than gold from solid materials and represent a novel type of microbial metal mobilization based on the ability of certain microbes to form HCN. The results might have the potential for industrial applications (biorecovery, bioremediation) regarding the treatment of metal-containing solids since metal cyanides can easily be separated by chromatographic means and be recovered by sorption onto activated carbon.

Clinical and Biological Relevance of Genomic Heterogeneity in Chronic Lymphocytic Leukemia

PubMed Central

Friedman, Daphne R.; Lucas, Joseph E.; Weinberg, J. Brice

2013-01-01

Background Chronic lymphocytic leukemia (CLL) is typically regarded as an indolent B-cell malignancy. However, there is wide variability with regards to need for therapy, time to progressive disease, and treatment response. This clinical variability is due, in part, to biological heterogeneity between individual patients’ leukemias. While much has been learned about this biological variation using genomic approaches, it is unclear whether such efforts have sufficiently evaluated biological and clinical heterogeneity in CLL. Methods To study the extent of genomic variability in CLL and the biological and clinical attributes of genomic classification in CLL, we evaluated 893 unique CLL samples from fifteen publicly available gene expression profiling datasets. We used unsupervised approaches to divide the data into subgroups, evaluated the biological pathways and genetic aberrations that were associated with the subgroups, and compared prognostic and clinical outcome data between the subgroups. Results Using an unsupervised approach, we determined that approximately 600 CLL samples are needed to define the spectrum of diversity in CLL genomic expression. We identified seven genomically-defined CLL subgroups that have distinct biological properties, are associated with specific chromosomal deletions and amplifications, and have marked differences in molecular prognostic markers and clinical outcomes. Conclusions Our results indicate that investigations focusing on small numbers of patient samples likely provide a biased outlook on CLL biology. These findings may have important implications in identifying patients who should be treated with specific targeted therapies, which could have efficacy against CLL cells that rely on specific biological pathways. PMID:23468975

[Use of dinoflagellates as a metal toxicity assessment tool in aquatic system].

PubMed

Yuan, Li-juan; He, Meng-chang

2009-10-15

Although dinoflagellates have been used to assess biological toxicity of contaminants, this method still lacks of corresponding toxicity assessment standard. This study appraised the toxicity of selected heavy metals to dinoflagellates based on the dinoflagellates bioluminescence with QwikLite developed by the United States Navy. The results show that single heavy metal biological toxicity is in the order: Hg2+ > Cu2+ > Cd2+ > As5+ > Pb2+ > Cr6+; Two, three and four heavy metal mixture experiments show synergism primarily, antagonism is in minority. pH has not remarkable effect on dinoflagellates, they can be applied directly in natural water, but pH influence Hg2+ and Cu2+ toxicity greatly, eliminating the influence of pH is essential when doing these two kind of ions measurements. The nutrients has little influence on dinoflagellates, change in COD has obvious effect on the response relationships between dinoflagellates and Hg2+ or CU2+. Metal toxicity assessment using dinoflagellates shows great sensitivity, narrow response scope and high stability. Dinoflagellates are good species for heavy metal biological toxicity test in aquatic system.

Biologically relevant 3D tumor arrays: treatment response and the importance of stromal partners

NASA Astrophysics Data System (ADS)

Rizvi, Imran; Celli, Jonathan P.; Xu, Feng; Evans, Conor L.; Abu-Yousif, Adnan O.; Muzikansky, Alona; Elrington, Stefan A.; Pogue, Brian W.; Finkelstein, Dianne M.; Demirci, Utkan; Hasan, Tayyaba

2011-02-01

The development and translational potential of therapeutic strategies for cancer is limited, in part, by a lack of biological models that capture important aspects of tumor growth and treatment response. It is also becoming increasingly evident that no single treatment will be curative for this complex disease. Rationally-designed combination regimens that impact multiple targets provide the best hope of significantly improving clinical outcomes for cancer patients. Rapidly identifying treatments that cooperatively enhance treatment efficacy from the vast library of candidate interventions is not feasible, however, with current systems. There is a vital, unmet need to create cell-based research platforms that more accurately mimic the complex biology of human tumors than monolayer cultures, while providing the ability to screen therapeutic combinations more rapidly than animal models. We have developed a highly reproducible in vitro three-dimensional (3D) tumor model for micrometastatic ovarian cancer (OvCa), which in conjunction with quantitative image analysis routines to batch-process large datasets, serves as a high throughput reporter to screen rationally-designed combination regimens. We use this system to assess mechanism-based combination regimens with photodynamic therapy (PDT), which sensitizes OvCa to chemo and biologic agents, and has shown promise in clinic trials. We show that PDT synergistically enhances carboplatin efficacy in a sequence dependent manner. In printed heterocellular cultures we demonstrate that proximity of fibroblasts enhances 3D tumor growth and investigate co-cultures with endothelial cells. The principles described here could inform the design and evaluation of mechanism-based therapeutic options for a broad spectrum of metastatic solid tumors.

Bio-metals imaging and speciation in cells using proton and synchrotron radiation X-ray microspectroscopy

PubMed Central

Ortega, Richard; Devès, Guillaume; Carmona, Asunción

2009-01-01

The direct detection of biologically relevant metals in single cells and of their speciation is a challenging task that requires sophisticated analytical developments. The aim of this article is to present the recent achievements in the field of cellular chemical element imaging, and direct speciation analysis, using proton and synchrotron radiation X-ray micro- and nano-analysis. The recent improvements in focusing optics for MeV-accelerated particles and keV X-rays allow application to chemical element analysis in subcellular compartments. The imaging and quantification of trace elements in single cells can be obtained using particle-induced X-ray emission (PIXE). The combination of PIXE with backscattering spectrometry and scanning transmission ion microscopy provides a high accuracy in elemental quantification of cellular organelles. On the other hand, synchrotron radiation X-ray fluorescence provides chemical element imaging with less than 100 nm spatial resolution. Moreover, synchrotron radiation offers the unique capability of spatially resolved chemical speciation using micro-X-ray absorption spectroscopy. The potential of these methods in biomedical investigations will be illustrated with examples of application in the fields of cellular toxicology, and pharmacology, bio-metals and metal-based nano-particles. PMID:19605403

Molecular biomimetics: nanotechnology through biology.

PubMed

Sarikaya, Mehmet; Tamerler, Candan; Jen, Alex K-Y; Schulten, Klaus; Baneyx, François

2003-09-01

Proteins, through their unique and specific interactions with other macromolecules and inorganics, control structures and functions of all biological hard and soft tissues in organisms. Molecular biomimetics is an emerging field in which hybrid technologies are developed by using the tools of molecular biology and nanotechnology. Taking lessons from biology, polypeptides can now be genetically engineered to specifically bind to selected inorganic compounds for applications in nano- and biotechnology. This review discusses combinatorial biological protocols, that is, bacterial cell surface and phage-display technologies, in the selection of short sequences that have affinity to (noble) metals, semiconducting oxides and other technological compounds. These genetically engineered proteins for inorganics (GEPIs) can be used in the assembly of functional nanostructures. Based on the three fundamental principles of molecular recognition, self-assembly and DNA manipulation, we highlight successful uses of GEPI in nanotechnology.

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

PubMed

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

2016-03-15

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

The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

NASA Astrophysics Data System (ADS)

Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

2017-12-01

Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

Extracting metals directly from metal oxides

DOEpatents

Wai, Chien M.; Smart, Neil G.; Phelps, Cindy

1997-01-01

A method of extracting metals directly from metal oxides by exposing the oxide to a supercritical fluid solvent containing a chelating agent is described. Preferably, the metal is an actinide or a lanthanide. More preferably, the metal is uranium, thorium or plutonium. The chelating agent forms chelates that are soluble in the supercritical fluid, thereby allowing direct removal of the metal from the metal oxide. In preferred embodiments, the extraction solvent is supercritical carbon dioxide and the chelating agent is selected from the group consisting of .beta.-diketones, halogenated .beta.-diketones, phosphinic acids, halogenated phosphinic acids, carboxylic acids, halogenated carboxylic acids, and mixtures thereof. In especially preferred embodiments, at least one of the chelating agents is fluorinated. The method provides an environmentally benign process for removing metals from metal oxides without using acids or biologically harmful solvents. The chelate and supercritical fluid can be regenerated, and the metal recovered, to provide an economic, efficient process.

Extracting metals directly from metal oxides

DOEpatents

Wai, C.M.; Smart, N.G.; Phelps, C.

1997-02-25

A method of extracting metals directly from metal oxides by exposing the oxide to a supercritical fluid solvent containing a chelating agent is described. Preferably, the metal is an actinide or a lanthanide. More preferably, the metal is uranium, thorium or plutonium. The chelating agent forms chelates that are soluble in the supercritical fluid, thereby allowing direct removal of the metal from the metal oxide. In preferred embodiments, the extraction solvent is supercritical carbon dioxide and the chelating agent is selected from the group consisting of {beta}-diketones, halogenated {beta}-diketones, phosphinic acids, halogenated phosphinic acids, carboxylic acids, halogenated carboxylic acids, and mixtures thereof. In especially preferred embodiments, at least one of the chelating agents is fluorinated. The method provides an environmentally benign process for removing metals from metal oxides without using acids or biologically harmful solvents. The chelate and supercritical fluid can be regenerated, and the metal recovered, to provide an economic, efficient process. 4 figs.

Toxic metal(loid)-based pollutants and their possible role in autism spectrum disorder.

PubMed

Bjørklund, Geir; Skalny, Anatoly V; Rahman, Md Mostafizur; Dadar, Maryam; Yassa, Heba A; Aaseth, Jan; Chirumbolo, Salvatore; Skalnaya, Margarita G; Tinkov, Alexey A

2018-06-11

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social interaction, verbal and non-verbal communication, and stereotypic behaviors. Many studies support a significant relationship between many different environmental factors in ASD etiology. These factors include increased daily exposure to various toxic metal-based environmental pollutants, which represent a cause for concern in public health. This article reviews the most relevant toxic metals, commonly found, environmental pollutants, i.e., lead (Pb), mercury (Hg), aluminum (Al), and the metalloid arsenic (As). Additionally, it discusses how pollutants can be a possible pathogenetic cause of ASD through various mechanisms including neuroinflammation in different regions of the brain, fundamentally occurring through elevation of the proinflammatory profile of cytokines and aberrant expression of nuclear factor kappa B (NF-κB). Due to the worldwide increase in toxic environmental pollution, studies on the role of pollutants in neurodevelopmental disorders, including direct effects on the developing brain and the subjects' genetic susceptibility and polymorphism, are of utmost importance to achieve the best therapeutic approach and preventive strategies. Copyright © 2018 Elsevier Inc. All rights reserved.

Biological Hydropersulfides and Related Polysulfides: A New Concept and Perspective in Redox Biology.

PubMed

Fukuto, Jon M; Ignarro, Louis J; Nagy, Peter; Wink, David A; Kevil, Christopher G; Feelisch, Martin; Cortese-Krott, Miriam M; Bianco, Christopher L; Kumagai, Yoshito; Hobbs, Adrian J; Lin, Joseph; Ida, Tomoaki; Akaike, Takaaki

2018-05-12

The chemical biology of thiols (RSH, e.g., cysteine and cysteine containing proteins/peptides) has been a topic of extreme interest for many decades due to their reported roles in protein structure/folding, redox signaling, metal ligation, cellular protection and enzymology. While many of the studies on thiol/sulfur biochemistry have focused on thiols, relatively ignored have been hydropersulfides (RSSH) and higher order polysulfur species (RSS n H, RSS n R, n > 1). Recent and provocative work has alluded to the prevalence and likely physiological importance of RSSH and related RSS n H. RSSH of cysteine (Cys-SSH) has been found to be prevalent in mammalian systems along with Cys-SSH-containing proteins. The RSSH functionality has not been examined to the extent of other biologically relevant sulfur derivatives (e.g., sulfenic acids, disulfides, etc.), whose roles in cell signaling are strongly indicated. The recent finding of Cys-SSH biosynthesis and translational incorporation into proteins is an unequivocal indication of its fundamental importance and necessitates a more profound look into the physiology of RSSH. In this Review, we discuss the currently reported chemical biology of RSSH (and related species) as a prelude to discussing their possible physiological roles. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.