Leveraging advances in biology to design biomaterials

NASA Astrophysics Data System (ADS)

Darnell, Max; Mooney, David J.

2017-12-01

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

Rapid self-assembly of complex biomolecular architectures during mussel byssus biofabrication

PubMed Central

Priemel, Tobias; Degtyar, Elena; Dean, Mason N.; Harrington, Matthew J.

2017-01-01

Protein-based biogenic materials provide important inspiration for the development of high-performance polymers. The fibrous mussel byssus, for instance, exhibits exceptional wet adhesion, abrasion resistance, toughness and self-healing capacity–properties that arise from an intricate hierarchical organization formed in minutes from a fluid secretion of over 10 different protein precursors. However, a poor understanding of this dynamic biofabrication process has hindered effective translation of byssus design principles into synthetic materials. Here, we explore mussel byssus assembly in Mytilus edulis using a synergistic combination of histological staining and confocal Raman microspectroscopy, enabling in situ tracking of specific proteins during induced thread formation from soluble precursors to solid fibres. Our findings reveal critical insights into this complex biological manufacturing process, showing that protein precursors spontaneously self-assemble into complex architectures, while maturation proceeds in subsequent regulated steps. Beyond their biological importance, these findings may guide development of advanced materials with biomedical and industrial relevance. PMID:28262668

Imparting the unique properties of DNA into complex material architectures and functions.

PubMed

Xu, Phyllis F; Noh, Hyunwoo; Lee, Ju Hun; Domaille, Dylan W; Nakatsuka, Matthew A; Goodwin, Andrew P; Cha, Jennifer N

2013-07-01

While the remarkable chemical and biological properties of DNA have been known for decades, these properties have only been imparted into materials with unprecedented function much more recently. The inimitable ability of DNA to form programmable, complex assemblies through stable, specific, and reversible molecular recognition has allowed the creation of new materials through DNA's ability to control a material's architecture and properties. In this review we discuss recent progress in how DNA has brought unmatched function to materials, focusing specifically on new advances in delivery agents, devices, and sensors.

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

PubMed

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

2018-05-01

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

Additive manufacturing of biologically-inspired materials.

PubMed

Studart, André R

2016-01-21

Additive manufacturing (AM) technologies offer an attractive pathway towards the fabrication of functional materials featuring complex heterogeneous architectures inspired by biological systems. In this paper, recent research on the use of AM approaches to program the local chemical composition, structure and properties of biologically-inspired materials is reviewed. A variety of structural motifs found in biological composites have been successfully emulated in synthetic systems using inkjet-based, direct-writing, stereolithography and slip casting technologies. The replication in synthetic systems of design principles underlying such structural motifs has enabled the fabrication of lightweight cellular materials, strong and tough composites, soft robots and autonomously shaping structures with unprecedented properties and functionalities. Pushing the current limits of AM technologies in future research should bring us closer to the manufacturing capabilities of living organisms, opening the way for the digital fabrication of advanced materials with superior performance, lower environmental impact and new functionalities.

A probabilistic framework for identifying biosignatures using Pathway Complexity

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Student Performance along Axes of Scenario Novelty and Complexity in Introductory Biology: Lessons from a Unique Factorial Approach to Assessment.

PubMed

Deane-Coe, Kirsten K; Sarvary, Mark A; Owens, Thomas G

2017-01-01

In an undergraduate introductory biology laboratory course, we used a summative assessment to directly test the learning objective that students will be able to apply course material to increasingly novel and complex situations. Using a factorial framework, we developed multiple true-false questions to fall along axes of novelty and complexity, which resulted in four categories of questions: familiar content and low complexity (category A); novel content and low complexity (category B); familiar content and high complexity (category C); and novel content and high complexity (category D). On average, students scored more than 70% on all questions, indicating that the course largely met this learning objective. However, students scored highest on questions in category A, likely because they were most similar to course content, and lowest on questions in categories C and D. While we anticipated students would score equally on questions for which either novelty or complexity was altered (but not both), we observed that student scores in category C were lower than in category B. Furthermore, students performed equally poorly on all questions for which complexity was higher (categories C and D), even those containing familiar content, suggesting that application of course material to increasingly complex situations is particularly challenging to students. © 2017 K. K. Deane-Coe et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Information and material flows in complex networks

NASA Astrophysics Data System (ADS)

Helbing, Dirk; Armbruster, Dieter; Mikhailov, Alexander S.; Lefeber, Erjen

2006-04-01

In this special issue, an overview of the Thematic Institute (TI) on Information and Material Flows in Complex Systems is given. The TI was carried out within EXYSTENCE, the first EU Network of Excellence in the area of complex systems. Its motivation, research approach and subjects are presented here. Among the various methods used are many-particle and statistical physics, nonlinear dynamics, as well as complex systems, network and control theory. The contributions are relevant for complex systems as diverse as vehicle and data traffic in networks, logistics, production, and material flows in biological systems. The key disciplines involved are socio-, econo-, traffic- and bio-physics, and a new research area that could be called “biologistics”.

Development and Effectiveness of an Educational Card Game as Supplementary Material in Understanding Selected Topics in Biology

ERIC Educational Resources Information Center

Gutierrez, Arnel F.

2014-01-01

The complex concepts and vocabulary of biology classes discourage many students. In this study, a pretest-posttest model was used to test the effectiveness of an educational card game in reinforcing biological concepts in comparison with traditional teaching methods. The subjects of this study were two biology classes at Bulacan State…

Artificial 3D hierarchical and isotropic porous polymeric materials

PubMed Central

Musteata, Valentina-Elena; Behzad, Ali Reza

2018-01-01

Hierarchical porous materials that replicate complex living structures are attractive for a wide variety of applications, ranging from storage and catalysis to biological and artificial systems. However, the preparation of structures with a high level of complexity and long-range order at the mesoscale and microscale is challenging. We report a simple, nonextractive, and nonreactive method used to prepare three-dimensional porous materials that mimic biological systems such as marine skeletons and honeycombs. This method exploits the concurrent occurrence of the self-assembly of block copolymers in solution and macrophase separation by nucleation and growth. We obtained a long-range order of micrometer-sized compartments. These compartments are interconnected by ordered cylindrical nanochannels. The new approach is demonstrated using polystyrene-b-poly(t-butyl acrylate), which can be further explored for a broad range of applications, such as air purification filters for viruses and pollution particle removal or growth of bioinspired materials for bone regeneration.

Artificial 3D hierarchical and isotropic porous polymeric materials.

PubMed

Chisca, Stefan; Musteata, Valentina-Elena; Sougrat, Rachid; Behzad, Ali Reza; Nunes, Suzana P

2018-05-01

Hierarchical porous materials that replicate complex living structures are attractive for a wide variety of applications, ranging from storage and catalysis to biological and artificial systems. However, the preparation of structures with a high level of complexity and long-range order at the mesoscale and microscale is challenging. We report a simple, nonextractive, and nonreactive method used to prepare three-dimensional porous materials that mimic biological systems such as marine skeletons and honeycombs. This method exploits the concurrent occurrence of the self-assembly of block copolymers in solution and macrophase separation by nucleation and growth. We obtained a long-range order of micrometer-sized compartments. These compartments are interconnected by ordered cylindrical nanochannels. The new approach is demonstrated using polystyrene- b -poly( t -butyl acrylate), which can be further explored for a broad range of applications, such as air purification filters for viruses and pollution particle removal or growth of bioinspired materials for bone regeneration.

From precision polymers to complex materials and systems

NASA Astrophysics Data System (ADS)

Lutz, Jean-François; Lehn, Jean-Marie; Meijer, E. W.; Matyjaszewski, Krzysztof

2016-05-01

Complex chemical systems, such as living biological matter, are highly organized structures based on discrete molecules in constant dynamic interactions. These natural materials can evolve and adapt to their environment. By contrast, man-made materials exhibit simpler properties. In this Review, we highlight that most of the necessary elements for the development of more complex synthetic matter are available today. Using modern strategies, such as controlled radical polymerizations, supramolecular polymerizations or stepwise synthesis, polymers with precisely controlled molecular structures can be synthesized. Moreover, such tailored polymers can be folded or self-assembled into defined nanoscale morphologies. These self-organized macromolecular objects can be at thermal equilibrium or can be driven out of equilibrium. Recently, in the latter case, interesting dynamic materials have been developed. However, this is just a start, and more complex adaptive materials are anticipated.

Weathering of wood

Treesearch

R. Sam Williams

2005-01-01

Weathering is the general term used to define the slow degradation of materials exposed to the weather. The degradation mechanism depends on the type of material, but the cause is a combination of factors found in nature: moisture, sunlight, heat/cold, chemicals, abrasion by windblown materials, and biological agents. Tall mountains weather by the complex and...

In-Gel Direct Laser Writing for 3D-Designed Hydrogel Composites That Undergo Complex Self-Shaping.

PubMed

Nishiguchi, Akihiro; Mourran, Ahmed; Zhang, Hang; Möller, Martin

2018-01-01

Self-shaping and actuating materials inspired by biological system have enormous potential for biosensor, microrobotics, and optics. However, the control of 3D-complex microactuation is still challenging due to the difficulty in design of nonuniform internal stress of micro/nanostructures. Here, we develop in-gel direct laser writing (in-gel DLW) procedure offering a high resolution inscription whereby the two materials, resin and hydrogel, are interpenetrated on a scale smaller than the wavelength of the light. The 3D position and mechanical properties of the inscribed structures could be tailored to a resolution better than 100 nm over a wide density range. These provide an unparalleled means of inscribing a freely suspended microstructures of a second material like a skeleton into the hydrogel body and also to direct isotropic volume changes to bending and distortion motions. In the combination with a thermosensitive hydrogel rather small temperature variations could actuate large amplitude motions. This generates complex modes of motion through the rational engineering of the stresses present in the multicomponent material. More sophisticated folding design would realize a multiple, programmable actuation of soft materials. This method inspired by biological system may offer the possibility for functional soft materials capable of biomimetic actuation and photonic crystal application.

Drawing inspiration from biological optical systems

NASA Astrophysics Data System (ADS)

Wolpert, H. D.

2009-08-01

Bio-Mimicking/Bio-Inspiration: How can we not be inspired by Nature? Life has evolved on earth over the last 3.5 to 4 billion years. Materials formed during this time were not toxic; they were created at low temperatures and low pressures unlike many of the materials developed today. The natural materials formed are self-assembled, multifunctional, nonlinear, complex, adaptive, self-repairing and biodegradable. The designs that failed are fossils. Those that survived are the success stories. Natural materials are mostly formed from organics, inorganic crystals and amorphous phases. The materials make economic sense by optimizing the design of the structures or systems to meet multiple needs. We constantly "see" many similar strategies in approaches, between man and nature, but we seldom look at the details of natures approaches. The power of image processing, in many of natures creatures, is a detail that is often overlooked. Seldon does the engineer interact with the biologist and learn what nature has to teach us. The variety and complexity of biological materials and the optical systems formed should inspire us.

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

Complex coacervate-based materials for biomedicine.

PubMed

Blocher, Whitney C; Perry, Sarah L

2017-07-01

There has been increasing interest in complex coacervates for deriving and transporting biomaterials. Complex coacervates are a dense, polyelectrolyte-rich liquid that results from the electrostatic complexation of oppositely charged macroions. Coacervates have long been used as a strategy for encapsulation, particularly in food and personal care products. More recent efforts have focused on the utility of this class of materials for the encapsulation of small molecules, proteins, RNA, DNA, and other biomaterials for applications ranging from sensing to biomedicine. Furthermore, coacervate-related materials have found utility in other areas of biomedicine, including cartilage mimics, tissue culture scaffolds, and adhesives for wet, biological environments. Here, we discuss the self-assembly of complex coacervate-based materials, current challenges in the intelligent design of these materials, and their utility applications in the broad field of biomedicine. WIREs Nanomed Nanobiotechnol 2017, 9:e1442. doi: 10.1002/wnan.1442 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

The New Toxicology of Sophisticated Materials: Nanotoxicology and Beyond

PubMed Central

Maynard, Andrew D.; Warheit, David B.; Philbert, Martin A.

2011-01-01

It has long been recognized that the physical form of materials can mediate their toxicity—the health impacts of asbestiform materials, industrial aerosols, and ambient particulate matter are prime examples. Yet over the past 20 years, toxicology research has suggested complex and previously unrecognized associations between material physicochemistry at the nanoscale and biological interactions. With the rapid rise of the field of nanotechnology and the design and production of increasingly complex nanoscale materials, it has become ever more important to understand how the physical form and chemical composition of these materials interact synergistically to determine toxicity. As a result, a new field of research has emerged—nanotoxicology. Research within this field is highlighting the importance of material physicochemical properties in how dose is understood, how materials are characterized in a manner that enables quantitative data interpretation and comparison, and how materials move within, interact with, and are transformed by biological systems. Yet many of the substances that are the focus of current nanotoxicology studies are relatively simple materials that are at the vanguard of a new era of complex materials. Over the next 50 years, there will be a need to understand the toxicology of increasingly sophisticated materials that exhibit novel, dynamic and multifaceted functionality. If the toxicology community is to meet the challenge of ensuring the safe use of this new generation of substances, it will need to move beyond “nano” toxicology and toward a new toxicology of sophisticated materials. Here, we present a brief overview of the current state of the science on the toxicology of nanoscale materials and focus on three emerging toxicology-based challenges presented by sophisticated materials that will become increasingly important over the next 50 years: identifying relevant materials for study, physicochemical characterization, and biointeractions. PMID:21177774

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

PubMed

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

2016-10-31

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

Cork Embedded Internal Features and Contrast Mechanisms with Del Using 18, 20, 30, 36 and 40 keV Synchrotron X-rays

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

Rao, D.V.; Zhong, Z.; Akatsuka, T.

Images of the cork used for wine and other bottles are visualized with the use of diffraction-enhanced imaging (DEI) technique. Present experimental studies allowed us to identify the cracks, holes, porosity, and importance of soft-matter (soft-material) and associated biology by visualization of the embedded internal complex features of the biological material such as cork and its microstructure. Highlighted the contrast mechanisms above and below the K-absorption edge of iodine and studied the attenuation through a combination of weakly and strongly attenuating materials.

Cork Embedded Internal Features and Contrast Mechanisms with DEI using 18, 20, 30, 36, and 40 kev Synchrotron X-rays

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

Donepudi, R.; Cesareo, R; Brunetti, A

Images of the cork used for wine and other bottles are visualized with the use of diffraction-enhanced imaging (DEI) technique. Present experimental studies allowed us to identify the cracks, holes, porosity, and importance of soft-matter (soft-material) and associated biology by visualization of the embedded internal complex features of the biological material such as cork and its microstructure. Highlighted the contrast mechanisms above and below the K-absorption edge of iodine and studied the attenuation through a combination of weakly and strongly attenuating materials.

Diversification and enrichment of clinical biomaterials inspired by Darwinian evolution.

PubMed

Green, D W; Watson, G S; Watson, J A; Lee, D-J; Lee, J-M; Jung, H-S

2016-09-15

Regenerative medicine and biomaterials design are driven by biomimicry. There is the essential requirement to emulate human cell, tissue, organ and physiological complexity to ensure long-lasting clinical success. Biomimicry projects for biomaterials innovation can be re-invigorated with evolutionary insights and perspectives, since Darwinian evolution is the original dynamic process for biological organisation and complexity. Many existing human inspired regenerative biomaterials (defined as a nature generated, nature derived and nature mimicking structure, produced within a biological system, which can deputise for, or replace human tissues for which it closely matches) are without important elements of biological complexity such as, hierarchy and autonomous actions. It is possible to engineer these essential elements into clinical biomaterials via bioinspired implementation of concepts, processes and mechanisms played out during Darwinian evolution; mechanisms such as, directed, computational, accelerated evolutions and artificial selection contrived in the laboratory. These dynamos for innovation can be used during biomaterials fabrication, but also to choose optimal designs in the regeneration process. Further evolutionary information can help at the design stage; gleaned from the historical evolution of material adaptations compared across phylogenies to changes in their environment and habitats. Taken together, harnessing evolutionary mechanisms and evolutionary pathways, leading to ideal adaptations, will eventually provide a new class of Darwinian and evolutionary biomaterials. This will provide bioengineers with a more diversified and more efficient innovation tool for biomaterial design, synthesis and function than currently achieved with synthetic materials chemistry programmes and rational based materials design approach, which require reasoned logic. It will also inject further creativity, diversity and richness into the biomedical technologies that we make. All of which are based on biological principles. Such evolution-inspired biomaterials have the potential to generate innovative solutions, which match with existing bioengineering problems, in vital areas of clinical materials translation that include tissue engineering, gene delivery, drug delivery, immunity modulation, and scar-less wound healing. Evolution by natural selection is a powerful generator of innovations in molecular, materials and structures. Man has influenced evolution for thousands of years, to create new breeds of farm animals and crop plants, but now molecular and materials can be molded in the same way. Biological molecules and simple structures can be evolved, literally in the laboratory. Furthermore, they are re-designed via lessons learnt from evolutionary history. Through a 3-step process to (1) create variants in material building blocks, (2) screen the variants with beneficial traits/properties and (3) select and support their self-assembly into usable materials, improvements in design and performance can emerge. By introducing biological molecules and small organisms into this process, it is possible to make increasingly diversified, sophisticated and clinically relevant materials for multiple roles in biomedicine. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Teaching Electrostatics and Entropy in Introductory Physics

NASA Astrophysics Data System (ADS)

Reeves, Mark

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 courses is important contribution of the entropy in driving fundamental biological processes towards equilibrium. I will present material developed to teach electrostatic screening in solutions and the function of nerve cells where entropic effects act to counterbalance electrostatic attraction. These ideas are taught in an introductory, calculus-based physics course to biomedical engineers using SCALEUP pedagogy. Results of student mastering of complex problems that cross disciplinary boundaries between biology and physics, as well as the challenges that they face in learning this material will be presented.

CPTC and NIST-sponsored Yeast Reference Material Now Publicly Available | Office of Cancer Clinical Proteomics Research

Cancer.gov

The yeast protein extract (RM8323) developed by National Institute of Standards and Technology (NIST) under the auspices of NCI's CPTC initiative is currently available to the public at https://www-s.nist.gov/srmors/view_detail.cfm?srm=8323. The yeast proteome offers researchers a unique biological reference material. RM8323 is the most extensively characterized complex biological proteome and the only one associated with several large-scale studies to estimate protein abundance across a wide concentration range.

Two-Dimensional Spectroscopy Is Being Used to Address Core Scientific Questions in Biology and Materials Science.

PubMed

Petti, Megan K; Lomont, Justin P; Maj, Michał; Zanni, Martin T

2018-02-15

Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photosynthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy.

Analysis of biosurfaces by neutron reflectometry: From simple to complex interfaces

DOE PAGES

Junghans, Ann; Watkins, Erik B.; Barker, Robert D.; ...

2015-03-16

Because of its high sensitivity for light elements and the scattering contrast manipulation via isotopic substitutions, neutron reflectometry (NR) is an excellent tool for studying the structure of soft-condensed material. These materials include model biophysical systems as well as in situ living tissue at the solid–liquid interface. The penetrability of neutrons makes NR suitable for probing thin films with thicknesses of 5–5000 Å at various buried, for example, solid–liquid, interfaces [J. Daillant and A. Gibaud, Lect. Notes Phys. 770, 133 (2009); G. Fragneto-Cusani, J. Phys.: Condens. Matter 13, 4973 (2001); J. Penfold, Curr. Opin. Colloid Interface Sci. 7, 139 (2002)].more » Over the past two decades, NR has evolved to become a key tool in the characterization of biological and biomimetic thin films. Highlighted In the current report are some of the authors' recent accomplishments in utilizing NR to study highly complex systems, including in-situ experiments. Such studies will result in a much better understanding of complex biological problems, have significant medical impact by suggesting innovative treatment, and advance the development of highly functionalized biomimetic materials.« less

Short-term bioassay of complex organic mixtures. Part II. Mutagenicity testing

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

Epler, J.L.; Clark, B.R.; Ho, C.

1978-01-01

The feasibility of using short-term mutagenicity assays to predict the potential biohazard of various crude and complex test materials has been examined in a coupled chemical and biological approach. The principal focus of the research has involved the preliminary chemical characterizatiion and preparation for bioassay, followed by testing in the Salmonella histidine reversion assay system. The mutagenicity tests are intended to act as predictors of profound long-range health effects such as mutagenesis and/or carcinogenesis; act as a mechanism to rapidly isolate and identify a hazardous agent in a complex mixture; and function as a measure of biological activity correlating baselinemore » data with changes in process conditions. Since complex mixtures can be fractionated and approached in these short-term assays, information reflecting on the actual compounds responsible for the biological effect may be accumulated.« less

Thermal Stabilization of Biologics with Photoresponsive Hydrogels.

PubMed

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

2018-03-12

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

Testing Effect and Complex Comprehension in a Large Introductory Undergraduate Biology Course

ERIC Educational Resources Information Center

Pagliarulo, Christopher L.

2011-01-01

Traditional undergraduate biology courses are content intensive, requiring students to understand and remember large amounts of information in short periods of time. Yet most students maintain little of the material encountered during their education. Poor knowledge retention is a main cause of academic failure and high undergraduate attrition…

Magnetic separation techniques in sample preparation for biological analysis: a review.

PubMed

He, Jincan; Huang, Meiying; Wang, Dongmei; Zhang, Zhuomin; Li, Gongke

2014-12-01

Sample preparation is a fundamental and essential step in almost all the analytical procedures, especially for the analysis of complex samples like biological and environmental samples. In past decades, with advantages of superparamagnetic property, good biocompatibility and high binding capacity, functionalized magnetic materials have been widely applied in various processes of sample preparation for biological analysis. In this paper, the recent advancements of magnetic separation techniques based on magnetic materials in the field of sample preparation for biological analysis were reviewed. The strategy of magnetic separation techniques was summarized. The synthesis, stabilization and bio-functionalization of magnetic nanoparticles were reviewed in detail. Characterization of magnetic materials was also summarized. Moreover, the applications of magnetic separation techniques for the enrichment of protein, nucleic acid, cell, bioactive compound and immobilization of enzyme were described. Finally, the existed problems and possible trends of magnetic separation techniques for biological analysis in the future were proposed. Copyright © 2014 Elsevier B.V. All rights reserved.

CryoTEM as an Advanced Analytical Tool for Materials Chemists.

PubMed

Patterson, Joseph P; Xu, Yifei; Moradi, Mohammad-Amin; Sommerdijk, Nico A J M; Friedrich, Heiner

2017-07-18

Morphology plays an essential role in chemistry through the segregation of atoms and/or molecules into different phases, delineated by interfaces. This is a general process in materials synthesis and exploited in many fields including colloid chemistry, heterogeneous catalysis, and functional molecular systems. To rationally design complex materials, we must understand and control morphology evolution. Toward this goal, we utilize cryogenic transmission electron microscopy (cryoTEM), which can track the structural evolution of materials in solution with nanometer spatial resolution and a temporal resolution of <1 s. In this Account, we review examples of our own research where direct observations by cryoTEM have been essential to understanding morphology evolution in macromolecular self-assembly, inorganic nucleation and growth, and the cooperative evolution of hybrid materials. These three different research areas are at the heart of our approach to materials chemistry where we take inspiration from the myriad examples of complex materials in Nature. Biological materials are formed using a limited number of chemical components and under ambient conditions, and their formation pathways were refined during biological evolution by enormous trial and error approaches to self-organization and biomineralization. By combining the information on what is possible in nature and by focusing on a limited number of chemical components, we aim to provide an essential insight into the role of structure evolution in materials synthesis. Bone, for example, is a hierarchical and hybrid material which is lightweight, yet strong and hard. It is formed by the hierarchical self-assembly of collagen into a macromolecular template with nano- and microscale structure. This template then directs the nucleation and growth of oriented, nanoscale calcium phosphate crystals to form the composite material. Fundamental insight into controlling these structuring processes will eventually allow us to design such complex materials with predetermined and potentially unique properties.

Quantitative Interpretation of Multifrequency Multimode EPR Spectra of Metal Containing Proteins, Enzymes, and Biomimetic Complexes.

PubMed

Petasis, Doros T; Hendrich, Michael P

2015-01-01

Electron paramagnetic resonance (EPR) spectroscopy has long been a primary method for characterization of paramagnetic centers in materials and biological complexes. Transition metals in biological complexes have valence d-orbitals that largely define the chemistry of the metal centers. EPR spectra are distinctive for metal type, oxidation state, protein environment, substrates, and inhibitors. The study of many metal centers in proteins, enzymes, and biomimetic complexes has led to the development of a systematic methodology for quantitative interpretation of EPR spectra from a wide array of metal containing complexes. The methodology is now contained in the computer program SpinCount. SpinCount allows simulation of EPR spectra from any sample containing multiple species composed of one or two metals in any spin state. The simulations are quantitative, thus allowing determination of all species concentrations in a sample directly from spectra. This chapter will focus on applications to transition metals in biological systems using EPR spectra from multiple microwave frequencies and modes. © 2015 Elsevier Inc. All rights reserved.

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

PubMed

Bhat, Ramray; Pally, Dharma

2017-07-01

The term complexity means several things to biologists.When qualifying morphological phenotype, on the one hand, it is used to signify the sheer complicatedness of living systems, especially as a result of the multicomponent aspect of biological form. On the other hand, it has been used to represent the intricate nature of the connections between constituents that make up form: a more process-based explanation. In the context of evolutionary arguments, complexity has been defined, in a quantifiable fashion, as the amount of information, an informatic template such as a sequence of nucleotides or amino acids stores about its environment. In this perspective, we begin with a brief review of the history of complexity theory. We then introduce a developmental and an evolutionary understanding of what it means for biological systems to be complex.We propose that the complexity of living systems can be understood through two interdependent structural properties: multiscalarity of interconstituent mechanisms and excitability of the biological materials. The answer to whether a system becomes more or less complex over time depends on the potential for its constituents to interact in novel ways and combinations to give rise to new structures and functions, as well as on the evolution of excitable properties that would facilitate the exploration of interconstituent organization in the context of their microenvironments and macroenvironments.

Category Theoretic Analysis of Hierarchical Protein Materials and Social Networks

PubMed Central

Spivak, David I.; Giesa, Tristan; Wood, Elizabeth; Buehler, Markus J.

2011-01-01

Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting functional properties of biological protein materials by developing so-called ologs. An olog is like a “concept web” or “semantic network” except that it follows a rigorous mathematical formulation based on category theory. This key difference ensures that an olog is unambiguous, highly adaptable to evolution and change, and suitable for sharing concepts with other olog. We consider simple cases of beta-helical and amyloid-like protein filaments subjected to axial extension and develop an olog representation of their structural and resulting mechanical properties. We also construct a representation of a social network in which people send text-messages to their nearest neighbors and act as a team to perform a task. We show that the olog for the protein and the olog for the social network feature identical category-theoretic representations, and we proceed to precisely explicate the analogy or isomorphism between them. The examples presented here demonstrate that the intrinsic nature of a complex system, which in particular includes a precise relationship between structure and function at different hierarchical levels, can be effectively represented by an olog. This, in turn, allows for comparative studies between disparate materials or fields of application, and results in novel approaches to derive functionality in the design of de novo hierarchical systems. We discuss opportunities and challenges associated with the description of complex biological materials by using ologs as a powerful tool for analysis and design in the context of materiomics, and we present the potential impact of this approach for engineering, life sciences, and medicine. PMID:21931622

The Physics of Life and Quantum Complex Matter: A Case of Cross-Fertilization

PubMed Central

Poccia, Nicola; Bianconi, Antonio

2011-01-01

Progress in the science of complexity, from the Big Bang to the coming of humankind, from chemistry and biology to geosciences and medicine, and from materials engineering to energy sciences, is leading to a shift of paradigm in the physical sciences. The focus is on the understanding of the non-equilibrium process in fine tuned systems. Quantum complex materials such as high temperature superconductors and living matter are both non-equilibrium and fine tuned systems. These topics have been subbjects of scientific discussion in the Rome Symposium on the “Quantum Physics of Living Matter”. PMID:26791661

Three-Dimensional Printing and Cell Therapy for Wound Repair.

PubMed

van Kogelenberg, Sylvia; Yue, Zhilian; Dinoro, Jeremy N; Baker, Christopher S; Wallace, Gordon G

2018-05-01

Significance: Skin tissue damage is a major challenge and a burden on healthcare systems, from burns and other trauma to diabetes and vascular disease. Although the biological complexities are relatively well understood, appropriate repair mechanisms are scarce. Three-dimensional bioprinting is a layer-based approach to regenerative medicine, whereby cells and cell-based materials can be dispensed in fine spatial arrangements to mimic native tissue. Recent Advances: Various bioprinting techniques have been employed in wound repair-based skin tissue engineering, from laser-induced forward transfer to extrusion-based methods, and with the investigation of the benefits and shortcomings of each, with emphasis on biological compatibility and cell proliferation, migration, and vitality. Critical issues: Development of appropriate biological inks and the vascularization of newly developed tissues remain a challenge within the field of skin tissue engineering. Future Directions: Progress within bioprinting requires close interactions between material scientists, tissue engineers, and clinicians. Microvascularization, integration of multiple cell types, and skin appendages will be essential for creation of complex skin tissue constructs.

Investigating Processes of Materials Formation via Liquid Phase and Cryogenic TEM

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

De Yoreo, James J.; Sommerdijk, Nico

2016-06-14

The formation of materials in solutions is a widespread phenomenon in synthetic, biological and geochemical systems, occurring through dynamic processes of nucleation, self-assembly, crystal growth, and coarsening. The recent advent of liquid phase TEM and advances in cryogenic TEM are transforming our understanding of these phenomena by providing new insights into the underlying physical and chemical mechanisms. The techniques have been applied to metallic and semiconductor nanoparticles, geochemical and biological minerals, electrochemical systems, macromolecular complexes, and selfassembling systems, both organic and inorganic. New instrumentation and methodologies currently on the horizon promise new opportunities for advancing the science of materials synthesis.

Installing logic-gate responses to a variety of biological substances in supramolecular hydrogel-enzyme hybrids.

PubMed

Ikeda, Masato; Tanida, Tatsuya; Yoshii, Tatsuyuki; Kurotani, Kazuya; Onogi, Shoji; Urayama, Kenji; Hamachi, Itaru

2014-06-01

Soft materials that exhibit stimuli-responsive behaviour under aqueous conditions (such as supramolecular hydrogels composed of self-assembled nanofibres) have many potential biological applications. However, designing a macroscopic response to structurally complex biochemical stimuli in these materials still remains a challenge. Here we show that redox-responsive peptide-based hydrogels have the ability to encapsulate enzymes and still retain their activities. Moreover, cooperative coupling of enzymatic reactions with the gel response enables us to construct unique stimuli-responsive soft materials capable of sensing a variety of disease-related biomarkers. The programmable gel-sol response (even to biological samples) is visible to the naked eye. Furthermore, we built Boolean logic gates (OR and AND) into the hydrogel-enzyme hybrid materials, which were able to sense simultaneously plural specific biochemicals and execute a controlled drug release in accordance with the logic operation. The intelligent soft materials that we have developed may prove valuable in future medical diagnostics or treatments.

Installing logic-gate responses to a variety of biological substances in supramolecular hydrogel-enzyme hybrids

NASA Astrophysics Data System (ADS)

Ikeda, Masato; Tanida, Tatsuya; Yoshii, Tatsuyuki; Kurotani, Kazuya; Onogi, Shoji; Urayama, Kenji; Hamachi, Itaru

2014-06-01

Soft materials that exhibit stimuli-responsive behaviour under aqueous conditions (such as supramolecular hydrogels composed of self-assembled nanofibres) have many potential biological applications. However, designing a macroscopic response to structurally complex biochemical stimuli in these materials still remains a challenge. Here we show that redox-responsive peptide-based hydrogels have the ability to encapsulate enzymes and still retain their activities. Moreover, cooperative coupling of enzymatic reactions with the gel response enables us to construct unique stimuli-responsive soft materials capable of sensing a variety of disease-related biomarkers. The programmable gel-sol response (even to biological samples) is visible to the naked eye. Furthermore, we built Boolean logic gates (OR and AND) into the hydrogel-enzyme hybrid materials, which were able to sense simultaneously plural specific biochemicals and execute a controlled drug release in accordance with the logic operation. The intelligent soft materials that we have developed may prove valuable in future medical diagnostics or treatments.

Deconstructing the core dynamics from a complex time-lagged regulatory biological circuit.

PubMed

Eriksson, O; Brinne, B; Zhou, Y; Björkegren, J; Tegnér, J

2009-03-01

Complex regulatory dynamics is ubiquitous in molecular networks composed of genes and proteins. Recent progress in computational biology and its application to molecular data generate a growing number of complex networks. Yet, it has been difficult to understand the governing principles of these networks beyond graphical analysis or extensive numerical simulations. Here the authors exploit several simplifying biological circumstances which thereby enable to directly detect the underlying dynamical regularities driving periodic oscillations in a dynamical nonlinear computational model of a protein-protein network. System analysis is performed using the cell cycle, a mathematically well-described complex regulatory circuit driven by external signals. By introducing an explicit time delay and using a 'tearing-and-zooming' approach the authors reduce the system to a piecewise linear system with two variables that capture the dynamics of this complex network. A key step in the analysis is the identification of functional subsystems by identifying the relations between state-variables within the model. These functional subsystems are referred to as dynamical modules operating as sensitive switches in the original complex model. By using reduced mathematical representations of the subsystems the authors derive explicit conditions on how the cell cycle dynamics depends on system parameters, and can, for the first time, analyse and prove global conditions for system stability. The approach which includes utilising biological simplifying conditions, identification of dynamical modules and mathematical reduction of the model complexity may be applicable to other well-characterised biological regulatory circuits. [Includes supplementary material].

3D bioprinting of tissues and organs.

PubMed

Murphy, Sean V; Atala, Anthony

2014-08-01

Additive manufacturing, otherwise known as three-dimensional (3D) printing, is driving major innovations in many areas, such as engineering, manufacturing, art, education and medicine. Recent advances have enabled 3D printing of biocompatible materials, cells and supporting components into complex 3D functional living tissues. 3D bioprinting is being applied to regenerative medicine to address the need for tissues and organs suitable for transplantation. Compared with non-biological printing, 3D bioprinting involves additional complexities, such as the choice of materials, cell types, growth and differentiation factors, and technical challenges related to the sensitivities of living cells and the construction of tissues. Addressing these complexities requires the integration of technologies from the fields of engineering, biomaterials science, cell biology, physics and medicine. 3D bioprinting has already been used for the generation and transplantation of several tissues, including multilayered skin, bone, vascular grafts, tracheal splints, heart tissue and cartilaginous structures. Other applications include developing high-throughput 3D-bioprinted tissue models for research, drug discovery and toxicology.

Biologically inspired dynamic material systems.

PubMed

Studart, André R

2015-03-09

Numerous examples of material systems that dynamically interact with and adapt to the surrounding environment are found in nature, from hair-based mechanoreceptors in animals to self-shaping seed dispersal units in plants to remodeling bone in vertebrates. Inspired by such fascinating biological structures, a wide range of synthetic material systems have been created to replicate the design concepts of dynamic natural architectures. Examples of biological structures and their man-made counterparts are herein revisited to illustrate how dynamic and adaptive responses emerge from the intimate microscale combination of building blocks with intrinsic nanoscale properties. By using top-down photolithographic methods and bottom-up assembly approaches, biologically inspired dynamic material systems have been created 1) to sense liquid flow with hair-inspired microelectromechanical systems, 2) to autonomously change shape by utilizing plantlike heterogeneous architectures, 3) to homeostatically influence the surrounding environment through self-regulating adaptive surfaces, and 4) to spatially concentrate chemical species by using synthetic microcompartments. The ever-increasing complexity and remarkable functionalities of such synthetic systems offer an encouraging perspective to the rich set of dynamic and adaptive properties that can potentially be implemented in future man-made material systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and Effectiveness of an Educational Card Game as Supplementary Material in Understanding Selected Topics in Biology

PubMed Central

Gutierrez, Arnel F.

2014-01-01

The complex concepts and vocabulary of biology classes discourage many students. In this study, a pretest–posttest model was used to test the effectiveness of an educational card game in reinforcing biological concepts in comparison with traditional teaching methods. The subjects of this study were two biology classes at Bulacan State University–Sarmiento Campus. Both classes received conventional instruction; however, the experimental group's instruction was supplemented with the card game, while the control group's instruction was reinforced with traditional exercises and assignments. The score increases from pretest to posttest showed that both methods effectively reinforced biological concepts, but a t test showed that the card game is more effective than traditional teaching methods. Additionally, students from the experimental group evaluated the card game using five criteria: goals, design, organization, playability, and usefulness. The students rated the material very satisfactory. PMID:24591506

Development and effectiveness of an educational card game as supplementary material in understanding selected topics in biology.

PubMed

Gutierrez, Arnel F

2014-01-01

The complex concepts and vocabulary of biology classes discourage many students. In this study, a pretest-posttest model was used to test the effectiveness of an educational card game in reinforcing biological concepts in comparison with traditional teaching methods. The subjects of this study were two biology classes at Bulacan State University-Sarmiento Campus. Both classes received conventional instruction; however, the experimental group's instruction was supplemented with the card game, while the control group's instruction was reinforced with traditional exercises and assignments. The score increases from pretest to posttest showed that both methods effectively reinforced biological concepts, but a t test showed that the card game is more effective than traditional teaching methods. Additionally, students from the experimental group evaluated the card game using five criteria: goals, design, organization, playability, and usefulness. The students rated the material very satisfactory.

Brushing Your Spacecrafts Teeth: A Review of Biological Reduction Processes for Planetary Protection Missions

NASA Technical Reports Server (NTRS)

Pugel, D. E. (Betsy); Rummel, J. D.; Conley, Catharine

2017-01-01

Much like keeping your teeth clean, where you brush away biofilms that your dentist calls "plaque," there are various methods to clean spaceflight hardware of biological contamination, known as biological reduction processes. Different approaches clean your hardware's "teeth" in different ways and with different levels of effectiveness. We know that brushing at home with a simple toothbrush is convenient and has a different level of impact vs. getting your teeth cleaned at the dentist. In the same way, there are some approaches to biological reduction that may require simple tools or more complex implementation approaches (think about sonicating or just soaking your dentures, vs. brushing them). There are also some that are more effective for different degrees of cleanliness and still some that have materials compatibility concerns. In this article, we review known and NASA-certified approaches for biological reduction, pointing out materials compatibility concerns and areas where additional research is needed.

Brushing Your Spacecrafts Teeth: A Review of Biological Reduction Processes for Planetary Protection Missions

NASA Technical Reports Server (NTRS)

Pugel, D.E. (Betsy); Rummel, J. D.; Conley, C. A.

2017-01-01

Much like keeping your teeth clean, where you brush away biofilms that your dentist calls plaque, there are various methods to clean spaceflight hardware of biological contamination, known as biological reduction processes. Different approaches clean your hardwares teeth in different ways and with different levels of effectiveness. We know that brushing at home with a simple toothbrush is convenient and has a different level of impact vs. getting your teeth cleaned at the dentist. In the same way, there are some approaches to biological reduction that may require simple tools or more complex implementation approaches (think about sonicating or just soaking your dentures, vs. brushing them). There are also some that are more effective for different degrees of cleanliness and still some that have materials compatibility concerns. In this article, we review known and NASA-certified approaches for biological reduction, pointing out materials compatibility concerns and areas where additional research is needed.

Using simple manipulatives to improve student comprehension of a complex biological process: protein synthesis.

PubMed

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article describes an exercise that was developed to illustrate the process of translation using simple objects to represent complex molecules. Animations, 3D physical models, computer simulations, laboratory experiments and classroom lectures are also used to reinforce the students' understanding of translation, but by focusing on the simple manipulatives in this exercise, students are better able to visualize concepts that can elude them when using the other methods. The translation exercise is described along with suggestions for background material, questions used to evaluate student comprehension and tips for using the manipulatives to identify common misconceptions. Copyright © 2012 Wiley Periodicals, Inc.

Deterministic Integration of Biological and Soft Materials onto 3D Microscale Cellular Frameworks

PubMed Central

McCracken, Joselle M.; Xu, Sheng; Badea, Adina; Jang, Kyung-In; Yan, Zheng; Wetzel, David J.; Nan, Kewang; Lin, Qing; Han, Mengdi; Anderson, Mikayla A.; Lee, Jung Woo; Wei, Zijun; Pharr, Matt; Wang, Renhan; Su, Jessica; Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2018-01-01

Complex 3D organizations of materials represent ubiquitous structural motifs found in the most sophisticated forms of matter, the most notable of which are in life-sustaining hierarchical structures found in biology, but where simpler examples also exist as dense multilayered constructs in high-performance electronics. Each class of system evinces specific enabling forms of assembly to establish their functional organization at length scales not dissimilar to tissue-level constructs. This study describes materials and means of assembly that extend and join these disparate systems—schemes for the functional integration of soft and biological materials with synthetic 3D microscale, open frameworks that can leverage the most advanced forms of multilayer electronic technologies, including device-grade semiconductors such as monocrystalline silicon. Cellular migration behaviors, temporal dependencies of their growth, and contact guidance cues provided by the nonplanarity of these frameworks illustrate design criteria useful for their functional integration with living matter (e.g., NIH 3T3 fibroblast and primary rat dorsal root ganglion cell cultures). PMID:29552634

Bioinspired microrobots

NASA Astrophysics Data System (ADS)

Palagi, Stefano; Fischer, Peer

2018-06-01

Microorganisms can move in complex media, respond to the environment and self-organize. The field of microrobotics strives to achieve these functions in mobile robotic systems of sub-millimetre size. However, miniaturization of traditional robots and their control systems to the microscale is not a viable approach. A promising alternative strategy in developing microrobots is to implement sensing, actuation and control directly in the materials, thereby mimicking biological matter. In this Review, we discuss design principles and materials for the implementation of robotic functionalities in microrobots. We examine different biological locomotion strategies, and we discuss how they can be artificially recreated in magnetic microrobots and how soft materials improve control and performance. We show that smart, stimuli-responsive materials can act as on-board sensors and actuators and that `active matter' enables autonomous motion, navigation and collective behaviours. Finally, we provide a critical outlook for the field of microrobotics and highlight the challenges that need to be overcome to realize sophisticated microrobots, which one day might rival biological machines.

Systematic toxicological analysis: computer-assisted identification of poisons in biological materials.

PubMed

Stimpfl, Th; Demuth, W; Varmuza, K; Vycudilik, W

2003-06-05

A new software was developed to improve the chances for identification of a "general unknown" in complex biological materials. To achieve this goal, the total ion current chromatogram was simplified by filtering the acquired mass spectra via an automated subtraction procedure, which removed mass spectra originating from the sample matrix, as well as interfering substances from the extraction procedure. It could be shown that this tool emphasizes mass spectra of exceptional compounds, and therefore provides the forensic toxicologist with further evidence-even in cases where mass spectral data of the unknown compound are not available in "standard" spectral libraries.

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

Development of hydrogels for regenerative engineering.

PubMed

Guan, Xiaofei; Avci-Adali, Meltem; Alarçin, Emine; Cheng, Hao; Kashaf, Sara Saheb; Li, Yuxiao; Chawla, Aditya; Jang, Hae Lin; Khademhosseini, Ali

2017-05-01

The aim of regenerative engineering is to restore complex tissues and biological systems through convergence in the fields of advanced biomaterials, stem cell science, and developmental biology. Hydrogels are one of the most attractive biomaterials for regenerative engineering, since they can be engineered into tissue mimetic 3D scaffolds to support cell growth due to their similarity to native extracellular matrix. Advanced nano- and micro-technologies have dramatically increased the ability to control properties and functionalities of hydrogel materials by facilitating biomimetic fabrication of more sophisticated compositions and architectures, thus extending our understanding of cell-matrix interactions at the nanoscale. With this perspective, this review discusses the most commonly used hydrogel materials and their fabrication strategies for regenerative engineering. We highlight the physical, chemical, and functional modulation of hydrogels to design and engineer biomimetic tissues based on recent achievements in nano- and micro-technologies. In addition, current hydrogel-based regenerative engineering strategies for treating multiple tissues, such as musculoskeletal, nervous and cardiac tissue, are also covered in this review. The interaction of multiple disciplines including materials science, cell biology, and chemistry, will further play an important role in the design of functional hydrogels for the regeneration of complex tissues. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Passive film growth on titanium alloys: physicochemical and biologic considerations.

PubMed

Eliades, T

1997-01-01

The role of reactive oxygen derivatives (hydroxy peroxide, hydroxyl radical, and singlet oxygen) on the precipitation of inorganic and organic complexes onto the surface of titanium implant alloys is discussed in this review. In addition, the effect of possible implication of several biologic entities surrounding the implant on the implant-tissue interface constituents is described. Evidence from relevant studies suggests that local microenvironmental byproducts and factors associated with the inflammatory response resulting from the implant-induced tissue insult may enhance the expressivity of the inherent, clinically important property of titanium to form oxides. Growth of titanium oxide may be explained through several processes derived from biologic, thermodynamic, and electrochemical approaches. The models proposed to interpret this phenomenon are often contradictory, demonstrating inward or outward from the bulk material passive film growth, with increasing or self-limiting levels of oxide formation as a function of time. However, in vivo observations are consistent with aging-induced thickening of the complexes precipitated on the implant material surface. This review attempts to clarify several critical issues pertaining to passive film formation and kinetics on titanium-alloy surfaces.

Materials as stem cell regulators

PubMed Central

Murphy, William L.; McDevitt, Todd C.; Engler, Adam J.

2014-01-01

The stem cell/material interface is a complex, dynamic microenvironment in which the cell and the material cooperatively dictate one another's fate: the cell by remodelling its surroundings, and the material through its inherent properties (such as adhesivity, stiffness, nanostructure or degradability). Stem cells in contact with materials are able to sense their properties, integrate cues via signal propagation and ultimately translate parallel signalling information into cell fate decisions. However, discovering the mechanisms by which stem cells respond to inherent material characteristics is challenging because of the highly complex, multicomponent signalling milieu present in the stem cell environment. In this Review, we discuss recent evidence that shows that inherent material properties may be engineered to dictate stem cell fate decisions, and overview a subset of the operative signal transduction mechanisms that have begun to emerge. Further developments in stem cell engineering and mechanotransduction are poised to have substantial implications for stem cell biology and regenerative medicine. PMID:24845994

Present systems and future needs for risk assessment of veterinary biologicals in Australia: the perspective of the regulator.

PubMed

Doyle, K A

1995-12-01

The increasing range and complexity of biologicals, and the greater demand for these products, have resulted in a greater volume of trade in animal-based biological material. This has given rise, in turn, to many approaches to the regulation of importation of these materials, as countries seek protection against the introduction of disease. Harmonization of these regulatory approaches would contribute significantly to the availability of veterinary biologicals, to their manufacture and trade, and to disease security. Australia has developed systems for the categorisation and evaluation of biologicals, control by import permits, and specific procedures at point-of-entry and in institutions where these products are used. Computerised records and precedents assist in evaluation and in the issuing of permits. Recognition that some materials must be subject to further control has led to a system of registration of institutions based on levels of biosecurity, and approved use and disposal programmes. Institutions vary from high-security animal health laboratories to human in vitro fertilisation clinics, which use animal-derived media and materials. Such institutions are regulated through quality assurance contracts. Quarantine authorities have linkages with other agencies which have an interest in these products. These linkages reflect the administrative structures of government in Australia, and provide for management of all forms of risk. The author describes these systems and overviews their biological basis.

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

Preparation and Luminescent Properties of the antibacterial materials of the La3+ Doped Sm3+-Hydroxyapatite

NASA Astrophysics Data System (ADS)

Lv, Yuguang; Shi, Qi; Jin, Yuling; Ren, Hengxin; Qin, Yushan; Wang, Bo; Song, Shanshan

2018-03-01

In this paper, the La3+-doped Sm3+ hydroxyapatite (La/Sm/HAP) complexes were prepared by a precipitation method. The sample was defined by IR spectra, fluorescence spectra and X ray diffraction analysis et al. The structure of complexes were discussed. The emission wavelength of heat treatment of Sm3+ do not change, but will affect the intensity of the peak Sm3+ luminescence properties and the occupy hydroxyapatite in the lattice Ca( II )and Ca( I ) loci with Sm3+ doped concentration and the proportion of the sintering temperature change and change: The nano hydroxyapatite complex of the La3+ doped samarium obtain the good fluorescence intensity, by La3+ doping content of Sm3+ were hydroxyapatite 6% (La3+, Sm3+ mole ratio) device. The complex of La3+ doped samarium HAP have Stable chemical property, fluorescence property and excellent biological activity. The ligand HAP absorbs energy or captures an electron-hole pair and then transfers it to the lanthanide ions. The catalytic activity influence of the La3+-doped Sm3+hydroxyapatite was discussed, the La/Sm/HAP had excellent antibacterial property, which used as potential biological antibacterial material.

Connecting qualitative observation and quantitative measurement for enhancing quantitative literacy in plant anatomy course

NASA Astrophysics Data System (ADS)

Nuraeni, E.; Rahmat, A.

2018-05-01

Forming of cognitive schemes of plant anatomy concepts is performed by processing of qualitative and quantitative data obtained from microscopic observations. To enhancing student’s quantitative literacy, strategy of plant anatomy course was modified by adding the task to analyze quantitative data produced by quantitative measurement of plant anatomy guided by material course. Participant in this study was 24 biology students and 35 biology education students. Quantitative Literacy test, complex thinking in plant anatomy test and questioner used to evaluate the course. Quantitative literacy capability data was collected by quantitative literacy test with the rubric from the Association of American Colleges and Universities, Complex thinking in plant anatomy by test according to Marzano and questioner. Quantitative literacy data are categorized according to modified Rhodes and Finley categories. The results showed that quantitative literacy of biology education students is better than biology students.

Wood preservatives and pressure-treated wood: considerations for historic-preservation projects

Treesearch

Ronald W. Anthony; Stan T. Lebow

2015-01-01

Wood, an abundant resource throughout most of the world, has been used as a building material for thousands of years. Many historic buildings have been built primarily of wood, and masonry and stone buildings generally have wood elements, both structural and architectural. As a biological material, wood is both remarkably complex and yet quite durable if well...

Biological and Clinical Aspects of Lanthanide Coordination Compounds

PubMed Central

Misra, Sudhindra N.; M., Indira Devi; Shukla, Ram S.

2004-01-01

The coordinating chemistry of lanthanides, relevant to the biological, biochemical and medical aspects, makes a significant contribution to understanding the basis of application of lanthanides, particularly in biological and medical systems. The importance of the applications of lanthanides, as an excellent diagnostic and prognostic probe in clinical diagnostics, and an anticancer material, is remarkably increasing. Lanthanide complexes based X-ray contrast imaging and lanthanide chelates based contrast enhancing agents for magnetic resonance imaging (MRI) are being excessively used in radiological analysis in our body systems. The most important property of the chelating agents, in lanthanide chelate complex, is its ability to alter the behaviour of lanthanide ion with which it binds in biological systems, and the chelation markedly modifies the biodistribution and excretion profile of the lanthanide ions. The chelating agents, especially aminopoly carboxylic acids, being hydrophilic, increase the proportion of their complex excreted from complexed lanthanide ion form biological systems. Lanthanide polyamino carboxylate-chelate complexes are used as contrast enhancing agents for Magnetic Resonance Imaging. Conjugation of antibodies and other tissue specific molecules to lanthanide chelates has led to a new type of specific MRI contrast agents and their conjugated MRI contrast agents with improved relaxivity, functioning in the body similar to drugs. Many specific features of contrast agent assisted MRI make it particularly effective for musculoskeletal and cerebrospinal imaging. Lanthanide-chelate contrast agents are effectively used in clinical diagnostic investigations involving cerebrospinal diseases and in evaluation of central nervous system. Chelated lanthanide complexes shift reagent aided 23Na NMR spectroscopic analysis is used in cellular, tissue and whole organ systems. PMID:18365075

Ultrafast electron microscopy in materials science, biology, and chemistry

NASA Astrophysics Data System (ADS)

King, Wayne E.; Campbell, Geoffrey H.; Frank, Alan; Reed, Bryan; Schmerge, John F.; Siwick, Bradley J.; Stuart, Brent C.; Weber, Peter M.

2005-06-01

The use of pump-probe experiments to study complex transient events has been an area of significant interest in materials science, biology, and chemistry. While the emphasis has been on laser pump with laser probe and laser pump with x-ray probe experiments, there is a significant and growing interest in using electrons as probes. Early experiments used electrons for gas-phase diffraction of photostimulated chemical reactions. More recently, scientists are beginning to explore phenomena in the solid state such as phase transformations, twinning, solid-state chemical reactions, radiation damage, and shock propagation. This review focuses on the emerging area of ultrafast electron microscopy (UEM), which comprises ultrafast electron diffraction (UED) and dynamic transmission electron microscopy (DTEM). The topics that are treated include the following: (1) The physics of electrons as an ultrafast probe. This encompasses the propagation dynamics of the electrons (space-charge effect, Child's law, Boersch effect) and extends to relativistic effects. (2) The anatomy of UED and DTEM instruments. This includes discussions of the photoactivated electron gun (also known as photogun or photoelectron gun) at conventional energies (60-200 keV) and extends to MeV beams generated by rf guns. Another critical aspect of the systems is the electron detector. Charge-coupled device cameras and microchannel-plate-based cameras are compared and contrasted. The effect of various physical phenomena on detective quantum efficiency is discussed. (3) Practical aspects of operation. This includes determination of time zero, measurement of pulse-length, and strategies for pulse compression. (4) Current and potential applications in materials science, biology, and chemistry. UEM has the potential to make a significant impact in future science and technology. Understanding of reaction pathways of complex transient phenomena in materials science, biology, and chemistry will provide fundamental knowledge for discovery-class science.

Plasmonic Interrogation of Biomimetic Systems for Enhanced Toxicity Assays

NASA Astrophysics Data System (ADS)

Hinman, Samuel Stuart

In light of their escalating exposure to possible environmental toxicants, there are many biological systems that need to be evaluated in a resource and time efficient manner. Understanding how toxicants behave in relation to their physicochemical properties and within complex biological media is especially important toward developing a stronger scientific foundation of these systems so that adequate regulatory decisions may be made. While there are many emerging methods available for the detection and characterization of these chemicals, nanotechnology has presented itself as a promising alternative toward creating more efficient assays. In particular, metallic nanoparticles and thin films exhibit unique optical properties that allow for highly sensitive and multiplexed studies to be performed. These plasmonic materials often preclude the use of molecular tags and labels, enabling direct characterizations and enhancing the throughput of biomolecular studies. However, their lack of specificity toward certain targets and potential toxicity has thus far precluded their widespread use in toxicity testing. The cell membrane, a natural signal transducer, represents one of the fundamental structures for biological recognition and communication. These interfaces principally function as a selective barrier to exogenous materials, including ions, signaling molecules, growth factors, and toxins; therefore, understanding interactions at membrane interfaces is a vital step in elucidating how biological responses are effected. Supported lipid bilayers, which may easily be tailored in composition and complexity, are ideal interfaces for coupling to plasmonic assays since they may be supported in close proximity to metallic nanoparticles and thin films, where measurements are most sensitive. This research will focus on the coupling of plasmonic materials and biomimetic interfaces to increase the sensitivity, efficiency, and throughput of conventional toxicity assays. The fabrication of new plasmonic materials for membrane-based assays is presented, as well as method developments in membrane array formation and opportunities for hyphenation with complementary analytical techniques.

Conferring biological activity to native spider silk: A biofunctionalized protein-based microfiber.

PubMed

Wu, Hsuan-Chen; Quan, David N; Tsao, Chen-Yu; Liu, Yi; Terrell, Jessica L; Luo, Xiaolong; Yang, Jen-Chang; Payne, Gregory F; Bentley, William E

2017-01-01

Spider silk is an extraordinary material with physical properties comparable to the best scaffolding/structural materials, and as a fiber it can be manipulated with ease into a variety of configurations. Our work here demonstrates that natural spider silk fibers can also be used to organize biological components on and in devices through rapid and simple means. Micron scale spider silk fibers (5-10 μm in diameter) were surface modified with a variety of biological entities engineered with pentaglutamine tags via microbial transglutaminase (mTG). Enzymes, enzyme pathways, antibodies, and fluorescent proteins were all assembled onto spider silk fibers using this biomolecular engineering/biofabrication process. Additionally, arrangement of biofunctionalized fiber should in of itself generate a secondary level of biomolecular organization. Toward this end, as proofs of principle, spatially defined arrangement of biofunctionalized spider silk fiber was shown to generate effects specific to silk position in two cases. In one instance, arrangement perpendicular to a flow produced selective head and neck carcinoma cell capture on silk with antibodies complexed to conjugated protein G. In a second scenario, asymmetric bacterial chemotaxis arose from asymmetric conjugation of enzymes to arranged silk. Overall, the biofabrication processes used here were rapid, required no complex chemistries, were biologically benign, and also the resulting engineered silk microfibers were flexible, readily manipulated and functionally active. Deployed here in microfluidic environments, biofunctional spider silk fiber provides a means to convey complex biological functions over a range of scales, further extending its potential as a biomaterial in biotechnological settings. Biotechnol. Bioeng. 2017;114: 83-95. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Roadmap on semiconductor-cell biointerfaces

NASA Astrophysics Data System (ADS)

Tian, Bozhi; Xu, Shuai; Rogers, John A.; Cestellos-Blanco, Stefano; Yang, Peidong; Carvalho-de-Souza, João L.; Bezanilla, Francisco; Liu, Jia; Bao, Zhenan; Hjort, Martin; Cao, Yuhong; Melosh, Nicholas; Lanzani, Guglielmo; Benfenati, Fabio; Galli, Giulia; Gygi, Francois; Kautz, Rylan; Gorodetsky, Alon A.; Kim, Samuel S.; Lu, Timothy K.; Anikeeva, Polina; Cifra, Michal; Krivosudský, Ondrej; Havelka, Daniel; Jiang, Yuanwen

2018-05-01

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world.

Recent advances, and unresolved issues, in the application of computational modelling to the prediction of the biological effects of nanomaterials

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

Winkler, David A., E-mail: dave.winkler@csiro.au

2016-05-15

Nanomaterials research is one of the fastest growing contemporary research areas. The unprecedented properties of these materials have meant that they are being incorporated into products very quickly. Regulatory agencies are concerned they cannot assess the potential hazards of these materials adequately, as data on the biological properties of nanomaterials are still relatively limited and expensive to acquire. Computational modelling methods have much to offer in helping understand the mechanisms by which toxicity may occur, and in predicting the likelihood of adverse biological impacts of materials not yet tested experimentally. This paper reviews the progress these methods, particularly those QSAR-based,more » have made in understanding and predicting potentially adverse biological effects of nanomaterials, and also the limitations and pitfalls of these methods. - Highlights: • Nanomaterials regulators need good information to make good decisions. • Nanomaterials and their interactions with biology are very complex. • Computational methods use existing data to predict properties of new nanomaterials. • Statistical, data driven modelling methods have been successfully applied to this task. • Much more must be learnt before robust toolkits will be widely usable by regulators.« less

A simple formula for the effective complex conductivity of periodic fibrous composites with interfacial impedance and applications to biological tissues

NASA Astrophysics Data System (ADS)

Bisegna, Paolo; Caselli, Federica

2008-06-01

This paper presents a simple analytical expression for the effective complex conductivity of a periodic hexagonal arrangement of conductive circular cylinders embedded in a conductive matrix, with interfaces exhibiting a capacitive impedance. This composite material may be regarded as an idealized model of a biological tissue comprising tubular cells, such as skeletal muscle. The asymptotic homogenization method is adopted, and the corresponding local problem is solved by resorting to Weierstrass elliptic functions. The effectiveness of the present analytical result is proved by convergence analysis and comparison with finite-element solutions and existing models.

Differential Multiscale Modeling of Chemically Complex Materials under Heavy Deformation: Biological, Bioinspired and Synthetic Hierarchical Materials

DTIC Science & Technology

2010-06-01

Buehler, “Meso- Origami : Folding Multilayer Graphene Sheets”, Applied Physics Letters, Vol. 95, paper #: 123121, 2009 D. Sen and M.J. Buehler, “Size and... geometry effects on flow stress in bioinspired de novo metal-matrix nanocomposites”, Advanced Engineering Materials, Vol. 11(10), pp. 774-781, 2009...behavior is recovered. Second, a subset of all geometries shows the inverse banana curve behavior. Interestingly, only 2% of all structures give the

Tissue Engineered Bone Using Polycaprolactone Scaffolds Made by Selective Laser Sintering

DTIC Science & Technology

2005-01-01

temporo - mandibular joint (TMJ) pose many challenges for bone tissue engineering. Adverse reactions to alloplastic, non- biological materials result in...producing a prototype mandibular condyle scaffold based on an actual pig condyle. INTRODUCTION Repair and reconstruction of complex joints such as the...computed tomography (CT) data with a designed porous architecture to build a complex scaffold that mimics a mandibular condyle. Results show that

A Fast Algorithm for Massively Parallel, Long-Term, Simulation of Complex Molecular Dynamics Systems

NASA Technical Reports Server (NTRS)

Jaramillo-Botero, Andres; Goddard, William A, III; Fijany, Amir

1997-01-01

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems,.

Dynamism & Detail

ERIC Educational Resources Information Center

Flannery, Maura C.

2004-01-01

New material discovered in the study of cell research is presented for the benefit of biology teachers. Huge amounts of data are being generated in fields like cellular dynamics, and it is felt that people's understanding of the cell is becoming much more complex and detailed.

New Directions in X-Ray Light Sources

ScienceCinema

Falcone, Roger

2017-12-09

July 15, 2008 Berkeley Lab lecture: Molecular movies of chemical reactions and material phase transformations need a strobe of x-rays, the penetrating light that reveals how atoms and molecules assemble in chemical and biological systems and complex materials. Roger Falcone, Director of the Advanced Light Source,will discuss a new generation of x ray sources that will enable a new science of atomic dynamics on ultrafast timescales.

Preprogramming Complex Hydrogel Responses using Enzymatic Reaction Networks.

PubMed

Postma, Sjoerd G J; Vialshin, Ilia N; Gerritsen, Casper Y; Bao, Min; Huck, Wilhelm T S

2017-02-06

The creation of adaptive matter is heavily inspired by biological systems. However, it remains challenging to design complex material responses that are governed by reaction networks, which lie at the heart of cellular complexity. The main reason for this slow progress is the lack of a general strategy to integrate reaction networks with materials. Herein we use a systematic approach to preprogram the response of a hydrogel to a trigger, in this case the enzyme trypsin, which activates a reaction network embedded within the hydrogel. A full characterization of all the kinetic rate constants in the system enabled the construction of a computational model, which predicted different hydrogel responses depending on the input concentration of the trigger. The results of the simulation are in good agreement with experimental findings. Our methodology can be used to design new, adaptive materials of which the properties are governed by reaction networks of arbitrary complexity. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

New Platforms for Characterization of Biological Material Failure and Resilience Properties

NASA Astrophysics Data System (ADS)

Brown, Katherine; Butler, Benjamin J.; Nguyen, Thuy-Tien N.; Sorry, David; Williams, Alun; Proud, William G.

2017-06-01

Obtaining information about the material responses of viscoelastic soft matter, such as polymers and foams has, required adaptation of techniques traditionally used with hard condensed matter. More recently it has been recognized that understanding the strain-rate behavior of natural and synthetic soft biological materials poses even greater challenges for materials research due their heterogeneous composition and structural complexity. Expanding fundamental knowledge about how these classes of biomaterials function under different loading regimes is of considerable interest in both fundamental and applied research. A comparative overview of methods, developed in our laboratory or elsewhere, for determining material responses of cells and soft tissues over a wide range of strain rates (quasi-static to blast loading) will be presented. Examples will illustrate how data are obtained for studying material responses of cells and tissues. Strengths and weaknesses of current approaches will be discussed, with particular emphasis on challenges associated with the development of realistic experimental and computational models for trauma and other disease indications.

Rheology of Soft Materials

NASA Astrophysics Data System (ADS)

Chen, Daniel T. N.; Wen, Qi; Janmey, Paul A.; Crocker, John C.; Yodh, Arjun G.

2010-04-01

Research on soft materials, including colloidal suspensions, glasses, pastes, emulsions, foams, polymer networks, liquid crystals, granular materials, and cells, has captured the interest of scientists and engineers in fields ranging from physics and chemical engineering to materials science and cell biology. Recent advances in rheological methods to probe mechanical responses of these complex media have been instrumental for producing new understanding of soft matter and for generating novel technological applications. This review surveys these technical developments and current work in the field, with partial aim to illustrate open questions for future research.

Biofabrication and biomaterials for urinary tract reconstruction

PubMed Central

Elsawy, Moustafa M; de Mel, Achala

2017-01-01

Reconstructive urologists are constantly facing diverse and complex pathologies that require structural and functional restoration of urinary organs. There is always a demand for a biocompatible material to repair or substitute the urinary tract instead of using patient’s autologous tissues with its associated morbidity. Biomimetic approaches are tissue-engineering tactics aiming to tailor the material physical and biological properties to behave physiologically similar to the urinary system. This review highlights the different strategies to mimic urinary tissues including modifications in structure, surface chemistry, and cellular response of a range of biological and synthetic materials. The article also outlines the measures to minimize infectious complications, which might lead to graft failure. Relevant experimental and preclinical studies are discussed, as well as promising biomimetic approaches such as three-dimensional bioprinting. PMID:28546955

Biomimetics: lessons from nature--an overview.

PubMed

Bhushan, Bharat

2009-04-28

Nature has developed materials, objects and processes that function from the macroscale to the nanoscale. These have gone through evolution over 3.8 Gyr. The emerging field of biomimetics allows one to mimic biology or nature to develop nanomaterials, nanodevices and processes. Properties of biological materials and surfaces result from a complex interplay between surface morphology and physical and chemical properties. Hierarchical structures with dimensions of features ranging from the macroscale to the nanoscale are extremely common in nature to provide properties of interest. Molecular-scale devices, superhydrophobicity, self-cleaning, drag reduction in fluid flow, energy conversion and conservation, high adhesion, reversible adhesion, aerodynamic lift, materials and fibres with high mechanical strength, biological self-assembly, antireflection, structural coloration, thermal insulation, self-healing and sensory-aid mechanisms are some of the examples found in nature that are of commercial interest. This paper provides a broad overview of the various objects and processes of interest found in nature and applications under development or available in the marketplace.

Checkpoints for vesicular traffic?

PubMed

Fiset, A; Faure, R

2001-01-01

During interphase the transport of material between different intracellular organelles requires accurate regulation of fusiogenic domains. Recent studies on hepatic endosomes indicated that compartmentalized Cdk2-cyclin E complexes act by braking fusion events. These Cdk2 complexes integrate tyrosine phosphorylation and dephosphorylation inputs, resulting in the control of the number of rounds of fusion at discrete domains. This leads to changes in the intracellular location of internalized receptors and ultimately their biological response.

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

DOE PAGES

Harrison, Jesse P.; Berry, David

2017-04-13

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

Vibrational spectroscopy for imaging single microbial cells in complex biological samples

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

Harrison, Jesse P.; Berry, David

Here, vibrational spectroscopy is increasingly used for the rapid and non-destructive imaging of environmental and medical samples. Both Raman and Fourier-transform infrared (FT-IR) imaging have been applied to obtain detailed information on the chemical composition of biological materials, ranging from single microbial cells to tissues. Due to its compatibility with methods such as stable isotope labeling for the monitoring of cellular activities, vibrational spectroscopy also holds considerable power as a tool in microbial ecology. Chemical imaging of undisturbed biological systems (such as live cells in their native habitats) presents unique challenges due to the physical and chemical complexity of themore » samples, potential for spectral interference, and frequent need for real-time measurements. This Mini Review provides a critical synthesis of recent applications of Raman and FT-IR spectroscopy for characterizing complex biological samples, with a focus on developments in single-cell imaging. We also discuss how new spectroscopic methods could be used to overcome current limitations of singlecell analyses. Given the inherent complementarity of Raman and FT-IR spectroscopic methods, we discuss how combining these approaches could enable us to obtain new insights into biological activities either in situ or under conditions that simulate selected properties of the natural environment.« less

Dynamic Self-Stiffening in Liquid Crystal Elastomers

PubMed Central

Agrawal, Aditya; Chipara, Alin C.; Shamoo, Yousif; Patra, Prabir K.; Carey, Brent J.; Ajayan, Pulickel M.; Chapman, Walter G.

2013-01-01

Biological tissues have the remarkable ability to remodel and repair in response to disease, injury, and mechanical stresses. Synthetic materials lack the complexity of biological tissues, and man-made materials which respond to external stresses through a permanent increase in stiffness are uncommon. Here, we report that polydomain nematic liquid crystal elastomers increase in stiffness by up to 90% when subjected to a low-amplitude (5%), repetitive (dynamic) compression. Elastomer stiffening is influenced by liquid crystal content, the presence of a nematic liquid crystal phase and the use of a dynamic as opposed to static deformation. Through rheological and X-ray diffraction measurements, stiffening can be attributed to a nematic director which rotates in response to dynamic compression. Stiffening under dynamic compression has not been previously observed in liquid crystal elastomers and may be useful for the development of self-healing materials or for the development of biocompatible, adaptive materials for tissue replacement. PMID:23612280

A Search for Signs of Life and Habitability on Europa

NASA Technical Reports Server (NTRS)

Fonda, Mark (Technical Monitor); McKay, Christoper P.; Eicken, H.; Neuer, S.; Sogin, M.; Waite, H.; Warmflash, D.

2003-01-01

Europa is a key target in the search for life beyond the Earth because of consistent evidence that below the icy surface there is liquid water. Future missions to Europa could confirm the presence and nature of the ocean and determine the thickness of the ice layer. Confirming the presence of an ocean and determining the habitability of Europa are key astrobiology science objectives. Nevertheless, the highest priority objective for astrobiology will be a search for life. How could a search for life be accomplished on a near-term mission given the thick ice cover? One answer may lie in the surface materials. If Europa has an ocean, and if that ocean contains life, and if water from the ocean is carried up to the surface, then signs of life may be contained in organic material on the surface. Organics that derive from biological processes (dead organisms) are distinct from organics derived from non-biological processes in several aspects. First, biology is selective and specific in its use of molecules. For example, Earth life uses 20 left-handed amino acids. Second, biology can leave characteristic isotopic patterns. Third, biology often produces large complex molecules in high concentrations, for example lipids. Organic material that has been on the surface of Europa for long periods of time would be reprocessed by the strong radiation field probably erasing any signature of biological origin. Evidence of life in the ocean may be found on the surface of Europa if regions of the surface contained relatively recent material carried up from the ocean through cracks in the icy lithosphere. But organic material that has been on the surface of Europa for long periods of time would be reprocessed by the strong radiation field probably erasing any signature of biological origin. Thus, the detailed analysis required may not be possible via remote sensing but direct sampling of the material below the radiation processed upper meter is probably required.

Bottom-up tissue engineering

PubMed Central

Elbert, Donald L.

2011-01-01

Recapitulating the elegant structures formed during development is an extreme synthetic and biological challenge. Great progress has been made in developing materials to support transplanted cells, yet the complexity of tissues is far beyond that found in even the most advanced scaffolds. Self-assembly is a motif used in development and a route for the production of complex materials. Self-assembly of peptides, proteins and other molecules at the nanoscale is promising, but in addition, intriguing ideas are emerging for self-assembly of micron-scale structures. In this brief review, very recent advances in the assembly of micron-scale cell aggregates and microgels will be described and discussed. PMID:21524904

Semiconductor nanowires: A platform for nanoscience and nanotechnology

PubMed Central

Lieber, Charles M.

2012-01-01

Advances in nanoscience and nanotechnology critically depend on the development of nanostructures whose properties are controlled during synthesis. We focus on this critical concept using semiconductor nanowires, which provide the capability through design and rational synthesis to realize unprecedented structural and functional complexity in building blocks as a platform material. First, a brief review of the synthesis of complex modulated nanowires in which rational design and synthesis can be used to precisely control composition, structure, and, most recently, structural topology is discussed. Second, the unique functional characteristics emerging from our exquisite control of nanowire materials are illustrated using several selected examples from nanoelectronics and nano-enabled energy. Finally, the remarkable power of nanowire building blocks is further highlighted through their capability to create unprecedented, active electronic interfaces with biological systems. Recent work pushing the limits of both multiplexed extracellular recording at the single-cell level and the first examples of intracellular recording is described, as well as the prospects for truly blurring the distinction between nonliving nanoelectronic and living biological systems. PMID:22707850

Tagging and purifying proteins to teach molecular biology and advanced biochemistry.

PubMed

Roecklein-Canfield, Jennifer A; Lopilato, Jane

2004-11-01

Two distinct courses, "Molecular Biology" taught by the Biology Department and "Advanced Biochemistry" taught by the Chemistry Department, complement each other and, when taught in a coordinated and integrated way, can enhance student learning and understanding of complex material. "Molecular Biology" is a comprehensive lecture-based course with a 3-h laboratory once a week, while "Advanced Biochemistry" is a completely laboratory-based course with lecture fully integrated around independent student projects. Both courses emphasize and utilize cutting-edge technology. Teaching across departmental boundaries allows students access to faculty expertise and techniques rarely used at the undergraduate level, namely the tagging of proteins and their use in protein purification. Copyright © 2004 International Union of Biochemistry and Molecular Biology, Inc.

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges.

PubMed

Thakur, Indu Shekhar; Kumar, Manish; Varjani, Sunita J; Wu, Yonghong; Gnansounou, Edgard; Ravindran, Sindhu

2018-05-01

To meet the CO 2 emission reduction targets, carbon dioxide capture and utilization (CCU) comes as an evolve technology. CCU concept is turning into a feedstock and technologies have been developed for transformation of CO 2 into useful organic products. At industrial scale, utilization of CO 2 as raw material is not much significant as compare to its abundance. Mechanisms in nature have evolved for carbon concentration, fixation and utilization. Assimilation and subsequent conversion of CO 2 into complex molecules are performed by the photosynthetic and chemolithotrophic organisms. In the last three decades, substantial research is carry out to discover chemical and biological conversion of CO 2 in various synthetic and biological materials, such as carboxylic acids, esters, lactones, polymer biodiesel, bio-plastics, bio-alcohols, exopolysaccharides. This review presents an over view of catalytic transformation of CO 2 into biofuels and biomaterials by chemical and biological methods. Copyright © 2018 Elsevier Ltd. All rights reserved.

Synthetic biology engineering of biofilms as nanomaterials factories.

PubMed

Nguyen, Peter Q

2017-06-15

Bottom-up fabrication of nanoscale materials has been a significant focus in materials science for expanding our technological frontiers. This assembly concept, however, is old news to biology - all living organisms fabricate themselves using bottom-up principles through a vast self-organizing system of incredibly complex biomolecules, a marvelous dynamic that we are still attempting to unravel. Can we use what we have gleaned from biology thus far to illuminate alternative strategies for designer nanomaterial manufacturing? In the present review article, new synthetic biology efforts toward using bacterial biofilms as platforms for the synthesis and secretion of programmable nanomaterials are described. Particular focus is given to self-assembling functional amyloids found in bacterial biofilms as re-engineerable modular nanomolecular components. Potential applications and existing challenges for this technology are also explored. This novel approach for repurposing biofilm systems will enable future technologies for using engineered living systems to grow artificial nanomaterials. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Exploring the significance of structural hierarchy in material systems-A review

NASA Astrophysics Data System (ADS)

Pan, Ning

2014-06-01

Structural hierarchy and heterogeneity are inherent features in biological materials, but their significance in affecting the system behaviors is yet to be fully understood. In Sec. I, this article first identifies the major characteristics that manifest, or are resulted from, such hierarchy and heterogeneity in materials. Then in Sec. II, it presents several typical natural material systems including wood, bone, and others from animals to illustrate the proposed views. The paper also discusses a man-made smart material, textiles, to demonstrate that textiles are hierarchal, multifunctional, highly complex, and arguably the engineered material closest on a par with biological materials in complexity, and, more importantly, we can still learn quite a few new things from them in development of novel materials. In Sec. III, the paper summarizes several general approaches in developing a hierarchal material system at various scales, including structure thinning and splitting, laminating and layering, spatial and angular orientation, heterogenization and hybridization, and analyzes the advantages associated with them. It also stresses the adverse consequences once the existing structural hierarchy breaks down due to various mutations in biological systems. It discusses, in particular, the influences of moisture and air on material properties, given the near ubiquitousness of both air and water in materials. It next deals with in Sec. IV, some theoretical issues in material research including packing and ordering, the bi-modular mechanics, the behavior non-affinities due to disparity in hierarchal levels, the importance of system dimensionality in a hierarchal material system, and more philosophically, the issues of Nature's wisdom versus Intelligent Design. Section V then offers some concluding remarks, including a recap of the major issues covered in this article, and some general conclusions derived from the analyses and discussions. The main purpose of this paper is to make an effort to explore, identify, derive, or theorize some generic principles based on the existing results, not to offer another comprehensive review of current research activities in the fields for that there already exist some excellent ones. This paper examines the related topics with several approaches to not only reveal the underlying geometrical and physical mechanisms but also to emphasize the ways in which such mechanisms may be applied to developing engineered material systems with novel properties.

Methods of biological dosimetry employing chromosome-specific staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

2000-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Morphogenesis and mechanostabilization of complex natural and 3D printed shapes

PubMed Central

Tiwary, Chandra Sekhar; Kishore, Sharan; Sarkar, Suman; Mahapatra, Debiprosad Roy; Ajayan, Pulickel M.; Chattopadhyay, Kamanio

2015-01-01

The natural selection and the evolutionary optimization of complex shapes in nature are closely related to their functions. Mechanostabilization of shape of biological structure via morphogenesis has several beautiful examples. With the help of simple mechanics-based modeling and experiments, we show an important causality between natural shape selection as evolutionary outcome and the mechanostabilization of seashells. The effect of biological growth on the mechanostabilization process is identified with examples of two natural shapes of seashells, one having a diametrically converging localization of stresses and the other having a helicoidally concentric localization of stresses. We demonstrate how the evolved shape enables predictable protection of soft body parts of the species. The effect of bioavailability of natural material is found to be a secondary factor compared to shape selectivity, where material microstructure only acts as a constraint to evolutionary optimization. This is confirmed by comparing the mechanostabilization behavior of three-dimensionally printed synthetic polymer structural shapes with that of natural seashells consisting of ceramic and protein. This study also highlights interesting possibilities in achieving a new design of structures made of ordinary materials which have bio-inspired optimization objectives. PMID:26601170

The complexity of silk under the spotlight of synthetic biology.

PubMed

Vollrath, Fritz

2016-08-15

For centuries silkworm filaments have been the focus of R&D innovation centred on textile manufacture with high added value. Most recently, silk research has focused on more fundamental issues concerning bio-polymer structure-property-function relationships. This essay outlines the complexity and fundamentals of silk spinning, and presents arguments for establishing this substance as an interesting and important subject at the interface of systems biology (discovery) and synthetic biology (translation). It is argued that silk is a generic class of materials where each type of silk presents a different embodiment of emergent properties that combine genetically determined (anticipatory) and environmentally responsive components. In spiders' webs the various silks have evolved to form the interactive components of an intricate fabric that provides an extended phenotype to the spider's body morphology. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

The Effect of Salt on the Complex Coacervation of Vinyl Polyelectrolytes

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

Perry, Sarah; Li, Yue; Priftis, Dimitrios

2014-06-01

Complex coacervation is an electrostatically-driven phase separation phenomenon that is utilized in a wide range of everyday applications and is of great interest for the creation of self-assembled materials. Here, we utilized turbidity to characterize the effect of salt type on coacervate formation using two vinyl polyelectrolytes, poly(acrylic acid sodium salt) (pAA) and poly(allylamine hydrochloride) (pAH), as simple models for industrial and biological coacervates. We confirmed the dominant role of salt valence on the extent of coacervate formation, while demonstrating the presence of significant secondary effects, which can be described by Hofmeister-like behavior. These results revealed the importance of ion-specificmore » interactions, which are crucial for the informed design of coacervate-based materials for use in complex ionic environments, and can enable more detailed theoretical investigations on the role of subtle electrostatic and thermodynamic effects in complex coacervation.« less

Modeling of biological intelligence for SCM system optimization.

PubMed

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms.

Modeling of Biological Intelligence for SCM System Optimization

PubMed Central

Chen, Shengyong; Zheng, Yujun; Cattani, Carlo; Wang, Wanliang

2012-01-01

This article summarizes some methods from biological intelligence for modeling and optimization of supply chain management (SCM) systems, including genetic algorithms, evolutionary programming, differential evolution, swarm intelligence, artificial immune, and other biological intelligence related methods. An SCM system is adaptive, dynamic, open self-organizing, which is maintained by flows of information, materials, goods, funds, and energy. Traditional methods for modeling and optimizing complex SCM systems require huge amounts of computing resources, and biological intelligence-based solutions can often provide valuable alternatives for efficiently solving problems. The paper summarizes the recent related methods for the design and optimization of SCM systems, which covers the most widely used genetic algorithms and other evolutionary algorithms. PMID:22162724

Soils, peatlands, and biomonitoring

Treesearch

James Doolittle

2009-01-01

Soils are three-dimensional (3D) natural bodies conSlStmg of unconsolidated mineral and organic materials that form a continuous blanket over most of the earth's land sUlface. At all sca les of measurements, soils are exceedingly complex and variable in biological, chemical, physical, mineralogical, and electromagnetic properties....

Herbal medicine, radical scavenger and metal detoxification: bioinorganic, complexity and nano science perspectives

NASA Astrophysics Data System (ADS)

Sumitro, Sutiman B.; Alit, Sukmaningsih

2018-03-01

Developing Complexity Science and Nano Biological perspective giving the ideas of interfacing between modern physical and biological sciences for more comprehensive understanding of life. The study of bioinorganic is a trans-disciplinary, and will initiate the way to more comprehensive and better understanding life. We can talk about energy generation, motive forces and energy transfer at the level of macromolecules. We can then develop understanding biological behavior on nano size biological materials and its higher order using modern physics as well as thermodynamic law. This is a necessity to ovoid partial understanding of life that are not match with holism. In animal tissues, the accumulation or overwhelmed production of free radicals can damage cells and are believed to accelerate the progression of cancer, cardiovascular disease, and age-related diseases. Thus a guarded balance of radical species is imperative. Edward Kosower [1] proposed an idea of biradical in an aromatic organic compounds. Each of which having unpaired electrons. The magnetic force of this compound used for making agregation based on their magnetic characters. Bioinorganic low molecular weight complex compounds composing herbal medicine can bind toxic metals. This low molecular weight complex molecules then easily excerted the metals from the body, removing them from their either intracellular or extracellular existences. This bioinorganic chelation potential is now inspiring a new therapeutic strategies.

Hierarchical nanostructures for functional materials.

PubMed

Qin, Zhao; Buehler, Markus J

2018-07-13

Naturally occurring biomaterials often have amazing functions, such as mechanical, thermal, electromagnetic, biological, optical and acoustic. These superior performances are often due to their hierarchical organizations of natural materials, starting from the nanoscopic scale and extending all the way to the macroscopic level. This topical issue features articles dedicated to understanding, designing and characterizing complex de novo hierarchical materials for a variety of applications. This research area is quickly evolving, and we hope that future work will drive the rational designs of innovative functional materials and generate deep impacts to broad engineering fields that address major societal challenges and needs.

Hierarchical nanostructures for functional materials

NASA Astrophysics Data System (ADS)

Qin, Zhao; Buehler, Markus J.

2018-07-01

Naturally occurring biomaterials often have amazing functions, such as mechanical, thermal, electromagnetic, biological, optical and acoustic. These superior performances are often due to their hierarchical organizations of natural materials, starting from the nanoscopic scale and extending all the way to the macroscopic level. This topical issue features articles dedicated to understanding, designing and characterizing complex de novo hierarchical materials for a variety of applications. This research area is quickly evolving, and we hope that future work will drive the rational designs of innovative functional materials and generate deep impacts to broad engineering fields that address major societal challenges and needs.

Bio-Inspired Metal-Coordination Dynamics: A Unique Tool for Engineering Soft Matter Mechanics

NASA Astrophysics Data System (ADS)

Holten-Andersen, Niels

Growing evidence supports a critical role of metal-coordination in soft biological material properties such as self-healing, underwater adhesion and autonomous wound plugging. Using bio-inspired metal-binding polymers, initial efforts to mimic these properties with metal-coordination crosslinked polymer materials have shown promise. In addition, with polymer network mechanics strongly coupled to coordinate crosslink dynamics material properties can be easily tuned from visco-elastic fluids to solids. Given their exploitation in desirable material applications in Nature, bio-inspired metal-coordinate complex crosslinking provides an opportunity to further advance synthetic polymer materials design. Early lessons from this pursuit are presented.

Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants

PubMed Central

Regan, Kelly; Wang, Kanix; Doughty, Emily; Li, Haiquan; Li, Jianrong; Lee, Younghee; Kann, Maricel G

2012-01-01

Objective Although trait-associated genes identified as complex versus single-gene inheritance differ substantially in odds ratio, the authors nonetheless posit that their mechanistic concordance can reveal fundamental properties of the genetic architecture, allowing the automated interpretation of unique polymorphisms within a personal genome. Materials and methods An analytical method, SPADE-gen, spanning three biological scales was developed to demonstrate the mechanistic concordance between Mendelian and complex inheritance of Alzheimer's disease (AD) genes: biological functions (BP), protein interaction modeling, and protein domain implicated in the disease-associated polymorphism. Results Among Gene Ontology (GO) biological processes (BP) enriched at a false detection rate <5% in 15 AD genes of Mendelian inheritance (Online Mendelian Inheritance in Man) and independently in those of complex inheritance (25 host genes of intragenic AD single-nucleotide polymorphisms confirmed in genome-wide association studies), 16 overlapped (empirical p=0.007) and 45 were similar (empirical p<0.009; information theory). SPAN network modeling extended the canonical pathway of AD (KEGG) with 26 new protein interactions (empirical p<0.0001). Discussion The study prioritized new AD-associated biological mechanisms and focused the analysis on previously unreported interactions associated with the biological processes of polymorphisms that affect specific protein domains within characterized AD genes and their direct interactors using (1) concordant GO-BP and (2) domain interactions within STRING protein–protein interactions corresponding to the genomic location of the AD polymorphism (eg, EPHA1, APOE, and CD2AP). Conclusion These results are in line with unique-event polymorphism theory, indicating how disease-associated polymorphisms of Mendelian or complex inheritance relate genetically to those observed as ‘unique personal variants’. They also provide insight for identifying novel targets, for repositioning drugs, and for personal therapeutics. PMID:22319180

Preparation of Degradable Biological Carrier With LCC and its Application in Culture of Hepatocytes

NASA Astrophysics Data System (ADS)

Zhao, H. K.; Chen, X. K.; Wu, H. F.; Li, J. L.; Xie, Y. M.

2018-05-01

The purpose of this article is to extract lignin-carbohydrate complexes (LCC) with poplar as raw material, which was used to prepare bio-carrier by freeze-drying method. The chemical properties and morphological of LCC porous biological carriers were analyzed by GPC, FT-IR, scanning electron microscopy (SEM) and optical microscopy. The FT-IR spectrum results indicated that LCC which are composed of lignin and polysaccharide, with a typical LCC structure. Galactose have a specific ability to recognize liver cells owing to the presence of receptors on hepatocytes. Cell counting results showed that the cells increases fastest while the proliferation rate of the liver cell in LCC is obviously higher than that of control group. These results indicated that poplar LCC is very biocompatible, in which it might be a great potential biological carrier material for human hepatocyte culture.

Matrix Assisted Ionization Vacuum (MAIV), a New Ionization Method for Biological Materials Analysis Using Mass Spectrometry*

PubMed Central

Inutan, Ellen D.; Trimpin, Sarah

2013-01-01

The introduction of electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) for the mass spectrometric analysis of peptides and proteins had a dramatic impact on biological science. We now report that a wide variety of compounds, including peptides, proteins, and protein complexes, are transported directly from a solid-state small molecule matrix to gas-phase ions when placed into the vacuum of a mass spectrometer without the use of high voltage, a laser, or added heat. This ionization process produces ions having charge states similar to ESI, making the method applicable for high performance mass spectrometers designed for atmospheric pressure ionization. We demonstrate highly sensitive ionization using intermediate pressure MALDI and modified ESI sources. This matrix and vacuum assisted soft ionization method is suitable for the direct surface analysis of biological materials, including tissue, via mass spectrometry. PMID:23242551

Nanomaterial interactions with biomembranes: Bridging the gap between soft matter models and biological context.

PubMed

Werner, Marco; Auth, Thorsten; Beales, Paul A; Fleury, Jean Baptiste; Höök, Fredrik; Kress, Holger; Van Lehn, Reid C; Müller, Marcus; Petrov, Eugene P; Sarkisov, Lev; Sommer, Jens-Uwe; Baulin, Vladimir A

2018-04-03

Synthetic polymers, nanoparticles, and carbon-based materials have great potential in applications including drug delivery, gene transfection, in vitro and in vivo imaging, and the alteration of biological function. Nature and humans use different design strategies to create nanomaterials: biological objects have emerged from billions of years of evolution and from adaptation to their environment resulting in high levels of structural complexity; in contrast, synthetic nanomaterials result from minimalistic but controlled design options limited by the authors' current understanding of the biological world. This conceptual mismatch makes it challenging to create synthetic nanomaterials that possess desired functions in biological media. In many biologically relevant applications, nanomaterials must enter the cell interior to perform their functions. An essential transport barrier is the cell-protecting plasma membrane and hence the understanding of its interaction with nanomaterials is a fundamental task in biotechnology. The authors present open questions in the field of nanomaterial interactions with biological membranes, including: how physical mechanisms and molecular forces acting at the nanoscale restrict or inspire design options; which levels of complexity to include next in computational and experimental models to describe how nanomaterials cross barriers via passive or active processes; and how the biological media and protein corona interfere with nanomaterial functionality. In this Perspective, the authors address these questions with the aim of offering guidelines for the development of next-generation nanomaterials that function in biological media.

Physical Principles of Development of the State Standard of Biological Cell Polarizability

NASA Astrophysics Data System (ADS)

Shuvalov, G. V.; Generalov, K. V.; Generalov, V. M.; Kruchinina, M. V.; Koptev, E. S.; Minin, O. V.; Minin, I. V.

2018-03-01

A new state standard of biological cell polarizability based on micron-size latex particles has been developed. As a standard material, it is suggested to use polystyrene. Values of the polarizability calculated for erythrocytes and values of the polarizability of micron-size spherical latex particles measured with measuring-computing complexes agree within the limits of satisfactory relative error. The Standard allows one the unit of polarizability measurements [m3] to be assigned to cells and erythrocytes for the needs of medicine.

Biology of Nanobots

NASA Astrophysics Data System (ADS)

Duan, Wentao; Pavlick, Ryan; Sen, Ayusman

2013-12-01

One of the more interesting recent discoveries has been the ability to design nano/microbots which catalytically harness the chemical energy in their environment to move autonomously. Their potential applications include delivery of materials, self-assembly of superstructures, and roving sensors. One emergent area of research is the study of their collective behavior and how they emulate living systems. The aim of this chapter is to describe the "biology" of nanobots, summarizing the fundamentals physics behind their motion and how the bots interact with each other to initiate complex emergent behavior.

Molecular biomimetics: GEPI-based biological routes to technology.

PubMed

Tamerler, Candan; Khatayevich, Dmitriy; Gungormus, Mustafa; Kacar, Turgay; Oren, E Emre; Hnilova, Marketa; Sarikaya, Mehmet

2010-01-01

In nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single-celled to the most complex multicellular species. Biomolecule-material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe-target interactions, e.g., ligand-receptor, antigen-antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide-material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self-assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide-sequence similarity analysis is developed to design higher generation function-specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide-range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we describe lessons from biology with examples of protein-mediated functional biological materials, explain how novel peptides can be designed with specific affinity to inorganic solids using evolutionary engineering approaches, give examples of their potential utilizations in technology and medicine, and, finally, provide a summary of challenges and future prospects. (c) 2010 Wiley Periodicals, Inc.

Insights to regenerate materials: learning from nature

NASA Astrophysics Data System (ADS)

García-Aznar, J. M.; Valero, C.; Gómez-Benito, M. J.; Javierre, E.

2016-08-01

Self-healing materials, both biological and engineered, integrate the ability to repair themselves and recover their functionality using the resources inherently available to them. Although significant advances have been made, in recent years, for the design of different concepts of self-healing materials, this work aims to provide some insights into how living materials are able to regenerate or heal when a fracture or injury occurs. The main sensors that regulate this adaptive and regenerative behavior are the cells. These are able to sense the mechanical alterations in their surroundings and regulate their activity in order to remove dead tissue and/or create new tissue. Therefore, understanding how cells are able to regenerate tissues under complex and multiphysics conditions can define the biomimetics guidelines to heal through inert or traditional engineering materials. In this work, we present a combination of experiments and different kinds of multiscale and multiphysics models in order to understand how mechanics regulate some mechanisms at cell and tissue level. This combination of results aims to gain insight into the development of novel strategies for self-healing materials, mimicking the behavior induced by cells and biological tissues.

Using eDNA to estimate distribution of fish species in a complex river system (presentation)

EPA Science Inventory

Environmental DNA (eDNA) analysis of biological material shed by aquatic organisms is a noninvasive genetic tool that can improve efficiency and reduce costs associated with species detection in aquatic systems. eDNA methods are widely used to assess presence/absence of a target ...

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

Holm, Christian; Gompper, Gerhard; Dill, Ken A.

This special issue highlights new developments in theory and coarse-graining in biological and synthetic macromolecules and membranes. Such approaches give unique insights into the principles and design of the structures, dynamics, and assembly processes of these complex fluids and soft materials, where the length and time scales are often prohibitively long for fully atomistic modeling.

Analysis of volatile metabolites in biological fluids as indicators of prodromal disease condition

NASA Technical Reports Server (NTRS)

Zlatkis, A.

1982-01-01

The volatile profile cannot be defined as a single class of substances, rather it is a broad spectrum of materials of different polarities characterized by having a boiling-point in the low to medium range (up to approximately 300 C) and the fact that the compounds are suitable for gas chromatography without derivatization. The organic volatile profiles are very complex mixtures of metabolic byproducts, intermediates, and terminal products of enzymatic degradations composed mainly of alcohols, ketones, aldehydes, pyrazines, sulfides, isothiocyanates, pyrroles, and furans. The concentration of organic volatiles in biological fluids covers a wide range with many important components present at trace levels. The complexity of the organic volatile fraction requires the use of capillary columns for their separation.

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

Yusufoglu, Yusuf

Nature offers many exciting ideas and inspiration for the development of new materials and processes. The toughness of spider silk, the strength and lightweight of bone, and the adhesion abilities of the gecko's feet are some of the many examples of highperformance natural materials, which have attracted the interest of scientist to duplicate their properties in man-made materials. Materials found in nature combine many inspiring properties such as miniaturization, sophistication, hierarchical organization, hybridization, and adaptability. In all biological systems, whether very basic or highly complex, nature provides a multiplicity of materials, architectures, systems and functions. Generally, the architectural configurations andmore » material characteristics are the important features that have been duplicated from nature for building synthetic structural composites.« less

Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels

PubMed Central

Hinton, Thomas J.; Jallerat, Quentin; Palchesko, Rachelle N.; Park, Joon Hyung; Grodzicki, Martin S.; Shue, Hao-Jan; Ramadan, Mohamed H.; Hudson, Andrew R.; Feinberg, Adam W.

2015-01-01

We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and fibrin. Computer-aided design models of 3D optical, computed tomography, and magnetic resonance imaging data were 3D printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures. PMID:26601312

Towards XNA nanotechnology: new materials from synthetic genetic polymers

PubMed Central

Pinheiro, Vitor B.; Holliger, Philipp

2014-01-01

Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry. PMID:24745974

A simple and low-cost chip bonding solution for high pressure, high temperature and biological applications.

PubMed

Serra, M; Pereiro, I; Yamada, A; Viovy, J-L; Descroix, S; Ferraro, D

2017-02-14

The sealing of microfluidic devices remains a complex and time-consuming process requiring specific equipment and protocols: a universal method is thus highly desirable. We propose here the use of a commercially available sealing tape as a robust, versatile, reversible solution, compatible with cell and molecular biology protocols, and requiring only the application of manually achievable pressures. The performance of the seal was tested with regards to the most commonly used chip materials. For most materials, the bonding resisted 5 bars at room temperature and 1 bar at 95 °C. This method should find numerous uses, ranging from fast prototyping in the laboratory to implementation in low technology environments or industrial production.

A direct biocombinatorial strategy toward next generation, mussel-glue inspired saltwater adhesives.

PubMed

Wilke, Patrick; Helfricht, Nicolas; Mark, Andreas; Papastavrou, Georg; Faivre, Damien; Börner, Hans G

2014-09-10

Biological materials exhibit remarkable, purpose-adapted properties that provide a source of inspiration for designing new materials to meet the requirements of future applications. For instance, marine mussels are able to attach to a broad spectrum of hard surfaces under hostile conditions. Controlling wet-adhesion of synthetic macromolecules by analogue processes promises to strongly impact materials sciences by offering advanced coatings, adhesives, and glues. The de novo design of macromolecules to mimic complex aspects of mussel adhesion still constitutes a challenge. Phage display allows material scientists to design specifically interacting molecules with tailored affinity to material surfaces. Here, we report on the integration of enzymatic processing steps into phage display biopanning to expand the biocombinatorial procedure and enable the direct selection of enzymatically activable peptide adhesion domains. Adsorption isotherms and single molecule force spectroscopy show that those de novo peptides mimic complex aspects of bioadhesion, such as enzymatic activation (by tyrosinase), the switchability from weak to strong binders, and adsorption under hostile saltwater conditions. Furthermore, peptide-poly(ethylene oxide) conjugates are synthesized to generate protective coatings, which possess anti-fouling properties and suppress irreversible interactions with blood-plasma protein cocktails. The extended phage display procedure provides a generic way to non-natural peptide adhesion domains, which not only mimic nature but also improve biological sequence sections extractable from mussel-glue proteins. The de novo peptides manage to combine several tasks in a minimal 12-mer sequence and thus pave the way to overcome major challenges of technical wet glues.

Fractals in biology and medicine

NASA Technical Reports Server (NTRS)

Havlin, S.; Buldyrev, S. V.; Goldberger, A. L.; Mantegna, R. N.; Ossadnik, S. M.; Peng, C. K.; Simons, M.; Stanley, H. E.

1995-01-01

Our purpose is to describe some recent progress in applying fractal concepts to systems of relevance to biology and medicine. We review several biological systems characterized by fractal geometry, with a particular focus on the long-range power-law correlations found recently in DNA sequences containing noncoding material. Furthermore, we discuss the finding that the exponent alpha quantifying these long-range correlations ("fractal complexity") is smaller for coding than for noncoding sequences. We also discuss the application of fractal scaling analysis to the dynamics of heartbeat regulation, and report the recent finding that the normal heart is characterized by long-range "anticorrelations" which are absent in the diseased heart.

Integrated Micro/nanoengineered Functional Biomaterials for Cell Mechanics and Mechanobiology: A Materials Perspective

PubMed Central

Shao, Yue

2014-01-01

The rapid development of micro/nanoengineered functional biomaterials in the last two decades has empowered materials scientists and bioengineers to precisely control different aspects of the in vitro cell microenvironment. Following a philosophy of reductionism, many studies using synthetic functional biomaterials have revealed instructive roles of individual extracellular biophysical and biochemical cues in regulating cellular behaviors. Development of integrated micro/nanoengineered functional biomaterials to study complex and emergent biological phenomena has also thrived rapidly in recent years, revealing adaptive and integrated cellular behaviors closely relevant to human physiological and pathological conditions. Working at the interface between materials science and engineering, biology, and medicine, we are now at the beginning of a great exploration using micro/nanoengineered functional biomaterials for both fundamental biology study and clinical and biomedical applications such as regenerative medicine and drug screening. In this review, we present an overview of state of the art micro/nanoengineered functional biomaterials that can control precisely individual aspects of cell-microenvironment interactions and highlight them as well-controlled platforms for mechanistic studies of mechano-sensitive and -responsive cellular behaviors and integrative biology research. We also discuss the recent exciting trend where micro/nanoengineered biomaterials are integrated into miniaturized biological and biomimetic systems for dynamic multiparametric microenvironmental control of emergent and integrated cellular behaviors. The impact of integrated micro/nanoengineered functional biomaterials for future in vitro studies of regenerative medicine, cell biology, as well as human development and disease models are discussed. PMID:24339188

Systems Biology of Industrial Microorganisms

NASA Astrophysics Data System (ADS)

Papini, Marta; Salazar, Margarita; Nielsen, Jens

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

Systems biology of industrial microorganisms.

PubMed

Papini, Marta; Salazar, Margarita; Nielsen, Jens

2010-01-01

The field of industrial biotechnology is expanding rapidly as the chemical industry is looking towards more sustainable production of chemicals that can be used as fuels or building blocks for production of solvents and materials. In connection with the development of sustainable bioprocesses, it is a major challenge to design and develop efficient cell factories that can ensure cost efficient conversion of the raw material into the chemical of interest. This is achieved through metabolic engineering, where the metabolism of the cell factory is engineered such that there is an efficient conversion of sugars, the typical raw materials in the fermentation industry, into the desired product. However, engineering of cellular metabolism is often challenging due to the complex regulation that has evolved in connection with adaptation of the different microorganisms to their ecological niches. In order to map these regulatory structures and further de-regulate them, as well as identify ingenious metabolic engineering strategies that full-fill mass balance constraints, tools from systems biology can be applied. This involves both high-throughput analysis tools like transcriptome, proteome and metabolome analysis, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies. It is in fact expected that systems biology may substantially improve the process of cell factory development, and we therefore propose the term Industrial Systems Biology for how systems biology will enhance the development of industrial biotechnology for sustainable chemical production.

A review on powder-based additive manufacturing for tissue engineering: selective laser sintering and inkjet 3D printing

PubMed Central

Shirazi, Seyed Farid Seyed; Gharehkhani, Samira; Mehrali, Mehdi; Yarmand, Hooman; Metselaar, Hendrik Simon Cornelis; Adib Kadri, Nahrizul; Osman, Noor Azuan Abu

2015-01-01

Since most starting materials for tissue engineering are in powder form, using powder-based additive manufacturing methods is attractive and practical. The principal point of employing additive manufacturing (AM) systems is to fabricate parts with arbitrary geometrical complexity with relatively minimal tooling cost and time. Selective laser sintering (SLS) and inkjet 3D printing (3DP) are two powerful and versatile AM techniques which are applicable to powder-based material systems. Hence, the latest state of knowledge available on the use of AM powder-based techniques in tissue engineering and their effect on mechanical and biological properties of fabricated tissues and scaffolds must be updated. Determining the effective setup of parameters, developing improved biocompatible/bioactive materials, and improving the mechanical/biological properties of laser sintered and 3D printed tissues are the three main concerns which have been investigated in this article. PMID:27877783

Zonal Articular Cartilage Possesses Complex Mechanical Behavior Spanning Multiple Length Scales: Dependence on Chemical Heterogeneity, Anisotropy, and Microstructure

NASA Astrophysics Data System (ADS)

Wahlquist, Joseph A.

This work focused on characterizing the mechanical behavior of biological material in physiologically relevant conditions and at sub millimeter length scales. Elucidating the time, length scale, and directionally dependent mechanical behavior of cartilage and other biological materials is critical to adequately recapitulate native mechanosensory cues for cells, create computational models that mimic native tissue behavior, and assess disease progression. This work focused on three broad aspects of characterizing the mechanical behavior of articular cartilage. First, we sought to reveal the causes of time-dependent deformation and variation of mechanical properties with distance from the articular surface. Second, we investigated size dependence of mechanical properties. Finally, we examined material anisotropy of both the calcified and uncalcified tissues of the osteochondral interface. This research provides insight into how articular cartilage serves to support physiologic loads and simultaneously sustain chondrocyte viability.

3D-printing and mechanics of bio-inspired articulated and multi-material structures.

PubMed

Porter, Michael M; Ravikumar, Nakul; Barthelat, Francois; Martini, Roberto

2017-09-01

3D-printing technologies allow researchers to build simplified physical models of complex biological systems to more easily investigate their mechanics. In recent years, a number of 3D-printed structures inspired by the dermal armors of various fishes have been developed to study their multiple mechanical functionalities, including flexible protection, improved hydrodynamics, body support, or tail prehensility. Natural fish armors are generally classified according to their shape, material and structural properties as elasmoid scales, ganoid scales, placoid scales, carapace scutes, or bony plates. Each type of dermal armor forms distinct articulation patterns that facilitate different functional advantages. In this paper, we highlight recent studies that developed 3D-printed structures not only to inform the design and application of some articulated and multi-material structures, but also to explain the mechanics of the natural biological systems they mimic. Copyright © 2017 Elsevier Ltd. All rights reserved.

A review on powder-based additive manufacturing for tissue engineering: selective laser sintering and inkjet 3D printing.

PubMed

Shirazi, Seyed Farid Seyed; Gharehkhani, Samira; Mehrali, Mehdi; Yarmand, Hooman; Metselaar, Hendrik Simon Cornelis; Adib Kadri, Nahrizul; Osman, Noor Azuan Abu

2015-06-01

Since most starting materials for tissue engineering are in powder form, using powder-based additive manufacturing methods is attractive and practical. The principal point of employing additive manufacturing (AM) systems is to fabricate parts with arbitrary geometrical complexity with relatively minimal tooling cost and time. Selective laser sintering (SLS) and inkjet 3D printing (3DP) are two powerful and versatile AM techniques which are applicable to powder-based material systems. Hence, the latest state of knowledge available on the use of AM powder-based techniques in tissue engineering and their effect on mechanical and biological properties of fabricated tissues and scaffolds must be updated. Determining the effective setup of parameters, developing improved biocompatible/bioactive materials, and improving the mechanical/biological properties of laser sintered and 3D printed tissues are the three main concerns which have been investigated in this article.

Materials learning from life: concepts for active, adaptive and autonomous molecular systems.

PubMed

Merindol, Rémi; Walther, Andreas

2017-09-18

Bioinspired out-of-equilibrium systems will set the scene for the next generation of molecular materials with active, adaptive, autonomous, emergent and intelligent behavior. Indeed life provides the best demonstrations of complex and functional out-of-equilibrium systems: cells keep track of time, communicate, move, adapt, evolve and replicate continuously. Stirred by the understanding of biological principles, artificial out-of-equilibrium systems are emerging in many fields of soft matter science. Here we put in perspective the molecular mechanisms driving biological functions with the ones driving synthetic molecular systems. Focusing on principles that enable new levels of functionalities (temporal control, autonomous structures, motion and work generation, information processing) rather than on specific material classes, we outline key cross-disciplinary concepts that emerge in this challenging field. Ultimately, the goal is to inspire and support new generations of autonomous and adaptive molecular devices fueled by self-regulating chemistry.

Biodegradability of Plastics: Challenges and Misconceptions.

PubMed

Kubowicz, Stephan; Booth, Andy M

2017-11-07

Plastics are one of the most widely used materials and, in most cases, they are designed to have long life times. Thus, plastics contain a complex blend of stabilizers that prevent them from degrading too quickly. Unfortunately, many of the most advantageous properties of plastics such as their chemical, physical and biological inertness and durability present challenges when plastic is released into the environment. Common plastics such as polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyethylene terephthalate (PET) are extremely persistent in the environment, where they undergo very slow fragmentation (projected to take centuries) into small particles through photo-, physical, and biological degradation processes 1 . The fragmentation of the material into increasingly smaller pieces is an unavoidable stage of the degradation process. Ultimately, plastic materials degrade to micron-sized particles (microplastics), which are persistent in the environment and present a potential source of harm for organisms.

Examination of Deteriogenic Biofilms on Building Facades with Scanning Electron Microscopy / Badanie Deteriogennych Nalotów Biologicznych Na Elewacjach Budynków Metodą Elektronowej Mikroskopii Skaningowej

NASA Astrophysics Data System (ADS)

Piontek, Marlena; Lechów, Hanna; Paradowska, Ewa; Nycz, Marta

2016-03-01

Destruction of facades is a complex process in which technical material changes its properties, and which is caused by depositing biological agents. The examination of biofilms from building facades is difficult because sampling for tests may result in the damage to the structure of the facade's material. Also biological analysis of the material obtained from a biofilm is arduous. Some species of microorganisms are impossible to be isolated and their pure cultures cannot be cultivated in laboratory conditions. It is multispecies cultures that most frequently develop on the surfaces of the facade's technical material. Clustered in a group, they cooperate with each other and reveal different features than single cells. It is essential to identify organisms present in the biofilms, since they may initiate deterioration processes. The aim of the research was the observation of the biofilm, collected from two facades, in a micrometer scale with the use of a scanning electron microscope.

From bacteria to mollusks: the principles underlying the biomineralization of iron oxide materials.

PubMed

Faivre, Damien; Godec, Tina Ukmar

2015-04-13

Various organisms possess a genetic program that enables the controlled formation of a mineral, a process termed biomineralization. The variety of biological material architectures is mind-boggling and arises from the ability of organisms to exert control over crystal nucleation and growth. The structure and composition of biominerals equip biomineralizing organisms with properties and functionalities that abiotically formed materials, made of the same mineral, usually lack. Therefore, elucidating the mechanisms underlying biomineralization and morphogenesis is of interdisciplinary interest to extract design principles that will enable the biomimetic formation of functional materials with similar capabilities. Herein, we summarize what is known about iron oxides formed by bacteria and mollusks for their magnetic and mechanical properties. We describe the chemical and biological machineries that are involved in controlling mineral precipitation and organization and show how these organisms are able to form highly complex structures under physiological conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modular and Orthogonal Synthesis of Hybrid Polymers and Networks

PubMed Central

Liu, Shuang; Dicker, Kevin T.; Jia, Xinqiao

2015-01-01

Biomaterials scientists strive to develop polymeric materials with distinct chemical make-up, complex molecular architectures, robust mechanical properties and defined biological functions by drawing inspirations from biological systems. Salient features of biological designs include (1) repetitive presentation of basic motifs; and (2) efficient integration of diverse building blocks. Thus, an appealing approach to biomaterials synthesis is to combine synthetic and natural building blocks in a modular fashion employing novel chemical methods. Over the past decade, orthogonal chemistries have become powerful enabling tools for the modular synthesis of advanced biomaterials. These reactions require building blocks with complementary functionalities, occur under mild conditions in the presence of biological molecules and living cells and proceed with high yield and exceptional selectivity. These chemistries have facilitated the construction of complex polymers and networks in a step-growth fashion, allowing facile modulation of materials properties by simple variations of the building blocks. In this review, we first summarize features of several types of orthogonal chemistries. We then discuss recent progress in the synthesis of step growth linear polymers, dendrimers and networks that find application in drug delivery, 3D cell culture and tissue engineering. Overall, orthogonal reactions and modulular synthesis have not only minimized the steps needed for the desired chemical transformations but also maximized the diversity and functionality of the final products. The modular nature of the design, combined with the potential synergistic effect of the hybrid system, will likely result in novel hydrogel matrices with robust structures and defined functions. PMID:25572255

Graphene sheets stabilized on genetically engineered M13 viral templates as conducting frameworks for hybrid energy-storage materials.

PubMed

Oh, Dahyun; Dang, Xiangnan; Yi, Hyunjung; Allen, Mark A; Xu, Kang; Lee, Yun Jung; Belcher, Angela M

2012-04-10

Utilization of the material-specific peptide-substrate interactions of M13 virus broadens colloidal stability window of graphene. The homogeneous distribution of graphene is maintained in weak acids and increased ionic strengths by complexing with virus. This graphene/virus conducting template is utilized in the synthesis of energy-storage materials to increase the conductivity of the composite electrode. Successful formation of the hybrid biological template is demonstrated by the mineralization of bismuth oxyfluoride as a cathode material for lithium-ion batteries, with increased loading and improved electronic conductivity. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Faking It Won't Make It in Science

ERIC Educational Resources Information Center

Cavanagh, Sean

2004-01-01

For years, educators and researchers have seen teachers at all grade levels attempt to upgrade their grasp of physics, chemistry, and biology, from basic theories to complex material. Now, the pressure on schools and instructors to improve science instruction is likely to intensify, with approaching federal requirements on states to test students…

Utilization of the wastes of vital activity

NASA Technical Reports Server (NTRS)

Gusarov, B. G.; Drigo, Y. A.; Novikov, V. M.; Samsonov, N. M.; Farafonov, N. S.; Chizhov, S. V.; Yazdovskiy, V. I.

1979-01-01

The recycling of wastes from the biological complex for use in life-support systems is discussed. Topics include laboratory equipment, heat treatment of waste materials, mineralization of waste products, methods for production of ammonium hydroxide and nitric acid, the extraction of sodium chloride from mineralized products, and the recovery of nutrient substances for plants from urine.

The Use of Percolating Filters in Teaching Ecology.

ERIC Educational Resources Information Center

Gray, N. F.

1982-01-01

Using percolating filters (components of sewage treatment process) reduces problems of organization, avoids damage to habitats, and provides a local study site for field work or rapid collection of biological material throughout the year. Component organisms are easily identified and the habitat can be studied as a simple or complex system.…

Differential Variance Analysis: a direct method to quantify and visualize dynamic heterogeneities

NASA Astrophysics Data System (ADS)

Pastore, Raffaele; Pesce, Giuseppe; Caggioni, Marco

2017-03-01

Many amorphous materials show spatially heterogenous dynamics, as different regions of the same system relax at different rates. Such a signature, known as Dynamic Heterogeneity, has been crucial to understand the nature of the jamming transition in simple model systems and is currently considered very promising to characterize more complex fluids of industrial and biological relevance. Unfortunately, measurements of dynamic heterogeneities typically require sophisticated experimental set-ups and are performed by few specialized groups. It is now possible to quantitatively characterize the relaxation process and the emergence of dynamic heterogeneities using a straightforward method, here validated on video microscopy data of hard-sphere colloidal glasses. We call this method Differential Variance Analysis (DVA), since it focuses on the variance of the differential frames, obtained subtracting images at different time-lags. Moreover, direct visualization of dynamic heterogeneities naturally appears in the differential frames, when the time-lag is set to the one corresponding to the maximum dynamic susceptibility. This approach opens the way to effectively characterize and tailor a wide variety of soft materials, from complex formulated products to biological tissues.

Microfluidic chambers using fluid walls for cell biology.

PubMed

Soitu, Cristian; Feuerborn, Alexander; Tan, Ann Na; Walker, Henry; Walsh, Pat A; Castrejón-Pita, Alfonso A; Cook, Peter R; Walsh, Edmond J

2018-06-12

Many proofs of concept have demonstrated the potential of microfluidics in cell biology. However, the technology remains inaccessible to many biologists, as it often requires complex manufacturing facilities (such as soft lithography) and uses materials foreign to cell biology (such as polydimethylsiloxane). Here, we present a method for creating microfluidic environments by simply reshaping fluids on a substrate. For applications in cell biology, we use cell media on a virgin Petri dish overlaid with an immiscible fluorocarbon. A hydrophobic/fluorophilic stylus then reshapes the media into any pattern by creating liquid walls of fluorocarbon. Microfluidic arrangements suitable for cell culture are made in minutes using materials familiar to biologists. The versatility of the method is demonstrated by creating analogs of a common platform in cell biology, the microtiter plate. Using this vehicle, we demonstrate many manipulations required for cell culture and downstream analysis, including feeding, replating, cloning, cryopreservation, lysis plus RT-PCR, transfection plus genome editing, and fixation plus immunolabeling (when fluid walls are reconfigured during use). We also show that mammalian cells grow and respond to stimuli normally, and worm eggs develop into adults. This simple approach provides biologists with an entrée into microfluidics. Copyright © 2018 the Author(s). Published by PNAS.

Designed Proteins Induce the Formation of Nanocage-containing Extracellular Vesicles

PubMed Central

Votteler, Jörg; Ogohara, Cassandra; Yi, Sue; Hsia, Yang; Nattermann, Una; Belnap, David M.; King, Neil P.; Sundquist, Wesley I.

2017-01-01

Complex biological processes are often performed by self-organizing nanostructures comprising multiple classes of macromolecules, such as ribosomes (proteins and RNA) or enveloped viruses (proteins, nucleic acids, and lipids). Approaches have been developed for designing self-assembling structures consisting of either nucleic acids1,2 or proteins3–5, but strategies for engineering hybrid biological materials are only beginning to emerge6,7. Here, we describe the design of self-assembling protein nanocages that direct their own release from human cells inside small vesicles in a manner that resembles some viruses. We refer to these hybrid biomaterials as Enveloped Protein Nanocages (EPNs). Robust EPN biogenesis required protein sequence elements that encode three distinct functions: membrane binding, self-assembly, and recruitment of the Endosomal Sorting Complexes Required for Transport (ESCRT) machinery8. A variety of synthetic proteins with these functional elements induced EPN biogenesis, highlighting the modularity and generality of the design strategy. Biochemical and electron cryomicroscopic (cryo-EM) analyses revealed that one design, EPN-01, comprised small (~100 nm) vesicles containing multiple protein nanocages that closely matched the structure of the designed 60-subunit self-assembling scaffold9. EPNs that incorporated the vesicular stomatitis viral glycoprotein (VSV-G) could fuse with target cells and deliver their contents, thereby transferring cargoes from one cell to another. These studies show how proteins can be programmed to direct the formation of hybrid biological materials that perform complex tasks, and establish EPNs as a novel class of designed, modular, genetically-encoded nanomaterials that can transfer molecules between cells. PMID:27919066

Silk-polypyrrole biocompatible actuator performance under biologically relevant conditions

NASA Astrophysics Data System (ADS)

Hagler, Jo'elen; Peterson, Ben; Murphy, Amanda; Leger, Janelle

Biocompatible actuators that are capable of controlled movement and can function under biologically relevant conditions are of significant interest in biomedical fields. Previously, we have demonstrated that a composite material of silk biopolymer and the conducting polymer polypyrrole (PPy) can be formed into a bilayer device that can bend under applied voltage. Further, these silk-PPy composites can generate forces comparable to human muscle (>0.1 MPa) making them ideal candidates for interfacing with biological tissues. Here silk-PPy composite films are tested for performance under biologically relevant conditions including exposure to a complex protein serum and biologically relevant temperatures. Free-end bending actuation performance, current response, force generation and, mass degradation were investigated . Preliminary results show that when exposed to proteins and biologically relevant temperatures, these silk-PPy composites show minimal degradation and are able to generate forces and conduct currents comparable to devices tested under standard conditions. NSF.

Quantitative biological surface science: challenges and recent advances.

PubMed

Höök, Fredrik; Kasemo, Bengt; Grunze, Michael; Zauscher, Stefan

2008-12-23

Biological surface science is a broad, interdisciplinary subfield of surface science, where properties and processes at biological and synthetic surfaces and interfaces are investigated, and where biofunctional surfaces are fabricated. The need to study and to understand biological surfaces and interfaces in liquid environments provides sizable challenges as well as fascinating opportunities. Here, we report on recent progress in biological surface science that was described within the program assembled by the Biomaterial Interface Division of the Science and Technology of Materials, Interfaces and Processes (www.avs.org) during their 55th International Symposium and Exhibition held in Boston, October 19-24, 2008. The selected examples show that the rapid progress in nanoscience and nanotechnology, hand-in-hand with theory and simulation, provides increasingly sophisticated methods and tools to unravel the mechanisms and details of complex processes at biological surfaces and in-depth understanding of biomolecular surface interactions.

Mix-and-match nanobiosensor design: Logical and spatial programming of biosensors using self-assembled DNA nanostructures.

PubMed

Liu, Ying; Kumar, Sriram; Taylor, Rebecca E

2018-04-06

The evergrowing need to understand and engineer biological and biochemical mechanisms has led to the emergence of the field of nanobiosensing. Structural DNA nanotechnology, encompassing methods such as DNA origami and single-stranded tiles, involves the base pairing-driven knitting of DNA into discrete one-, two-, and three-dimensional shapes at nanoscale. Such nanostructures enable a versatile design and fabrication of nanobiosensors. These systems benefit from DNA's programmability, inherent biocompatibility, and the ability to incorporate and organize functional materials such as proteins and metallic nanoparticles. In this review, we present a mix-and-match taxonomy and approach to designing nanobiosensors in which the choices of bioanalyte and transduction mechanism are fully independent of each other. We also highlight opportunities for greater complexity and programmability of these systems that are built using structural DNA nanotechnology. This article is categorized under: Implantable Materials and Surgical Technologies > Nanomaterials and Implants Diagnostic Tools > Biosensing Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology. © 2018 Wiley Periodicals, Inc.

New Directions in X-Ray Light Sources or Fiat Lux: what's under the dome and watching atoms with x-rays (LBNL Summer Lecture Series)

ScienceCinema

Falcone, Roger [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Advanced Light Source (ALS); Univ. of California, Berkeley, CA (United States). Dept. of Physics

2018-05-04

Summer Lecture Series 2008: Molecular movies of chemical reactions and material phase transformations need a strobe of x-rays, the penetrating light that reveals how atoms and molecules assemble in chemical and biological systems and complex materials. Roger Falcone, Director of the Advanced Light Source,will discuss a new generation of x ray sources that will enable a new science of atomic dynamics on ultrafast timescales.

Experiments in Natural and Synthetic Dental Materials: A Mouthful of Experiments

NASA Technical Reports Server (NTRS)

Masi, James V.

1996-01-01

The objectives of these experiments are to show that the area of biomaterials, especially dental materials (natural and synthetic), contain all of the elements of good and bad design, with the caveat that a person's health is directly involved. The students learn the process of designing materials for the complex interactions in the oral cavity, analyze those already used, and suggest possible solutions to the problems involved with present technology. The N.I.O.S.H. Handbook is used extensively by the students and judgement calls are made, even without extensive biology education.

Tapping bioremediation's potential -- A matter of sweat and tiers

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

Merski, A.T.; Griffin, W.M.

Bioremediation's potential for treating environmental contamination is gaining greater recognition among regulators and the regulated community. For example, biological treatment is routinely applied to municipal wastewater, which typically contains readily biodegradable materials. Industrial wastewaters, by contrast, often contain higher concentrations of materials that present unique challenges to biological treatment. In both areas, biological treatment has succeeded by using contained, relatively controlled systems engineered to optimize performance of the biological component. Uncontrolled releases into such matrices as soil, and fresh and marine waters increase the complexity of the biological challenge, requiring development of novel products and procedures for efficient biological treatmentmore » and monitoring. One of the goals of the National Environmental Technology Applications Corporation (NETAC; Pittsburgh) is to support scientific development of bioremediation technology. NETAC is a non-profit corporation formed in 1988 through a cooperative agreement between EPA and the University of Pittsburgh Trust. Its overall mission is to accelerate development, application and commercialization of priority environmental technologies for national and international markets. NETAC provides technical and business expertise to assist in evaluating, commercializing and publicizing new environmental technologies. The organization assumes no financial interest in any technology but provides independent third-party support and analysis on a fee-for-service basis to technology users and developers.« less

Major review: Exfoliation syndrome; advances in disease genetics, molecular biology, and epidemiology.

PubMed

Aboobakar, Inas F; Johnson, William M; Stamer, W Daniel; Hauser, Michael A; Allingham, R Rand

2017-01-01

Exfoliation syndrome (XFS) is a common age-related disorder that leads to deposition of extracellular fibrillar material throughout the body. The most recognized disease manifestation is exfoliation glaucoma (XFG), which is a common cause of blindness worldwide. Recent developments in XFS genetics, cell biology and epidemiology have greatly improved our understanding of the etiology of this complex inherited disease. This review summarizes current knowledge of XFS pathogenesis, identifies gaps in knowledge, and discusses areas for future research. Copyright © 2016. Published by Elsevier Ltd.

Progress and Opportunities in Soft Photonics and Biologically Inspired Optics.

PubMed

Kolle, Mathias; Lee, Seungwoo

2018-01-01

Optical components made fully or partially from reconfigurable, stimuli-responsive, soft solids or fluids-collectively referred to as soft photonics-are poised to form the platform for tunable optical devices with unprecedented functionality and performance characteristics. Currently, however, soft solid and fluid material systems still represent an underutilized class of materials in the optical engineers' toolbox. This is in part due to challenges in fabrication, integration, and structural control on the nano- and microscale associated with the application of soft components in optics. These challenges might be addressed with the help of a resourceful ally: nature. Organisms from many different phyla have evolved an impressive arsenal of light manipulation strategies that rely on the ability to generate and dynamically reconfigure hierarchically structured, complex optical material designs, often involving soft or fluid components. A comprehensive understanding of design concepts, structure formation principles, material integration, and control mechanisms employed in biological photonic systems will allow this study to challenge current paradigms in optical technology. This review provides an overview of recent developments in the fields of soft photonics and biologically inspired optics, emphasizes the ties between the two fields, and outlines future opportunities that result from advancements in soft and bioinspired photonics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomaterials in light amplification

NASA Astrophysics Data System (ADS)

Mysliwiec, Jaroslaw; Cyprych, Konrad; Sznitko, Lech; Miniewicz, Andrzej

2017-03-01

Biologically produced or inspired materials can serve as optical gain media, i.e. they can exhibit the phenomenon of light amplification. Some of these materials, under suitable dye-doping and optical pumping conditions, show lasing phenomena. The emerging branch of research focused on obtaining lasing action in highly disordered and highly light scattering materials, i.e. research on random lasing, is perfectly suited for biological materials. The use of biomaterials in light amplification has been extensively reported in the literature. In this review we attempt to report on progress in the development of biologically derived systems able to show the phenomena of light amplification and random lasing together with the contribution of our group to this field. The rich world of biopolymers modified with molecular aggregates and nanocrystals, and self-organized at the nanoscale, offers a multitude of possibilities for tailoring luminescent and light scattering properties that are not easily replicated in conventional organic or inorganic materials. Of particular importance and interest are light amplification and lasing, or random lasing studies in biological cells and tissues. In this review we will describe nucleic acids and their complexes employed as gain media due to their favorable optical properties and ease of manipulation. We will report on research conducted on various biomaterials showing structural analogy to nucleic acids such as fluorescent proteins, gelatins in which the first distributed feedback laser was realized, and also amyloids or silks, which, due to their dye-doped fiber-like structure, allow for light amplification. Other materials that were investigated in that respect include polysaccharides, like starch exhibiting favorable photostability in comparison to other biomaterials, and chitosan, which forms photonic crystals or cellulose. Light amplification and random lasing was not only observed in processed biomaterials but also in living cells and tissues or separated phase systems like phosphatydylcholine liposomes. All of the above-mentioned light amplification possibilities of biomaterials also have potential for several interesting applications in biology, medicine, sensing and imaging, which will be described and discussed in this review.

Evaluation of the Methods of portective Treatment against microbiological damages and prolonged antimicrobic protection of the interior and the equipment of space objects

NASA Astrophysics Data System (ADS)

Deshevaya, E.; Novikova, N.; Polycarpov, N.; Poddubko, S.; Shumilina, G.; Bragina, M.; Zarubina, K.; Tverskoy, V.; Akova, M. D.

The researches which have been carried out onboard the orbital complex (? C) MIR, testify that environment of the manned space object may be considered as peculiar ecological niche for development of the microbial community generated by microorganisms of various physiological and taxonomic groups. As a result of vital activity of fungi during OC MIR operation zones of fungi growth on various elements of interior and equipment, cases of destruction of the materials and attributes of corrosion of metals were noted. Existing methods of development of microorganisms on a surface of constructional materials using sanitary treatment of the accessible surfaces with disinfectants, represent the big labour input for the crew. More radical solution of the problem is the development and use of methods of superficial modification of constructional materials and use of methods of superficial modification of constructional materials and treatment of their surface of varnish or paint, resistant to biocontamination and growth of the microorganisms. As a result of the conducted research, the following methods of protection of constructional materials against development of microorganisms were chosen: - fluorination, sylilition, radiating graft polymerization etc., resulting in formation of the functional groups having biocide action; For varnish and paint coverings - coverings on a basis stoichiometrical interpolymeric polyelectrolytic complexes, organosilicone coverings, etc. For testing of the biological effects of samples of the materials subjected to the different methods of surface modification, researches were carried out and experimental models of typical biodestructive processes of the constructional materials are developed considering microclimatic parameters of local zones (the increased temperature and humidity), resistance of the materials to the influence of fungi and increased radiating background influence. Biological testing testifying the efficiency of developed methods and ways of protection of materials on experimental samples of the materials subjected superficial modification is conducted and optimum concentration of reagents and biocides in varnish coverings are determined.

Using the Tools and Resources of the RCSB Protein Data Bank.

PubMed

Costanzo, Luigi Di; Ghosh, Sutapa; Zardecki, Christine; Burley, Stephen K

2016-09-07

The Protein Data Bank (PDB) archive is the worldwide repository of experimentally determined three-dimensional structures of large biological molecules found in all three kingdoms of life. Atomic-level structures of these proteins, nucleic acids, and complex assemblies thereof are central to research and education in molecular, cellular, and organismal biology, biochemistry, biophysics, materials science, bioengineering, ecology, and medicine. Several types of information are associated with each PDB archival entry, including atomic coordinates, primary experimental data, polymer sequence(s), and summary metadata. The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves as the U.S. data center for the PDB, distributing archival data and supporting both simple and complex queries that return results. These data can be freely downloaded, analyzed, and visualized using RCSB PDB tools and resources to gain a deeper understanding of fundamental biological processes, molecular evolution, human health and disease, and drug discovery. © 2016 by John Wiley & Sons, Inc. Copyright © 2016 John Wiley & Sons, Inc.

Trends in biotechnological production of fuel ethanol from different feedstocks.

PubMed

Sánchez, Oscar J; Cardona, Carlos A

2008-09-01

Present work deals with the biotechnological production of fuel ethanol from different raw materials. The different technologies for producing fuel ethanol from sucrose-containing feedstocks (mainly sugar cane), starchy materials and lignocellulosic biomass are described along with the major research trends for improving them. The complexity of the biomass processing is recognized through the analysis of the different stages involved in the conversion of lignocellulosic complex into fermentable sugars. The features of fermentation processes for the three groups of studied feedstocks are discussed. Comparative indexes for the three major types of feedstocks for fuel ethanol production are presented. Finally, some concluding considerations on current research and future tendencies in the production of fuel ethanol regarding the pretreatment and biological conversion of the feedstocks are presented.

Physics through the 1990s: Scientific interfaces and technological applications

NASA Technical Reports Server (NTRS)

1986-01-01

The volume examines the scientific interfaces and technological applications of physics. Twelve areas are dealt with: biological physics-biophysics, the brain, and theoretical biology; the physics-chemistry interface-instrumentation, surfaces, neutron and synchrotron radiation, polymers, organic electronic materials; materials science; geophysics-tectonics, the atmosphere and oceans, planets, drilling and seismic exploration, and remote sensing; computational physics-complex systems and applications in basic research; mathematics-field theory and chaos; microelectronics-integrated circuits, miniaturization, future trends; optical information technologies-fiber optics and photonics; instrumentation; physics applications to energy needs and the environment; national security-devices, weapons, and arms control; medical physics-radiology, ultrasonics, MNR, and photonics. An executive summary and many chapters contain recommendations regarding funding, education, industry participation, small-group university research and large facility programs, government agency programs, and computer database needs.

Adsorptive removal and separation of chemicals with metal-organic frameworks: Contribution of π-complexation.

PubMed

Khan, Nazmul Abedin; Jhung, Sung Hwa

2017-03-05

Efficient removal and separation of chemicals from the environment has become a vital issue from a biological and environmental point of view. Currently, adsorptive removal/separation is one of the most promising approaches for cleaning purposes. Selective adsorption/removal of various sulfur- and nitrogen-containing compounds, olefins, and π-electron-rich gases via π-complex formation between an adsorbent and adsorbate molecules is very competitive. Porous metal-organic framework (MOF) materials are very promising in the adsorption/separation of various liquids and gases owing to their distinct characteristics. This review summarizes the literature on the adsorptive removal/separation of various π-electron-rich compounds mainly from fuel and gases using MOF materials containing metal ions that are active for π-complexation. Details of the π-complexation, including mechanism, pros/cons, applications, and efficient ways to form the complex, are discussed systematically. For in-depth understanding, molecular orbital calculations regarding charge transfer between the π-complexing species are also explained in a separate section. From this review, readers will gain an understanding of π-complexation for adsorption and separation, especially with MOFs, to develop new insight for future research. Copyright © 2016 Elsevier B.V. All rights reserved.

Bacillus spores as building blocks for stimuli-responsive materials and nanogenerators

NASA Astrophysics Data System (ADS)

Sahin, Ozgur; Chen, Xi

2014-03-01

Materials that mechanically respond to external chemical stimuli have applications in a wide range of fields. Inspired by biological systems, stimuli-responsive materials that can oscillate, transport fluid, mimic homeostasis, and undergo complex changes in shape have been previously demonstrated. However, the effectiveness of synthetic stimuli-responsive materials in generating work is limited when compared to mechanical actuators. During studies of bacterial sporulation, we have found that the mechanical response of Bacillus spores to water gradients exhibits an energy density of more than 10 MJ/m3, which is two orders of magnitude higher than synthetic water-responsive materials. We also identified mutations that can approximately double the energy density of the spores, and found that spores can self-assemble into dense, submicron-thick monolayers on substrates such as silicon microcantilevers and elastomer sheets, creating self-assembled actuators that can remotely generate electrical power from an evaporating body of water. The energy conversion mechanism of Bacillus spores may facilitate synthetic stimuli-responsive materials with significantly higher energy densities. We acknowledge support from the U.S. Dept. of Energy Early Career Research Program, the Wyss Institute for Biologically Inspired Engineering, and the Rowland Institute at Harvard.

A Novel Silicone-Magnetite Composite Material Used in the Fabrication of Biomimetic Cilia

NASA Astrophysics Data System (ADS)

Carstens, B. L.; Evans, B. A.; Shields, A. R.; Su, J.; Washburn, S.; Falvo, M. R.; Superfine, R.

2008-10-01

We have developed a novel polymer-magnetite composite that we use to fabricate arrays of magnetically actuable biomimetic cilia. Biomimetic cilia are flexible nanorods 750 nm in diameter and 25 microns tall. They generate fluid flows similar to those produced by biological cilia. Polymer-magnetic nanoparticle materials such as ours are becoming increasingly useful in biomedical applications and microelectromechanical systems (MEMS). Comprised of magnetite (Fe3O4), the nanoparticles have a diameter of 5-7 nm and are complexed with a silicone copolymer and crosslinked into a flexible, magnetic solid. Amine groups make up 6-7 percent of the silicone copolymer, providing a simple means of functionalization. We present a detailed mechanical and magnetic analysis of our bulk crosslinked material. The high-aspect ratio biomimetic cilia we create with this magnetite-copolymer complex may have applications in microfluidic mixing, biofouling, and MEMS.

Nanoscale Structure and Interaction of Compact Assemblies of Carbon Nano-Materials

NASA Astrophysics Data System (ADS)

Timsina, Raju; Qiu, Xiangyun

Carbon-based nano-materials (CNM) are a diverse family of multi-functional materials under research and development world wide. Our work is further motivated by the predictive power of the physical understanding of the underlying structure-interaction-function relationships. Here we present results form recent studies of the condensed phases of several model CNMs in complexation with biologically derived molecules. Specifically, we employ X-ray diffraction (XRD) to determine nanoscale structures and use the osmotic stress method to quantify their interactions. The systems under investigation are dsDNA-dispersed carbon nanotubes (dsDNA-CNT), bile-salt-dispersed carbon nanotubes, and surfactant-assisted assemblies of graphene oxides. We found that salt and molecular crowding are both effective in condensing CNMs but the resultant structures show disparate phase behaviors. The molecular interactions driving the condensation/assembly sensitively depend on the nature of CNM complex surface chemistry and range from hydrophobic to electrostatic to entropic forces.

Materials science. Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling.

PubMed

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G; Huang, Yonggang; Zhang, Yihui; Rogers, John A

2015-01-09

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations. Copyright © 2015, American Association for the Advancement of Science.

Integrated micro/nanoengineered functional biomaterials for cell mechanics and mechanobiology: a materials perspective.

PubMed

Shao, Yue; Fu, Jianping

2014-03-12

The rapid development of micro/nanoengineered functional biomaterials in the last two decades has empowered materials scientists and bioengineers to precisely control different aspects of the in vitro cell microenvironment. Following a philosophy of reductionism, many studies using synthetic functional biomaterials have revealed instructive roles of individual extracellular biophysical and biochemical cues in regulating cellular behaviors. Development of integrated micro/nanoengineered functional biomaterials to study complex and emergent biological phenomena has also thrived rapidly in recent years, revealing adaptive and integrated cellular behaviors closely relevant to human physiological and pathological conditions. Working at the interface between materials science and engineering, biology, and medicine, we are now at the beginning of a great exploration using micro/nanoengineered functional biomaterials for both fundamental biology study and clinical and biomedical applications such as regenerative medicine and drug screening. In this review, an overview of state of the art micro/nanoengineered functional biomaterials that can control precisely individual aspects of cell-microenvironment interactions is presented and they are highlighted them as well-controlled platforms for mechanistic studies of mechano-sensitive and -responsive cellular behaviors and integrative biology research. The recent exciting trend where micro/nanoengineered biomaterials are integrated into miniaturized biological and biomimetic systems for dynamic multiparametric microenvironmental control of emergent and integrated cellular behaviors is also discussed. The impact of integrated micro/nanoengineered functional biomaterials for future in vitro studies of regenerative medicine, cell biology, as well as human development and disease models are discussed. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

Advances in the analysis of biological samples using ionic liquids.

PubMed

Clark, Kevin D; Trujillo-Rodríguez, María J; Anderson, Jared L

2018-02-12

Ionic liquids are a class of solvents and materials that hold great promise in bioanalytical chemistry. Task-specific ionic liquids have recently been designed for the selective extraction, separation, and detection of proteins, peptides, nucleic acids, and other physiologically relevant analytes from complex biological samples. To facilitate rapid bioanalysis, ionic liquids have been integrated in miniaturized and automated procedures. Bioanalytical separations have also benefited from the modification of nonspecific magnetic materials with ionic liquids or the implementation of ionic liquids with inherent magnetic properties. Furthermore, the direct detection of the extracted molecules in the analytical instrument has been demonstrated with structurally tuned ionic liquids and magnetic ionic liquids, providing a significant advantage in the analysis of low-abundance analytes. This article gives an overview of these advances that involve the application of ionic liquids and derivatives in bioanalysis. Graphical abstract Ionic liquids, magnetic ionic liquids, and ionic liquid-based sorbents are increasing the speed, selectivity, and sensitivity in the analysis of biological samples.

Nanolayered Features of Collagen-like Peptides

NASA Technical Reports Server (NTRS)

Valluzzi, Regina; Bini, Elisabetta; Haas, Terry; Cebe, Peggy; Kaplan, David L.

2003-01-01

We have been investigating collagen-like model oligopeptides as molecular bases for complex ordered biomimetic materials. The collagen-like molecules incorporate aspects of native collagen sequence and secondary structure. Designed modifications to native primary and secondary structure have been incorporated to control the nanostructure and microstructure of the collagen-like materials produced. We find that the collagen-like molecules form a number of lyotropic rod liquid crystalline phases, which because of their strong temperature dependence in the liquid state can also be viewed as solvent intercalated thermotropic liquid crystals. The liquid crystalline phases formed by the molecules can be captured in the solid state by drying off solvent, resulting in solid nanopatterned (chemically and physically) thermally stable (to greater than 100 C) materials. Designed sequences which stabilize smectic phases have allowed a variety of nanoscale multilayered biopolymeric materials to be developed. Preliminary investigations suggest that chemical patterns running perpendicular to the smectic layer plane can be functionalized and used to localize a variety of organic, inorganic, and organometallic moieties in very simple multilayered nanocomposites. The phase behavior of collagen-like oligopeptide materials is described, emphasizing the correlation between mesophase, molecular orientation, and chemical patterning at the microscale and nanoscale. In many cases, the textures observed for smectic and hexatic phase collagens are remarkably similar to the complex (and not fully understood) helicoids observed in biological collagen-based tissues. Comparisons between biological morphologies and collagen model liquid crystalline (and solidified materials) textures may help us understand the molecular features which impart order and function to the extracellular matrix and to collagen-based mineralized tissues. Initial studies have utilized synthetic collagen-like peptides while future work will also focus on similar sequences generated via genetic engineering methods.

Use of Multimedia in an Introductory College Biology Course to Improve Comprehension of Complex Material

ERIC Educational Resources Information Center

Rhodes, Ashley; Rozell, Tim; Shroyer, Gail

2014-01-01

Many students who have the ability to succeed in science, technology, engineering and math (STEM) disciplines are often alienated by the traditional instructional methods encountered within introductory courses; as a result, attrition from STEM fields is highest after completion of these courses. This is especially true for females. The present…

Fundamental Physics Program and the NASA Mission

NASA Technical Reports Server (NTRS)

Trinh, Eugene

2003-01-01

The accomplishments of Physics, the increasing power of its instruments, and its expanding reach into other sciences have generated an unprecedented set of scientific opportunities. The committee has identified six such Grand Challenges listed below in no particular order: Developing quantum technologies. Creating new materials. Understanding complex systems. Unifying the forces of Nature. Exploring the universe Applying Physics to Biology.

Benzoin Condensation: Monitoring a Chemical Reaction by High-Pressure Liquid Chromatography

ERIC Educational Resources Information Center

Bhattacharya, Apurba; Purohit, Vikram C.; Bellar, Nicholas R.

2004-01-01

High-pressure liquid chromatography (HPLC) is the preferred method of separating a variety of materials in complex mixtures such as pharmaceuticals, polymers, soils, food products and biological fluids and is also considered to be a powerful analytical tool in both academia and industry. The use of HPLC analysis as a means of monitoring and…

Application of Nanoparticle Technology to Reduce the Anti-Microbial Resistance through β-Lactam Antibiotic-Polymer Inclusion Nano-Complex.

PubMed

Salamanca, Constain H; Yarce, Cristhian J; Roman, Yony; Davalos, Andrés F; Rivera, Gustavo R

2018-02-10

Biocompatible polymeric materials with potential to form functional structures in association with different therapeutic molecules have a high potential for biological, medical and pharmaceutical applications. Therefore, the capability of the inclusion of nano-Complex formed between the sodium salt of poly(maleic acid- alt -octadecene) and a β-lactam drug (ampicillin trihydrate) to avoid the chemical and enzymatic degradation and enhance the biological activity were evaluated. PAM-18Na was produced and characterized, as reported previously. The formation of polymeric hydrophobic aggregates in aqueous solution was determined, using pyrene as a fluorescent probe. Furthermore, the formation of polymer-drug nano-complexes was characterized by Differential Scanning Calorimetry-DSC, viscometric, ultrafiltration/centrifugation assays, zeta potential and size measurements were determined by dynamic light scattering-DLS. The PAM-18Na capacity to avoid the chemical degradation was studied through stress stability tests. The enzymatic degradation was evaluated from a pure β-lactamase, while the biological degradation was determined by different β-lactamase producing Staphylococcus aureus strains. When ampicillin was associated with PAM-18Na, the half-life time in acidic conditions increased, whereas both the enzymatic degradation and the minimum inhibitory concentration decreased to a 90 and 75%, respectively. These results suggest a promissory capability of this polymer to protect the β-lactam drugs against chemical, enzymatic and biological degradation.

Application of Nanoparticle Technology to Reduce the Anti-Microbial Resistance through β-Lactam Antibiotic-Polymer Inclusion Nano-Complex

PubMed Central

Yarce, Cristhian J.; Roman, Yony; Davalos, Andrés F.; Rivera, Gustavo R.

2018-01-01

Biocompatible polymeric materials with potential to form functional structures in association with different therapeutic molecules have a high potential for biological, medical and pharmaceutical applications. Therefore, the capability of the inclusion of nano-Complex formed between the sodium salt of poly(maleic acid-alt-octadecene) and a β-lactam drug (ampicillin trihydrate) to avoid the chemical and enzymatic degradation and enhance the biological activity were evaluated. PAM-18Na was produced and characterized, as reported previously. The formation of polymeric hydrophobic aggregates in aqueous solution was determined, using pyrene as a fluorescent probe. Furthermore, the formation of polymer-drug nano-complexes was characterized by Differential Scanning Calorimetry-DSC, viscometric, ultrafiltration/centrifugation assays, zeta potential and size measurements were determined by dynamic light scattering-DLS. The PAM-18Na capacity to avoid the chemical degradation was studied through stress stability tests. The enzymatic degradation was evaluated from a pure β-lactamase, while the biological degradation was determined by different β-lactamase producing Staphylococcus aureus strains. When ampicillin was associated with PAM-18Na, the half-life time in acidic conditions increased, whereas both the enzymatic degradation and the minimum inhibitory concentration decreased to a 90 and 75%, respectively. These results suggest a promissory capability of this polymer to protect the β-lactam drugs against chemical, enzymatic and biological degradation. PMID:29439391

"Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology.

PubMed

Sato, Naoki

2018-05-01

"What is life?" is an ultimate biological quest for the principle that makes organisms alive. This 'WIL problem' is not, however, a simple one that we have a straightforward strategy to attack. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. A dominating idea behind these mainstream biological studies relies on the identification of life-bearing molecules, which themselves are models of life. Another, prevalent idea emphasizes that life resides in the whole system of an organism, but not in some particular molecules. The behavior of a complex system may be considered to embody the essence of life. The thermodynamic view of life system in the early 20th century was remodeled as physics of complex systems and systems biology. The two views contrast with each other, but they are no longer heritage of the historical dualism in biology, such as mechanism/materialism versus vitalism, or reductionism versus holism. These two views are both materialistic and mechanistic, and act as driving forces of modern biology. In reality, molecules function in a context of systems, whereas systems presuppose functional molecules. A key notion to reconcile this conflict is that subjects of biological studies are given before we start to study them. Cell- or organism-level biology is destined to the dialectic of molecules and systems, but this antagonism can be resolved by dynamic thinking involving biological evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthetic biology to access and expand nature’s chemical diversity

PubMed Central

Smanski, Michael J.; Zhou, Hui; Claesen, Jan; Shen, Ben; Fischbach, Michael; Voigt, Christopher A.

2016-01-01

Bacterial genomes encode the biosynthetic potential to produce hundreds of thousands of complex molecules with diverse applications, from medicine to agriculture and materials. Economically accessing the potential encoded within sequenced genomes promises to reinvigorate waning drug discovery pipelines and provide novel routes to intricate chemicals. This is a tremendous undertaking, as the pathways often comprise dozens of genes spanning as much as 100+ kiliobases of DNA, are controlled by complex regulatory networks, and the most interesting molecules are made by non-model organisms. Advances in synthetic biology address these issues, including DNA construction technologies, genetic parts for precision expression control, synthetic regulatory circuits, computer aided design, and multiplexed genome engineering. Collectively, these technologies are moving towards an era when chemicals can be accessed en mass based on sequence information alone. This will enable the harnessing of metagenomic data and massive strain banks for high-throughput molecular discovery and, ultimately, the ability to forward design pathways to complex chemicals not found in nature. PMID:26876034

Schiff's Bases and Crown Ethers as Supramolecular Sensing Materials in the Construction of Potentiometric Membrane Sensors

PubMed Central

Faridbod, Farnoush; Ganjali, Mohammad Reza; Dinarvand, Rassoul; Norouzi, Parviz; Riahi, Siavash

2008-01-01

Ionophore incorporated PVC membrane sensors are well-established analytical tools routinely used for the selective and direct measurement of a wide variety of different ions in complex biological and environmental samples. Potentiometric sensors have some outstanding advantages including simple design and operation, wide linear dynamic range, relatively fast response and rational selectivity. The vital component of such plasticized PVC members is the ionophore involved, defining the selectivity of the electrodes' complex formation. Molecular recognition causes the formation of many different supramolecules. Different types of supramolecules, like calixarenes, cyclodextrins and podands, have been used as a sensing material in the construction of ion selective sensors. Schiff's bases and crown ethers, which feature prominently in supramolecular chemistry, can be used as sensing materials in the construction of potentiometric ion selective electrodes. Up to now, more than 200 potentiometric membrane sensors for cations and anions based on Schiff's bases and crown ethers have been reported. In this review cation binding and anion complexes will be described. Liquid membrane sensors based on Schiff's bases and crown ethers will then be discussed. PMID:27879786

An Energetic Concept of Habitability for the Deep Subsurface

NASA Technical Reports Server (NTRS)

Hoehler, Tori M.

2006-01-01

Universally, life must be characterized by a characteristic level of order and complexity. In the most general sense, habitability could then be defined as the set of factors required to allow the creation and maintenance of molecular complexity. These factors are: chemical raw materials; energy with which to assemble those materials into complex molecules and sustain the resultant state of complexity; a solvent that allows the interaction of complex molecules, promotes tertiary structure, and permits compartmentalization; and environmental conditions that permit the assembly and maintenance of complex molecules. On Earth, these general requirements correspond to the major biogenic elements C, H, O, N, P, S; chemical or light energy; the solvent water; and specific ranges of temperature, pH, radiation, ionic strength, and so forth, which have thus far been determined on and exclusively empirical basis. Importantly, while the complete absence of any of these factors ensures uninhabitable conditions, the mere presence of all four does not guarantee habitability. In each case - even that of water - it is a question of degree. This question can be couched in quantitative terms by considering the impact of each of these factors on cellular energy balance. More "extreme" conditions (e.g., high temperature, high or low pH, etc.), lower water activity, and low concentrations of nutrients incur or have potential to be addressed by increased investment of energy on the part of the cell. This must be balanced by energy conservation in the cell, noting that biochemical, mass transport, and abiotic chemical limitations intervene between environmental energy availability and biological energy capture. Similarly, lower boundary conditions are emplaced on useful environmental energy yields by the "quantized" nature of biological energy conservation, and upper boundary conditions are emplaced by energy levels or fluxes that are destructive with respect to complexity. This energetic framework, with boundary conditions supplied by the specifics of the biochemistry in question, offers a generalized, yet quantitative means of assessing the habitability of any system with respect to complex life.

Interfacing nanostructures to biological cells

DOEpatents

Chen, Xing; Bertozzi, Carolyn R.; Zettl, Alexander K.

2012-09-04

Disclosed herein are methods and materials by which nanostructures such as carbon nanotubes, nanorods, etc. are bound to lectins and/or polysaccharides and prepared for administration to cells. Also disclosed are complexes comprising glycosylated nanostructures, which bind selectively to cells expressing glycosylated surface molecules recognized by the lectin. Exemplified is a complex comprising a carbon nanotube functionalized with a lipid-like alkane, linked to a polymer bearing repeated .alpha.-N-acetylgalactosamine sugar groups. This complex is shown to selectively adhere to the surface of living cells, without toxicity. In the exemplified embodiment, adherence is mediated by a multivalent lectin, which binds both to the cells and the .alpha.-N-acetylgalactosamine groups on the nanostructure.

The Effectiveness of an Online Curriculum on High School Students' Understanding of Biological Evolution

NASA Astrophysics Data System (ADS)

Marsteller, Robert B.; Bodzin, Alec M.

2015-12-01

An online curriculum about biological evolution was designed to promote increased student content knowledge and evidentiary reasoning. A feasibility study was conducted with 77 rural high school biology students who learned with the online biological evolution unit. Data sources included the Biological Evolution Assessment Measure (BEAM), an analysis of discussion forum posts, and a post-implementation perceptions and attitudes questionnaire. BEAM posttest scores were significantly higher than the pretest scores. However, the findings revealed that the students required additional support to develop evidentiary reasoning. Many students perceived that the Web-based curriculum would have been enhanced by increased immediate interaction and feedback. Students required greater scaffolding to support complex, process-oriented tasks. Implications for designing Web-based science instruction with curriculum materials to support students' acquisition of content knowledge and science process skills in a Web-based setting are discussed.

A Multicenter Study To Evaluate the Performance of High-Throughput Sequencing for Virus Detection

PubMed Central

Ng, Siemon H. S.; Vandeputte, Olivier; Aljanahi, Aisha; Deyati, Avisek; Cassart, Jean-Pol; Charlebois, Robert L.; Taliaferro, Lanyn P.

2017-01-01

ABSTRACT The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics. Four model viruses were selected based upon different physical and biochemical properties and commercial availability: human respiratory syncytial virus (RSV), Epstein-Barr virus (EBV), feline leukemia virus (FeLV), and human reovirus (REO). Additionally, porcine circovirus (PCV) was tested by one laboratory. Independent samples were prepared for HTS by spiking intact viruses or extracted viral nucleic acids, singly or mixed, into different HeLa cell matrices (resuspended whole cells, cell lysate, or total cellular RNA). Data were obtained using different sequencing platforms (Roche 454, Illumina HiSeq1500 or HiSeq2500). Bioinformatic analyses were performed independently by each laboratory using available tools, pipelines, and databases. The results showed that comparable virus detection was obtained in the three laboratories regardless of sample processing, library preparation, sequencing platform, and bioinformatic analysis: between 0.1 and 3 viral genome copies per cell were detected for all of the model viruses used. This study highlights the potential for using HTS for sensitive detection of adventitious viruses in complex biological samples containing cellular background. IMPORTANCE Recent high-throughput sequencing (HTS) investigations have resulted in unexpected discoveries of known and novel viruses in a variety of sample types, including research materials, clinical materials, and biological products. Therefore, HTS can be a powerful tool for supplementing current methods for demonstrating the absence of adventitious or unwanted viruses in biological products, particularly when using a new cell line. However, HTS is a complex technology with different platforms, which needs standardization for evaluation of biologics. This collaborative study was undertaken to investigate detection of different virus types using two different HTS platforms. The results of the independently performed studies demonstrated a similar sensitivity of virus detection, regardless of the different sample preparation and processing procedures and bioinformatic analyses done in the three laboratories. Comparable HTS detection of different virus types supports future development of reference virus materials for standardization and validation of different HTS platforms. PMID:28932815

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

PubMed Central

Russo, Marco; La Corte, Daniele; Pisciotta, Annalisa; Riela, Serena; Alduina, Rosa

2017-01-01

Three polyaminocyclodextrin materials, obtained by direct reaction between heptakis(6-deoxy-6-iodo)-β-cyclodextrin and the proper linear polyamines, were investigated for their binding properties, in order to assess their potential applications in biological systems, such as vectors for simultaneous drug and gene cellular uptake or alternatively for the protection of macromolecules. In particular, we exploited polarimetry to test their interaction with some model p-nitroaniline derivatives, chosen as probe guests. The data obtained indicate that binding inside the host cavity is mainly affected by interplay between Coulomb interactions and conformational restraints. Moreover, simultaneous interaction of the cationic polyamine pendant bush at the primary rim was positively assessed. Insights on quantitative aspects of the interaction between our materials and polyanions were investigated by studying the binding with sodium alginate. Finally, the complexation abilities of the same materials towards polynucleotides were assessed by studying their interaction with the model plasmid pUC19. Our results positively highlight the ability of our materials to exploit both the cavity and the polycationic branches, thus functioning as bimodal ligands. PMID:29564010

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution.

PubMed

Rothschild, Lynn J

2010-04-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested.

Collaborative study for the establishment of the 2(nd) International Standard for Bleomycin Complex A2/B2.

PubMed

Jorajuria, S; Raphalen, C; Dujardin, V; Daas, A

2015-01-01

Organization (WHO) International Standard (IS) for bleomycin complex A2/B2. Eight laboratories from different countries participated. Potencies of the candidate material were estimated by microbiological assays with sensitive micro-organisms. To ensure continuity between consecutive batches, the 1(st) IS for bleomycin complex A2/B2 was used as a reference. Based on the results of the study, the 2(nd) IS for bleomycin complex A2/B2 was adopted at the meeting of the WHO Expert Committee for Biological Standardization (ECBS) in 2014 with an assigned potency of 12 500 International Units (IU) per vial. The 2(nd) IS for bleomycin complex A2/B2 is available from the European Directorate for the Quality of Medicines & HealthCare (EDQM).

A Critical Review on Clinical Application of Separation Techniques for Selective Recognition of Uracil and 5-Fluorouracil.

PubMed

Pandey, Khushaboo; Dubey, Rama Shankar; Prasad, Bhim Bali

2016-03-01

The most important objectives that are frequently found in bio-analytical chemistry involve applying tools to relevant medical/biological problems and refining these applications. Developing a reliable sample preparation step, for the medical and biological fields is another primary objective in analytical chemistry, in order to extract and isolate the analytes of interest from complex biological matrices. Since, main inborn errors of metabolism (IEM) diagnosable through uracil analysis and the therapeutic monitoring of toxic 5-fluoruracil (an important anti-cancerous drug) in dihydropyrimidine dehydrogenase deficient patients, require an ultra-sensitive, reproducible, selective, and accurate analytical techniques for their measurements. Therefore, keeping in view, the diagnostic value of uracil and 5-fluoruracil measurements, this article refines several analytical techniques involved in selective recognition and quantification of uracil and 5-fluoruracil from biological and pharmaceutical samples. The prospective study revealed that implementation of molecularly imprinted polymer as a solid-phase material for sample preparation and preconcentration of uracil and 5-fluoruracil had proven to be effective as it could obviates problems related to tedious separation techniques, owing to protein binding and drastic interferences, from the complex matrices in real samples such as blood plasma, serum samples.

Antifouling aptasensor for the detection of adenosine triphosphate in biological media based on mixed self-assembled aptamer and zwitterionic peptide.

PubMed

Wang, Guixiang; Su, Xiaoli; Xu, Qingjun; Xu, Guiyun; Lin, Jiehua; Luo, Xiliang

2018-03-15

Direct detection of targets in complex biological media with conventional biosensors is an enormous challenge due to the nonspecific adsorption and severe biofouling. In this work, a facile strategy for sensitive and low fouling detection of adenosine triphosphate (ATP) is developed through the construction of a mixed self-assembled biosensing interface, which was composed of zwitterionic peptide (antifouling material) and ATP aptamer (bio-recognition element). The peptide and aptamer (both containing thiol groups) were simultaneously self-assembled onto gold electrode surface electrodeposited with gold nanoparticles. The developed aptasensor possessed high selectivity and sensitivity for ATP, and it showed a wide linear response range towards ATP from 0.1pM to 5nM. Owing to the presence of peptide with excellent antifouling property in the biosensing interface, the aptasensor can detect ATP in complex biological media with remarkably reduced biofouling or nonspecific adsorption effect. Moreover, it can directly detect ATP in 1% human whole blood without suffering from any significant interference, indicating its great potential for practical assaying of ATP in biological samples. Copyright © 2017 Elsevier B.V. All rights reserved.

A Unifying Review of Bioassay-Guided Fractionation, Effect-Directed Analysis and Related Techniques

PubMed Central

Weller, Michael G.

2012-01-01

The success of modern methods in analytical chemistry sometimes obscures the problem that the ever increasing amount of analytical data does not necessarily give more insight of practical relevance. As alternative approaches, toxicity- and bioactivity-based assays can deliver valuable information about biological effects of complex materials in humans, other species or even ecosystems. However, the observed effects often cannot be clearly assigned to specific chemical compounds. In these cases, the establishment of an unambiguous cause-effect relationship is not possible. Effect-directed analysis tries to interconnect instrumental analytical techniques with a biological/biochemical entity, which identifies or isolates substances of biological relevance. Successful application has been demonstrated in many fields, either as proof-of-principle studies or even for complex samples. This review discusses the different approaches, advantages and limitations and finally shows some practical examples. The broad emergence of effect-directed analytical concepts might lead to a true paradigm shift in analytical chemistry, away from ever growing lists of chemical compounds. The connection of biological effects with the identification and quantification of molecular entities leads to relevant answers to many real life questions. PMID:23012539

Theory of meiotic spindle assembly

NASA Astrophysics Data System (ADS)

Furthauer, Sebastian; Foster, Peter; Needleman, Daniel; Shelley, Michael

2016-11-01

The meiotic spindle is a biological structure that self assembles from the intracellular medium to separate chromosomes during meiosis. It consists of filamentous microtubule (MT) proteins that interact through the fluid in which they are suspended and via the associated molecules that orchestrate their behavior. We aim to understand how the interplay between fluid medium, MTs, and regulatory proteins allows this material to self-organize into the spindle's highly stereotyped shape. To this end we develop a continuum model that treats the spindle as an active liquid crystal with MT turnover. In this active material, molecular motors, such as dyneins which collect MT minus ends and kinesins which slide MTs past each other, generate active fluid and material stresses. Moreover nucleator proteins that are advected with and transported along MTs control the nucleation and depolymerization of MTs. This theory captures the growth process of meiotic spindles, their shapes, and the essential features of many perturbation experiments. It thus provides a framework to think about the physics of this complex biological suspension.

[Presence of lactoferrin (LF) in lymphocutaneous sporotrichosis. Yeast-bound antimicrobial peptide].

PubMed

Palma-Ramos, Alejandro; Castrillón-Rivera, Laura E; Vega-Mémije, María Elisa; Arenas-Guzmán, Roberto; Rangel-Gamboa, Lucía

Sporotrichosis is a common subcutaneous mycosis in Latin America, produced by dimorphic fungi belong to Sporothrix schenckii complex of cryptic species. Infection is acquired by traumatic inoculation with contaminated organic material. Host immune response includes polymorphonuclear neutrophils chemotaxis and release of granular components. Lactoferrin is a protein member of the transferrin family of iron-binding proteins, present inside polymorphonuclear granular structure, and has been reported to affect growth and development of infectious agents, including fungal organisms. Nevertheless, lactoferrin expression in sporotrichosis infections has not been reported yet. To determine the expression of lactoferrin using immunohistochemical staining in sporotrichosis human infection. The dermatology department's files during a period of five years were reviewed; cases with a diagnosis of sporotrichosis were selected and lactoferrin immunostaining was performed when enough biological material was available. Three cases with a diagnosis of sporotrichosis and adequate biological material on paraffin block were identified. In all cases, lactoferrin immunostaining was positive around yeast cell.

Nano- and microstructured materials for in vitro studies of the physiology of vascular cells

PubMed Central

Chen, Hao; Biela, Sarah A; Kaufmann, Dieter

2016-01-01

The extracellular environment of vascular cells in vivo is complex in its chemical composition, physical properties, and architecture. Consequently, it has been a great challenge to study vascular cell responses in vitro, either to understand their interaction with their native environment or to investigate their interaction with artificial structures such as implant surfaces. New procedures and techniques from materials science to fabricate bio-scaffolds and surfaces have enabled novel studies of vascular cell responses under well-defined, controllable culture conditions. These advancements are paving the way for a deeper understanding of vascular cell biology and materials–cell interaction. Here, we review previous work focusing on the interaction of vascular smooth muscle cells (SMCs) and endothelial cells (ECs) with materials having micro- and nanostructured surfaces. We summarize fabrication techniques for surface topographies, materials, geometries, biochemical functionalization, and mechanical properties of such materials. Furthermore, various studies on vascular cell behavior and their biological responses to micro- and nanostructured surfaces are reviewed. Emphasis is given to studies of cell morphology and motility, cell proliferation, the cytoskeleton and cell-matrix adhesions, and signal transduction pathways of vascular cells. We finalize with a short outlook on potential interesting future studies. PMID:28144512

Supramolecular effects as driving force of dipyrrin based functional materials engineering

NASA Astrophysics Data System (ADS)

Banakova, E.; Bobrov, A.; Kazak, A.; Marfin, Yu; Merkushev, D.; Molchanov, E.; Rumyantsev, E.; Shipalova, M.; Usoltsev, S.; Vodyanova, O.

2018-01-01

Dipyrrin based luminophores are of major interest in different areas of chemistry, material science and molecular biology. Vast variety of the structures with dipyrrin motif were synthesized and investigated up to date. Modern trend in the dipyrrin chemistry is the aimed functionalization of the ligand or complex structure allowing to gain the mechanism based on supramolecular interactions for controlling spectral and photophysical characteristics of compounds for tuning practically valuable properties for specific tasks. Presented paper summarize the results of our research group, working in the field of dipyrrin complexes with p-elements: synthesis, spectral characteristics evaluation and possibilities of practical application investigation. Discussion is focused on the opportunities of molecules preorganization for achieving the supramolecular interactions causing the tuning of fluorescence of the compounds in solutions, polymeric matrices and thin films.

The Characterization of Material Properties and Structural Dynamics of the Manduca Sexta Forewing for Application to Flapping Wing Micro Air Vehicle Design

DTIC Science & Technology

2012-09-13

2.1.1 Wing Morphology. Insect wings are formed from a complex makeup of polymer based chains, Chitin , that form the Cuticle, which provides the strong... Chitin , a long-chain polymer and a deriva- tive of glucose, is the main component of the exoskeletons and wings of insects . Due to the ability of the...biological specimen to vary the bonding chains, assemblage of nanofibers, and crystalline structure, the material properties of chitin can vary over a

Employing ASHRAE Standard 62-1989 in urban building environments

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

Meckler, M.

1991-01-01

Indoor air quality (IAQ) is a result of a complex relationship between the contamination sources in a building, the ventilation rate, and the dilution of the indoor air contaminant concentrations with outdoor air. This complex relationship is further complicated by outdoor sources used for dilution air and pollution sinks in a building which may modify or remove contaminants. This paper reports that the factors influencing IAQ in a building are: emissions from indoor contamination sources, dilution rate of outdoor ventilation air, quality of the outdoor dilution air, and systems and materials in a building that change the concentrations of contaminants.more » Emissions from contaminant sources in a building are the primary determinant of IAQ. They include building materials, consumer products, cleaners, furnishings, combustion appliances and processes, biological growth from standing water and damp surfaces and building occupants. These factors combined with the emissions from indoor air contamination sources such as synthetic building materials, modern office equipment, and cleaning and biological agents are believed to increase the levels of indoor air contamination. The physiological reactions to these contaminants, coupled with the psychosocial stresses of the modern office environment, and the wide range of human susceptibility to indoor air contaminants led to the classification of acute building sicknesses: sick building syndrome (SBS), building-related illness (BRI), and multiple chemical sensitivity (MCS).« less

Facile synthesis of zwitterionic polymer-coated core-shell magnetic nanoparticles for highly specific capture of N-linked glycopeptides

NASA Astrophysics Data System (ADS)

Chen, Yajing; Xiong, Zhichao; Zhang, Lingyi; Zhao, Jiaying; Zhang, Quanqing; Peng, Li; Zhang, Weibing; Ye, Mingliang; Zou, Hanfa

2015-02-01

Highly selective and efficient capture of glycosylated proteins and peptides from complex biological samples is of profound significance for the discovery of disease biomarkers in biological systems. Recently, hydrophilic interaction liquid chromatography (HILIC)-based functional materials have been extensively utilized for glycopeptide enrichment. However, the low amount of immobilized hydrophilic groups on the affinity material has limited its specificity, detection sensitivity and binding capacity in the capture of glycopeptides. Herein, a novel affinity material was synthesized to improve the binding capacity and detection sensitivity for glycopeptides by coating a poly(2-(methacryloyloxy)ethyl)-dimethyl-(3-sulfopropyl) ammonium hydroxide (PMSA) shell onto Fe3O4@SiO2 nanoparticles, taking advantage of reflux-precipitation polymerization for the first time (denoted as Fe3O4@SiO2@PMSA). The thick polymer shell endows the nanoparticles with excellent hydrophilic property and several functional groups on the polymer chains. The resulting Fe3O4@SiO2@PMSA demonstrated an outstanding ability for glycopeptide enrichment with high selectivity, extremely high detection sensitivity (0.1 fmol), large binding capacity (100 mg g-1), high enrichment recovery (above 73.6%) and rapid magnetic separation. Furthermore, in the analysis of real complicated biological samples, 905 unique N-glycosylation sites from 458 N-glycosylated proteins were reliably identified in three replicate analyses of a 65 μg protein sample extracted from mouse liver, showing the great potential of Fe3O4@SiO2@PMSA in the detection and identification of low-abundance N-linked glycopeptides in biological samples.Highly selective and efficient capture of glycosylated proteins and peptides from complex biological samples is of profound significance for the discovery of disease biomarkers in biological systems. Recently, hydrophilic interaction liquid chromatography (HILIC)-based functional materials have been extensively utilized for glycopeptide enrichment. However, the low amount of immobilized hydrophilic groups on the affinity material has limited its specificity, detection sensitivity and binding capacity in the capture of glycopeptides. Herein, a novel affinity material was synthesized to improve the binding capacity and detection sensitivity for glycopeptides by coating a poly(2-(methacryloyloxy)ethyl)-dimethyl-(3-sulfopropyl) ammonium hydroxide (PMSA) shell onto Fe3O4@SiO2 nanoparticles, taking advantage of reflux-precipitation polymerization for the first time (denoted as Fe3O4@SiO2@PMSA). The thick polymer shell endows the nanoparticles with excellent hydrophilic property and several functional groups on the polymer chains. The resulting Fe3O4@SiO2@PMSA demonstrated an outstanding ability for glycopeptide enrichment with high selectivity, extremely high detection sensitivity (0.1 fmol), large binding capacity (100 mg g-1), high enrichment recovery (above 73.6%) and rapid magnetic separation. Furthermore, in the analysis of real complicated biological samples, 905 unique N-glycosylation sites from 458 N-glycosylated proteins were reliably identified in three replicate analyses of a 65 μg protein sample extracted from mouse liver, showing the great potential of Fe3O4@SiO2@PMSA in the detection and identification of low-abundance N-linked glycopeptides in biological samples. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05955g

The design and construction of a cost-efficient confocal laser scanning microscope

NASA Astrophysics Data System (ADS)

Xi, Peng; Rajwa, Bartlomiej; Jones, James T.; Robinson, J. Paul

2007-03-01

The optical dissection ability of confocal microscopy makes it a powerful tool for biological materials. However, the cost and complexity of confocal scanning laser microscopy hinders its wide application in education. We describe the construction of a simplified confocal scanning laser microscope and demonstrate three-dimensional projection based on cost-efficient commercial hardware, together with available open source software.

Cysteamine-based cell-permeable Zn(2+)-specific molecular bioimaging materials: from animal to plant cells.

PubMed

Sinha, Sougata; Dey, Gourab; Kumar, Sunil; Mathew, Jomon; Mukherjee, Trinetra; Mukherjee, Subhrakanti; Ghosh, Subrata

2013-11-27

Structure-interaction/fluorescence relationship studies led to the development of a small chemical library of Zn(2+)-specific cysteamine-based molecular probes. The probe L5 with higher excitation/emission wavelengths, which absorbs in the visible region and emits in the green, was chosen as a model imaging material for biological studies. After successful imaging of intracellular zinc in four different kinds of cells including living organisms, plant, and animal cells, in vivo imaging potential of L5 was evaluated using plant systems. In vivo imaging of translocation of zinc through the stem of a small herb with a transparent stem, Peperomia pellucida, confirmed the stability of L5 inside biological systems and the suitability of L5 for real-time analysis. Similarly, fluorescence imaging of zinc in gram sprouts revealed the efficacy of the probe in the detection and localization of zinc in cereal crops. This imaging technique will help in knowing the efficiency of various techniques used for zinc enrichment of cereal crops. Computational analyses were carried out to better understand the structure, the formation of probe-Zn(2+) complexes, and the emission properties of these complexes.

Isolation, Separation, and Preconcentration of Biologically Active Compounds from Plant Matrices by Extraction Techniques.

PubMed

Raks, Victoria; Al-Suod, Hossam; Buszewski, Bogusław

2018-01-01

Development of efficient methods for isolation and separation of biologically active compounds remains an important challenge for researchers. Designing systems such as organomineral composite materials that allow extraction of a wide range of biologically active compounds, acting as broad-utility solid-phase extraction agents, remains an important and necessary task. Selective sorbents can be easily used for highly selective and reliable extraction of specific components present in complex matrices. Herein, state-of-the-art approaches for selective isolation, preconcentration, and separation of biologically active compounds from a range of matrices are discussed. Primary focus is given to novel extraction methods for some biologically active compounds including cyclic polyols, flavonoids, and oligosaccharides from plants. In addition, application of silica-, carbon-, and polymer-based solid-phase extraction adsorbents and membrane extraction for selective separation of these compounds is discussed. Potential separation process interactions are recommended; their understanding is of utmost importance for the creation of optimal conditions to extract biologically active compounds including those with estrogenic properties.

On the Use of Machine Learning Techniques for the Mechanical Characterization of Soft Biological Tissues.

PubMed

Cilla, M; Pérez-Rey, I; Martínez, M A; Peña, Estefania; Martínez, Javier

2018-06-23

Motivated by the search for new strategies for fitting a material model, a new approach is explored in the present work. The use of numerical and complex algorithms based on machine learning techniques such as support vector machines for regression, bagged decision trees and artificial neural networks is proposed for solving the parameter identification of constitutive laws for soft biological tissues. First, the mathematical tools were trained with analytical uniaxial data (circumferential and longitudinal directions) as inputs, and their corresponding material parameters of the Gasser, Ogden and Holzapfel strain energy function as outputs. The train and test errors show great efficiency during the training process in finding correlations between inputs and outputs; besides, the correlation coefficients were very close to 1. Second, the tool was validated with unseen observations of analytical circumferential and longitudinal uniaxial data. The results show an excellent agreement between the prediction of the material parameters of the SEF and the analytical curves. Finally, data from real circumferential and longitudinal uniaxial tests on different cardiovascular tissues were fitted, thus the material model of these tissues was predicted. We found that the method was able to consistently identify model parameters, and we believe that the use of these numerical tools could lead to an improvement in the characterization of soft biological tissues. This article is protected by copyright. All rights reserved.

Modified Organosilica Core-Shell Nanoparticles for Stable pH Sensing in Biological Solutions.

PubMed

Robinson, Kye J; Huynh, Gabriel T; Kouskousis, Betty P; Fletcher, Nicholas L; Houston, Zachary H; Thurecht, Kristofer J; Corrie, Simon R

2018-04-19

Continuous monitoring using nanoparticle-based sensors has been successfully employed in complex biological systems, yet the sensors still suffer from poor long-term stability partially because of the scaffold materials chosen to date. Organosilica core-shell nanoparticles containing a mixture of covalently incorporated pH-sensitive (shell) and pH-insensitive (core) fluorophores is presented as a continuous pH sensor for application in biological media. In contrast to previous studies focusing on similar materials, we sought to investigate the sensor characteristics (dynamic range, sensitivity, response time, stability) as a function of material properties. The ratio of the fluorescence intensities at specific wavelengths was found to be highly sensitive to pH over a physiologically relevant range (4.5-8) with a response time of <100 ms, significantly faster than that of previously reported response times using silica-based particles. Particles produced stable, pH-specific signals when stored at room temperature for more than 80 days. Finally, we demonstrated that the nanosensors successfully monitored the pH of a bacterial culture over 15 h and that pH changes in the skin of mouse cadavers could also be observed via in vivo fluorescence imaging following subcutaneous injection. The understanding gained from linking sensor characteristics and material properties will inform the next generation of optical nanosensors for continuous-monitoring applications.

Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns

PubMed Central

König, Harald; Frank, Daniel; Heil, Reinhard; Coenen, Christopher

2013-01-01

New organisms and biological systems designed to satisfy human needs are among the aims of synthetic genomics and synthetic biology. Synthetic biology seeks to model and construct biological components, functions and organisms that do not exist in nature or to redesign existing biological systems to perform new functions. Synthetic genomics, on the other hand, encompasses technologies for the generation of chemically-synthesized whole genomes or larger parts of genomes, allowing to simultaneously engineer a myriad of changes to the genetic material of organisms. Engineering complex functions or new organisms in synthetic biology are thus progressively becoming dependent on and converging with synthetic genomics. While applications from both areas have been predicted to offer great benefits by making possible new drugs, renewable chemicals or clean energy, they have also given rise to concerns about new safety, environmental and socio-economic risks – stirring an increasingly polarizing debate. Here we intend to provide an overview on recent progress in biomedical and biotechnological applications of synthetic genomics and synthetic biology as well as on arguments and evidence related to their possible benefits, risks and governance implications. PMID:23997647

Detection and drug delivery from superhydrophobic materials

NASA Astrophysics Data System (ADS)

Falde, Eric John

The wetting of a rough material is controlled by surface chemistry and morphology, the liquid phase, solutes, and surfactants that affect the surface tension with the gas phase, and environmental conditions such as temperature and pressure. Materials with high (>150°) apparent contact angles are known as superhydrophobic and are very resistant to wetting. However, in complex biological mixtures eventually protein adsorbs, fouling the surface and facilitating wetting on time scales from seconds to months. The work here uses the partially-wetted (Cassie-Baxter) to fully-wetted (Wenzel) state transition to control drug delivery and to perform surfactant detection via surface tension using hydrophobic and superhydrophobic materials. First there is an overview of the physics of the non-wetting state and the transition to wetting. Then there is a review of how wetting can be controlled by outside stimuli and applications of these materials. Next there is work presented on controlling drug release using superhydrophobic materials with controlled wetting rates, with both in vitro and in vivo results. Then there is work on developing a sensor based on this wetting state transition and its applications toward detecting solute levels in biological fluids for point-of-care diagnosis. Finally, there is work presented on using these sensors for detecting the alcohol content in wine and spirits.

Controlled droplet microfluidic systems for multistep chemical and biological assays.

PubMed

Kaminski, T S; Garstecki, P

2017-10-16

Droplet microfluidics is a relatively new and rapidly evolving field of science focused on studying the hydrodynamics and properties of biphasic flows at the microscale, and on the development of systems for practical applications in chemistry, biology and materials science. Microdroplets present several unique characteristics of interest to a broader research community. The main distinguishing features include (i) large numbers of isolated compartments of tiny volumes that are ideal for single cell or single molecule assays, (ii) rapid mixing and negligible thermal inertia that all provide excellent control over reaction conditions, and (iii) the presence of two immiscible liquids and the interface between them that enables new or exotic processes (the synthesis of new functional materials and structures that are otherwise difficult to obtain, studies of the functions and properties of lipid and polymer membranes and execution of reactions at liquid-liquid interfaces). The most frequent application of droplet microfluidics relies on the generation of large numbers of compartments either for ultrahigh throughput screens or for the synthesis of functional materials composed of millions of droplets or particles. Droplet microfluidics has already evolved into a complex field. In this review we focus on 'controlled droplet microfluidics' - a portfolio of techniques that provide convenient platforms for multistep complex reaction protocols and that take advantage of automated and passive methods of fluid handling on a chip. 'Controlled droplet microfluidics' can be regarded as a group of methods capable of addressing and manipulating droplets in series. The functionality and complexity of controlled droplet microfluidic systems can be positioned between digital microfluidics (DMF) addressing each droplet individually using 2D arrays of electrodes and ultrahigh throughput droplet microfluidics focused on the generation of hundreds of thousands or even millions of picoliter droplets that cannot be individually addressed by their location on a chip.

Ferrocene-containing non-interlocked molecular machines.

PubMed

Scottwell, Synøve Ø; Crowley, James D

2016-02-11

Ferrocene is the prototypical organometallic sandwich complex and despite over 60 years passing since the discovery and elucidation of ferrocene's structure, research into ferrocene-containing compounds continues to grow as potential new applications in catalysis, biology and the material sciences are found. Ferrocene is chemically robust and readily functionalized which enables its facile incorporation into more complex molecular systems. This coupled with ferrocene's reversible redox properties and ability function as a "molecular ball bearing" has led to the use of ferrocene as a component in wide range of interlocked and non-interlocked synthetic molecular machine systems. This review will focus on the exploitation of ferrocene (and related sandwich complexes) for the development of non-interlocked synthetic molecular machines.

Realisation of a holographic microlaser scalpel using a digital micromirror device

NASA Astrophysics Data System (ADS)

Zwick, Susanne; Warber, Michael; Haist, Tobias; Osten, Wolfgang

2007-06-01

Modern spatial light modulators (SLM) enable the generation of more or less arbitrary light fields in three dimensions. Such light fields can be used for different future applications in the field of biomedical optics. One example is the processing/cutting of biological material on a microscopic scale. By displaying computer generated holograms by suitable SLMs it is possible to ablate complex structures into three-dimensional objects without scanning with very high accuracy on a microscopic scale. To effectively cut biological materials by light, pulsed ultraviolet light is preferable. We will present a combined setup of a holographic laser scalpel using a digital micromirror device (DMD) and holographic optical tweezers using a liquid crystal display (LCD). The setup enables to move and cut or process micro-scaled objects like biological cells or tissue in three dimensions with high accuracy and without any mechanical movements just by changing the hologram displayed by the SLMs. We will show that holograms can be used to compensate aberrations implemented by the DMD or other optical components of the setup. Also we can generate arbitrary light fields like stripes, circles or arbitrary curves. Additionally we will present results for the fast optimization of holograms for the system. In particular we will show results obtained by implementing iterative Fourier transform based algorithms on a standard consumer graphics board (Nvidia 8800GLX). By this approach we are able to compute more than 360 complex 2D FFTs (512 × 512 pixels) per second with floating point precision.

Syntheses and Functionalizations of Porphyrin Macrocycles

PubMed Central

Vicente, Maria da G.H.; Smith, Kevin M.

2014-01-01

Porphyrin macrocycles have been the subject of intense study in the last century because they are widely distributed in nature, usually as metal complexes of either iron or magnesium. As such, they serve as the prosthetic groups in a wide variety of primary metabolites, such as hemoglobins, myoglobins, cytochromes, catalases, peroxidases, chlorophylls, and bacteriochlorophylls; these compounds have multiple applications in materials science, biology and medicine. This article describes current methodology for preparation of simple, symmetrical model porphyrins, as well as more complex protocols for preparation of unsymmetrically substituted porphyrin macrocycles similar to those found in nature. The basic chemical reactivity of porphyrins and metalloporphyrin is also described, including electrophilic and nucleophilic reactions, oxidations, reductions, and metal-mediated cross-coupling reactions. Using the synthetic approaches and reactivity profiles presented, eventually almost any substituted porphyrin system can be prepared for applications in a variety of areas, including in catalysis, electron transport, model biological systems and therapeutics. PMID:25484638

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials.

PubMed

Le Feuvre, Rosalind A; Scrutton, Nigel S

2018-06-01

Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials , where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal.

Chlorodifluoromethane-triggered formation of difluoromethylated arenes catalysed by palladium

NASA Astrophysics Data System (ADS)

Feng, Zhang; Min, Qiao-Qiao; Fu, Xia-Ping; An, Lun; Zhang, Xingang

2017-09-01

Difluoromethylated aromatic compounds are of increasing importance in pharmaceuticals, agrochemicals and materials. Chlorodifluoromethane (ClCF2H), an inexpensive, abundant and widely used industrial raw material, represents the ideal and most straightforward difluoromethylating reagent, but introduction of the difluoromethyl group (CF2H) from ClCF2H into aromatics has not been reported. Here, we describe a direct palladium-catalysed difluoromethylation method for coupling ClCF2H with arylboronic acids and esters to generate difluoromethylated arenes with high efficiency. The reaction exhibits a remarkably broad substrate scope, including heteroarylboronic acids, and was used for difluoromethylation of a range of pharmaceuticals and biologically active compounds. Preliminary mechanistic studies revealed that a palladium difluorocarbene intermediate is involved in the reaction. Although numerous metal-difluorocarbene complexes have been prepared, the catalytic synthesis of difluoromethylated or difluoromethylenated compounds involving metal-difluorocarbene complexes has not received much attention. This new reaction therefore also opens the door to understand metal-difluorocarbene complex catalysed reactions.

Synthetic Biomaterials to Rival Nature's Complexity-a Path Forward with Combinatorics, High-Throughput Discovery, and High-Content Analysis.

PubMed

Zhang, Douglas; Lee, Junmin; Kilian, Kristopher A

2017-10-01

Cells in tissue receive a host of soluble and insoluble signals in a context-dependent fashion, where integration of these cues through a complex network of signal transduction cascades will define a particular outcome. Biomaterials scientists and engineers are tasked with designing materials that can at least partially recreate this complex signaling milieu towards new materials for biomedical applications. In this progress report, recent advances in high throughput techniques and high content imaging approaches that are facilitating the discovery of efficacious biomaterials are described. From microarrays of synthetic polymers, peptides and full-length proteins, to designer cell culture systems that present multiple biophysical and biochemical cues in tandem, it is discussed how the integration of combinatorics with high content imaging and analysis is essential to extracting biologically meaningful information from large scale cellular screens to inform the design of next generation biomaterials. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Calcifying tissue regeneration via biomimetic materials chemistry

PubMed Central

Green, David W.; Goto, Tazuko K.; Kim, Kye-Seong; Jung, Han-Sung

2014-01-01

Materials chemistry is making a fundamental impact in regenerative sciences providing many platforms for tissue development. However, there is a surprising paucity of replacements that accurately mimic the structure and function of the structural fabric of tissues or promote faithful tissue reconstruction. Methodologies in biomimetic materials chemistry have shown promise in replicating morphologies, architectures and functional building blocks of acellular mineralized tissues dentine, enamel and bone or that can be used to fully regenerate them with integrated cell populations. Biomimetic materials chemistry encompasses the two processes of crystal formation and mineralization of crystals into inorganic formations on organic templates. This review will revisit the successes of biomimetics materials chemistry in regenerative medicine, including coccolithophore simulants able to promote in vivo bone formation. In-depth knowledge of biomineralization throughout evolution informs the biomimetic materials chemist of the most effective techniques for regenerative framework construction exemplified via exploitation of liquid crystals (LCs) and complex self-organizing media. Therefore, a new innovative direction would be to create chemical environments that perform reaction–diffusion exchanges as the basis for building complex biomimetic inorganic structures. This has evolved widely in biology, as have LCs, serving as self-organizing templates in pattern formation of structural biomaterials. For instance, a study is highlighted in which artificially fabricated chiral LCs, made from bacteriophages are transformed into a faithful copy of enamel. While chemical-based strategies are highly promising at creating new biomimetic structures there are limits to the degree of complexity that can be generated. Thus, there may be good reason to implement living or artificial cells in ‘morphosynthesis’ of complex inorganic constructs. In the future, cellular construction is probably key to instruct building of ultimate biomimetic hierarchies with a totality of functions. PMID:25320063

37 CFR 1.801 - Biological material.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Biological material. 1.801... Biological Material § 1.801 Biological material. For the purposes of these regulations pertaining to the deposit of biological material for purposes of patents for inventions under 35 U.S.C. 101, the term...

37 CFR 1.801 - Biological material.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Biological material. 1.801... Biological Material § 1.801 Biological material. For the purposes of these regulations pertaining to the deposit of biological material for purposes of patents for inventions under 35 U.S.C. 101, the term...

37 CFR 1.801 - Biological material.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Biological material. 1.801... Biological Material § 1.801 Biological material. For the purposes of these regulations pertaining to the deposit of biological material for purposes of patents for inventions under 35 U.S.C. 101, the term...

Connectivity of streams and wetlands to downstream waters: An integrated systems framework

USGS Publications Warehouse

Leibowitz, Scott G.; Wigington, Parker J.; Schoefield, Kate A.; Alexander, Laurie C.; Vanderhoof, Melanie; Golden, Heather E.

2018-01-01

Interest in connectivity has increased in the aquatic sciences, partly because of its relevance to the Clean Water Act. This paper has two objectives: (1) provide a framework to understand hydrological, chemical, and biological connectivity, focusing on how headwater streams and wetlands connect to and contribute to rivers; and (2) briefly review methods to quantify hydrological and chemical connectivity. Streams and wetlands affect river structure and function by altering material and biological fluxes to the river; this depends on two factors: (1) functions within streams and wetlands that affect material fluxes; and (2) connectivity (or isolation) from streams and wetlands to rivers that allows (or prevents) material transport between systems. Connectivity can be described in terms of frequency, magnitude, duration, timing, and rate of change. It results from physical characteristics of a system, e.g., climate, soils, geology, topography, and the spatial distribution of aquatic components. Biological connectivity is also affected by traits and behavior of the biota. Connectivity can be altered by human impacts, often in complex ways. Because of variability in these factors, connectivity is not constant but varies over time and space. Connectivity can be quantified with field‐based methods, modeling, and remote sensing. Further studies using these methods are needed to classify and quantify connectivity of aquatic ecosystems and to understand how impacts affect connectivity.

Biologically inspired crack delocalization in a high strain-rate environment.

PubMed

Knipprath, Christian; Bond, Ian P; Trask, Richard S

2012-04-07

Biological materials possess unique and desirable energy-absorbing mechanisms and structural characteristics worthy of consideration by engineers. For example, high levels of energy dissipation at low strain rates via triggering of crack delocalization combined with interfacial hardening by platelet interlocking are observed in brittle materials such as nacre, the iridescent material in seashells. Such behaviours find no analogy in current engineering materials. The potential to mimic such toughening mechanisms on different length scales now exists, but the question concerning their suitability under dynamic loading conditions and whether these mechanisms retain their energy-absorbing potential is unclear. This paper investigates the kinematic behaviour of an 'engineered' nacre-like structure within a high strain-rate environment. A finite-element (FE) model was developed which incorporates the pertinent biological design features. A parametric study was carried out focusing on (i) the use of an overlapping discontinuous tile arrangement for crack delocalization and (ii) application of tile waviness (interfacial hardening) for improved post-damage behaviour. With respect to the material properties, the model allows the permutation and combination of a variety of different material datasets. The advantage of such a discontinuous material shows notable improvements in sustaining high strain-rate deformation relative to an equivalent continuous morphology. In the case of the continuous material, the shockwaves propagating through the material lead to localized failure while complex shockwave patterns are observed in the discontinuous flat tile arrangement, arising from platelet interlocking. The influence of the matrix properties on impact performance is investigated by varying the dominant material parameters. The results indicate a deceleration of the impactor velocity, thus delaying back face nodal displacement. A final series of FE models considered the identification of an optimized configuration as a function of tile waviness and matrix properties. In the combined model, the optimized configuration was capable of stopping the ballistic threat, thus indicating the potential for bioinspired toughened synthetic systems to defeat high strain-rate threats.

Biologically inspired crack delocalization in a high strain-rate environment

PubMed Central

Knipprath, Christian; Bond, Ian P.; Trask, Richard S.

2012-01-01

Biological materials possess unique and desirable energy-absorbing mechanisms and structural characteristics worthy of consideration by engineers. For example, high levels of energy dissipation at low strain rates via triggering of crack delocalization combined with interfacial hardening by platelet interlocking are observed in brittle materials such as nacre, the iridescent material in seashells. Such behaviours find no analogy in current engineering materials. The potential to mimic such toughening mechanisms on different length scales now exists, but the question concerning their suitability under dynamic loading conditions and whether these mechanisms retain their energy-absorbing potential is unclear. This paper investigates the kinematic behaviour of an ‘engineered’ nacre-like structure within a high strain-rate environment. A finite-element (FE) model was developed which incorporates the pertinent biological design features. A parametric study was carried out focusing on (i) the use of an overlapping discontinuous tile arrangement for crack delocalization and (ii) application of tile waviness (interfacial hardening) for improved post-damage behaviour. With respect to the material properties, the model allows the permutation and combination of a variety of different material datasets. The advantage of such a discontinuous material shows notable improvements in sustaining high strain-rate deformation relative to an equivalent continuous morphology. In the case of the continuous material, the shockwaves propagating through the material lead to localized failure while complex shockwave patterns are observed in the discontinuous flat tile arrangement, arising from platelet interlocking. The influence of the matrix properties on impact performance is investigated by varying the dominant material parameters. The results indicate a deceleration of the impactor velocity, thus delaying back face nodal displacement. A final series of FE models considered the identification of an optimized configuration as a function of tile waviness and matrix properties. In the combined model, the optimized configuration was capable of stopping the ballistic threat, thus indicating the potential for bioinspired toughened synthetic systems to defeat high strain-rate threats. PMID:21880614

Electro-Statically Stricted Polymers (ESSP)

NASA Technical Reports Server (NTRS)

Liu, C.; Bar-Cohen, Y.; Leary, S.

1999-01-01

Miniature, lightweight, miser actuators that operate similar to biological muscles can be used to develop robotic devices with unmatched capabilities and impact many technology areas. Electroactive polymers (EAP) offer the potential to producing such actuators and their main attractive feature is their ability to induce relatively large bending or longitudinal strain. EAP actuators can change the paradigm about the complexity of robots, where robotic components such as motors, gears, bearings, and others can be eliminated with simple drive mechanisms. Generally, these materials produce a relatively low force and the applications that can be considered at the current state of the art are relatively limited. While improved material are being developed there is a need for methods to develop longitudinal actuators that can contract similar to muscles. In this study, the authors began investigating the electromechanical behavior of polymers in reaction to a complex configuration of electric fields. A computer model was used to simulate the electromechanical response. Efforts were made to develop both the material basis as well as the electromechanical modeling of the actuator.

Development of force-detected THz-ESR measurement system and its application to metal porphyrin complexes

NASA Astrophysics Data System (ADS)

Takahashi, Hideyuki; Okamoto, Tsubasa; Ohmichi, Eiji; Ohta, Hitoshi

Electron spin resonance spectroscopy in the terahertz region (THz-ESR) is a promising technique to study biological materials such as metalloproteins because it directly probes the metal ion sites that play an important role in the emergence of functionality. By combining THz-ESR with force detection, the samples mass is reduced to the order of ng. This feature is of great advantage because the sample preparation process of biological materials is time-consuming. We developed a force-detected THz-ESR system utilizing optical interferometry for precise cantilever displacement measurement. In order to suppress the sensitivity fluctuation and instability of cantilever dynamics under high magnetic field, the tuning of interferometer is feedback-controlled during a measurement. By using this system, we successfully observed the ESR signal of hemin, which is a model substance of hemoglobin and myoglobin, in THz region.

Fort Collins Science Center Ecosystem Dynamics Branch

USGS Publications Warehouse

Wilson, Jim; Melcher, C.; Bowen, Z.

2009-01-01

Complex natural resource issues require understanding a web of interactions among ecosystem components that are (1) interdisciplinary, encompassing physical, chemical, and biological processes; (2) spatially complex, involving movements of animals, water, and airborne materials across a range of landscapes and jurisdictions; and (3) temporally complex, occurring over days, weeks, or years, sometimes involving response lags to alteration or exhibiting large natural variation. Scientists in the Ecosystem Dynamics Branch of the U.S. Geological Survey, Fort Collins Science Center, investigate a diversity of these complex natural resource questions at the landscape and systems levels. This Fact Sheet describes the work of the Ecosystems Dynamics Branch, which is focused on energy and land use, climate change and long-term integrated assessments, herbivore-ecosystem interactions, fire and post-fire restoration, and environmental flows and river restoration.

Molecular Library Synthesis Using Complex Substrates: Expanding the Framework of Triterpenoids

PubMed Central

Ignatenko, Vasily A.; Han, Yong; Tochtrop, Gregory P.

2013-01-01

The remodelling of a natural product core framework by means of diversity-oriented synthesis (DOS) is a valuable approach to access diverse/biologically relevant chemical space and to overcome the limitations of combinatorial-type compounds. Here we provide proof of principle and a thorough conformational analysis for a general strategy whereby the inherent complexity of a starting material is used to define the regio- and stereochemical outcomes of reactions in chemical library construction. This is in contrast to the traditional DOS logic employing reaction development and catalysis to drive library diversity PMID:23245400

Development of new smart materials and spinning systems inspired by natural silks and their applications

NASA Astrophysics Data System (ADS)

Cheng, Jie; Lee, Sang-Hoon

2015-12-01

Silks produced by spiders and silkworms are charming natural biological materials with highly optimized hierarchical structures and outstanding physicomechanical properties. The superior performance of silks relies on the integration of a unique protein sequence, a distinctive spinning process, and complex hierarchical structures. Silks have been prepared to form a variety of morphologies and are widely used in diverse applications, for example, in the textile industry, as drug delivery vehicles, and as tissue engineering scaffolds. This review presents an overview of the organization of natural silks, in which chemical and physical functions are optimized, as well as a range of new materials inspired by the desire to mimic natural silk structure and synthesis.

Flow-controlled magnetic particle manipulation

DOEpatents

Grate, Jay W [West Richland, WA; Bruckner-Lea, Cynthia J [Richland, WA; Holman, David A [Las Vegas, NV

2011-02-22

Inventive methods and apparatus are useful for collecting magnetic materials in one or more magnetic fields and resuspending the particles into a dispersion medium, and optionally repeating collection/resuspension one or more times in the same or a different medium, by controlling the direction and rate of fluid flow through a fluid flow path. The methods provide for contacting derivatized particles with test samples and reagents, removal of excess reagent, washing of magnetic material, and resuspension for analysis, among other uses. The methods are applicable to a wide variety of chemical and biological materials that are susceptible to magnetic labeling, including, for example, cells, viruses, oligonucleotides, proteins, hormones, receptor-ligand complexes, environmental contaminants and the like.

Hydrolysis kinetics in anaerobic degradation of particulate organic material: an overview.

PubMed

Vavilin, V A; Fernandez, B; Palatsi, J; Flotats, X

2008-01-01

The applicability of different kinetics to the hydrolysis of particulate organic material in anaerobic digestion is discussed. Hydrolysis has traditionally been modelled according to the first-order kinetics. For complex substrate, the first-order kinetics should be modified in order to take into account hardly degradable material. It has been shown that models in which hydrolysis is coupled to the growth of hydrolytic bacteria work well at high or at fluctuant organic loading. In particular, the surface-related two-phase and the Contois models showed good fits to experimental data from a wide range of organic waste. Both models tend to the first-order kinetics at a high biomass-to-waste ratio and, for this reason, they can be considered as more general models. Examples on different inhibition processes that might affect the degradation of solid waste are reported. Acetogenesis or methanogenesis might be the rate-limiting stages in complex waste. In such cases, stimulation of hydrolysis (mechanically, chemically or biologically) may lead to a further inhibition of these stages, which ultimately affects hydrolysis as well. Since the hydrolysis process is characterized by surface and transport phenomena, new developments in spatially distributed models are considered fundamental to provide new insights in this complex process.

Assembly of micro/nanomaterials into complex, three-dimensional architectures by compressive buckling

NASA Astrophysics Data System (ADS)

Xu, Sheng; Yan, Zheng; Jang, Kyung-In; Huang, Wen; Fu, Haoran; Kim, Jeonghyun; Wei, Zijun; Flavin, Matthew; McCracken, Joselle; Wang, Renhan; Badea, Adina; Liu, Yuhao; Xiao, Dongqing; Zhou, Guoyan; Lee, Jungwoo; Chung, Ha Uk; Cheng, Huanyu; Ren, Wen; Banks, Anthony; Li, Xiuling; Paik, Ungyu; Nuzzo, Ralph G.; Huang, Yonggang; Zhang, Yihui; Rogers, John A.

2015-01-01

Complex three-dimensional (3D) structures in biology (e.g., cytoskeletal webs, neural circuits, and vasculature networks) form naturally to provide essential functions in even the most basic forms of life. Compelling opportunities exist for analogous 3D architectures in human-made devices, but design options are constrained by existing capabilities in materials growth and assembly. We report routes to previously inaccessible classes of 3D constructs in advanced materials, including device-grade silicon. The schemes involve geometric transformation of 2D micro/nanostructures into extended 3D layouts by compressive buckling. Demonstrations include experimental and theoretical studies of more than 40 representative geometries, from single and multiple helices, toroids, and conical spirals to structures that resemble spherical baskets, cuboid cages, starbursts, flowers, scaffolds, fences, and frameworks, each with single- and/or multiple-level configurations.

Synthesis and property investigation of metal-based nanomaterials for biotechnological applications

NASA Astrophysics Data System (ADS)

Darsanasiri, Nalin Dammika

Luminescent lanthanide-based materials have drawn recent interest due to their applications in in vitro cellular imaging. Sensitive biological analysis requires optical labels with high water dispersibility & stability and excellent luminescent properties. Most literature reported lanthanide complexes with high luminescence intensity are hydrophobic and unstable, limiting their biological applications. This project was designed to incorporate a highly luminescent lanthanide beta-diketonate complex in a silica nanoparticle. Eu(btfa)3dmph complex was synthesized, which exhibits red luminescence at 614 nm with a narrow (15 nm) full with half-maximum (btfa=4,4,4-trifluoro-1-phenyl-1,3-butanedione, dmph=4,7-dimethyl,1,10-phenanthroline). A synthetic procedure was optimized to incorporate the Eu-complex in a silica-based nanoparticle with an average particle diameter of 36 nm. Eu-complex based silica nanoparticles exhibit high stability and water-dispersibility with a luminescence quantum yield of 10 %. The nanoparticles showed antimicrobial activity against clinically important E.coli, S.aureus and S.epidermidis. Synthesis, materials characterization, and antimicrobial studies of the complex and the nanoparticles was discussed in the first part of this thesis. Nanotechnology is emerging as a new interdisciplinary field combining biology, chemistry, physics, and material science. Recent advances promise developments in the synthesis, modification and practical applications of polymer-coated manganese (Mn)-based zinc oxide (ZnO) nanoparticles (NPs). The size distribution, shape, and surface modification of metal-based ZnO nanoparticles are the key factors determining their specific physical properties. Due to the strong antibacterial properties and low toxicity towards mammalian cells, ZnO NPs have been successfully used in a wide range of applications including wound dressing, protective clothing, antibacterial surfaces, food preservation, and cosmetics as biocidal and disinfecting agents. In this study, cotton textiles with antimicrobial activity were developed by incorporating polymer-coated Mn-doped ZnO nanoparticles. Antimicrobial potential of synthesized Mn-doped zinc oxide (ZnO) nanoparticles against two bacteria strains ( Escherichia coli as Gram-negative bacteria, Staphylococcus aureus as Gram-positive bacteria) in liquid and solid phases was studied in this work. Polymer-coated Mn-doped ZnO nanoparticles were prepared by the modified co-precipitation method. Characterization of the nanoparticles was carried out using Ultra-violet visible spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray powder diffraction (XRD). The average particle size of the nanoparticles was found to be less than 15 nm. The antibacterial activity of the nanoparticles was evaluated using minimum inhibitory concentration (MIC) and agar diffusion method. Disk diffusion studies revealed that the nanoparticles have excellent antimicrobial activity against E.coli and S.aureus bacterial species. Therefore, it was concluded that the polymer-coated Mn-doped ZnO nanoparticles were excellent antibacterial agents with potential clinical applications.

Role of carbon nano-materials in the analysis of biological materials by laser desorption/ionization-mass spectrometry.

PubMed

Najam-ul-Haq, M; Rainer, M; Szabó, Z; Vallant, R; Huck, C W; Bonn, G K

2007-03-10

At present, carbon nano-materials are being utilized in various procedures, especially in laser desorption/ionization-mass spectrometry (LDI-MS) for analyzing a range of analytes, which include peptides, proteins, metabolites, and polymers. Matrix-oriented LDI-MS techniques are very well established, with weak organic acids as energy-absorbing substances. Carbon materials, such as nano-tubes and fullerenes are being successfully applied in the small-mass range, where routine matrices have strong background signals. In addition, the role of carbon nano-materials is very well established in the fractionation and purification fields. Modified diamond powder and surfaces are utilized in binding peptides and proteins from complex biological fluids and analyzed by matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS). Polylysine-coated diamond is used for solid-phase extraction to pre-concentrate DNA oligonucleotides. Graphite is useful for desalting, pre-concentration, and as energy-absorbing material (matrix) in desorption/ionization. Carbon nano-tubes in their different derivatized forms are used as matrix materials for the analysis of a range of analytes, such as carbohydrates, amino acids, peptides, proteins, and some environmental samples by LDI-MS. Fullerenes are modified in different ways to bind serum entities analyzed through MALDI/TOF-MS and are subsequently utilized in their identifications. In addition, the fullerenes are a promising matrix in LDI-MS, but improvements are needed.

Leaf LIMS: A Flexible Laboratory Information Management System with a Synthetic Biology Focus.

PubMed

Craig, Thomas; Holland, Richard; D'Amore, Rosalinda; Johnson, James R; McCue, Hannah V; West, Anthony; Zulkower, Valentin; Tekotte, Hille; Cai, Yizhi; Swan, Daniel; Davey, Robert P; Hertz-Fowler, Christiane; Hall, Anthony; Caddick, Mark

2017-12-15

This paper presents Leaf LIMS, a flexible laboratory information management system (LIMS) designed to address the complexity of synthetic biology workflows. At the project's inception there was a lack of a LIMS designed specifically to address synthetic biology processes, with most systems focused on either next generation sequencing or biobanks and clinical sample handling. Leaf LIMS implements integrated project, item, and laboratory stock tracking, offering complete sample and construct genealogy, materials and lot tracking, and modular assay data capture. Hence, it enables highly configurable task-based workflows and supports data capture from project inception to completion. As such, in addition to it supporting synthetic biology it is ideal for many laboratory environments with multiple projects and users. The system is deployed as a web application through Docker and is provided under a permissive MIT license. It is freely available for download at https://leaflims.github.io .

Therapeutic synthetic gene networks.

PubMed

Karlsson, Maria; Weber, Wilfried

2012-10-01

The field of synthetic biology is rapidly expanding and has over the past years evolved from the development of simple gene networks to complex treatment-oriented circuits. The reprogramming of cell fate with open-loop or closed-loop synthetic control circuits along with biologically implemented logical functions have fostered applications spanning over a wide range of disciplines, including artificial insemination, personalized medicine and the treatment of cancer and metabolic disorders. In this review we describe several applications of interactive gene networks, a synthetic biology-based approach for future gene therapy, as well as the utilization of synthetic gene circuits as blueprints for the design of stimuli-responsive biohybrid materials. The recent progress in synthetic biology, including the rewiring of biosensing devices with the body's endogenous network as well as novel therapeutic approaches originating from interdisciplinary work, generates numerous opportunities for future biomedical applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

Biological Soft Robotics.

PubMed

Feinberg, Adam W

2015-01-01

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

Fibrous materials on polyhydroxybutyrate and ferric iron (III)-based porphyrins basis: physical-chemical and antibacterial properties

NASA Astrophysics Data System (ADS)

Olkhov, A.; Lobanov, A.; Staroverova, O.; Tyubaeva, P.; Zykova, A.; Pantyukhov, P.; Popov, A.; Iordanskii, A.

2017-02-01

Ferric iron (III)-based complexes with porphyrins are the homogenous catalysts of auto-oxidation of several biogenic substances. The most perspective carrier for functional low-molecular substances is the polymer fibers with nano-dimensional parameters. Application of natural polymers, poly-(3-hydroxybutyrate) or polylactic acid for instance, makes possible to develop fiber and matrice systems to solve ecological problem in biomedicine The aim of the article is to obtain fibrous material on poly-(3-hydroxybutyrate) and ferric iron (III)-based porphyrins basis and to examine its physical-chemical and antibacterial properties. The work is focused on possibility to apply such material to biomedical purposes. Microphotographs of obtained material showed that addition of 1% wt. ferric iron (III)-based porphyrins to PHB led to increased average diameter and disappeared spindly structures in comparison with initial PHB. Biological tests of nonwoven fabrics showed that fibers, containing ferric iron (III)-based tetraphenylporphyrins, were active in relation to bacterial test-cultures. It was found that materials on polymer and metal complexes with porphyrins basis can be applied to production of decontamination equipment in relation to pathogenic and opportunistic microorganisms.

The social neuroscience and the theory of integrative levels.

PubMed

Bello-Morales, Raquel; Delgado-García, José María

2015-01-01

The theory of integrative levels provides a general description of the evolution of matter through successive orders of complexity and integration. Along its development, material forms pass through different levels of organization, such as physical, chemical, biological or sociological. The appearance of novel structures and dynamics during this process of development of matter in complex systems has been called emergence. Social neuroscience (SN), an interdisciplinary field that aims to investigate the biological mechanisms that underlie social structures, processes, and behavior and the influences between social and biological levels of organization, has affirmed the necessity for including social context as an essential element to understand the human behavior. To do this, SN proposes a multilevel integrative approach by means of three principles: multiple determinism, nonadditive determinism and reciprocal determinism. These theoretical principles seem to share the basic tenets of the theory of integrative levels but, in this paper, we aim to reveal the differences among both doctrines. First, SN asserts that combination of neural and social variables can produce emergent phenomena that would not be predictable from a neuroscientific or social psychological analysis alone; SN also suggests that to achieve a complete understanding of social structures we should use an integrative analysis that encompasses levels of organization ranging from the genetic level to the social one; finally, SN establishes that there can be mutual influences between biological and social factors in determining behavior, accepting, therefore, a double influence, upward from biology to social level, and downward, from social level to biology. In contrast, following the theory of integrative levels, emergent phenomena are not produced by the combination of variables from two levels, but by the increment of complexity at one level. In addition, the social behavior and structures might be contemplated not as the result of mixing or summing social and biological influences, but as emergent phenomena that should be described with its own laws. Finally, following the integrative levels view, influences upward, from biology to social level, and downward, from social level to biology, might not be equivalent, since the bottom-up processes are emergent and the downward causation (DC) is not.

The social neuroscience and the theory of integrative levels

PubMed Central

Bello-Morales, Raquel; Delgado-García, José María

2015-01-01

The theory of integrative levels provides a general description of the evolution of matter through successive orders of complexity and integration. Along its development, material forms pass through different levels of organization, such as physical, chemical, biological or sociological. The appearance of novel structures and dynamics during this process of development of matter in complex systems has been called emergence. Social neuroscience (SN), an interdisciplinary field that aims to investigate the biological mechanisms that underlie social structures, processes, and behavior and the influences between social and biological levels of organization, has affirmed the necessity for including social context as an essential element to understand the human behavior. To do this, SN proposes a multilevel integrative approach by means of three principles: multiple determinism, nonadditive determinism and reciprocal determinism. These theoretical principles seem to share the basic tenets of the theory of integrative levels but, in this paper, we aim to reveal the differences among both doctrines. First, SN asserts that combination of neural and social variables can produce emergent phenomena that would not be predictable from a neuroscientific or social psychological analysis alone; SN also suggests that to achieve a complete understanding of social structures we should use an integrative analysis that encompasses levels of organization ranging from the genetic level to the social one; finally, SN establishes that there can be mutual influences between biological and social factors in determining behavior, accepting, therefore, a double influence, upward from biology to social level, and downward, from social level to biology. In contrast, following the theory of integrative levels, emergent phenomena are not produced by the combination of variables from two levels, but by the increment of complexity at one level. In addition, the social behavior and structures might be contemplated not as the result of mixing or summing social and biological influences, but as emergent phenomena that should be described with its own laws. Finally, following the integrative levels view, influences upward, from biology to social level, and downward, from social level to biology, might not be equivalent, since the bottom-up processes are emergent and the downward causation (DC) is not. PMID:26578909

Synthetic biology, inspired by synthetic chemistry.

PubMed

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

2012-07-16

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

Complexity reduction of biochemical rate expressions.

PubMed

Schmidt, Henning; Madsen, Mads F; Danø, Sune; Cedersund, Gunnar

2008-03-15

The current trend in dynamical modelling of biochemical systems is to construct more and more mechanistically detailed and thus complex models. The complexity is reflected in the number of dynamic state variables and parameters, as well as in the complexity of the kinetic rate expressions. However, a greater level of complexity, or level of detail, does not necessarily imply better models, or a better understanding of the underlying processes. Data often does not contain enough information to discriminate between different model hypotheses, and such overparameterization makes it hard to establish the validity of the various parts of the model. Consequently, there is an increasing demand for model reduction methods. We present a new reduction method that reduces complex rational rate expressions, such as those often used to describe enzymatic reactions. The method is a novel term-based identifiability analysis, which is easy to use and allows for user-specified reductions of individual rate expressions in complete models. The method is one of the first methods to meet the classical engineering objective of improved parameter identifiability without losing the systems biology demand of preserved biochemical interpretation. The method has been implemented in the Systems Biology Toolbox 2 for MATLAB, which is freely available from http://www.sbtoolbox2.org. The Supplementary Material contains scripts that show how to use it by applying the method to the example models, discussed in this article.

Large area sub-micron chemical imaging of magnesium in sea urchin teeth.

PubMed

Masic, Admir; Weaver, James C

2015-03-01

The heterogeneous and site-specific incorporation of inorganic ions can profoundly influence the local mechanical properties of damage tolerant biological composites. Using the sea urchin tooth as a research model, we describe a multi-technique approach to spatially map the distribution of magnesium in this complex multiphase system. Through the combined use of 16-bit backscattered scanning electron microscopy, multi-channel energy dispersive spectroscopy elemental mapping, and diffraction-limited confocal Raman spectroscopy, we demonstrate a new set of high throughput, multi-spectral, high resolution methods for the large scale characterization of mineralized biological materials. In addition, instrument hardware and data collection protocols can be modified such that several of these measurements can be performed on irregularly shaped samples with complex surface geometries and without the need for extensive sample preparation. Using these approaches, in conjunction with whole animal micro-computed tomography studies, we have been able to spatially resolve micron and sub-micron structural features across macroscopic length scales on entire urchin tooth cross-sections and correlate these complex morphological features with local variability in elemental composition. Copyright © 2015 Elsevier Inc. All rights reserved.

Harnessing QbD, Programming Languages, and Automation for Reproducible Biology.

PubMed

Sadowski, Michael I; Grant, Chris; Fell, Tim S

2016-03-01

Building robust manufacturing processes from biological components is a task that is highly complex and requires sophisticated tools to describe processes, inputs, and measurements and administrate management of knowledge, data, and materials. We argue that for bioengineering to fully access biological potential, it will require application of statistically designed experiments to derive detailed empirical models of underlying systems. This requires execution of large-scale structured experimentation for which laboratory automation is necessary. This requires development of expressive, high-level languages that allow reusability of protocols, characterization of their reliability, and a change in focus from implementation details to functional properties. We review recent developments in these areas and identify what we believe is an exciting trend that promises to revolutionize biotechnology. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Carbon dioxide evolution rate as a method to monitor and control an aerobic biological waste treatment system

NASA Technical Reports Server (NTRS)

Lee, S. S.; Shuler, M. L.

1986-01-01

An experimental system was developed to study the microbial growth kinetic of an undefined mixed culture in an erobic biological waste treatment process. The experimental results were used to develop a mathematical model that can predict the performance of a bioreactor. The bioreactor will be used to regeneratively treat waste material which is expected to be generated during a long term manned space mission. Since the presence of insoluble particles in the chemically undefined complex media made estimating biomass very difficult in the real system, a clean system was devised to study the microbial growth from the soluble substrate.

Living matter—nexus of physics and biology in the 21st century

PubMed Central

Gardel, Margaret L.

2012-01-01

Cells are made up of complex assemblies of cytoskeletal proteins that facilitate force transmission from the molecular to cellular scale to regulate cell shape and force generation. The “living matter” formed by the cytoskeleton facilitates versatile and robust behaviors of cells, including their migration, adhesion, division, and morphology, that ultimately determine tissue architecture and mechanics. Elucidating the underlying physical principles of such living matter provides great opportunities in both biology and physics. For physicists, the cytoskeleton provides an exceptional toolbox to study materials far from equilibrium. For biologists, these studies will provide new understanding of how molecular-scale processes determine cell morphological changes. PMID:23112229

On residual stresses and homeostasis: an elastic theory of functional adaptation in living matter.

PubMed

Ciarletta, P; Destrade, M; Gower, A L

2016-04-26

Living matter can functionally adapt to external physical factors by developing internal tensions, easily revealed by cutting experiments. Nonetheless, residual stresses intrinsically have a complex spatial distribution, and destructive techniques cannot be used to identify a natural stress-free configuration. This work proposes a novel elastic theory of pre-stressed materials. Imposing physical compatibility and symmetry arguments, we define a new class of free energies explicitly depending on the internal stresses. This theory is finally applied to the study of arterial remodelling, proving its potential for the non-destructive determination of the residual tensions within biological materials.

Precision manufacturing for clinical-quality regenerative medicines.

PubMed

Williams, David J; Thomas, Robert J; Hourd, Paul C; Chandra, Amit; Ratcliffe, Elizabeth; Liu, Yang; Rayment, Erin A; Archer, J Richard

2012-08-28

Innovations in engineering applied to healthcare make a significant difference to people's lives. Market growth is guaranteed by demographics. Regulation and requirements for good manufacturing practice-extreme levels of repeatability and reliability-demand high-precision process and measurement solutions. Emerging technologies using living biological materials add complexity. This paper presents some results of work demonstrating the precision automated manufacture of living materials, particularly the expansion of populations of human stem cells for therapeutic use as regenerative medicines. The paper also describes quality engineering techniques for precision process design and improvement, and identifies the requirements for manufacturing technology and measurement systems evolution for such therapies.

Efficient separation of conjugated polymers using a water soluble glycoprotein matrix: from fluorescence materials to light emitting devices.

PubMed

Hendler, Netta; Wildeman, Jurjen; Mentovich, Elad D; Schnitzler, Tobias; Belgorodsky, Bogdan; Prusty, Deepak K; Rimmerman, Dolev; Herrmann, Andreas; Richter, Shachar

2014-03-01

Optically active bio-composite blends of conjugated polymers or oligomers are fabricated by complexing them with bovine submaxilliary mucin (BSM) protein. The BSM matrix is exploited to host hydrophobic extended conjugated π-systems and to prevent undesirable aggregation and render such materials water soluble. This method allows tuning the emission color of solutions and films from the basic colors to the technologically challenging white emission. Furthermore, electrically driven light emitting biological devices are prepared and operated. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Freezing-Out Technique Applied to the Concentration of Biologically Active Materials

PubMed Central

Wilson, T. E.; Evans, D. J.; Theriot, Mary L.

1964-01-01

When applied to a dilute solution of folic acid and glucose, a freezing-out (with agitation) technique was shown to be an effective method of achieving a 20-fold reduction in volume with a loss of 10% of the active material being concentrated. Concentration of a stimulatory factor for Lactobacillus casei produced by Candida albicans in a complex medium was limited by the total solute concentration. Salts in the medium were concentrated to levels inhibitory for L. casei. The process is not selective and all solutes are concentrated. Images FIG. 2 FIG. 3 PMID:14131370

Evaluation of the toxicity of superfine materials to change the physiological functions of aquatic organisms of different trophic levels

NASA Astrophysics Data System (ADS)

Morgalev, S.; Morgaleva, T.; Gosteva, I.; Morgalev, Yu

2015-11-01

We assessed ecological and biological effects caused by the physical and chemical properties of nanomaterials on the basis of the laboratory researches into water test-organisms of different trophic levels. We studied the physiological functions of water organisms on adding into the environment superfine materials of various chemical nature and structural characteristics: metallic nanoparticles of nikel (nNi), argentum (nAg), platinum (nPt), aurum (nAu), binary NPs (powder of titanium dioxide - nTiO2, aluminum oxide - nAl2O3, zink oxide - nZnO, silicon nitride - nSi3N4, silicon carbide (nSiC) and carbon nanotubes (BT-50, MCD- material). We observed the dependence of developing the complex of unfavourable biological effects in water plants and entomostracans’ organisms on the physical and chemical properties of superfine materials. We determined the values of NOEC, L(E)C20 and L(E)C50 for aquatic organisms of various regular groups. We found out the most vulnerable elements of the communities’ trophic structure and the possibility of a breakdown in the water ecosystem food pyramid.

Analysis of working conditions focusing on biological risk: firefighters in Campo Grande, MS, Brazil.

PubMed

Contrera-Moreno, Luciana; de Andrade, Sonia Maria Oliveira; Motta-Castro, Ana Rita Coimbra; Pinto, Alexandra Maria Almeida Carvalho; Salas, Frederico Reis Pouso; Stief, Alcione Cavalheiros Faro

2012-01-01

Firefighters are exposed to a wide range of risks, among them, biological risk. The objective was to analyze working conditions of firefighters in the city of Campo Grande, MS, Brazil, focusing on risk conditions of exposure to biological material. Three hundred and seven (307) firefighters were interviewed for data collection and observed for ergonomic job analysis (AET). 63.5% of the firefighters suffered some kind of job related accident with blood or body fluids. Statistically significant association was found between having suffered accidents at work and incomplete use of personal protective equipment (PPE). About AET regarding the biological risks, 57.1% of all patients had blood or secretions, which corresponds in average to 16.0% of the total work time, based on a working day of 24 h. Besides biological risks, other stressing factors were identified: emergency and complexity of decision, high responsibility regarding patients and environment, and conflicts. Health promotion and accident prevention actions must be emphasized as measures to minimize these risks.

Artificially Engineered Protein Polymers.

PubMed

Yang, Yun Jung; Holmberg, Angela L; Olsen, Bradley D

2017-06-07

Modern polymer science increasingly requires precise control over macromolecular structure and properties for engineering advanced materials and biomedical systems. The application of biological processes to design and synthesize artificial protein polymers offers a means for furthering macromolecular tunability, enabling polymers with dispersities of ∼1.0 and monomer-level sequence control. Taking inspiration from materials evolved in nature, scientists have created modular building blocks with simplified monomer sequences that replicate the function of natural systems. The corresponding protein engineering toolbox has enabled the systematic development of complex functional polymeric materials across areas as diverse as adhesives, responsive polymers, and medical materials. This review discusses the natural proteins that have inspired the development of key building blocks for protein polymer engineering and the function of these elements in material design. The prospects and progress for scalable commercialization of protein polymers are reviewed, discussing both technology needs and opportunities.

Investigation of engineered bacterial adhesins for opportunity to interface cells with abiotic materials

NASA Astrophysics Data System (ADS)

Terrell, Jessica L.; Dong, Hong; Holthoff, Ellen L.; Small, Meagan C.; Sarkes, Deborah A.; Hurley, Margaret M.; Stratis-Cullum, Dimitra N.

2016-05-01

The convenience of cellular genetic engineering has afforded the power to build `smart' synthetic biological tools with novel applications. Here, we have explored opportunities to hybridize engineered cells with inorganic materials toward the development of 'living' device-compatible systems. Cellular structural biology is engineerable based on the ability to rewrite genetic code to generate recombinant, foreign, or even unnatural proteins. With this capability on the biological end, it should be possible to achieve superior abio-compatibility with the inorganic materials that compose current microfabricated technology. This work investigated the hair-like appendages of Escherichia coli known as Type 1 fimbriae that enable natural adhesion to glycosylated substrates. Sequence alterations within the fimbrial gene cluster were found to be well-tolerated, evidenced by tagging the fimbriae with peptide-based probes. As a further development, fimbriae tips could be reconfigured to, in turn, alter cell binding. In particular, the fimbriae were fused with a genetically optimized peptide-for-inorganics to enable metal binding. This work established methodologies to systematically survey cell adhesion properties across a suite of fimbriae-modified cell types as well as to direct patterned cell adhesion. Cell types were further customized for added complexity including turning on secondary gene expression and binding to gold surfaces. The former demonstrates potential for programmable gene switches and the latter for interfacing biology with inorganic materials. In general, the incorporation of 'programmed' cells into devices can be used to provide the feature of dynamic and automated cell response. The outcomes of this study are foundational toward the critical feature of deliberate positioning of cells as configurable biocomponentry. Overall, cellular integration into bioMEMs will yield advanced sensing and actuation.

Copper Capture in a Thioether-Functionalized Porous Polymer Applied to the Detection of Wilson’s Disease

PubMed Central

2016-01-01

Copper is an essential nutrient for life, but at the same time, hyperaccumulation of this redox-active metal in biological fluids and tissues is a hallmark of pathologies such as Wilson’s and Menkes diseases, various neurodegenerative diseases, and toxic environmental exposure. Diseases characterized by copper hyperaccumulation are currently challenging to identify due to costly diagnostic tools that involve extensive technical workup. Motivated to create simple yet highly selective and sensitive diagnostic tools, we have initiated a program to develop new materials that can enable monitoring of copper levels in biological fluid samples without complex and expensive instrumentation. Herein, we report the design, synthesis, and properties of PAF-1-SMe, a robust three-dimensional porous aromatic framework (PAF) densely functionalized with thioether groups for selective capture and concentration of copper from biofluids as well as aqueous samples. PAF-1-SMe exhibits a high selectivity for copper over other biologically relevant metals, with a saturation capacity reaching over 600 mg/g. Moreover, the combination of PAF-1-SMe as a material for capture and concentration of copper from biological samples with 8-hydroxyquinoline as a colorimetric indicator affords a method for identifying aberrant elevations of copper in urine samples from mice with Wilson’s disease and also tracing exogenously added copper in serum. This divide-and-conquer sensing strategy, where functional and robust porous materials serve as molecular recognition elements that can be used to capture and concentrate analytes in conjunction with molecular indicators for signal readouts, establishes a valuable starting point for the use of porous polymeric materials in noninvasive diagnostic applications. PMID:27285482

Microfabrication of hierarchical structures for engineered mechanical materials

NASA Astrophysics Data System (ADS)

Vera Canudas, Marc

Materials found in nature present, in some cases, unique properties from their constituents that are of great interest in engineered materials for applications ranging from structural materials for the construction of bridges, canals and buildings to the fabrication of new lightweight composites for airplane and automotive bodies, to protective thin film coatings, amongst other fields. Research in the growing field of biomimetic materials indicates that the micro-architectures present in natural materials are critical to their macroscopic mechanical properties. A better understanding of the effect that structure and hierarchy across scales have on the material properties will enable engineered materials with enhanced properties. At the moment, very few theoretical models predict mechanical properties of simple materials based on their microstructures. Moreover these models are based on observations from complex biological systems. One way to overcome this challenge is through the use of microfabrication techniques to design and fabricate simple materials, more appropriate for the study of hierarchical organizations and microstructured materials. Arrays of structures with controlled geometry and dimension can be designed and fabricated at different length scales, ranging from a few hundred nanometers to centimeters, in order to mimic similar systems found in nature. In this thesis, materials have been fabricated in order to gain fundamental insight into the complex hierarchical materials found in nature and to engineer novel materials with enhanced mechanical properties. The materials fabricated here were mechanically characterized and compared to simple mechanics models to describe their behavior with the goal of applying the knowledge acquired to the design and synthesis of future engineered materials with novel properties.

ON THE BIOMECHANICAL FUNCTION OF SCAFFOLDS FOR ENGINEERING LOAD BEARING SOFT TISSUES

PubMed Central

Stella, John A.; D’Amore, Antonio; Wagner, William R.; Sacks, Michael S.

2010-01-01

Replacement or regeneration of load bearing soft tissues has long been the impetus for the development bioactive materials. While maturing, current efforts continue to be confounded by our lack of understanding of the intricate multi-scale hierarchical arrangements and interactions typically found in native tissues. The current state of the art in biomaterial processing enables a degree of controllable microstructure that can be used for the development of model systems to deduce fundamental biological implications of matrix morphologies on cell function. Furthermore, the development of computational frameworks which allow for the simulation of experimentally derived observations represents a positive departure from what has mostly been an empirically driven field, enabling a deeper understanding of the highly complex biological mechanisms we wish to ultimately emulate. Ongoing research is actively pursuing new materials and processing methods to control material structure down to the micro-scale to sustain or improve cell viability, guide tissue growth, and provide mechanical integrity all while exhibiting the capacity to degrade in a controlled manner. The purpose of this review is not to focus solely on material processing but to assess the ability of these techniques to produce mechanically sound tissue surrogates, highlight the unique structural characteristics produced in these materials, and discuss how this translates to distinct macroscopic biomechanical behaviors. PMID:20060509

Materials by Design—A Perspective From Atoms to Structures

PubMed Central

Buehler, Markus J.

2013-01-01

Biological materials are effectively synthesized, controlled, and used for a variety of purposes—in spite of limitations in energy, quality, and quantity of their building blocks. Whereas the chemical composition of materials in the living world plays a some role in achieving functional properties, the way components are connected at different length scales defines what material properties can be achieved, how they can be altered to meet functional requirements, and how they fail in disease states and other extreme conditions. Recent work has demonstrated this by using large-scale computer simulations to predict materials properties from fundamental molecular principles, combined with experimental work and new mathematical techniques to categorize complex structure-property relationships into a systematic framework. Enabled by such categorization, we discuss opportunities based on the exploitation of concepts from distinct hierarchical systems that share common principles in how function is created, linking music to materials science. PMID:24163499

Processing and properties of Titanium alloy based materials with tailored porosity and composition

NASA Astrophysics Data System (ADS)

Cabezas-Villa, Jose Luis; Olmos, Luis; Lemus-Ruiz, Jose; Bouvard, Didier; Chavez, Jorge; Jimenez, Omar; Manuel Solorio, Victor

2017-06-01

This paper deals with powder processing of Ti6Al4V titanium alloy based materials with tailored porosity and composition. Ti6Al4V powder was mixed either with salt particles acting as space holder, so as to provide two-scale porosity, or with hard TiN particles that significantly modified the microstructure of the material and increased its hardness. Finally an original three-layer component was produced. Sample microstructure was observed by SEM and micro-tomography with special interest in pore size and shape, inclusion distribution and connectivity. Compression tests provided elastic modulus and yield stress as functions of density. These materials are representative of bone implants subjected to complex biological and mechanical conditions. These results thus open avenues for processing personalized implants by powder metallurgy.

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.

Silica biomineralization via the self-assembly of helical biomolecules.

PubMed

Liu, Ben; Cao, Yuanyuan; Huang, Zhehao; Duan, Yingying; Che, Shunai

2015-01-21

The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A rapid and repeatable method to deposit bioaerosols on material surfaces.

PubMed

Calfee, M Worth; Lee, Sang Don; Ryan, Shawn P

2013-03-01

A simple method for repeatably inoculating surfaces with a precise quantity of aerosolized spores was developed. Laboratory studies were conducted to evaluate the variability of the method within and between experiments, the spatial distribution of spore deposition, the applicability of the method to complex surface types, and the relationship between material surface roughness and spore recoveries. Surface concentrations, as estimated by recoveries from wetted-wipe sampling, were between 5×10(3) and 1.5×10(4)CFUcm(-2) across the entire area (930cm(2)) inoculated. Between-test variability (Cv) in spore recoveries was 40%, 81%, 66%, and 20% for stainless steel, concrete, wood, and drywall, respectively. Within-test variability was lower, and did not exceed 33%, 47%, 52%, and 20% for these materials. The data demonstrate that this method is repeatable, is effective at depositing spores across a target surface area, and can be used to dose complex materials such as concrete, wood, and drywall. In addition, the data demonstrate that surface sampling recoveries vary by material type, and this variability can partially be explained by the material surface roughness index. This deposition method was developed for use in biological agent detection, sampling, and decontamination studies, however, is potentially beneficial to any scientific discipline that investigates surfaces containing aerosol-borne particles. Published by Elsevier B.V.

Within-storm and Seasonal Differences in Particulate Organic Material Composition and Sources in White Clay Creek, USA

NASA Astrophysics Data System (ADS)

Karwan, D. L.; Aufdenkampe, A. K.; Aalto, R. E.; Newbold, J. D.; Pizzuto, J. E.

2011-12-01

The material exported from a watershed reflects its origin and the processes it undergoes during downhill and downstream transport. Due to its nature as a complex mixture of material, the composition of POM integrates the physical, biological, and chemical processes effecting watershed material. In this study, we integrate sediment fingerprint analyses common in geomorphological studies of mineral suspended particulate material (SPM) with biological and ecological characterizations of particulate organic carbon (POC). Through this combination, we produce quantifiable budgets of particulate organic carbon and mineral material, as well as integrate our calculations of carbon and mineral cycling in a complex, human-influenced watershed. More specifically, we quantify the composition and sources of POM in the third-order White Clay Creek Watershed, and examine the differences in composition and source with hydrologic variations produced by storms and seasonality. POM and watershed sources have been analyzed for particle size, mineral surface area, total mineral elemental composition, fallout radioisotope activity for common erosion tracers (7Be, 210Pb, 137Cs), and organic carbon and nitrogen content with stable isotope (13C, 15N) abundance. Results indicate a difference in POM source with season as well as within individual storms. Beryllium-7 activity, an indicator of landscape surface erosion, nearly triples within a single spring storm, from 389 mBq/g on the rising limb and 1190 mBq/g at the storm hydrograph peak. Fall storms have even lower 7Be concentrations, below 100 mBq/g. Furthermore, weight-percent of organic carbon nearly doubles from 4 - 5% during spring storms to over 8% during fall storms, with smaller variation occurring within individual storms. Despite changes in percent organic carbon, organic carbon to mineral surface area ratios and carbon to nitrogen molar ratios remain similar within storms and across seasons.

New Methods of Simulation of Mn(II) EPR Spectra: Single Crystals, Polycrystalline and Amorphous (Biological) Materials

NASA Astrophysics Data System (ADS)

Misra, Sushil K.

Biological systems exhibit properties of amorphous materials. The Mn(II) ion in amorphous materials is characterized by distributions of spin-Hamiltonian parameters around mean values. It has a certain advantage over other ions, being one of the most abundant elements on the earth. The extent to which living organisms utilize manganese varies from one organism to the other. There is a fairly high concentration of the Mn(II) ion in green plants, which use it in the O2 evolution reaction of photosynthesis (Sauer, 1980). Structure-reactivity relationships in Mn(II)-O2 complexes are given in a review article by Coleman and Taylor (1980). Manganese is a trace requirement in animal nutrition; highly elevated levels of manganese in the diet can be toxic, probably because of an interference with iron homeostasis (Underwood, 1971). On the other hand, animals raised with a dietary deficiency of manganese exhibit severe abnormalities in connective tissue; these problems have been attributed to the obligatory role of Mn(II) in mucopolysaccharide metabolism (Leach, 1971). Mn(II) has been detected unequivocally in living organisms.

Functionalization of 3D scaffolds with protein-releasing biomaterials for intracellular delivery.

PubMed

Seras-Franzoso, Joaquin; Steurer, Christoph; Roldán, Mònica; Vendrell, Meritxell; Vidaurre-Agut, Carla; Tarruella, Anna; Saldaña, Laura; Vilaboa, Nuria; Parera, Marc; Elizondo, Elisa; Ratera, Imma; Ventosa, Nora; Veciana, Jaume; Campillo-Fernández, Alberto J; García-Fruitós, Elena; Vázquez, Esther; Villaverde, Antonio

2013-10-10

Appropriate combinations of mechanical and biological stimuli are required to promote proper colonization of substrate materials in regenerative medicine. In this context, 3D scaffolds formed by compatible and biodegradable materials are under continuous development in an attempt to mimic the extracellular environment of mammalian cells. We have here explored how novel 3D porous scaffolds constructed by polylactic acid, polycaprolactone or chitosan can be decorated with bacterial inclusion bodies, submicron protein particles formed by releasable functional proteins. A simple dipping-based decoration method tested here specifically favors the penetration of the functional particles deeper than 300μm from the materials' surface. The functionalized surfaces support the intracellular delivery of biologically active proteins to up to more than 80% of the colonizing cells, a process that is slightly influenced by the chemical nature of the scaffold. The combination of 3D soft scaffolds and protein-based sustained release systems (Bioscaffolds) offers promise in the fabrication of bio-inspired hybrid matrices for multifactorial control of cell proliferation in tissue engineering under complex architectonic setting-ups. © 2013.

Hydrogel microparticles for biosensing

PubMed Central

Le Goff, Gaelle C.; Srinivas, Rathi L.; Hill, W. Adam; Doyle, Patrick S.

2015-01-01

Due to their hydrophilic, biocompatible, and highly tunable nature, hydrogel materials have attracted strong interest in the recent years for numerous biotechnological applications. In particular, their solution-like environment and non-fouling nature in complex biological samples render hydrogels as ideal substrates for biosensing applications. Hydrogel coatings, and later, gel dot surface microarrays, were successfully used in sensitive nucleic acid assays and immunoassays. More recently, new microfabrication techniques for synthesizing encoded particles from hydrogel materials have enabled the development of hydrogel-based suspension arrays. Lithography processes and droplet-based microfluidic techniques enable generation of libraries of particles with unique spectral or graphical codes, for multiplexed sensing in biological samples. In this review, we discuss the key questions arising when designing hydrogel particles dedicated to biosensing. How can the hydrogel material be engineered in order to tune its properties and immobilize bioprobes inside? What are the strategies to fabricate and encode gel particles, and how can particles be processed and decoded after the assay? Finally, we review the bioassays reported so far in the literature that have used hydrogel particle arrays and give an outlook of further developments of the field. PMID:26594056

Materials and Techniques for Implantable Nutrient Sensing Using Flexible Sensors Integrated with Metal-Organic Frameworks.

PubMed

Ling, Wei; Liew, Guoguang; Li, Ya; Hao, Yafeng; Pan, Huizhuo; Wang, Hanjie; Ning, Baoan; Xu, Hang; Huang, Xian

2018-06-01

The combination of novel materials with flexible electronic technology may yield new concepts of flexible electronic devices that effectively detect various biological chemicals to facilitate understanding of biological processes and conduct health monitoring. This paper demonstrates single- or multichannel implantable flexible sensors that are surface modified with conductive metal-organic frameworks (MOFs) such as copper-MOF and cobalt-MOF with large surface area, high porosity, and tunable catalysis capability. The sensors can monitor important nutriments such as ascorbicacid, glycine, l-tryptophan (l-Trp), and glucose with detection resolutions of 14.97, 0.71, 4.14, and 54.60 × 10 -6 m, respectively. In addition, they offer sensing capability even under extreme deformation and complex surrounding environment with continuous monitoring capability for 20 d due to minimized use of biological active chemicals. Experiments using live cells and animals indicate that the MOF-modified sensors are biologically safe to cells, and can detect l-Trp in blood and interstitial fluid. This work represents the first effort in integrating MOFs with flexible sensors to achieve highly specific and sensitive implantable electrochemical detection and may inspire appearance of more flexible electronic devices with enhanced capability in sensing, energy storage, and catalysis using various properties of MOFs. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nucleic acid purification from plants, animals and microbes in under 30 seconds

PubMed Central

Zou, Yiping; Wang, Yuling; Wee, Eugene; Turni, Conny; Blackall, Patrick J.; Trau, Matt; Botella, Jose Ramon

2017-01-01

Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries. PMID:29161268

Biotemplated materials for sustainable energy and environment: current status and challenges.

PubMed

Zhou, Han; Fan, Tongxiang; Zhang, Di

2011-10-17

Materials science will play a key role in the further development of emerging solutions for the increasing problems of energy and environment. Materials found in nature have many inspiring structures, such as hierarchical organizations, periodic architectures, or nanostructures, that endow them with amazing functions, such as energy harvesting and conversion, antireflection, structural coloration, superhydrophobicity, and biological self-assembly. Biotemplating is an effective strategy to obtain morphology-controllable materials with structural specificity, complexity, and related unique functions. Herein, we highlight the synthesis and application of biotemplated materials for six key areas of energy and environment technologies, namely, photocatalytic hydrogen evolution, CO(2) reduction, solar cells, lithium-ion batteries, photocatalytic degradation, and gas/vapor sensing. Although the applications differ from each other, a common fundamental challenge is to realize optimum structures for improved performances. We highlight the role of four typical structures derived from biological systems exploited to optimize properties: hierarchical (porous) structures, periodic (porous) structures, hollow structures, and nanostructures. We also provide examples of using biogenic elements (e.g., C, Si, N, I, P, S) for the creation of active materials. Finally, we disscuss the challenges of achieving the desired performance for large-scale commercial applications and provide some useful prototypes from nature for the biomimetic design of new materials or systems. The emphasis is mainly focused on the structural effects and compositional utilization of biotemplated materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biomedically relevant chemical and physical properties of coal combustion products.

PubMed Central

Fisher, G L

1983-01-01

The evaluation of the potential public and occupational health hazards of developing and existing combustion processes requires a detailed understanding of the physical and chemical properties of effluents available for human and environmental exposures. These processes produce complex mixtures of gases and aerosols which may interact synergistically or antagonistically with biological systems. Because of the physicochemical complexity of the effluents, the biomedically relevant properties of these materials must be carefully assessed. Subsequent to release from combustion sources, environmental interactions further complicate assessment of the toxicity of combustion products. This report provides an overview of the biomedically relevant physical and chemical properties of coal fly ash. Coal fly ash is presented as a model complex mixture for health and safety evaluation of combustion processes. PMID:6337824

Bioinspired peony-like beta-Ni(OH)2 nanostructures with enhanced electrochemical activity and superhydrophobicity.

PubMed

Cao, Huaqiang; Zheng, He; Liu, Kaiyu; Warner, Jamie H

2010-02-01

Constructing complex nanostructures has become increasingly important in the development of hydrogen storage, self-cleaning materials, and the formation of chiral branched nanowires. Several approaches have been developed to generate complex nanostructures, which have led to novel applications. Combining biology and nanotechnology through the utilization of biomolecules to chemically template the growth of complex nanostructures during synthesis has aroused great interest. Herein, we use a biomolecule-assisted hydrothermal method to synthesize beta-phase Ni(OH)(2) peony-like complex nanostructures with second-order structure nanoplate structure. The novel beta-Ni(OH)(2) nanostructures exhibit high-power Ni/MH battery performance, close to the theoretical capacity of Ni(OH)(2), as well as controlled wetting behavior. We demonstrate that this bioinspired route to generate a complex nanostructure has applications in environmental protection and green secondary cells. This approach opens up opportunities for the synthesis and potential applications of new kinds of nanostructures.

Status and Prospects of Hirfl Experiments on Nuclear Physics

NASA Astrophysics Data System (ADS)

Xu, H. S.; Zheng, C.; Xiao, G. Q.; Zhan, W. L.; Zhou, X. H.; Zhang, Y. H.; Sun, Z. Y.; Wang, J. S.; Gan, Z. G.; Huang, W. X.; Ma, X. W.

HIRFL is an accelerator complex consisting of 3 accelerators, 2 radioactive beams lines, 1 storage rings and a number of experimental setups. The research activities at HIRFL cover the fields of radio-biology, material science, atomic physics, and nuclear physics. This report mainly concentrates on the experiments of nuclear physics with the existing and planned experimental setups such as SHANS, RIBLL1, ETF, CSRe, PISA and HPLUS at HIRFL.

From supramolecular polymers to multi-component biomaterials.

PubMed

Goor, Olga J G M; Hendrikse, Simone I S; Dankers, Patricia Y W; Meijer, E W

2017-10-30

The most striking and general property of the biological fibrous architectures in the extracellular matrix (ECM) is the strong and directional interaction between biologically active protein subunits. These fibers display rich dynamic behavior without losing their architectural integrity. The complexity of the ECM taking care of many essential properties has inspired synthetic chemists to mimic these properties in artificial one-dimensional fibrous structures with the aim to arrive at multi-component biomaterials. Due to the dynamic character required for interaction with natural tissue, supramolecular biomaterials are promising candidates for regenerative medicine. Depending on the application area, and thereby the design criteria of these multi-component fibrous biomaterials, they are used as elastomeric materials or hydrogel systems. Elastomeric materials are designed to have load bearing properties whereas hydrogels are proposed to support in vitro cell culture. Although the chemical structures and systems designed and studied today are rather simple compared to the complexity of the ECM, the first examples of these functional supramolecular biomaterials reaching the clinic have been reported. The basic concept of many of these supramolecular biomaterials is based on their ability to adapt to cell behavior as a result of dynamic non-covalent interactions. In this review, we show the translation of one-dimensional supramolecular polymers into multi-component functional biomaterials for regenerative medicine applications.

Bioinspired synthesis and self-assembly of hybrid organic–inorganic nanomaterials

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

Zhang, Honghu

Nature is replete with complex organic–inorganic hierarchical materials of diverse yet specific functions. These materials are intricately designed under physiological conditions through biomineralization and biological self-assembly processes. Tremendous efforts have been devoted to investigating mechanisms of such biomineralization and biological self-assembly processes as well as gaining inspiration to develop biomimetic methods for synthesis and self-assembly of functional nanomaterials. In this work, we focus on the bioinspired synthesis and self-assembly of functional inorganic nanomaterials templated by specialized macromolecules including proteins, DNA and polymers. The in vitro biomineralization process of the magnetite biomineralizing protein Mms6 has been investigated using small-angle X-ray scattering.more » Templated by Mms6, complex magnetic nanomaterials can be synthesized on surfaces and in the bulk. DNA and synthetic polymers have been exploited to construct macroscopic two- and three-dimensional (2D and 3D) superlattices of gold nanocrystals. Employing X-ray scattering and spectroscopy techniques, the self-assembled structures and the self-assembly mechanisms have been studied, and theoretical models have been developed. Our results show that specialized macromolecules including proteins, DNA and polymers act as effective templates for synthesis and self-assembly of nanomaterials. These bottom-up approaches provide promising routes to fabricate hybrid organic–inorganic nanomaterials with rationally designed hierarchical structures, targeting specific functions.« less

Recent advances in the development of extraction chromatographic materials for the isolation of radionuclides from biological and environmental samples.

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

Dietz, M. L.

1998-11-30

The determination of low levels of radionuclides in environmental and biological samples is often hampered by the complex and variable nature of the samples. One approach to circumventing this problem is to incorporate into the analytical scheme a separation and preconcentration step by which the species of interest can be isolated from the major constituents of the sample. Extraction chromatography (EXC), a form of liquid chromatography in which the stationary phase comprises an extractant or a solution of an extractant in an appropriate diluent coated onto an inert support, provides a simple and efficient means of performing a wide varietymore » of metal ion separations. Recent advances in extractant design, in particular the development of extractants capable of metal ion recognition or of strong complex formation even in acidic media, have substantially improved the utility of the method. For the preconcentration of actinides, for example, an EXC resin consisting of a liquid diphosphonic acid supported on a polymeric substrate has been shown to exhibit extraordinarily strong retention of these elements from acidic chloride media. This resin, together with other related materials, can provide the basis of a number of efficient and flexible schemes for the separation and preconcentration of radionuclides form a variety of samples for subsequent determination.« less

Engineering a clinically-useful matrix for cell therapy.

PubMed

Prestwich, Glenn D

2008-01-01

The design criteria for matrices for encapsulation of cells for cell therapy include chemical, biological, engineering, marketing, regulatory, and financial constraints. What is required is a biocompatible material for culture of cells in three-dimensions (3-D) that offers ease of use, experimental flexibility to alter composition and compliance, and a composition that would permit a seamless transition from in vitro to in vivo use. The challenge is to replicate the complexity of the native extracellular matrix (ECM) environment with the minimum number of components necessary to allow cells to rebuild a given tissue. Our approach is to deconstruct the ECM to a few modular components that can be reassembled into biomimetic materials that meet these criteria. These semi-synthetic ECMs (sECMs) employ thiol-modified derivatives of hyaluronic acid (HA) that can form covalently crosslinked, biodegradable hydrogels. These sECMs are "living" biopolymers, meaning that they can be crosslinked in the presence of cells or tissues to enable cell therapy and tissue engineering. Moreover, the sECMs allow inclusion of the appropriate biological cues needed to simulate the complexity of the ECM of a given tissue. Taken together, the sECM technology offers a manufacturable, highly reproducible, flexible, FDA-approvable, and affordable vehicle for cell expansion and differentiation in 3-D.

Biological issues in materials science and engineering: Interdisciplinarity and the bio-materials paradigm

NASA Astrophysics Data System (ADS)

Murr, L. E.

2006-07-01

Biological systems and processes have had, and continue to have, important implications and applications in materials extraction, processing, and performance. This paper illustrates some interdisciplinary, biological issues in materials science and engineering. These include metal extraction involving bacterial catalysis, galvanic couples, bacterial-assisted corrosion and degradation of materials, biosorption and bioremediation of toxic and other heavy metals, metal and material implants and prostheses and related dental and medical biomaterials developments and applications, nanomaterials health benefits and toxicity issue, and biomimetics and biologically inspired materials developments. These and other examples provide compelling evidence and arguments for emphasizing biological sicences in materials science and engineering curricula and the implementation of a bio-materials paradigm to facilitate the emergence of innovative interdisciplinarity involving the biological sciences and materials sciences and engineering.

Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

PubMed

Louridas, George E; Lourida, Katerina G

2017-02-21

Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

The genesis of craniofacial biology as a health science discipline.

PubMed

Sperber, G H; Sperber, S M

2014-06-01

The craniofacial complex encapsulates the brain and contains the organs for key functions of the body, including sight, hearing and balance, smell, taste, respiration and mastication. All these systems are intimately integrated within the head. The combination of these diverse systems into a new field was dictated by the dental profession's desire for a research branch of basic science devoted and attuned to its specific needs. The traditional subjects of genetics, embryology, anatomy, physiology, biochemistry, dental materials, odontology, molecular biology and palaeoanthropology pertaining to dentistry have been drawn together by many newly emerging technologies. These new technologies include gene sequencing, CAT scanning, MRI imaging, laser scanning, image analysis, ultrasonography, spectroscopy and visualosonics. A vibrant unitary discipline of investigation, craniofacial biology, has emerged that builds on the original concept of 'oral biology' that began in the 1960s. This paper reviews some of the developments that have led to the genesis of craniofacial biology as a fully-fledged health science discipline of significance in the advancement of clinical dental practice. Some of the key figures and milestones in craniofacial biology are identified. © 2014 Australian Dental Association.

Design, fabrication and control of origami robots

NASA Astrophysics Data System (ADS)

Rus, Daniela; Tolley, Michael T.

2018-06-01

Origami robots are created using folding processes, which provide a simple approach to fabricating a wide range of robot morphologies. Inspired by biological systems, engineers have started to explore origami folding in combination with smart material actuators to enable intrinsic actuation as a means to decouple design from fabrication complexity. The built-in crease structure of origami bodies has the potential to yield compliance and exhibit many soft body properties. Conventional fabrication of robots is generally a bottom-up assembly process with multiple low-level steps for creating subsystems that include manual operations and often multiple iterations. By contrast, natural systems achieve elegant designs and complex functionalities using top-down parallel transformation approaches such as folding. Folding in nature creates a wide spectrum of complex morpho-functional structures such as proteins and intestines and enables the development of structures such as flowers, leaves and insect wings. Inspired by nature, engineers have started to explore folding powered by embedded smart material actuators to create origami robots. The design and fabrication of origami robots exploits top-down, parallel transformation approaches to achieve elegant designs and complex functionalities. In this Review, we first introduce the concept of origami robotics and then highlight advances in design principles, fabrication methods, actuation, smart materials and control algorithms. Applications of origami robots for a variety of devices are investigated, and future directions of the field are discussed, examining both challenges and opportunities.

Synthesis, spectroscopic, fluorescence properties and biological evaluation of novel Pd(II) and Cd(II) complexes of NOON tetradentate Schiff bases.

PubMed

Ali, Omyma A M

2014-01-01

The solid complexes of Pd(II) and Cd(II) with N,N/bis(salicylaldehyde)4,5-dimethyl-1,2-phenylenediamine (H2L(1)), and N,N/bis(salicylaldehyde)4,5-dichloro-1,2-phenylenediamine (H2L(2)) have been synthesized and characterized by several techniques using elemental analysis (CHN), FT-IR, (1)H NMR, UV-Vis spectra and thermal analysis. Elemental analysis data proved 1:1 stoichiometry for the reported complexes while spectroscopic data indicated square planar and octahedral geometries for Pd(II) and Cd(II) complexes, respectively. The prepared ligands, Pd(II) and Cd(II) complexes exhibited intraligand (π-π(∗)) fluorescence and can potentially serve as photoactive materials. Thermal behavior of the complexes was studied and kinetic parameters were determined by Coats-Redfern method. Both the ligands and their complexes have been screened for antimicrobial activities. Copyright © 2013 Elsevier B.V. All rights reserved.

Advanced Engineering Strategies for Periodontal Complex Regeneration.

PubMed

Park, Chan Ho; Kim, Kyoung-Hwa; Lee, Yong-Moo; Seol, Yang-Jo

2016-01-18

The regeneration and integration of multiple tissue types is critical for efforts to restore the function of musculoskeletal complex. In particular, the neogenesis of periodontal constructs for systematic tooth-supporting functions is a current challenge due to micron-scaled tissue compartmentalization, oblique/perpendicular orientations of fibrous connective tissues to the tooth root surface and the orchestration of multiple regenerated tissues. Although there have been various biological and biochemical achievements, periodontal tissue regeneration remains limited and unpredictable. The purpose of this paper is to discuss current advanced engineering approaches for periodontal complex formations; computer-designed, customized scaffolding architectures; cell sheet technology-based multi-phasic approaches; and patient-specific constructs using bioresorbable polymeric material and 3-D printing technology for clinical application. The review covers various advanced technologies for periodontal complex regeneration and state-of-the-art therapeutic avenues in periodontal tissue engineering.

Stability and dynamical properties of material flow systems on random networks

NASA Astrophysics Data System (ADS)

Anand, K.; Galla, T.

2009-04-01

The theory of complex networks and of disordered systems is used to study the stability and dynamical properties of a simple model of material flow networks defined on random graphs. In particular we address instabilities that are characteristic of flow networks in economic, ecological and biological systems. Based on results from random matrix theory, we work out the phase diagram of such systems defined on extensively connected random graphs, and study in detail how the choice of control policies and the network structure affects stability. We also present results for more complex topologies of the underlying graph, focussing on finitely connected Erdös-Réyni graphs, Small-World Networks and Barabási-Albert scale-free networks. Results indicate that variability of input-output matrix elements, and random structures of the underlying graph tend to make the system less stable, while fast price dynamics or strong responsiveness to stock accumulation promote stability.

Biosorption: current perspectives on concept, definition and application.

PubMed

Fomina, Marina; Gadd, Geoffrey Michael

2014-05-01

Biosorption is a physico-chemical and metabolically-independent process based on a variety of mechanisms including absorption, adsorption, ion exchange, surface complexation and precipitation. Biosorption processes are highly important in the environment and conventional biotreatment processes. As a branch of biotechnology, biosorption has been aimed at the removal or recovery of organic and inorganic substances from solution by biological material which can include living or dead microorganisms and their components, seaweeds, plant materials, industrial and agricultural wastes and natural residues. For decades biosorption has been heralded as a promising cost-effective clean-up biotechnology. Despite significant progress in our understanding of this complex phenomenon and a dramatic increase in publications in this research area, commercialization of biosorption technologies has been limited so far. This article summarizes existing knowledge on various aspects of the fundamentals and applications of biosorption and critically reviews the obstacles to commercial success and future perspectives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Three-dimensional distribution of polymorphs and magnesium in a calcified underwater attachment system by diffraction tomography

PubMed Central

Leemreize, Hanna; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik

2013-01-01

Biological materials display complicated three-dimensional hierarchical structures. Determining these structures is essential in understanding the link between material design and properties. Herein, we show how diffraction tomography can be used to determine the relative placement of the calcium carbonate polymorphs calcite and aragonite in the highly mineralized holdfast system of the bivalve Anomia simplex. In addition to high fidelity and non-destructive mapping of polymorphs, we use detailed analysis of X-ray diffraction peak positions in reconstructed powder diffraction data to determine the local degree of Mg substitution in the calcite phase. These data show how diffraction tomography can provide detailed multi-length scale information on complex materials in general and of biomineralized tissues in particular. PMID:23804437

Creating biological nanomaterials using synthetic biology.

PubMed

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

[Cooperations between biology laboratories of the establishments of healthcare].

PubMed

Burnat, Pascal; Payen, Catherine; Mérens, Audrey; Ceppa, Franck; Renard, Christophe

2013-01-01

In France, the cooperations between biological laboratories of the healthcare establishments increased after those realized in the private laboratories. The biologists are confronted with various hypotheses of organization. They are often complex because they may preserve the quality of the care and their continuity while realizing financial economies. These economies are mostly based on the global reduction in the staff and in the equipments by mutualising the biological tests with varying degrees. We describe the various elements to be taken into account (staff, activities, budget, quality, transport, materials) and propose many scenarios of cooperations, from a unique central shape to the transfer of very specialized tests, with their advantages and their inconveniences. The management of human aspects in these cooperations is determining to facilitate their success as well as a reliable preliminary inventory of fixtures.

A multiscale MD-FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure.

PubMed

Kojic, M; Milosevic, M; Kojic, N; Kim, K; Ferrari, M; Ziemys, A

2014-02-01

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts.

A multiscale MD–FE model of diffusion in composite media with internal surface interaction based on numerical homogenization procedure

PubMed Central

Kojic, M.; Milosevic, M.; Kojic, N.; Kim, K.; Ferrari, M.; Ziemys, A.

2014-01-01

Mass transport by diffusion within composite materials may depend not only on internal microstructural geometry, but also on the chemical interactions between the transported substance and the material of the microstructure. Retrospectively, there is a gap in methods and theory to connect material microstructure properties with macroscale continuum diffusion characteristics. Here we present a new hierarchical multiscale model for diffusion within composite materials that couples material microstructural geometry and interactions between diffusing particles and the material matrix. This model, which bridges molecular dynamics (MD) and the finite element (FE) method, is employed to construct a continuum diffusion model based on a novel numerical homogenization procedure. The procedure is general and robust for evaluating constitutive material parameters of the continuum model. These parameters include the traditional bulk diffusion coefficients and, additionally, the distances from the solid surface accounting for surface interaction effects. We implemented our models to glucose diffusion through the following two geometrical/material configurations: tightly packed silica nanospheres, and a complex fibrous structure surrounding nanospheres. Then, rhodamine 6G diffusion analysis through an aga-rose gel network was performed, followed by a model validation using our experimental results. The microstructural model, numerical homogenization and continuum model offer a new platform for modeling and predicting mass diffusion through complex biological environment and within composite materials that are used in a wide range of applications, like drug delivery and nanoporous catalysts. PMID:24578582

Tandem catalysis: a new approach to polymers.

PubMed

Robert, Carine; Thomas, Christophe M

2013-12-21

The creation of polymers by tandem catalysis represents an exciting frontier in materials science. Tandem catalysis is one of the strategies used by Nature for building macromolecules. Living organisms generally synthesize macromolecules by in vivo enzyme-catalyzed chain growth polymerization reactions using activated monomers that have been formed within cells during complex metabolic processes. However, these biological processes rely on highly complex biocatalysts, thus limiting their industrial applications. In order to obtain polymers by tandem catalysis, homogeneous and enzyme catalysts have played a leading role in the last two decades. In the following feature article, we will describe selected published efforts to achieve these research goals.

Dinitrosyl iron complexes with thiol-containing ligands as a "working form" of endogenous nitric oxide.

PubMed

Vanin, Anatoly F

2016-04-01

The material presented herein is an overview of the results obtained by our research team during the many years' study of biological activities and occurrence of dinitrosyl iron complexes (DNIC) with thiol-containing ligands in human and animal organisms. With regard to their dose dependence and vast diversity of biological activities, DNIC are similar to the system of endogenous NO, one of the most universal regulators of biological processes. The role of biologically active components in DNIC is played by their iron-dinitrosyl fragments, [Fe(NO)2], endowed with the ability to generate neutral NO molecules and nitrosonium ions (NO(+)). Their release is effected by heme-and thiol-containing proteins, which fulfill the function of biological targets and acceptors of NO and NO(+). Beneficial regulatory effects of DNIC on physiological and metabolic processes are numerous and diverse and include, among other things, lowering of arterial pressure and accelerated healing of skin wounds. In the course of fast decomposition of their Fe(NO)2 fragments (e.g., in the presence of iron chelators), DNIC produce adverse (cytotoxic) effects, which can best be exemplified by their ability to suppress the development of experimental endometriosis in animals. In animal tissues, DNIC with thiol-containing ligands are predominantly represented by the binuclear form, which, contrary to mononuclear DNIC detectable by the 2.03 signal, is EPR-silent. The ample body of evidence on biological activities and occurrence of DNIC gained so far clearly demonstrates that in human and animal organisms DNIC with thiol-containing ligands represent a "working form" of the system of endogenous NO responsible for its accumulation and stabilization in animal tissues as well as its further transfer to its biological targets. Copyright © 2016 Elsevier Inc. All rights reserved.

Facile synthesis of zwitterionic polymer-coated core-shell magnetic nanoparticles for highly specific capture of N-linked glycopeptides.

PubMed

Chen, Yajing; Xiong, Zhichao; Zhang, Lingyi; Zhao, Jiaying; Zhang, Quanqing; Peng, Li; Zhang, Weibing; Ye, Mingliang; Zou, Hanfa

2015-02-21

Highly selective and efficient capture of glycosylated proteins and peptides from complex biological samples is of profound significance for the discovery of disease biomarkers in biological systems. Recently, hydrophilic interaction liquid chromatography (HILIC)-based functional materials have been extensively utilized for glycopeptide enrichment. However, the low amount of immobilized hydrophilic groups on the affinity material has limited its specificity, detection sensitivity and binding capacity in the capture of glycopeptides. Herein, a novel affinity material was synthesized to improve the binding capacity and detection sensitivity for glycopeptides by coating a poly(2-(methacryloyloxy)ethyl)-dimethyl-(3-sulfopropyl) ammonium hydroxide (PMSA) shell onto Fe3O4@SiO2 nanoparticles, taking advantage of reflux-precipitation polymerization for the first time (denoted as Fe3O4@SiO2@PMSA). The thick polymer shell endows the nanoparticles with excellent hydrophilic property and several functional groups on the polymer chains. The resulting Fe3O4@SiO2@PMSA demonstrated an outstanding ability for glycopeptide enrichment with high selectivity, extremely high detection sensitivity (0.1 fmol), large binding capacity (100 mg g(-1)), high enrichment recovery (above 73.6%) and rapid magnetic separation. Furthermore, in the analysis of real complicated biological samples, 905 unique N-glycosylation sites from 458 N-glycosylated proteins were reliably identified in three replicate analyses of a 65 μg protein sample extracted from mouse liver, showing the great potential of Fe3O4@SiO2@PMSA in the detection and identification of low-abundance N-linked glycopeptides in biological samples.

Quantitative volumetric Raman imaging of three dimensional cell cultures

NASA Astrophysics Data System (ADS)

Kallepitis, Charalambos; Bergholt, Mads S.; Mazo, Manuel M.; Leonardo, Vincent; Skaalure, Stacey C.; Maynard, Stephanie A.; Stevens, Molly M.

2017-03-01

The ability to simultaneously image multiple biomolecules in biologically relevant three-dimensional (3D) cell culture environments would contribute greatly to the understanding of complex cellular mechanisms and cell-material interactions. Here, we present a computational framework for label-free quantitative volumetric Raman imaging (qVRI). We apply qVRI to a selection of biological systems: human pluripotent stem cells with their cardiac derivatives, monocytes and monocyte-derived macrophages in conventional cell culture systems and mesenchymal stem cells inside biomimetic hydrogels that supplied a 3D cell culture environment. We demonstrate visualization and quantification of fine details in cell shape, cytoplasm, nucleus, lipid bodies and cytoskeletal structures in 3D with unprecedented biomolecular specificity for vibrational microspectroscopy.

The past, present and future of ligament regenerative engineering

PubMed Central

Mengsteab, Paulos Y; Nair, Lakshmi S; Laurencin, Cato T

2016-01-01

Regenerative engineering has been defined as the convergence of Advanced Materials Sciences, Stem Cell Sciences, Physics, Developmental Biology and Clinical Translation for the regeneration of complex tissues and organ systems. Anterior cruciate ligament (ACL) reconstruction necessitates the regeneration of bone, ligament and their interface to achieve superior clinical results. In the past, the ACL has been repaired with the use of autologous and allogeneic grafts, which have their respective drawbacks. Currently, investigations on the use of biodegradable matrices to achieve knee stability and permit tissue regeneration are making promising advancements. In the future, utilizing regenerative biology cues to induce an endogenous regenerative response may aid the enhancement of clinical ACL reconstruction outcomes. PMID:27879170

Spatial transcriptomics: paving the way for tissue-level systems biology.

PubMed

Moor, Andreas E; Itzkovitz, Shalev

2017-08-01

The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates. In this review we describe how recent advances in spatial transcriptomics open the way for tissue-level systems biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

BIOINFORMATICS IN THE K-8 CLASSROOM: DESIGNING INNOVATIVE ACTIVITIES FOR TEACHER IMPLEMENTATION

PubMed Central

Shuster, Michele; Claussen, Kira; Locke, Melly; Glazewski, Krista

2016-01-01

At the intersection of biology and computer science is the growing field of bioinformatics—the analysis of complex datasets of biological relevance. Despite the increasing importance of bioinformatics and associated practical applications, these are not standard topics in elementary and middle school classrooms. We report on a pilot project and its evolution to support implementation of bioinformatics-based activities in elementary and middle school classrooms. Specifically, we ultimately designed a multi-day summer teacher professional development workshop, in which teachers design innovative classroom activities. By focusing on teachers, our design leverages enhanced teacher knowledge and confidence to integrate innovative instructional materials into K-8 classrooms and contributes to capacity building in STEM instruction. PMID:27429860

The past, present and future of ligament regenerative engineering.

PubMed

Mengsteab, Paulos Y; Nair, Lakshmi S; Laurencin, Cato T

2016-12-01

Regenerative engineering has been defined as the convergence of Advanced Materials Sciences, Stem Cell Sciences, Physics, Developmental Biology and Clinical Translation for the regeneration of complex tissues and organ systems. Anterior cruciate ligament (ACL) reconstruction necessitates the regeneration of bone, ligament and their interface to achieve superior clinical results. In the past, the ACL has been repaired with the use of autologous and allogeneic grafts, which have their respective drawbacks. Currently, investigations on the use of biodegradable matrices to achieve knee stability and permit tissue regeneration are making promising advancements. In the future, utilizing regenerative biology cues to induce an endogenous regenerative response may aid the enhancement of clinical ACL reconstruction outcomes.

Green biorefinery - Industrial implementation.

PubMed

Kamm, B; Schönicke, P; Hille, Ch

2016-04-15

Oil refineries currently generate a multitude of products for almost every sphere of life at very high efficiency. However, fossil raw materials are just available in limited quantities. The development of comparable BIOREFINERIES is necessary to make a variety of competitive biological products regarding their equivalent products based on fossil raw materials. The product range of a biorefinery comprises products that can be manufactured on the basis of crude oil, as well as such products that cannot be produced on the basis of crude oil (Kamm, Gruber, & Kamm, 2011). GREEN BIOREFINERIES [GBR's] are complex systems of sustainable, environment- and resource-friendly technologies for a comprehensive material and energy use or recovery of renewable raw materials in form of green and waste biomasses from a sustainable land use as target (Kamm et al., 2009; Digman, Runge, Shinners, & Hatfield, 2013). Copyright © 2015. Published by Elsevier Ltd.

Butterfly effects: novel functional materials inspired from the wings scales.

PubMed

Zhang, Wang; Gu, Jiajun; Liu, Qinglei; Su, Huilan; Fan, Tongxiang; Zhang, Di

2014-10-07

Through millions of years of evolutionary selection, nature has created biological materials with various functional properties for survival. Many complex natural architectures, such as shells, bones, and honeycombs, have been studied and imitated in the design and fabrication of materials with enhanced hardness and stiffness. Recently, more and more researchers have started to research the wings of butterflies, mostly because of their dazzling colors. It was found that most of these iridescent colors are caused by periodic photonic structures on the scales that make up the surfaces of these wings. These materials have recently become a focus of multidiscipline research because of their promising applications in the display of structural colors, and in advanced sensors, photonic crystals, and solar cells. This paper review aims to provide a perspective overview of the research inspired by these wing structures in recent years.

Photochemical mineralization of europium, titanium, and iron oxyhydroxide nanoparticles in the ferritin protein cage.

PubMed

Klem, Michael T; Mosolf, Jesse; Young, Mark; Douglas, Trevor

2008-04-07

The Fe storage protein ferritin was used as a size-constrained reaction vessel for the photoreduction and reoxidation of complexed Eu, Fe, and Ti precursors for the formation of oxyhydroxide nanoparticles. The resultant materials were characterized by dynamic light scattering, gel electrophoresis, UV-vis spectroscopy, and transmission electron microscopy. The photoreduction and reoxidation process is inspired by biological sequestration mechanisms observed in some marine siderophore systems.

Engineering Lipid Bilayer Membranes for Protein Studies

PubMed Central

Khan, Muhammad Shuja; Dosoky, Noura Sayed; Williams, John Dalton

2013-01-01

Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques. PMID:24185908

The bioartificial pancreas (BAP): Biological, chemical and engineering challenges.

PubMed

Iacovacci, Veronica; Ricotti, Leonardo; Menciassi, Arianna; Dario, Paolo

2016-01-15

The bioartificial pancreas (BAP) represents a viable solution for the treatment of type 1 diabetes (T1D). By encapsulating pancreatic cells in a semipermeable membrane to allow nutrient, insulin and glucose exchange, the side effects produced by islets and whole organ transplantation-related immunosuppressive therapy can be circumvented. Several factors, mainly related to materials properties, capsule morphology and biological environment, play a key role in optimizing BAP systems. The BAP is an extremely complex delivery system for insulin. Despite considerable efforts, in some instances meeting with limited degree of success, a BAP capable of restoring physiological pancreas functions without the need for immunosuppressive drugs and of controlling blood glucose levels especially in large animal models and a few clinical trials, does not exist. The state of the art in terms of materials, fabrication techniques and cell sources, as well as the current status of commercial devices and clinical trials, are described in this overview from an interdisciplinary viewpoint. In addition, challenges to the creation of effective BAP systems are highlighted including future perspectives in terms of component integration from both a biological and an engineering viewpoint. Copyright © 2015 Elsevier Inc. All rights reserved.

The viking biological investigation: preliminary results.

PubMed

Klein, H P; Horowitz, N H; Levin, G V; Oyama, V I; Lederberg, J; Rich, A; Hubbard, J S; Hobby, G L; Straat, P A; Berdahl, B J; Carle, G C; Brown, F S; Johnson, R D

1976-10-01

Three different types of biological experiments on samples of martian surface material ("soil") were conducted inside the Viking lander. In the carbon assimilation or pyrolytic release experiment, (14)CO(2) and (14)CO were exposed to soil in the presence of light. A small amount of gas was found to be converted into organic material. Heat treatment of a duplicate sample prevented such conversion. In the gas exchange experiment, soil was first humidified (exposed to water vapor) for 6 sols and then wet with a complex aqueous solution of metabolites. The gas above the soil was monitored by gas chromatography. A substantial amount of O(2) was detected in the first chromatogram taken 2.8 hours after humidification. Subsequent analyses revealed that significant increases in CO(2) and only small changes in N(2) had also occurred. In the labeled release experiment, soil was moistened with a solution containing several (14)C-labeled organic compounds. A substantial evolution of radioactive gas was registered but did not occur with a duplicate heat-treated sample. Alternative chemical and biological interpretations are possible for these preliminary data. The experiments are still in process, and these results so far do not allow a decision regarding the existence of life on the plonet Mars.

Shape-programmable magnetic soft matter

PubMed Central

Lum, Guo Zhan; Ye, Zhou; Dong, Xiaoguang; Marvi, Hamid; Erin, Onder; Hu, Wenqi; Sitti, Metin

2016-01-01

Shape-programmable matter is a class of active materials whose geometry can be controlled to potentially achieve mechanical functionalities beyond those of traditional machines. Among these materials, magnetically actuated matter is particularly promising for achieving complex time-varying shapes at small scale (overall dimensions smaller than 1 cm). However, previous work can only program these materials for limited applications, as they rely solely on human intuition to approximate the required magnetization profile and actuating magnetic fields for their materials. Here, we propose a universal programming methodology that can automatically generate the required magnetization profile and actuating fields for soft matter to achieve new time-varying shapes. The universality of the proposed method can therefore inspire a vast number of miniature soft devices that are critical in robotics, smart engineering surfaces and materials, and biomedical devices. Our proposed method includes theoretical formulations, computational strategies, and fabrication procedures for programming magnetic soft matter. The presented theory and computational method are universal for programming 2D or 3D time-varying shapes, whereas the fabrication technique is generic only for creating planar beams. Based on the proposed programming method, we created a jellyfish-like robot, a spermatozoid-like undulating swimmer, and an artificial cilium that could mimic the complex beating patterns of its biological counterpart. PMID:27671658

Shape-programmable magnetic soft matter.

PubMed

Lum, Guo Zhan; Ye, Zhou; Dong, Xiaoguang; Marvi, Hamid; Erin, Onder; Hu, Wenqi; Sitti, Metin

2016-10-11

Shape-programmable matter is a class of active materials whose geometry can be controlled to potentially achieve mechanical functionalities beyond those of traditional machines. Among these materials, magnetically actuated matter is particularly promising for achieving complex time-varying shapes at small scale (overall dimensions smaller than 1 cm). However, previous work can only program these materials for limited applications, as they rely solely on human intuition to approximate the required magnetization profile and actuating magnetic fields for their materials. Here, we propose a universal programming methodology that can automatically generate the required magnetization profile and actuating fields for soft matter to achieve new time-varying shapes. The universality of the proposed method can therefore inspire a vast number of miniature soft devices that are critical in robotics, smart engineering surfaces and materials, and biomedical devices. Our proposed method includes theoretical formulations, computational strategies, and fabrication procedures for programming magnetic soft matter. The presented theory and computational method are universal for programming 2D or 3D time-varying shapes, whereas the fabrication technique is generic only for creating planar beams. Based on the proposed programming method, we created a jellyfish-like robot, a spermatozoid-like undulating swimmer, and an artificial cilium that could mimic the complex beating patterns of its biological counterpart.

Shape-programmable magnetic soft matter

NASA Astrophysics Data System (ADS)

Zhan Lum, Guo; Ye, Zhou; Dong, Xiaoguang; Marvi, Hamid; Erin, Onder; Hu, Wenqi; Sitti, Metin

2016-10-01

Shape-programmable matter is a class of active materials whose geometry can be controlled to potentially achieve mechanical functionalities beyond those of traditional machines. Among these materials, magnetically actuated matter is particularly promising for achieving complex time-varying shapes at small scale (overall dimensions smaller than 1 cm). However, previous work can only program these materials for limited applications, as they rely solely on human intuition to approximate the required magnetization profile and actuating magnetic fields for their materials. Here, we propose a universal programming methodology that can automatically generate the required magnetization profile and actuating fields for soft matter to achieve new time-varying shapes. The universality of the proposed method can therefore inspire a vast number of miniature soft devices that are critical in robotics, smart engineering surfaces and materials, and biomedical devices. Our proposed method includes theoretical formulations, computational strategies, and fabrication procedures for programming magnetic soft matter. The presented theory and computational method are universal for programming 2D or 3D time-varying shapes, whereas the fabrication technique is generic only for creating planar beams. Based on the proposed programming method, we created a jellyfish-like robot, a spermatozoid-like undulating swimmer, and an artificial cilium that could mimic the complex beating patterns of its biological counterpart.

Hydrolysates of lignocellulosic materials for biohydrogen production

PubMed Central

Chen, Rong; Wang, Yong-Zhong; Liao, Qiang; Zhu, Xun; Xu, Teng-Fei

2013-01-01

Lignocellulosic materials are commonly used in bio-H2 production for the sustainable energy resource development as they are abundant, cheap, renewable and highly biodegradable. In the process of the bio-H2 production, the pretreated lignocellulosic materials are firstly converted to monosaccharides by enzymolysis and then to H2 by fermentation. Since the structures of lignocellulosic materials are rather complex, the hydrolysates vary with the used materials. Even using the same lignocellulosic materials, the hydrolysates also change with different pretreatment methods. It has been shown that the appropriate hydrolysate compositions can dramatically improve the biological activities and bio-H2 production performances. Over the past decades, hydrolysis with respect to different lignocellulosic materials and pretreatments has been widely investigated. Besides, effects of the hydrolysates on the biohydrogen yields have also been examined. In this review, recent studies on hydrolysis as well as their effects on the biohydrogen production performance are summarized. [BMB Reports 2013; 46(5): 244-251] PMID:23710634

Microfluidic vascular channels in gels using commercial 3D printers

NASA Astrophysics Data System (ADS)

Selvaganapathy, P. Ravi; Attalla, Rana

2016-03-01

This paper details the development of a three dimensional (3D) printing system with a modified microfluidic printhead used for the generation of complex vascular tissue scaffolds. The print-head features an integrated coaxial nozzle that allows the fabrication of hollow, calcium-polymerized alginate tubes that can easily be patterned using 3Dbioprinting techniques. This microfluidic design allows the incorporation of a wide range of scaffold materials as well as biological constituents such as cells, growth factors, and ECM material. With this setup, gel constructs with embedded arrays of hollow channels can be created and used as a potential substitute for blood vessel networks.

Economics of abdominal wall reconstruction.

PubMed

Bower, Curtis; Roth, J Scott

2013-10-01

The economic aspects of abdominal wall reconstruction are frequently overlooked, although understandings of the financial implications are essential in providing cost-efficient health care. Ventral hernia repairs are frequently performed surgical procedures with significant economic ramifications for employers, insurers, providers, and patients because of the volume of procedures, complication rates, the significant rate of recurrence, and escalating costs. Because biological mesh materials add significant expense to the costs of treating complex abdominal wall hernias, the role of such costly materials needs to be better defined to ensure the most cost-efficient and effective treatments for ventral abdominal wall hernias. Copyright © 2013 Elsevier Inc. All rights reserved.

Platform construction and extraction mechanism study of magnetic mixed hemimicelles solid-phase extraction

NASA Astrophysics Data System (ADS)

Xiao, Deli; Zhang, Chan; He, Jia; Zeng, Rong; Chen, Rong; He, Hua

2016-12-01

Simple, accurate and high-throughput pretreatment method would facilitate large-scale studies of trace analysis in complex samples. Magnetic mixed hemimicelles solid-phase extraction has the power to become a key pretreatment method in biological, environmental and clinical research. However, lacking of experimental predictability and unsharpness of extraction mechanism limit the development of this promising method. Herein, this work tries to establish theoretical-based experimental designs for extraction of trace analytes from complex samples using magnetic mixed hemimicelles solid-phase extraction. We selected three categories and six sub-types of compounds for systematic comparative study of extraction mechanism, and comprehensively illustrated the roles of different force (hydrophobic interaction, π-π stacking interactions, hydrogen-bonding interaction, electrostatic interaction) for the first time. What’s more, the application guidelines for supporting materials, surfactants and sample matrix were also summarized. The extraction mechanism and platform established in the study render its future promising for foreseeable and efficient pretreatment under theoretical based experimental design for trace analytes from environmental, biological and clinical samples.

78 FR 58311 - Complex Issues in Developing Drug and Biological Products for Rare Diseases; Public Workshop...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-23

...] Complex Issues in Developing Drug and Biological Products for Rare Diseases; Public Workshop; Request for... Issues in Developing Drug and Biological Products for Rare Diseases.'' The purpose of the public workshop is twofold: To discuss complex issues in clinical trials for developing drug and biological products...

Biologically-inspired data decorrelation for hyper-spectral imaging

NASA Astrophysics Data System (ADS)

Picon, Artzai; Ghita, Ovidiu; Rodriguez-Vaamonde, Sergio; Iriondo, Pedro Ma; Whelan, Paul F.

2011-12-01

Hyper-spectral data allows the construction of more robust statistical models to sample the material properties than the standard tri-chromatic color representation. However, because of the large dimensionality and complexity of the hyper-spectral data, the extraction of robust features (image descriptors) is not a trivial issue. Thus, to facilitate efficient feature extraction, decorrelation techniques are commonly applied to reduce the dimensionality of the hyper-spectral data with the aim of generating compact and highly discriminative image descriptors. Current methodologies for data decorrelation such as principal component analysis (PCA), linear discriminant analysis (LDA), wavelet decomposition (WD), or band selection methods require complex and subjective training procedures and in addition the compressed spectral information is not directly related to the physical (spectral) characteristics associated with the analyzed materials. The major objective of this article is to introduce and evaluate a new data decorrelation methodology using an approach that closely emulates the human vision. The proposed data decorrelation scheme has been employed to optimally minimize the amount of redundant information contained in the highly correlated hyper-spectral bands and has been comprehensively evaluated in the context of non-ferrous material classification

Mechanical characterization of human brain tumors from patients and comparison to potential surgical phantoms.

PubMed

Stewart, Daniel C; Rubiano, Andrés; Dyson, Kyle; Simmons, Chelsey S

2017-01-01

While mechanical properties of the brain have been investigated thoroughly, the mechanical properties of human brain tumors rarely have been directly quantified due to the complexities of acquiring human tissue. Quantifying the mechanical properties of brain tumors is a necessary prerequisite, though, to identify appropriate materials for surgical tool testing and to define target parameters for cell biology and tissue engineering applications. Since characterization methods vary widely for soft biological and synthetic materials, here, we have developed a characterization method compatible with abnormally shaped human brain tumors, mouse tumors, animal tissue and common hydrogels, which enables direct comparison among samples. Samples were tested using a custom-built millimeter-scale indenter, and resulting force-displacement data is analyzed to quantify the steady-state modulus of each sample. We have directly quantified the quasi-static mechanical properties of human brain tumors with effective moduli ranging from 0.17-16.06 kPa for various pathologies. Of the readily available and inexpensive animal tissues tested, chicken liver (steady-state modulus 0.44 ± 0.13 kPa) has similar mechanical properties to normal human brain tissue while chicken crassus gizzard muscle (steady-state modulus 3.00 ± 0.65 kPa) has similar mechanical properties to human brain tumors. Other materials frequently used to mimic brain tissue in mechanical tests, like ballistic gel and chicken breast, were found to be significantly stiffer than both normal and diseased brain tissue. We have directly compared quasi-static properties of brain tissue, brain tumors, and common mechanical surrogates, though additional tests would be required to determine more complex constitutive models.

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

PubMed Central

Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

2010-01-01

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

Linking Microstructural Changes to Bulk Behavior in Shear Disordered Matter

NASA Astrophysics Data System (ADS)

Blair, Daniel

Soft and biological materials often exhibit disordered and heterogeneous microstructure. In most cases, the transmission and distribution of stresses through these complex materials reflects their inherent heterogeneity. Through the combination of rheology and 4D imaging we can directly alter and quantify the connection between microstructure and local stresses. We subject soft and biological materials to precise shear deformations while measuring real space information about the distribution and redistribution of the applied stress.In this talk, I will focus on the flow behavior of two distinct but related disordered materials; a flowing compressed emulsion above its yield stress and a strained collagen network. In the emulsion system, I will present experimental and computational results on the dynamical response, at the level of individual droplets, that directly links the particle motion and deformation to the rheology. I will also present results that utilize boundary stress microscopy to quantify the spatial distribution of surface stresses that arise from sheared in-vitro collagen networks. I will outline our main conclusions which is that the strain stiffening behavior observed in collagen networks can be parameterized by a single characteristic strain and associated stress. This characteristic rheological signature seems to describe both the strain stiffening regime and network yielding. NSF DMR: 0847490.

Fabrication of diverse pH-sensitive functional mesoporous silica for selective removal or depletion of highly abundant proteins from biological samples.

PubMed

Wang, Jiaojiao; Lan, Jingfeng; Li, Huihui; Liu, Xiaoyan; Zhang, Haixia

2017-01-01

In proteomic studies, poor detection of low abundant proteins is a major problem due to the presence of highly abundant proteins. Therefore, the specific removal or depletion of highly abundant proteins prior to analysis is necessary. In response to this problem, a series of pH-sensitive functional mesoporous silica materials composed of 2-(diethylamino)ethyl methacrylate and methacrylic acid units were designed and synthesized via atom transfer radical polymerization. These functional mesoporous silica materials were characterized and their ability for adsorption and separation of proteins was evaluated. Possessing a pH-sensitive feature, the synthesized functional materials showed selective adsorption of some proteins in aqueous or buffer solutions at certain pH values. The specific removal of a particular protein from a mixed protein solution was subsequently studied. The analytical results confirmed that all the target proteins (bovine serum albumin, ovalbumin, and lysozyme) can be removed by the proposed materials from a five-protein mixture in a single operation. Finally, the practical application of this approach was also evaluated by the selective removal of certain proteins from real biological samples. The results revealed that the maximum removal efficiencies of ovalbumin and lysozyme from egg white sample were obtained as 99% and 92%, respectively, while the maximum removal efficiency of human serum albumin from human serum sample was about 80% by the proposed method. It suggested that this treatment process reduced the complexity of real biological samples and facilitated the identification of hidden proteins in chromatograms. Copyright © 2016 Elsevier B.V. All rights reserved.

Synthetic fossilization of soft biological tissues and their shape-preserving transformation into silica or electron-conductive replicas

DOE PAGES

Townson, Jason L.; Lin, Yu-Shen; Chou, Stanley S.; ...

2014-12-08

Structural preservation of complex biological systems from the subcellular to whole organism level in robust forms, enabling dissection and imaging while preserving 3D context, represents an enduring grand challenge in biology. Here we report a simple immersion method for structurally preserving intact organisms via conformal stabilization within silica. This self-limiting process, which we refer to as silica bioreplication, occurs by condensation of water-soluble silicic acid proximally to biomolecular interfaces throughout the organism. Conformal nanoscopic silicification of all biomolecular features imparts structural rigidity enabling the preservation of shape and nano-to-macroscale dimensional features upon drying to form a biocomposite and further highmore » temperature oxidative calcination to form silica replicas or reductive pyrolysis to form electrically conductive carbon replicas of complete organisms. Ultimately, the simplicity and generalizability of this approach should facilitate efforts in biological preservation and analysis and could enable the development of new classes of biomimetic composite materials.« less

Remotely controlled fusion of selected vesicles and living cells: a key issue review

NASA Astrophysics Data System (ADS)

Bahadori, Azra; Moreno-Pescador, Guillermo; Oddershede, Lene B.; Bendix, Poul M.

2018-03-01

Remote control over fusion of single cells and vesicles has a great potential in biological and chemical research allowing both transfer of genetic material between cells and transfer of molecular content between vesicles. Membrane fusion is a critical process in biology that facilitates molecular transport and mixing of cellular cytoplasms with potential formation of hybrid cells. Cells precisely regulate internal membrane fusions with the aid of specialized fusion complexes that physically provide the energy necessary for mediating fusion. Physical factors like membrane curvature, tension and temperature, affect biological membrane fusion by lowering the associated energy barrier. This has inspired the development of physical approaches to harness the fusion process at a single cell level by using remotely controlled electromagnetic fields to trigger membrane fusion. Here, we critically review various approaches, based on lasers or electric pulses, to control fusion between individual cells or between individual lipid vesicles and discuss their potential and limitations for present and future applications within biochemistry, biology and soft matter.

e-Biologics: Fabrication of Sustainable Electronics with "Green" Biological Materials.

PubMed

Lovley, Derek R

2017-06-27

The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial components as the guide for synthesis, are a potential green solution. Some e-biologics can be fabricated from renewable feedstocks with relatively low energy inputs, often while avoiding the harsh chemicals used for synthesizing more traditional electronic materials. Several are completely free of toxic components, can be readily recycled, and offer unique features not found in traditional electronic materials in terms of size, performance, and opportunities for diverse functionalization. An appropriate investment in the concerted multidisciplinary collaborative research required to identify and characterize e-biologics and to engineer materials and devices based on e-biologics could be rewarded with a new "green age" of sustainable electronic materials and devices. Copyright © 2017 Lovley.

On the biomechanical function of scaffolds for engineering load-bearing soft tissues.

PubMed

Stella, John A; D'Amore, Antonio; Wagner, William R; Sacks, Michael S

2010-07-01

Replacement or regeneration of load-bearing soft tissues has long been the impetus for the development of bioactive materials. While maturing, current efforts continue to be confounded by our lack of understanding of the intricate multi-scale hierarchical arrangements and interactions typically found in native tissues. The current state of the art in biomaterial processing enables a degree of controllable microstructure that can be used for the development of model systems to deduce fundamental biological implications of matrix morphologies on cell function. Furthermore, the development of computational frameworks which allow for the simulation of experimentally derived observations represents a positive departure from what has mostly been an empirically driven field, enabling a deeper understanding of the highly complex biological mechanisms we wish to ultimately emulate. Ongoing research is actively pursuing new materials and processing methods to control material structure down to the micro-scale to sustain or improve cell viability, guide tissue growth, and provide mechanical integrity, all while exhibiting the capacity to degrade in a controlled manner. The purpose of this review is not to focus solely on material processing but to assess the ability of these techniques to produce mechanically sound tissue surrogates, highlight the unique structural characteristics produced in these materials, and discuss how this translates to distinct macroscopic biomechanical behaviors. Copyright 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Materiomics for Oral Disease Diagnostics and Personal Health Monitoring: Designer Biomaterials for the Next Generation Biomarkers

PubMed Central

Zhang, Wenjun; Wang, Ming L.; Khalili, Sammy

2016-01-01

Abstract We live in exciting times for a new generation of biomarkers being enabled by advances in the design and use of biomaterials for medical and clinical applications, from nano- to macro-materials, and protein to tissue. Key challenges arise, however, due to both scientific complexity and compatibility of the interface of biology and engineered materials. The linking of mechanisms across scales by using a materials science approach to provide structure–process–property relations characterizes the emerging field of ‘materiomics,’ which offers enormous promise to provide the hitherto missing tools for biomaterial development for clinical diagnostics and the next generation biomarker applications towards personal health monitoring. Put in other words, the emerging field of materiomics represents an essentially systematic approach to the investigation of biological material systems, integrating natural functions and processes with traditional materials science perspectives. Here we outline how materiomics provides a game-changing technology platform for disruptive innovation in biomaterial science to enable the design of tailored and functional biomaterials—particularly, the design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. Rigorous and complementary computational modeling and experimental techniques will provide an efficient means to develop new clinical technologies in silico, greatly accelerating the translation of materiomics-driven oral health diagnostics from concept to practice in the clinic. PMID:26760957

Imaging mass spectrometer with mass tags

DOEpatents

Felton, James S.; Wu, Kuang Jen; Knize, Mark G.; Kulp, Kristen S.; Gray, Joe W.

2010-06-01

A method of analyzing biological material by exposing the biological material to a recognition element, that is coupled to a mass tag element, directing an ion beam of a mass spectrometer to the biological material, interrogating at least one region of interest area from the biological material and producing data, and distributing the data in plots.

Source Identification of Human Biological Materials and Its Prospect in Forensic Science.

PubMed

Zou, K N; Gui, C; Gao, Y; Yang, F; Zhou, H G

2016-06-01

Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction. Copyright© by the Editorial Department of Journal of Forensic Medicine.

A 4-D dataset for validation of crystal growth in a complex three-phase material, ice cream

NASA Astrophysics Data System (ADS)

Rockett, P.; Karagadde, S.; Guo, E.; Bent, J.; Hazekamp, J.; Kingsley, M.; Vila-Comamala, J.; Lee, P. D.

2015-06-01

Four dimensional (4D, or 3D plus time) X-ray tomographic imaging of phase changes in materials is quickly becoming an accepted tool for quantifying the development of microstructures to both inform and validate models. However, most of the systems studied have been relatively simple binary compositions with only two phases. In this study we present a quantitative dataset of the phase evolution in a complex three-phase material, ice cream. The microstructure of ice cream is an important parameter in terms of sensorial perception, and therefore quantification and modelling of the evolution of the microstructure with time and temperature is key to understanding its fabrication and storage. The microstructure consists of three phases, air cells, ice crystals, and unfrozen matrix. We perform in situ synchrotron X-ray imaging of ice cream samples using in-line phase contrast tomography, housed within a purpose built cold-stage (-40 to +20oC) with finely controlled variation in specimen temperature. The size and distribution of ice crystals and air cells during programmed temperature cycling are determined using 3D quantification. The microstructural evolution of three-phase materials has many other important applications ranging from biological to structural and functional material, hence this dataset can act as a validation case for numerical investigations on faceted and non-faceted crystal growth in a range of materials.

[Development and application of artificial vertebral body].

PubMed

Liu, Jian-Tao; Zhang, Feng; Gao, Zheng-Chao; Niu, Bin-Bin; Li, Yu-Huan; He, Xi-Jing

2017-12-25

Artificial vertebral body has achieved good results in treating spinal tumors, tuberculosis, fracture and other diseases. Currently, artificial vertebral body with variety of kinds and pros and cons, is generally divided into two types: fusion type and movable type. The former according to whether the height could be adjusted and strength of self-stability is divided into three types: support-fixed type, adjust-fixed type and self-fixed type. Whether the height of self-fixed type could be adjusted is dependent on structure of collar thread rotation. The latter is due to mobile device of ball-and-socket joints or hollow structures instead of the disc which retains the activity of the spine to some extent. Materials of artificial vertebral body include metals, ceramics, biomaterials, polymer composites and other materials. Titanium with a dominant role in the metal has developed to the third generation, but there are still defects such as poor surface bioactivity; ceramics with the representative of hydroxyapatite composite, magnetic bioceramics, polycrystalline alumina ceramics and so on, which have the defects of processing complex and uneven mechanical properties; biological material is mainly dominated by xenogeneic bone, which is closest to human bone in structure and properties, but has defects of low toughness and complex production; polymer composites according to biological characteristics in general consists of biodegradable type and non-biodegradable type which are respectively represented by poly-lactide and polyethylene, each with advantages and disadvantages. Although the design and materials of prosthesis have made great progress, it is difficult to fully meet requirements of spinal implants and they need be further optimized. 3D printing technology makes process of the complex structure of prosthesis and individual customization possible and has broad development prospects. However, long production cycles and high cost of defect should be overcome. Although artificial vertebral body has achieved curative effect in treating spinal disease, there were reports of implant loosening or displacement. Combining with evaluation standards not unified, short follow-up time, its exact effect needs further observation. Copyright© 2017 by the China Journal of Orthopaedics and Traumatology Press.

The Development and Study of Surface Bound Ruthenium Organometallic Complexes

NASA Astrophysics Data System (ADS)

Abbott, Geoffrey Reuben

The focus of this project has been on the use of mono-diimine ruthenium organometallic complexes, of the general structure [H(Ru)(CO)(L)2(L') 2][PF6] (L=PPh3, DPPENE and L'=Bpy, DcBpy, MBpyC, Phen, AminoPhen) bound to surfaces as luminescent probes. Both biological and inorganic/organic hybrid surfaces have been studied. The complexes were characterized both bound and unbound using standard analytical techniques such as NMR, IR and X-ray crystallography, as well as through several photophysical methods as well. Initially the study focused on how the photophyscial properties of the complexes were affected by incorporation into biological membranes. It was found that by conjugating the probes to a more rigid cholesterol moiety that luminescence was conserved, compared to conjugation with a far more flexible lipid moiety, where luminescence was either lost or reduced. Both the cholesterol and lipid conjugates were able to insert into a lipid membrane, and in the more rigid environment some of the lipid conjugates regained some of their luminescence, but often blue shifted and reduced, depending on the conjugation site. Silica Polyamine Composites (SPCs) were a hybrid material developed in the Rosenberg Lab as useful metal separation materials, that could be easily modified, and had several benefits over current commercially available polymers, or inorganic materials. These SPCs also provided an opportunity for the development of a heterogeneous platform for luminescent complexes as either catalysts or sensors. Upon binding of the luminescent Ru complexes to the surface no loss, or major change in luminescence was seen, however, when bound to the rigid surface a significant increase in excited state lifetime was measured. It is likely that through binding and interacting with the surface that the complexes lost non-radiative decay pathways, resulting in the increase in lifetime, however, these interactions do not seem to affect the energy level of the MLCT band in a large way. With a better understanding of the effects of surface binding on the complexes, the study turned to possible applications, as either sensors or catalysts. Recently the bound complexes have been found to be very useful as toxic metal sensors, as the free amines left on the surface could bind toxic metal ions in close proximity leading to either a quenching or enhancement of the luminescence of the complexes, depending on the metal ion. This process was determined to be a static process, requiring the toxic metal to remain bound to the surface in order to affect the luminescence of the Ru complex. The quenching is thought to be due to a metal-centered electron-transfer reaction, in which the excited-state electron is transferred from the Ru to the toxic metal, but relaxes back to the Ru center. The enhancement of luminescence is due to the external heavy-atom effect, in which heavier atoms mixes MLCT singlet state with the triplet state through spin-orbit coupling.

Bioelectrical Impedance and The Frequency Dependent Current Conduction Through Biological Tissues: A Short Review

NASA Astrophysics Data System (ADS)

Kanti Bera, Tushar

2018-03-01

Biological tissues are developed with biological cells which exhibit complex electrical impedance called electrical bioimpedance. Under an alternating electrical excitation the bioimpedance varies with the tissue anatomy, composition and the signal frequency. The current penetration and conduction paths vary with frequency of the applied signal. Bioimpedance spectroscopy is used to study the frequency response of the electrical impedance of biological materials noninvasively. In bioimpedance spectroscopy, a low amplitude electrical signal is injected to the tissue sample or body parts to characterization the sample in terms of its bioimpedance. The electrical current conduction phenomena, which is highly influenced by the tissue impedance and the signal frequency, is an important phenomena which should be studied to understand the bioimpedance techniques like bioelectrical impedance analysis (BIA), EIS, or else. In this paper the origin of bioelectrical impedance and current conduction phenomena has been reviewed to present a brief summary of bioelectrical impedance and the frequency dependent current conduction through biological tissues. Simulation studies are conducted with alternation current injection through a two dimensional model of biological tissues containing finite number of biological cells suspended in extracellular fluid. The paper demonstrates the simulation of alternating current conduction through biological tissues conducted by COMSOL Multiphysics. Simulation studies also show the frequency response of the tissue impedance for different tissue compositions.

Organic Electronics for Point-of-Care Metabolite Monitoring.

PubMed

Pappa, Anna-Maria; Parlak, Onur; Scheiblin, Gaetan; Mailley, Pascal; Salleo, Alberto; Owens, Roisin M

2018-01-01

In this review we focus on demonstrating how organic electronic materials can solve key problems in biosensing thanks to their unique material properties and implementation in innovative device configurations. We highlight specific examples where these materials solve multiple issues related to complex sensing environments, and we benchmark these examples by comparing them to state-of-the-art commercially available sensing using alternative technologies. We have categorized our examples by sample type, focusing on sensing from body fluids in vitro and on wearable sensors, which have attracted significant interest owing to their integration with everyday life activities. We finish by describing a future trend for in vivo, implantable sensors, which aims to build on current progress from sensing in biological fluids ex vivo. Copyright © 2017 Elsevier Ltd. All rights reserved.

Engineering artificial cells by combining HeLa-based cell-free expression and ultra-thin double emulsion template

PubMed Central

Ho, Kwun Yin; Murray, Victoria L.; Liu, Allen P.

2015-01-01

Generation of artificial cells provides the bridge needed to cover the gap between studying the complexity of biological processes in whole cells and studying these same processes in an in vitro reconstituted system. Artificial cells are defined as the encapsulation of biologically active material in a biological or synthetic membrane. Here, we describe a robust and general method to produce artificial cells for the purpose of mimicking one or more behaviors of a cell. A microfluidic double emulsion system is used to encapsulate a mammalian cell free expression system that is able to express membrane proteins into the bilayer or soluble proteins inside the vesicles. The development of a robust platform that allows the assembly of artificial cells is valuable in understanding subcellular functions and emergent behaviors in a more cell-like environment as well as for creating novel signaling pathways to achieve specific cellular behaviors. PMID:25997354

Integrative biological analysis for neuropsychopharmacology.

PubMed

Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

2014-01-01

Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches--proteomics, transcriptomics, metabolomics, and glycomics--have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studies that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine.

Manufacturing, assembling and packaging of miniaturized implants for neural prostheses and brain-machine interfaces

NASA Astrophysics Data System (ADS)

Stieglitz, Thomas

2009-05-01

Implantable medical devices to interface with muscles, peripheral nerves, and the brain have been developed for many applications over the last decades. They have been applied in fundamental neuroscientific studies as well as in diagnosis, therapy and rehabilitation in clinical practice. Success stories of these implants have been written with help of precision mechanics manufacturing techniques. Latest cutting edge research approaches to restore vision in blind persons and to develop an interface with the human brain as motor control interface, however, need more complex systems and larger scales of integration and higher degrees of miniaturization. Microsystems engineering offers adequate tools, methods, and materials but so far, no MEMS based active medical device has been transferred into clinical practice. Silicone rubber, polyimide, parylene as flexible materials and silicon and alumina (aluminum dioxide ceramics) as substrates and insulation or packaging materials, respectively, and precious metals as electrodes have to be combined to systems that do not harm the biological target structure and have to work reliably in a wet environment with ions and proteins. Here, different design, manufacturing and packaging paradigms will be presented and strengths and drawbacks will be discussed in close relation to the envisioned biological and medical applications.

Electrospun microcrimped fibers with nonlinear mechanical properties enhance ligament fibroblast phenotype.

PubMed

Grace Chao, Pen-hsiu; Hsu, Hsiang-Yi; Tseng, Hsiao-Yun

2014-09-01

Fiber structure and order greatly impact the mechanical behavior of fibrous materials. In biological tissues, the nonlinear mechanics of fibrous scaffolds contribute to the functionality of the material. The nonlinear mechanical properties of the wavy structure (crimp) in collagen allow tissue flexibility while preventing over-extension. A number of approaches have tried to recreate this complex mechanical functionality. We generated microcrimped fibers by briefly heating electrospun parallel fibers over the glass transition temperature or by ethanol treatment. The crimp structure is similar to those of collagen fibers found in native aorta, intestines, or ligaments. Using poly-L-lactic acid fibers, we demonstrated that the bulk materials exhibit changed stress-strain behaviors with a significant increase in the toe region in correlation to the degree of crimp, similar to those observed in collagenous tissues. In addition to mimicking the stress-strain behavior of biological tissues, the microcrimped fibers are instructive in cell morphology and promote ligament phenotypic gene expression. This effect can be further enhanced by dynamic tensile loading, a physiological perturbation in vivo. This rapid and economical approach for microcrimped fiber production provides an accessible platform to study structure-function relationships and a novel functional scaffold for tissue engineering and cell mechanobiology studies.

Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

DOEpatents

Alfano, Robert R.; Wang, Wubao

2003-05-06

A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. A low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic transaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively.

Understanding Global Change (UGC) as a Unifying Conceptual Framework for Teaching Ecology: Using UGC in a High School Biology Program to Integrate Earth Science and Biology, and to Demonstrate the Value of Modeling Global Systems in Promoting Conceptual Learning

NASA Astrophysics Data System (ADS)

Levine, J.; Bean, J. R.

2017-12-01

Global change science is ideal for NGSS-informed teaching, but presents a serious challenge to K-12 educators because it is complex and interdisciplinary- combining earth science, biology, chemistry, and physics. Global systems are themselves complex. Adding anthropogenic influences on those systems creates a formidable list of topics - greenhouse effect, climate change, nitrogen enrichment, introduced species, land-use change among them - which are often presented as a disconnected "laundry list" of "facts." This complexity, combined with public and mass-media scientific illiteracy, leaves global change science vulnerable to misrepresentation and politicization, creating additional challenges to teachers in public schools. Ample stand-alone, one-off, online resources, many of them excellent, are (to date) underutilized by teachers in the high school science course taken by most students: biology. The Understanding Global Change project (UGC) from the UC Berkeley Museum of Paleontology has created a conceptual framework that organizes, connects, and explains global systems, human and non-human drivers of change in those systems, and measurable changes in those systems. This organization and framework employ core ideas, crosscutting concepts, structure/function relationships, and system models in a unique format that facilitates authentic understanding, rather than memorization. This system serves as an organizing framework for the entire ecology unit of a forthcoming mainstream high school biology program. The UGC system model is introduced up front with its core informational graphic. The model is elaborated, step by step, by adding concepts and processes as they are introduced and explained in each chapter. The informational graphic is thus used in several ways: to organize material as it is presented, to summarize topics in each chapter and put them in perspective, and for review and critical thinking exercises that supplement the usual end-of-chapter lists of key terms.

PREFACE: Nanobiology: from physics and engineering to biology

NASA Astrophysics Data System (ADS)

Nussinov, Ruth; Alemán, Carlos

2006-03-01

Biological systems are inherently nano in scale. Unlike nanotechnology, nanobiology is characterized by the interplay between physics, materials science, synthetic organic chemistry, engineering and biology. Nanobiology is a new discipline, with the potential of revolutionizing medicine: it combines the tools, ideas and materials of nanoscience and biology; it addresses biological problems that can be studied and solved by nanotechnology; it devises ways to construct molecular devices using biomacromolecules; and it attempts to build molecular machines utilizing concepts seen in nature. Its ultimate aim is to be able to predictably manipulate these, tailoring them to specified needs. Nanobiology targets biological systems and uses biomacromolecules. Hence, on the one hand, nanobiology is seemingly constrained in its scope as compared to general nanotechnology. Yet the amazing intricacy of biological systems, their complexity, and the richness of the shapes and properties provided by the biological polymers, enrich nanobiology. Targeting biological systems entails comprehension of how they work and the ability to use their components in design. From the physical standpoint, ultimately, if we are to understand biology we need to learn how to apply physical principles to figure out how these systems actually work. The goal of nanobiology is to assist in probing these systems at the appropriate length scale, heralding a new era in the biological, physical and chemical sciences. Biology is increasingly asking quantitative questions. Quantitation is essential if we are to understand how the cell works, and the details of its regulation. The physical sciences provide tools and strategies to obtain accurate measurements and simulate the information to allow comprehension of the processes. Nanobiology is at the interface of the physical and the biological sciences. Biology offers to the physical sciences fascinating problems, sophisticated systems and a rich repertoire of shapes and materials. Inspection of the protein structure databank illustrates the breadth of scaffolds, shapes and properties that protein molecules and their building blocks can provide. Via a shape-guided self-assembly strategy, these can be put together toward a specific function. Further, by inserting synthetic non-natural residues at judiciously selected positions, or synthetic peptide linkers, we may selectively rigidify the construct, or obtain a totally new world of shapes and scaffolds. Such broadening of the chemical space may lead to an almost unlimited range of nanosystems and architectures. Merging computation with experiment will accelerate nanodesign. Computational modeling will enhance the application of nanotechnology to key areas such as drug delivery and biomaterial design. Nanobiology is a field where interdisciplinary collaborations are essential and disciplines converge. Discipline convergence should enable the quantitation, leading to a better understanding of the regulatory networks within cells and between cells of an organism. These networks dictate how a cell responds to external stimuli, which in turn activate signaling cascades. It should allow the addressing of a broad range of questions on the structure and function of the cytoskeleton; the nuclear envelope; signal transduction by membrane embedded receptors; the nanomechanical properties of the extracellular matrix; nuclear transport; and voltage induced channel gating. For successful nanostructure design, we need to figure out and be able to control the intermolecular associations. For a stable functional construct, there are two key elements: first, the conformations of the building blocks in the designed structure should follow their natural tendencies; and second, the associations should be favorable. Molecules interact through their surfaces. Thus, favorable associations derive from shape complementarity and contributions of the various physical components. Nanobiology is in its infancy. Yet, biology provides an enormous range of engaging and stimulating problems with many in vivo examples of intricate, complex, fascinating biological systems. Understanding, mimicking and controlling the devices which target these processes and which are constructed from these molecules is a tremendous challenge to the converging disciplines in nanobiology.

e-Biologics: Fabrication of Sustainable Electronics with “Green” Biological Materials

PubMed Central

2017-01-01

ABSTRACT The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial components as the guide for synthesis, are a potential green solution. Some e-biologics can be fabricated from renewable feedstocks with relatively low energy inputs, often while avoiding the harsh chemicals used for synthesizing more traditional electronic materials. Several are completely free of toxic components, can be readily recycled, and offer unique features not found in traditional electronic materials in terms of size, performance, and opportunities for diverse functionalization. An appropriate investment in the concerted multidisciplinary collaborative research required to identify and characterize e-biologics and to engineer materials and devices based on e-biologics could be rewarded with a new “green age” of sustainable electronic materials and devices. PMID:28655820

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance*

PubMed Central

Paulovich, Amanda G.; Billheimer, Dean; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Tabb, David L.; Wang, Pei; Blackman, Ronald K.; Bunk, David M.; Cardasis, Helene L.; Clauser, Karl R.; Kinsinger, Christopher R.; Schilling, Birgit; Tegeler, Tony J.; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fenyo, David; Carr, Steven A.; Fisher, Susan J.; Gibson, Bradford W.; Mesri, Mehdi; Neubert, Thomas A.; Regnier, Fred E.; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E.; Tempst, Paul; Liebler, Daniel C.

2010-01-01

Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize preanalytical and analytical variation in comparative proteomics experiments. PMID:19858499

Electrospun poly(ε-caprolactone) matrices containing silver sulfadiazine complexed with β-cyclodextrin as a new pharmaceutical dosage form to wound healing: preliminary physicochemical and biological evaluation.

PubMed

Souza, Sarah Oliveira Lamas; Cotrim, Monique Alvarenga Pinto; Oréfice, Rodrigo Lambert; Carvalho, Suzana Gonçalves; Dutra, Jessyca Aparecida Paes; de Paula Careta, Francisco; Resende, Juliana Alves; Villanova, Janaina Cecília Oliveira

2018-05-10

Cooperation between researchers in the areas of medical, pharmaceutical and materials science has facilitated the development of pharmaceutical dosage forms that elicit therapeutic effects and protective action with a single product. In addition to optimizing pharmacologic action, such dosage forms provide greater patient comfort and increase success and treatment compliance. In the present work, we prepared semipermeable bioactive electrospun fibers for use as wound dressings containing silver sulfadiazine complexed with β-cyclodextrin in a poly(Ɛ-caprolactone) nanofiber matrix aiming to reduce the direct contact between silver and skin and to modulate the drug release. Wound dressings were prepared by electrospinning, and were subjected to ATR-FT-IR and TG/DTG assays to evaluate drug stability. The hydrophilicity of the fibrous nanostructure in water and PBS buffer was studied by goniometry. Electrospun fibers permeability and swelling capacity were assessed, and a dissolution test was performed. In vitro biological tests were realized to investigate the biological compatibility and antimicrobial activity. We obtained flexible matrices that were each approximately 1.0 g in weight. The electrospun fibers were shown to be semipermeable, with water vapor transmission and swelling indexes compatible with the proposed objective. The hydrophilicity was moderate. Matrices containing pure drug modulated drug release adequately during 24 h but presented a high hemolytic index. Complexation promoted a decrease in the hemolytic index and in the drug release but did not negatively impact antimicrobial activity. The drug was released predominantly by diffusion. These results indicate that electrospun PCL matrices containing β-cyclodextrin/silver sulfadiazine inclusion complexes are a promising pharmaceutical dosage form for wound healing.

Tutorial: Electroporation of cells in complex materials and tissue

NASA Astrophysics Data System (ADS)

Rems, L.; Miklavčič, D.

2016-05-01

Electroporation is being successfully used in biology, medicine, food processing, and biotechnology, and in some environmental applications. Recent applications also include in addition to classical electroporation, where cells are exposed to micro- or milliseconds long pulses, exposures to extremely short nanosecond pulses, i.e., high-frequency electroporation. Electric pulses are applied to cells in different structural configurations ranging from suspended cells to cells in tissues. Understanding electroporation of cells in tissues and other complex environments is a key to its successful use and optimization in various applications. Thus, explanation will be provided theoretically/numerically with relation to experimental observations by scaling our understanding of electroporation from the molecular level of the cell membrane up to the tissue level.

Light-fuelled transport of large dendrimers and proteins.

PubMed

Koskela, Jenni E; Liljeström, Ville; Lim, Jongdoo; Simanek, Eric E; Ras, Robin H A; Priimagi, Arri; Kostiainen, Mauri A

2014-05-14

This work presents a facile water-based supramolecular approach for light-induced surface patterning. The method is based upon azobenzene-functionalized high-molecular weight triazine dendrimers up to generation 9, demonstrating that even very large globular supramolecular complexes can be made to move in response to light. We also demonstrate light-fuelled macroscopic movements in native biomolecules, showing that complexes of apoferritin protein and azobenzene can effectively form light-induced surface patterns. Fundamentally, the results establish that thin films comprising both flexible and rigid globular particles of large diameter can be moved with light, whereas the presented material concepts offer new possibilities for the yet marginally explored biological applications of azobenzene surface patterning.

Biological tracer method

DOEpatents

Strong-Gunderson, Janet M.; Palumbo, Anthony V.

1998-01-01

The present invention is a biological tracer method for characterizing the movement of a material through a medium, comprising the steps of: introducing a biological tracer comprising a microorganism having ice nucleating activity into a medium; collecting at least one sample of the medium from a point removed from the introduction point; and analyzing the sample for the presence of the biological tracer. The present invention is also a method for using a biological tracer as a label for material identification by introducing a biological tracer having ice nucleating activity into a material, collecting a sample of a portion of the labelled material and analyzing the sample for the presence of the biological tracer.

Biological tracer method

DOEpatents

Strong-Gunderson, J.M.; Palumbo, A.V.

1998-09-15

The present invention is a biological tracer method for characterizing the movement of a material through a medium, comprising the steps of: introducing a biological tracer comprising a microorganism having ice nucleating activity into a medium; collecting at least one sample of the medium from a point removed from the introduction point; and analyzing the sample for the presence of the biological tracer. The present invention is also a method for using a biological tracer as a label for material identification by introducing a biological tracer having ice nucleating activity into a material, collecting a sample of a portion of the labelled material and analyzing the sample for the presence of the biological tracer. 2 figs.

Standoff laser-induced fluorescence of suspensions from different bacterial strains

NASA Astrophysics Data System (ADS)

Duschek, Frank; Walter, Arne; Fellner, Lea; Grünewald, Karin; Pargmann, Carsten; Handke, Jürgen; Tomaso, Herbert

2016-10-01

Biological hazardous substances like certain fungi and bacteria represent a high risk for the broad public if fallen into wrong hands. Incidents based on bio agents are commonly considered to have incalculable and complex consequences for first responders and people. The impact of such an event can be minimized by a combination of different sensor technologies that have been developed to detect bio-threats and to gather information after an incident. Sensors for bio-agents can be grouped into two categories. Sampling devices collect material from locations supposed to be contaminated, and they are able to identify biological material with high sensitivity and selectivity. However, these point sensors need to be positioned correctly in advance of an attack, and moving sources of biological material cannot be tracked. A different approach is based on optical standoff detection. For biological samples laser induced florescence (LIF) has been proven to get real time data on location and type of hazards without being in contact with the suspicious substance. This work is based on a bio-detector developed at the DLR Lampoldshausen. The LIF detection has been designed for outdoor operation at standoff distances from 20 m up to more than 100 m. The detector acquires LIF spectral data for two different excitation wavelengths (280 and 355 nm) as well as time resolved information for the fluorescence decay which can be used to classify suspicious samples. While the classification device had been trained on uncritical samples (like amino acids, NADH, yeast, chemicals, oils), this work presents the progress to more relevant, living bacteria of different strains. The low risk and non-pathogenic bacteria Bacillus thuringensis, Bacillus atrophaeus, Bacillus subtilis, Brevibacillus brevis, Micrococcus luteus, Oligella urethralis, Paenibacillus polymyxa and Escherichia coli (K12) have been investigated with the above set-up at both excitation wavelengths

Complex dielectric properties of anhydrous polycrystalline glucose in the terahertz region

NASA Astrophysics Data System (ADS)

Sun, P.; Liu, W.; Zou, Y.; Jia, Qiong Z.; Li, Jia Y.

2015-03-01

We utilized terahertz time-domain spectroscopy (THz-TDS) to investigate the complex dielectric properties of solid polycrystalline material of anhydrous glucose (D-(+)-glucose with purity >99.9%). THz transmission spectra of samples were measured from 0.2 to 2.2 THz. The samples were prepared into tablets with thicknesses of 0.362, 0.447, 0.504, 0.522 and 0.626 mm, respectively. The imaginary part of the complex dielectric function of polycrystalline glucose showed that there were multiple characteristic absorption peaks at 1.232, 1.445, 1.522, 1.608, 1.811 and 1.987 THz, respectively. Moreover, for a given characteristic absorption peak, the real part of the complex dielectric function showed anomalous dispersion within the full width half maximum (FWHM) of the absorption peak. Both finite difference time-domain (FDTD) numerical simulations and experimental results showed that the complex dielectric function of anhydrous polycrystalline glucose fits well with the Lorentz dielectric mode. The plasma oscillation frequency was below the frequency of the light waves suggesting that the light waves passed through the polycrystalline glucose tablets. Calculations based on density functional theory (DFT) showed that the characteristic absorption peaks of polycrystalline glucose originated mainly from collective intermolecular vibrations such as hydrogen bonds and crystal phonon modes. The THz radiation can excite the vibrational or rotational energy levels of the biological macromolecules. This leads to changes in their spatial configuration or interactions. This study showed that THz-TDS has potential applications in biological and pharmaceutical research and food industry.

Preface

NASA Astrophysics Data System (ADS)

Mallamace, Francesco; Quintana, Jacqueline

2002-03-01

Complex systems represent one of the richest and more fascinating fields of current scientific research. The reason behind this is the important role that the properties of complex systems and materials play in a variety of different but overlapping areas in physics, chemistry, biology, mathematics, and social sciences, like medicine and economy. Such unusually broad research field is, therefore, of primary interest nowadays in pure science and technology. The role of statistical physics in this new field of complex systems has been present since its onset and it has been accelerating recently. Methods developed for studying ordering phenomena in simple systems have been generalized for application to more complex forms of matter (polymers, biological macromolecules, glasses, etc) and complex processes (e.g. chaos, turbulence, economy, jamming, biological processes). In particular, many different phenomena (considered in the past to belong to separate research fields) have now a common description. Pillars of such a description are the concepts of scaling and universality. The International Conference on `Scaling Concepts and Complex Systems' (a satellite meeting of STATPHYS21) was devoted to give an overview on recent developments around these two concepts. The Conference took place in Merida, Yucatan, Mexico, in July 9-14 2001. The meeting was held in the Gordon Conference style and was attended by about 100 scientists, it covered a large variety of theoretical and experimental research topics of current interest in complex systems and materials. The meeting consisted of a total number of about 40 invited and contributed talks and a poster session. The topics covered included: scaling behaviour, supra-molecular systems, aggregation, aggregation kinetics, growth mechanisms, disordered systems, soft condensed matter (polymers, biological polymers, bio-colloids, gels, colloids, membranes and interfacial phenomena), granular matter, phase separation and out-of-equilibrium dynamics, non-linear dynamics, chaos, turbulence and chaotic dynamics. The present issue contains a substantial number of the invited and contributed talks presented at the meeting. We made an effort to arrange these papers with an order similar to that of presentation during the meeting. It is our pleasure to thank the scientific committee, all the speakers, the session chairs and all participants who contributed to the success of the conference. We are grateful to the Bonino-Pulejo Foundation (Messina-Italy), and to the President On. Nino Calarco, for the Patronage and the enthusiastic support. Our thanks goes also for the Messina University, the INFM (Istituto Nazionale per la Fisica della Materia, Italy), the Consejo Nacional de Ciencia y Tecnología (CONACyT, Mexico) and the Universidad Nacional Autonoma de Mexico (UNAM). The Conference was sponsored by the INFM-Sec.C, CONACyT, UNAM, the Bonino-Pulejo Foundation which contributed financial support to participants and to the publication of the present issue. We are grateful to them for the support. Last, but not the least, we express our warmest gratitude to all the members of the local organizing committee for their assistance and for the work spent in organizing this meeting and especially to Professor~Alberto Robledo for his valuable advice.

3D Printing of Materials with Tunable Failure via Bioinspired Mechanical Gradients.

PubMed

Kokkinis, Dimitri; Bouville, Florian; Studart, André R

2018-05-01

Mechanical gradients are useful to reduce strain mismatches in heterogeneous materials and thus prevent premature failure of devices in a wide range of applications. While complex graded designs are a hallmark of biological materials, gradients in manmade materials are often limited to 1D profiles due to the lack of adequate fabrication tools. Here, a multimaterial 3D-printing platform is developed to fabricate elastomer gradients spanning three orders of magnitude in elastic modulus and used to investigate the role of various bioinspired gradient designs on the local and global mechanical behavior of synthetic materials. The digital image correlation data and finite element modeling indicate that gradients can be effectively used to manipulate the stress state and thus circumvent the weakening effect of defect-rich interfaces or program the failure behavior of heterogeneous materials. Implementing this concept in materials with bioinspired designs can potentially lead to defect-tolerant structures and to materials whose tunable failure facilitates repair of biomedical implants, stretchable electronics, or soft robotics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quantitative nanoparticle tracking: applications to nanomedicine.

PubMed

Huang, Feiran; Dempsey, Christopher; Chona, Daniela; Suh, Junghae

2011-06-01

Particle tracking is an invaluable technique to extract quantitative and qualitative information regarding the transport of nanomaterials through complex biological environments. This technique can be used to probe the dynamic behavior of nanoparticles as they interact with and navigate through intra- and extra-cellular barriers. In this article, we focus on the recent developments in the application of particle-tracking technology to nanomedicine, including the study of synthetic and virus-based materials designed for gene and drug delivery. Specifically, we cover research where mean square displacements of nanomaterial transport were explicitly determined in order to quantitatively assess the transport of nanoparticles through biological environments. Particle-tracking experiments can provide important insights that may help guide the design of more intelligent and effective diagnostic and therapeutic nanoparticles.

Mass balances for a biological life support system simulation model

NASA Technical Reports Server (NTRS)

Volk, Tyler; Rummel, John D.

1987-01-01

Design decisions to aid the development of future space based biological life support systems (BLSS) can be made with simulation models. The biochemistry stoichiometry was developed for: (1) protein, carbohydrate, fat, fiber, and lignin production in the edible and inedible parts of plants; (2) food consumption and production of organic solids in urine, feces, and wash water by the humans; and (3) operation of the waste processor. Flux values for all components are derived for a steady state system with wheat as the sole food source. The large scale dynamics of a materially closed (BLSS) computer model is described in a companion paper. An extension of this methodology can explore multifood systems and more complex biochemical dynamics while maintaining whole system closure as a focus.

The Effects of Linear and Modified Linear Programed Materials on the Achievement of Slow Learners in Tenth Grade BSCS Special Materials Biology.

ERIC Educational Resources Information Center

Moody, John Charles

Assessed were the effects of linear and modified linear programed materials on the achievement of slow learners in tenth grade Biological Sciences Curriculum Study (BSCS) Special Materials biology. Two hundred and six students were randomly placed into four programed materials formats: linear programed materials, modified linear program with…

Microgel mechanics in biomaterial design.

PubMed

Saxena, Shalini; Hansen, Caroline E; Lyon, L Andrew

2014-08-19

The field of polymeric biomaterials has received much attention in recent years due to its potential for enhancing the biocompatibility of systems and devices applied to drug delivery and tissue engineering. Such applications continually push the definition of biocompatibility from relatively straightforward issues such as cytotoxicity to significantly more complex processes such as reducing foreign body responses or even promoting/recapitulating natural body functions. Hydrogels and their colloidal analogues, microgels, have been and continue to be heavily investigated as viable materials for biological applications because they offer numerous, facile avenues in tailoring chemical and physical properties to approach biologically harmonious integration. Mechanical properties in particular are recently coming into focus as an important manner in which biological responses can be altered. In this Account, we trace how mechanical properties of microgels have moved into the spotlight of research efforts with the realization of their potential impact in biologically integrative systems. We discuss early experiments in our lab and in others focused on synthetic modulation of particle structure at a rudimentary level for fundamental drug delivery studies. These experiments elucidated that microgel mechanics are a consequence of polymer network distribution, which can be controlled by chemical composition or particle architecture. The degree of deformability designed into the microgel allows for a defined response to an imposed external force. We have studied deformation in packed colloidal phases and in translocation events through confined pores; in all circumstances, microgels exhibit impressive deformability in response to their environmental constraints. Microgels further translate their mechanical properties when assembled in films to the properties of the bulk material. In particular, microgel films have been a large focus in our lab as building blocks for self-healing materials. We have shown that their ability to heal after damage arises from polymer mobility during hydration. Furthermore, we have shown film mobility dictates cell adhesion and spreading in a manner that is fundamentally different from previous work on mechanotransduction. In total, we hope that this Account presents a broad introduction to microgel research that intersects polymer chemistry, physics, and regenerative medicine. We expect that research intersection will continue to expand as we fill the knowledge gaps associated with soft materials in biological milieu.

A multidisciplinary database for global distribution

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

Wolfe, P.J.

The issue of selenium toxicity in the environment has been documented in the scientific literature for over 50 years. Recent studies reveal a complex connection between selenium and human and animal populations. This article introduces a bibliographic citation database on selenium in the environment developed for global distribution via the Internet by the University of Wyoming Libraries. The database incorporates material from commercial sources, print abstracts, indexes, and U.S. government literature, resulting in a multidisciplinary resource. Relevant disciplines include, biology, medicine, veterinary science, botany, chemistry, geology, pollution, aquatic sciences, ecology, and others. It covers the years 1985-1996 for most subjectmore » material, with additional years being added as resources permit.« less

Towards physical principles of biological evolution

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Programmable assembly of nanoarchitectures using genetically engineered viruses.

PubMed

Huang, Yu; Chiang, Chung-Yi; Lee, Soo Kwan; Gao, Yan; Hu, Evelyn L; De Yoreo, James; Belcher, Angela M

2005-07-01

Biological systems possess inherent molecular recognition and self-assembly capabilities and are attractive templates for constructing complex material structures with molecular precision. Here we report the assembly of various nanoachitectures including nanoparticle arrays, hetero-nanoparticle architectures, and nanowires utilizing highly engineered M13 bacteriophage as templates. The genome of M13 phage can be rationally engineered to produce viral particles with distinct substrate-specific peptides expressed on the filamentous capsid and the ends, providing a generic template for programmable assembly of complex nanostructures. Phage clones with gold-binding motifs on the capsid and streptavidin-binding motifs at one end are created and used to assemble Au and CdSe nanocrytals into ordered one-dimensional arrays and more complex geometries. Initial studies show such nanoparticle arrays can further function as templates to nucleate highly conductive nanowires that are important for addressing/interconnecting individual nanostructures.

Rahman Prize Lecture: Lattice Boltzmann simulation of complex states of flowing matter

NASA Astrophysics Data System (ADS)

Succi, Sauro

Over the last three decades, the Lattice Boltzmann (LB) method has gained a prominent role in the numerical simulation of complex flows across an impressively broad range of scales, from fully-developed turbulence in real-life geometries, to multiphase flows in micro-fluidic devices, all the way down to biopolymer translocation in nanopores and lately, even quark-gluon plasmas. After a brief introduction to the main ideas behind the LB method and its historical developments, we shall present a few selected applications to complex flow problems at various scales of motion. Finally, we shall discuss prospects for extreme-scale LB simulations of outstanding problems in the physics of fluids and its interfaces with material sciences and biology, such as the modelling of fluid turbulence, the optimal design of nanoporous gold catalysts and protein folding/aggregation in crowded environments.

Biodegradable Polyphosphazene-Based Blends for Regenerative Engineering

PubMed Central

Ogueri, Kenneth S.; Escobar Ivirico, Jorge L.; Nair, Lakshmi S.; Allcock, Harry R.; Laurencin, Cato T.

2017-01-01

The occurrence of musculoskeletal tissue injury or disease and the subsequent functional impairment is at an alarming rate. It continues to be one of the most challenging problems in the human health care. Regenerative engineering offers a promising transdisciplinary strategy for tissues regeneration based on the convergence of tissue engineering, advanced materials science, stem cell science, developmental biology and clinical translation. Biomaterials are emerging as extracellular-mimicking matrices designed to provide instructive cues to control cell behavior and ultimately, be applied as therapies to regenerate damaged tissues. Biodegradable polymers constitute an attractive class of biomaterials for the development of scaffolds due to their flexibility in chemistry and the ability to be excreted or resorbed by the body. Herein, the focus will be on biodegradable polyphosphazene-based blend systems. The synthetic flexibility of polyphosphazene, combined with the unique inorganic backbone, has provided a springboard for more research and subsequent development of numerous novel materials that are capable of forming miscible blends with poly (lactide-co-glycolide) (PLAGA). Laurencin and co-workers has demonstrated the exploitation of the synthetic flexibility of Polyphosphazene that will allow the design of novel polymers, which can form miscible blends with PLAGA for biomedical applications. These novel blends, due to their well-tuned biodegradability, and mechanical and biological properties coupled with the buffering capacity of the degradation products, constitute ideal materials for regeneration of various musculoskeletal tissues. Lay Summary Regenerative engineering aims to regenerate complex tissues to address the clinical challenge of organ damage. Tissue engineering has largely focused on the restoration and repair of individual tissues and organs, but over the past 25 years, scientific, engineering, and medical advances have led to the introduction of this new approach which involves the regeneration of complex tissues and biological systems such as a knee or a whole limb. While a number of excellent advanced biomaterials have been developed, the choice of biomaterials, however, has increased over the past years to include polymers that can be designed with a range of mechanical properties, degradation rates, and chemical functionality. The polyphosphazenes are one good example. Their chemical versatility and hydrogen bonding capability encourages blending with other biologically relevant polymers. The further development of Polyphosphazene-based blends will present a wide spectrum of advanced biomaterials that can be used as scaffolds for regenerative engineering and as well as other biomedical applications. PMID:28596987

Biodegradable Polyphosphazene-Based Blends for Regenerative Engineering.

PubMed

Ogueri, Kenneth S; Escobar Ivirico, Jorge L; Nair, Lakshmi S; Allcock, Harry R; Laurencin, Cato T

2017-03-01

The occurrence of musculoskeletal tissue injury or disease and the subsequent functional impairment is at an alarming rate. It continues to be one of the most challenging problems in the human health care. Regenerative engineering offers a promising transdisciplinary strategy for tissues regeneration based on the convergence of tissue engineering, advanced materials science, stem cell science, developmental biology and clinical translation. Biomaterials are emerging as extracellular-mimicking matrices designed to provide instructive cues to control cell behavior and ultimately, be applied as therapies to regenerate damaged tissues. Biodegradable polymers constitute an attractive class of biomaterials for the development of scaffolds due to their flexibility in chemistry and the ability to be excreted or resorbed by the body. Herein, the focus will be on biodegradable polyphosphazene-based blend systems. The synthetic flexibility of polyphosphazene, combined with the unique inorganic backbone, has provided a springboard for more research and subsequent development of numerous novel materials that are capable of forming miscible blends with poly (lactide-co-glycolide) (PLAGA). Laurencin and co-workers has demonstrated the exploitation of the synthetic flexibility of Polyphosphazene that will allow the design of novel polymers, which can form miscible blends with PLAGA for biomedical applications. These novel blends, due to their well-tuned biodegradability, and mechanical and biological properties coupled with the buffering capacity of the degradation products, constitute ideal materials for regeneration of various musculoskeletal tissues. Regenerative engineering aims to regenerate complex tissues to address the clinical challenge of organ damage. Tissue engineering has largely focused on the restoration and repair of individual tissues and organs, but over the past 25 years, scientific, engineering, and medical advances have led to the introduction of this new approach which involves the regeneration of complex tissues and biological systems such as a knee or a whole limb. While a number of excellent advanced biomaterials have been developed, the choice of biomaterials, however, has increased over the past years to include polymers that can be designed with a range of mechanical properties, degradation rates, and chemical functionality. The polyphosphazenes are one good example. Their chemical versatility and hydrogen bonding capability encourages blending with other biologically relevant polymers. The further development of Polyphosphazene-based blends will present a wide spectrum of advanced biomaterials that can be used as scaffolds for regenerative engineering and as well as other biomedical applications.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Surface biofunctionalization and production of miniaturized sensor structures using aerosol printing technologies.

PubMed

Grunwald, Ingo; Groth, Esther; Wirth, Ingo; Schumacher, Julian; Maiwald, Marcus; Zoellmer, Volker; Busse, Matthias

2010-03-01

The work described in this paper demonstrates that very small protein and DNA structures can be applied to various substrates without denaturation using aerosol printing technology. This technology allows high-resolution deposition of various nanoscaled metal and biological suspensions. Before printing, metal and biological suspensions were formulated and then nebulized to form an aerosol which is aerodynamically focused on the printing module of the system in order to achieve precise structuring of the nanoscale material on a substrate. In this way, it is possible to focus the aerosol stream at a distance of about 5 mm from the printhead to the surface. This technology is useful for printing fluorescence-marked proteins and printing enzymes without affecting their biological activity. Furthermore, higher molecular weight DNA can be printed without shearing. The advantages, such as printing on complex, non-planar 3D structured surfaces, and disadvantages of the aerosol printing technology are also discussed and are compared with other printing technologies. In addition, miniaturized sensor structures with line thicknesses in the range of a few micrometers are fabricated by applying a silver sensor structure to glass. After sintering using an integrated laser or in an oven process, electrical conductivity is achieved within the sensor structure. Finally, we printed BSA in small micrometre-sized areas within the sensor structure using the same deposition system. The aerosol printing technology combined with material development offers great advantages for future-oriented applications involving biological surface functionalization on small areas. This is important for innovative biomedical micro-device development and for production solutions which bridge the disciplines of biology and electronics.

Biosorption of heavy metal ions using wheat based biosorbents--a review of the recent literature.

PubMed

Farooq, Umar; Kozinski, Janusz A; Khan, Misbahul Ain; Athar, Makshoof

2010-07-01

Conventional technologies for the removal/remediation of toxic metal ions from wastewaters are proving expensive due to non-regenerable materials used and high costs. Biosorption is emerging as a technique offering the use of economical alternate biological materials for the purpose. Functional groups like carboxyl, hydroxyl, sulphydryl and amido present in these biomaterials, make it possible for them to attach metal ions from waters. Every year, large amounts of straw and bran from Triticum aestivum (wheat), a major food crop of the world, are produced as by-products/waste materials. The purpose of this article is to review rather scattered information on the utilization of straw and bran for the removal/minimization of metal ions from waters. High efficiency, high biosorption capacity, cost-effectiveness and renewability are the important parameters making these materials as economical alternatives for metal removal and waste remediation. Applications of available adsorption and kinetic models as well as influences of change in temperature and pH of medium on metal biosorption by wheat straw and wheat bran are reviewed. The biosorption mechanism has been found to be quite complex. It comprises a number of phenomena including adsorption, surface precipitation, ion-exchange and complexation. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Biological and Clinical Implications of Lysozyme Deposition on Soft Contact Lenses

PubMed Central

Omali, Negar Babaei; Subbaraman, Lakshman N.; Coles-Brennan, Chantal; Fadli, Zohra; Jones, Lyndon W.

2015-01-01

ABSTRACT Within a few minutes of wear, contact lenses become rapidly coated with a variety of tear film components, including proteins, lipids, and mucins. Tears have a rich and complex composition, allowing a wide range of interactions and competitive processes, with the first event observed at the interface between a contact lens and tear fluid being protein adsorption. Protein adsorption on hydrogel contact lenses is a complex process involving a variety of factors relating to both the protein in question and the lens material. Among tear proteins, lysozyme is a major protein that has both antibacterial and anti-inflammatory functions. Contact lens materials that have high ionicity and high water content have an increased affinity to accumulate lysozyme during wear, when compared with other soft lens materials, notably silicone hydrogel lenses. This review provides an overview of tear film proteins, with a specific focus on lysozyme, and examines various factors that influence protein deposition on contact lenses. In addition, the impact of lysozyme deposition on various ocular physiological responses and bacterial adhesion to lenses and the interaction of lysozyme with other tear proteins are reviewed. This comprehensive review suggests that deposition of lysozyme on contact lens materials may provide a number of beneficial effects during contact lens wear. PMID:26002002

A novel tantalum-based sol-gel packed microextraction syringe for highly specific enrichment of phosphopeptides in MALDI-MS applications.

PubMed

Çelikbıçak, Ömür; Atakay, Mehmet; Güler, Ülkü; Salih, Bekir

2013-08-07

A new tantalum-based sol-gel material was synthesized using a unique sol-gel synthesis pathway by PEG incorporation into the sol-gel structure without performing a calcination step. This improved its chemical and physical properties for the high capacity and selective enrichment of phosphopeptides from protein digests in complex biological media. The specificity of the tantalum-based sol-gel material for phosphopeptides was evaluated and compared with tantalum(V) oxide (Ta2O5) in different phosphopeptide enrichment applications. The tantalum-based sol-gel and tantalum(V) oxide were characterized in detail using FT-IR spectroscopy, X-ray diffraction (XRD) and scanning electron microscopy (SEM), and also using a surface area and pore size analyzer. In the characterization studies, the surface morphology, pore volume, crystallinity of the materials and PEG incorporation into the sol-gel structure to produce a more hydrophilic material were successfully demonstrated. The X-ray diffractograms of the two different materials were compared and it was noted that the broad signals of the tantalum-based sol-gel clearly represented the amorphous structure of the sol-gel material, which was more likely to create enough surface area and to provide more accessible tantalum atoms for phosphopeptides to be easily adsorbed when compared with the neat and more crystalline structure of Ta2O5. Therefore, the phosphopeptide enrichment performance of the tantalum-based sol-gels was found to be remarkably higher than the more crystalline Ta2O5 in our studies. Phosphopeptides at femtomole levels could be selectively enriched using the tantalum-based sol-gel and detected with a higher signal-to-noise ratio by matrix-assisted laser desorption/ionization-mass spectrometer (MALDI-MS). Moreover, phosphopeptides in a tryptic digest of non-fat bovine milk as a complex real-world biological sample were retained with higher yield using a tantalum-based sol-gel. Additionally, the sol-gel material was packed into a standard syringe (0.5 mL) to enhance the ease of use of the sol-gel material and for the elimination of additional mixing and separation procedures during the adsorption, washing and elution steps of the enrichment procedure. It was found that up to 28 phosphopeptides in milk digest were easily detectable by MALDI-MS at femtomole levels (around 20 fmol) using the microextraction syringe within less than one minute.

Animal models for periodontal regeneration and peri-implant responses.

PubMed

Kantarci, Alpdogan; Hasturk, Hatice; Van Dyke, Thomas E

2015-06-01

Translation of experimental data to the clinical setting requires the safety and efficacy of such data to be confirmed in animal systems before application in humans. In dental research, the animal species used is dependent largely on the research question or on the disease model. Periodontal disease and, by analogy, peri-implant disease, are complex infections that result in a tissue-degrading inflammatory response. It is impossible to explore the complex pathogenesis of periodontitis or peri-implantitis using only reductionist in-vitro methods. Both the disease process and healing of the periodontal and peri-implant tissues can be studied in animals. Regeneration (after periodontal surgery), in response to various biologic materials with potential for tissue engineering, is a continuous process involving various types of tissue, including epithelia, connective tissues and alveolar bone. The same principles apply to peri-implant healing. Given the complexity of the biology, animal models are necessary and serve as the standard for successful translation of regenerative materials and dental implants to the clinical setting. Smaller species of animal are more convenient for disease-associated research, whereas larger animals are more appropriate for studies that target tissue healing as the anatomy of larger animals more closely resembles human dento-alveolar architecture. This review focuses on the animal models available for the study of regeneration in periodontal research and implantology; the advantages and disadvantages of each animal model; the interpretation of data acquired; and future perspectives of animal research, with a discussion of possible nonanimal alternatives. Power calculations in such studies are crucial in order to use a sample size that is large enough to generate statistically useful data, whilst, at the same time, small enough to prevent the unnecessary use of animals. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Design Considerations for Developing Biodegradable Magnesium Implants

NASA Astrophysics Data System (ADS)

Brar, Harpreet S.; Keselowsky, Benjamin G.; Sarntinoranont, Malisa; Manuel, Michele V.

The integration of biodegradable and bioabsorbable magnesium implants into the human body is a complex undertaking that faces major challenges. The complexity arises from the fact that biomaterials must meet both engineering and physiological requirements to ensure the desired properties. Historically, efforts have been focused on the behavior of commercial magnesium alloys in biological environments and their resultant effect on cell-mediated processes. Developing causal relationships between alloy chemistry and micro structure, and its effect on cellular behavior can be a difficult and time intensive process. A systems design approach driven by thermodynamics has the power to provide significant contributions in developing the next generation of magnesium alloy implants with controlled degradability, biocompatibility, and optimized mechanical properties, at reduced time and cost. This approach couples experimental research with theory and mechanistic modeling for the accelerated development of materials. The aim of this article is to enumerate this strategy, design considerations and hurdles for developing new magnesium alloys for use as biodegradable implant materials [1].

A highly stretchable autonomous self-healing elastomer

NASA Astrophysics Data System (ADS)

Li, Cheng-Hui; Wang, Chao; Keplinger, Christoph; Zuo, Jing-Lin; Jin, Lihua; Sun, Yang; Zheng, Peng; Cao, Yi; Lissel, Franziska; Linder, Christian; You, Xiao-Zeng; Bao, Zhenan

2016-06-01

It is a challenge to synthesize materials that possess the properties of biological muscles—strong, elastic and capable of self-healing. Herein we report a network of poly(dimethylsiloxane) polymer chains crosslinked by coordination complexes that combines high stretchability, high dielectric strength, autonomous self-healing and mechanical actuation. The healing process can take place at a temperature as low as -20 °C and is not significantly affected by surface ageing and moisture. The crosslinking complexes used consist of 2,6-pyridinedicarboxamide ligands that coordinate to Fe(III) centres through three different interactions: a strong pyridyl-iron one, and two weaker carboxamido-iron ones through both the nitrogen and oxygen atoms of the carboxamide groups. As a result, the iron-ligand bonds can readily break and re-form while the iron centres still remain attached to the ligands through the stronger interaction with the pyridyl ring, which enables reversible unfolding and refolding of the chains. We hypothesize that this behaviour supports the high stretchability and self-healing capability of the material.

Silaffins in Silica Biomineralization and Biomimetic Silica Precipitation

PubMed Central

Lechner, Carolin C.; Becker, Christian F. W.

2015-01-01

Biomineralization processes leading to complex solid structures of inorganic material in biological systems are constantly gaining attention in biotechnology and biomedical research. An outstanding example for biomineral morphogenesis is the formation of highly elaborate, nano-patterned silica shells by diatoms. Among the organic macromolecules that have been closely linked to the tightly controlled precipitation of silica in diatoms, silaffins play an extraordinary role. These peptides typically occur as complex posttranslationally modified variants and are directly involved in the silica deposition process in diatoms. However, even in vitro silaffin-based peptides alone, with and without posttranslational modifications, can efficiently mediate biomimetic silica precipitation leading to silica material with different properties as well as with encapsulated cargo molecules of a large size range. In this review, the biomineralization process of silica in diatoms is summarized with a specific focus on silaffins and their in vitro silica precipitation properties. Applications in the area of bio- and nanotechnology as well as in diagnostics and therapy are discussed. PMID:26295401

High surface area silicon materials: fundamentals and new technology.

PubMed

Buriak, Jillian M

2006-01-15

Crystalline silicon forms the basis of just about all computing technologies on the planet, in the form of microelectronics. An enormous amount of research infrastructure and knowledge has been developed over the past half-century to construct complex functional microelectronic structures in silicon. As a result, it is highly probable that silicon will remain central to computing and related technologies as a platform for integration of, for instance, molecular electronics, sensing elements and micro- and nanoelectromechanical systems. Porous nanocrystalline silicon is a fascinating variant of the same single crystal silicon wafers used to make computer chips. Its synthesis, a straightforward electrochemical, chemical or photochemical etch, is compatible with existing silicon-based fabrication techniques. Porous silicon literally adds an entirely new dimension to the realm of silicon-based technologies as it has a complex, three-dimensional architecture made up of silicon nanoparticles, nanowires, and channel structures. The intrinsic material is photoluminescent at room temperature in the visible region due to quantum confinement effects, and thus provides an optical element to electronic applications. Our group has been developing new organic surface reactions on porous and nanocrystalline silicon to tailor it for a myriad of applications, including molecular electronics and sensing. Integration of organic and biological molecules with porous silicon is critical to harness the properties of this material. The construction and use of complex, hierarchical molecular synthetic strategies on porous silicon will be described.

Citrate-Based Biomaterials and Their Applications in Regenerative Engineering

PubMed Central

Tran, Richard T.; Yang, Jian; Ameer, Guillermo A.

2015-01-01

Advances in biomaterials science and engineering are crucial to translating regenerative engineering, an emerging field that aims to recreate complex tissues, into clinical practice. In this regard, citrate-based biomaterials have become an important tool owing to their versatile material and biological characteristics including unique antioxidant, antimicrobial, adhesive, and fluorescent properties. This review discusses fundamental design considerations, strategies to incorporate unique functionality, and examples of how citrate-based biomaterials can be an enabling technology for regenerative engineering. PMID:27004046

KSC-06pd1684

NASA Image and Video Library

2006-07-28

KENNEDY SPACE CENTER, FLA. - In the Space Station Processing Facility, Japan Aerospace Exploration Agency (JAXA) technicians install piping insulation on the Japanese Experiment Module (JEM). The JEM, developed by JAXA for use on the International Space Station, is named Kibo -- which means "hope" in Japanese -- and will enhance the unique research capabilities of the orbiting complex by providing an additional environment for astronauts to conduct science experiments. Research conducted in Kibo will focus on space medicine, biology, Earth observations, material production, biotechnology and communications. Photo credit: NASA/Amanda Diller

KSC-06pd1685

NASA Image and Video Library

2006-07-28

KENNEDY SPACE CENTER, FLA. - In the Space Station Processing Facility, Japan Aerospace Exploration Agency (JAXA) technicians install piping insulation on the Japanese Experiment Module (JEM). The JEM, developed by JAXA for use on the International Space Station, is named Kibo -- which means "hope" in Japanese -- and will enhance the unique research capabilities of the orbiting complex by providing an additional environment for astronauts to conduct science experiments. Research conducted in Kibo will focus on space medicine, biology, Earth observations, material production, biotechnology and communications. Photo credit: NASA/Amanda Diller

KSC-06pd1682

NASA Image and Video Library

2006-07-28

KENNEDY SPACE CENTER, FLA. - In the Space Station Processing Facility, a Japan Aerospace Exploration Agency (JAXA) technician inspects the wiring on the Japanese Experiment Module (JEM). The JEM, developed by JAXA for use on the International Space Station, is named Kibo -- which means "hope" in Japanese -- and will enhance the unique research capabilities of the orbiting complex by providing an additional environment for astronauts to conduct science experiments. Research conducted in Kibo will focus on space medicine, biology, Earth observations, material production, biotechnology and communications. Photo credit: NASA/Amanda Diller

KSC-06pd1683

NASA Image and Video Library

2006-07-28

KENNEDY SPACE CENTER, FLA. - In the Space Station Processing Facility, Japan Aerospace Exploration Agency (JAXA) technicians inspect the wiring on the Japanese Experiment Module (JEM). The JEM, developed by JAXA for use on the International Space Station, is named Kibo -- which means "hope" in Japanese -- and will enhance the unique research capabilities of the orbiting complex by providing an additional environment for astronauts to conduct science experiments. Research conducted in Kibo will focus on space medicine, biology, Earth observations, material production, biotechnology and communications. Photo credit: NASA/Amanda Diller

KSC-06pd1687

NASA Image and Video Library

2006-07-28

KENNEDY SPACE CENTER, FLA. - In the Space Station Processing Facility, the Japanese Experiment Module (JEM) awaits its flight to the International Space Station (ISS). The JEM, developed by the Japan Aerospace Exploration Agency (JAXA) for installation on the ISS, is named Kibo -- which means "hope" in Japanese -- and will enhance the unique research capabilities of the orbiting complex by providing an additional environment for astronauts to conduct science experiments. Research conducted in Kibo will focus on space medicine, biology, Earth observations, material production, biotechnology and communications. Photo credit: NASA/Amanda Diller

The Morphological Characterization of the Forewing of the Manduca sexta Species for the Application of Biomimetic Flapping Wing Micro Air Vehicles

DTIC Science & Technology

2012-01-01

16.64 Figure 3. Venation map of Manduca sexta forewing [11]. 2.4. Venation Insect wings are formed from a complex makeup of polymer based chains, Chitin ...for coloration, but may subtly influence flow patterns and boundary layer structure over wings [4, 24]. There is significant understanding of chitin ...biological specimen to vary the bonding chains, assemblage of nanofibers and crystalline structure, the material properties of chitin can vary over a

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine

PubMed Central

Seto, Jong; Ma, Yurong; Davis, Sean A.; Meldrum, Fiona; Gourrier, Aurelien; Kim, Yi-Yeoun; Schilde, Uwe; Sztucki, Michael; Burghammer, Manfred; Maltsev, Sergey; Jäger, Christian; Cölfen, Helmut

2012-01-01

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature’s demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials. PMID:22343283

Dynamics of bubble collapse under vessel confinement in 2D hydrodynamic experiments

NASA Astrophysics Data System (ADS)

Shpuntova, Galina; Austin, Joanna

2013-11-01

One trauma mechanism in biomedical treatment techniques based on the application of cumulative pressure pulses generated either externally (as in shock-wave lithotripsy) or internally (by laser-induced plasma) is the collapse of voids. However, prediction of void-collapse driven tissue damage is a challenging problem, involving complex and dynamic thermomechanical processes in a heterogeneous material. We carry out a series of model experiments to investigate the hydrodynamic processes of voids collapsing under dynamic loading in configurations designed to model cavitation with vessel confinement. The baseline case of void collapse near a single interface is also examined. Thin sheets of tissue-surrogate polymer materials with varying acoustic impedance are used to create one or two parallel material interfaces near the void. Shadowgraph photography and two-color, single-frame particle image velocimetry quantify bubble collapse dynamics including jetting, interface dynamics and penetration, and the response of the surrounding material. Research supported by NSF Award #0954769, ``CAREER: Dynamics and damage of void collapse in biological materials under stress wave loading.''

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine.

PubMed

Seto, Jong; Ma, Yurong; Davis, Sean A; Meldrum, Fiona; Gourrier, Aurelien; Kim, Yi-Yeoun; Schilde, Uwe; Sztucki, Michael; Burghammer, Manfred; Maltsev, Sergey; Jäger, Christian; Cölfen, Helmut

2012-03-06

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature's demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials.

A new mode of contrast in biological second harmonic generation microscopy.

PubMed

Green, Nicola H; Delaine-Smith, Robin M; Askew, Hannah J; Byers, Robert; Reilly, Gwendolen C; Matcher, Stephen J

2017-10-17

Enhanced image contrast in biological second harmonic imaging microscopy (SHIM) has previously been reported via quantitative assessments of forward- to epi-generated signal intensity ratio and by polarization analysis. Here we demonstrate a new form of contrast: the material-specific, wavelength-dependence of epi-generated second harmonic generation (SHG) excitation efficiency, and discriminate collagen and myosin by ratiometric epi-generated SHG images at 920 nm and 860 nm. Collagen shows increased SHG intensity at 920 nm, while little difference is detected between the two for myosin; allowing SHIM to characterize different SHG-generating components within a complex biological sample. We propose that momentum-space mapping of the second-order non-linear structure factor is the source of this contrast and develop a model for the forward and epi-generated SHG wavelength-dependence. Our model demonstrates that even very small changes in the assumed material fibrillar structure can produce large changes in the wavelength-dependency of epi-generated SHG. However, in the case of forward SHG, although the same changes impact upon absolute intensity at a given wavelength, they have very little effect on wavelength-dependency beyond the expected monotonic fall. We also propose that this difference between forward and epi-generated SHG provides an explanation for many of the wavelength-dependency discrepancies in the published literature.

Image processing for cryogenic transmission electron microscopy of symmetry-mismatched complexes.

PubMed

Huiskonen, Juha T

2018-02-08

Cryogenic transmission electron microscopy (cryo-TEM) is a high-resolution biological imaging method, whereby biological samples, such as purified proteins, macromolecular complexes, viral particles, organelles and cells, are embedded in vitreous ice preserving their native structures. Due to sensitivity of biological materials to the electron beam of the microscope, only relatively low electron doses can be applied during imaging. As a result, the signal arising from the structure of interest is overpowered by noise in the images. To increase the signal-to-noise ratio, different image processing-based strategies that aim at coherent averaging of signal have been devised. In such strategies, images are generally assumed to arise from multiple identical copies of the structure. Prior to averaging, the images must be grouped according to the view of the structure they represent and images representing the same view must be simultaneously aligned relatively to each other. For computational reconstruction of the three-dimensional structure, images must contain different views of the original structure. Structures with multiple symmetry-related substructures are advantageous in averaging approaches because each image provides multiple views of the substructures. However, the symmetry assumption may be valid for only parts of the structure, leading to incoherent averaging of the other parts. Several image processing approaches have been adapted to tackle symmetry-mismatched substructures with increasing success. Such structures are ubiquitous in nature and further computational method development is needed to understanding their biological functions. ©2018 The Author(s).

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

PubMed

Waliszewski, P; Molski, M; Konarski, J

1998-06-01

A keystone of the molecular reductionist approach to cellular biology is a specific deductive strategy relating genotype to phenotype-two distinct categories. This relationship is based on the assumption that the intermediary cellular network of actively transcribed genes and their regulatory elements is deterministic (i.e., a link between expression of a gene and a phenotypic trait can always be identified, and evolution of the network in time is predetermined). However, experimental data suggest that the relationship between genotype and phenotype is nonbijective (i.e., a gene can contribute to the emergence of more than just one phenotypic trait or a phenotypic trait can be determined by expression of several genes). This implies nonlinearity (i.e., lack of the proportional relationship between input and the outcome), complexity (i.e. emergence of the hierarchical network of multiple cross-interacting elements that is sensitive to initial conditions, possesses multiple equilibria, organizes spontaneously into different morphological patterns, and is controlled in dispersed rather than centralized manner), and quasi-determinism (i.e., coexistence of deterministic and nondeterministic events) of the network. Nonlinearity within the space of the cellular molecular events underlies the existence of a fractal structure within a number of metabolic processes, and patterns of tissue growth, which is measured experimentally as a fractal dimension. Because of its complexity, the same phenotype can be associated with a number of alternative sequences of cellular events. Moreover, the primary cause initiating phenotypic evolution of cells such as malignant transformation can be favored probabilistically, but not identified unequivocally. Thermodynamic fluctuations of energy rather than gene mutations, the material traits of the fluctuations alter both the molecular and informational structure of the network. Then, the interplay between deterministic chaos, complexity, self-organization, and natural selection drives formation of malignant phenotype. This concept offers a novel perspective for investigation of tumorigenesis without invalidating current molecular findings. The essay integrates the ideas of the sciences of complexity in a biological context.

Mechanical characterization of human brain tumors from patients and comparison to potential surgical phantoms

PubMed Central

Rubiano, Andrés; Dyson, Kyle; Simmons, Chelsey S.

2017-01-01

While mechanical properties of the brain have been investigated thoroughly, the mechanical properties of human brain tumors rarely have been directly quantified due to the complexities of acquiring human tissue. Quantifying the mechanical properties of brain tumors is a necessary prerequisite, though, to identify appropriate materials for surgical tool testing and to define target parameters for cell biology and tissue engineering applications. Since characterization methods vary widely for soft biological and synthetic materials, here, we have developed a characterization method compatible with abnormally shaped human brain tumors, mouse tumors, animal tissue and common hydrogels, which enables direct comparison among samples. Samples were tested using a custom-built millimeter-scale indenter, and resulting force-displacement data is analyzed to quantify the steady-state modulus of each sample. We have directly quantified the quasi-static mechanical properties of human brain tumors with effective moduli ranging from 0.17–16.06 kPa for various pathologies. Of the readily available and inexpensive animal tissues tested, chicken liver (steady-state modulus 0.44 ± 0.13 kPa) has similar mechanical properties to normal human brain tissue while chicken crassus gizzard muscle (steady-state modulus 3.00 ± 0.65 kPa) has similar mechanical properties to human brain tumors. Other materials frequently used to mimic brain tissue in mechanical tests, like ballistic gel and chicken breast, were found to be significantly stiffer than both normal and diseased brain tissue. We have directly compared quasi-static properties of brain tissue, brain tumors, and common mechanical surrogates, though additional tests would be required to determine more complex constitutive models. PMID:28582392

Three-Dimensional Printing Articular Cartilage: Recapitulating the Complexity of Native Tissue.

PubMed

Guo, Ting; Lembong, Josephine; Zhang, Lijie Grace; Fisher, John P

2017-06-01

In the past few decades, the field of tissue engineering combined with rapid prototyping (RP) techniques has been successful in creating biological substitutes that mimic tissues. Its applications in regenerative medicine have drawn efforts in research from various scientific fields, diagnostics, and clinical translation to therapies. While some areas of therapeutics are well developed, such as skin replacement, many others such as cartilage repair can still greatly benefit from tissue engineering and RP due to the low success and/or inefficiency of current existing, often surgical treatments. Through fabrication of complex scaffolds and development of advanced materials, RP provides a new avenue for cartilage repair. Computer-aided design and three-dimensional (3D) printing allow the fabrication of modeled cartilage scaffolds for repair and regeneration of damaged cartilage tissues. Specifically, the various processes of 3D printing will be discussed in details, both cellular and acellular techniques, covering the different materials, geometries, and operational printing conditions for the development of tissue-engineered articular cartilage. Finally, we conclude with some insights on future applications and challenges related to this technology, especially using 3D printing techniques to recapitulate the complexity of native structure for advanced cartilage regeneration.

Polymeric Biomaterials: Diverse Functions Enabled by Advances in Macromolecular Chemistry

PubMed Central

Liang, Yingkai; Li, Linqing; Scott, Rebecca A.; Kiick, Kristi L.

2017-01-01

Biomaterials have been extensively used to leverage beneficial outcomes in various therapeutic applications, such as providing spatial and temporal control over the release of therapeutic agents in drug delivery as well as engineering functional tissues and promoting the healing process in tissue engineering and regenerative medicine. This perspective presents important milestones in the development of polymeric biomaterials with defined structures and properties. Contemporary studies of biomaterial design have been reviewed with focus on constructing materials with controlled structure, dynamic functionality, and biological complexity. Examples of these polymeric biomaterials enabled by advanced synthetic methodologies, dynamic chemistry/assembly strategies, and modulated cell-material interactions have been highlighted. As the field of polymeric biomaterials continues to evolve with increased sophistication, current challenges and future directions for the design and translation of these materials are also summarized. PMID:29151616

Porous silicon and diatoms micro-shells: an example of inverse biomimetic

NASA Astrophysics Data System (ADS)

De Tommasi, Edoardo; Rea, Ilaria; Rendina, Ivo; De Stefano, Luca

2011-05-01

Porous silicon (PSi) is by far a very useful technological platform for optical monitoring of chemical and biological substances and due to its peculiar physical and morphological properties it is worldwide used in sensing experiments. On the other hand, we have discovered a natural material, the micro-shells of marine diatoms, ubiquitous unicellular algae, which are made of hydrated amorphous silica, but, most of all, show geometrical structures made of complex patterns of pores which are surprisingly similar to those of porous silicon. Moreover, under laser irradiation, this material is photoluminescent and the photoluminescence is very sensitive to the surrounding atmosphere, which means that the material can act as a transducer. Starting from our experience on PSi devices, we explore the optical and photonic properties of marine diatoms micro-shells in a sort of inverse biomimicry.

Conjugated Polymers in Bioelectronics.

PubMed

Inal, Sahika; Rivnay, Jonathan; Suiu, Andreea-Otilia; Malliaras, George G; McCulloch, Iain

2018-06-19

The emerging field of organic bioelectronics bridges the electronic world of organic-semiconductor-based devices with the soft, predominantly ionic world of biology. This crosstalk can occur in both directions. For example, a biochemical reaction may change the doping state of an organic material, generating an electronic readout. Conversely, an electronic signal from a device may stimulate a biological event. Cutting-edge research in this field results in the development of a broad variety of meaningful applications, from biosensors and drug delivery systems to health monitoring devices and brain-machine interfaces. Conjugated polymers share similarities in chemical "nature" with biological molecules and can be engineered on various forms, including hydrogels that have Young's moduli similar to those of soft tissues and are ionically conducting. The structure of organic materials can be tuned through synthetic chemistry, and their biological properties can be controlled using a variety of functionalization strategies. Finally, organic electronic materials can be integrated with a variety of mechanical supports, giving rise to devices with form factors that enable integration with biological systems. While these developments are innovative and promising, it is important to note that the field is still in its infancy, with many unknowns and immense scope for exploration and highly collaborative research. The first part of this Account details the unique properties that render conjugated polymers excellent biointerfacing materials. We then offer an overview of the most common conjugated polymers that have been used as active layers in various organic bioelectronics devices, highlighting the importance of developing new materials. These materials are the most popular ethylenedioxythiophene derivatives as well as conjugated polyelectrolytes and ion-free organic semiconductors functionalized for the biological interface. We then discuss several applications and operation principles of state-of-the-art bioelectronics devices. These devices include electrodes applied to sense/trigger electrophysiological activity of cells as well as electrolyte-gated field-effect and electrochemical transistors used for sensing of biochemical markers. Another prime application example of conjugated polymers is cell actuators. External modulation of the redox state of the underlying conjugated polymer films controls the adhesion behavior and viability of cells. These smart surfaces can be also designed in the form of three-dimensional architectures because of the processability of conjugated polymers. As such, cell-loaded scaffolds based on electroactive polymers enable integrated sensing or stimulation within the engineered tissue itself. A last application example is organic neuromorphic devices, an alternative computing architecture that takes inspiration from biology and, in particular, from the way the brain works. Leveraging ion redistribution inside a conjugated polymer upon application of an electrical field and its coupling with electronic charges, conjugated polymers can be engineered to act as artificial neurons or synapses with complex, history-dependent behavior. We conclude this Account by highlighting main factors that need to be considered for the design of a conjugated polymer for applications in bioelectronics-although there can be various figures of merit given the broad range of applications, as emphasized in this Account.

Methods And Compositions For Chromosome-Specific Staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

2003-08-19

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Compositions for chromosome-specific staining

DOEpatents

Gray, Joe W.; Pinkel, Daniel

1998-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Further, methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. Still further, the invention provides for automated means to detect and analyse chromosomal abnormalities.

Compositions for chromosome-specific staining

DOEpatents

Gray, J.W.; Pinkel, D.

1998-05-26

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. The methods produce staining patterns that can be tailored for specific cytogenetic analyses. The probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods are provided to disable the hybridization capacity of shared, high copy repetitive sequences and/or remove such sequences to provide for useful contrast. Still further methods are provided to produce chromosome-specific staining reagents which are made specific to the targeted chromosomal material, which can be one or more whole chromosomes, one or more regions on one or more chromosomes, subsets of chromosomes and/or the entire genome. Probes and test kits are provided for use in tumor cytogenetics, in the detection of disease related loci, in analysis of structural abnormalities, such as translocations, and for biological dosimetry. Methods and prenatal test kits are provided to stain targeted chromosomal material of fetal cells, including fetal cells obtained from maternal blood. The invention provides for automated means to detect and analyze chromosomal abnormalities. 17 figs.

Estimating material viscoelastic properties based on surface wave measurements: A comparison of techniques and modeling assumptions

PubMed Central

Royston, Thomas J.; Dai, Zoujun; Chaunsali, Rajesh; Liu, Yifei; Peng, Ying; Magin, Richard L.

2011-01-01

Previous studies of the first author and others have focused on low audible frequency (<1 kHz) shear and surface wave motion in and on a viscoelastic material comprised of or representative of soft biological tissue. A specific case considered has been surface (Rayleigh) wave motion caused by a circular disk located on the surface and oscillating normal to it. Different approaches to identifying the type and coefficients of a viscoelastic model of the material based on these measurements have been proposed. One approach has been to optimize coefficients in an assumed viscoelastic model type to match measurements of the frequency-dependent Rayleigh wave speed. Another approach has been to optimize coefficients in an assumed viscoelastic model type to match the complex-valued frequency response function (FRF) between the excitation location and points at known radial distances from it. In the present article, the relative merits of these approaches are explored theoretically, computationally, and experimentally. It is concluded that matching the complex-valued FRF may provide a better estimate of the viscoelastic model type and parameter values; though, as the studies herein show, there are inherent limitations to identifying viscoelastic properties based on surface wave measurements. PMID:22225067

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

PubMed

Kelty-Stephen, Damian; Dixon, James A

2012-01-01

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

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

NASA Astrophysics Data System (ADS)

De Domenico, Manlio

2018-03-01

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

"On the Dot"-The Timing of Self-Assembled Growth to the Quantum Scale.

PubMed

Sonkaria, Sanjiv; Ahn, Sung-Hoon; Lee, Caroline S; Khare, Varsha

2017-06-16

Understanding the complex world of material growth and tunability has mystified the minds of material scientists and has been met with increasing efforts to close the gap between controllability and applicability. The reality of this journey is frustratingly tortuous but is being eased through better conceptual appreciation of metal crystalline frameworks that originate from shape and size dependent solvent responsive growth patterns. The quantum confinement of TiO 2 in the range of 0.8-2 nm has been synthetically challenging to achieve but lessons from biomineralization processes have enabled alternative routes to be explored via self-induced pre-nucleation events. In driving this concept, we have incorporated many of these key features integrating aspects of low temperature annealing at the interface of complex heterogeneous nucleation between hard and soft materials to arrest the biomimetic amorphous phase of TiO 2 to a tunable crystalline quantumized state. The stabilization of metastable states of quantum sized TiO 2 driven by kinetic and thermodynamic processes show hallmarks of biomineralized controlled events that suggest the inter-play between new pathways and interfacial energies that preferentially favor low dimensionality at the quantum scale. This provides the potential to re-direct synthetic assemblies under tightly controlled parameters to generate a host of new materials with size, shape and anisotropic properties as smart stimuli responsive materials. These new stabilities leading to the growth arrest of TiO 2 are discussed in terms of molecular interactions and structural frameworks that were previously inaccessible via conventional routes. There exists an undiscovered parallel between synthetic and biomineralized routes enabling unprecedented access to the availability and tunability of novel quantum confined materials. The parametrics of complex material design at the crossroads of synthetically and biologically driven processes is only now surfacing. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-scale, multi-modal analysis uncovers complex relationship at the brain tissue-implant neural interface: new emphasis on the biological interface

NASA Astrophysics Data System (ADS)

Michelson, Nicholas J.; Vazquez, Alberto L.; Eles, James R.; Salatino, Joseph W.; Purcell, Erin K.; Williams, Jordan J.; Cui, X. Tracy; Kozai, Takashi D. Y.

2018-06-01

Objective. Implantable neural electrode devices are important tools for neuroscience research and have an increasing range of clinical applications. However, the intricacies of the biological response after implantation, and their ultimate impact on recording performance, remain challenging to elucidate. Establishing a relationship between the neurobiology and chronic recording performance is confounded by technical challenges related to traditional electrophysiological, material, and histological limitations. This can greatly impact the interpretations of results pertaining to device performance and tissue health surrounding the implant. Approach. In this work, electrophysiological activity and immunohistological analysis are compared after controlling for motion artifacts, quiescent neuronal activity, and material failure of devices in order to better understand the relationship between histology and electrophysiological outcomes. Main results. Even after carefully accounting for these factors, the presence of viable neurons and lack of glial scarring does not convey single unit recording performance. Significance. To better understand the biological factors influencing neural activity, detailed cellular and molecular tissue responses were examined. Decreases in neural activity and blood oxygenation in the tissue surrounding the implant, shift in expression levels of vesicular transporter proteins and ion channels, axon and myelin injury, and interrupted blood flow in nearby capillaries can impact neural activity around implanted neural interfaces. Combined, these tissue changes highlight the need for more comprehensive, basic science research to elucidate the relationship between biology and chronic electrophysiology performance in order to advance neural technologies.

NUTS and BOLTS: Applications of Fluorescence Detected Sedimentation

PubMed Central

Kroe, Rachel R.; Laue, Thomas M.

2008-01-01

Analytical ultracentrifugation is a widely used method for characterizing the solution behavior of macromolecules. However, the two commonly used detectors (absorbance and interference) impose some fundamental restrictions on the concentrations and complexity of the solutions that can be analyzed. The recent addition of a fluorescence detector for the XL-I analytical ultracentrifuge (AU-FDS) enables two different types of sedimentation experiments. First, the AU-FDS can detect picomolar concentrations of labeled solutes allowing the characterization of very dilute solutions of macromolecules, applications we call Normal Use Tracer Sedimentation (NUTS). The great sensitivity of NUTS analysis allows the characterization of small quantities of materials and high affinity interactions. Second, AU-FDS allows characterization of trace quantities of labeled molecules in solutions containing high concentrations and complex mixtures of unlabeled molecules, applications we call Biological On Line Tracer Sedimentation (BOLTS). The discrimination of BOLTS enables the size distribution of a labeled macromolecule to be determined in biological milieu such as cell lysates and serum. Examples are presented that embody features of both NUTS and BOLTS applications, along with our observations on these applications. PMID:19103145

Analytical Scheme Leading to Integrated High-Sensitivity Profiling of Glycosphingolipids Together with N- and O-Glycans from One Sample

NASA Astrophysics Data System (ADS)

Benktander, John D.; Gizaw, Solomon T.; Gaunitz, Stefan; Novotny, Milos V.

2018-05-01

Glycoconjugates are directly or indirectly involved in many biological processes. Due to their complex structures, the structural elucidation of glycans and the exploration of their role in biological systems have been challenging. Glycan pools generated through release from glycoprotein or glycolipid mixtures can often be very complex. For the sake of procedural simplicity, many glycan profiling studies choose to concentrate on a single class of glycoconjugates. In this paper, we demonstrate it feasible to cover glycosphingolipids, N-glycans, and O-glycans isolated from the same sample. Small volumes of human blood serum and ascites fluid as well as small mouse brain tissue samples are sufficient to profile sequentially glycans from all three classes of glycoconjugates and even positively identify some mixture components through MALDI-MS and LC-ESI-MS. The results show that comprehensive glycan profiles can be obtained from the equivalent of 500-μg protein starting material or possibly less. These methodological improvements can help accelerating future glycomic comprehensive studies, especially for precious clinical samples.

Platform construction and extraction mechanism study of magnetic mixed hemimicelles solid-phase extraction

PubMed Central

Xiao, Deli; Zhang, Chan; He, Jia; Zeng, Rong; Chen, Rong; He, Hua

2016-01-01

Simple, accurate and high-throughput pretreatment method would facilitate large-scale studies of trace analysis in complex samples. Magnetic mixed hemimicelles solid-phase extraction has the power to become a key pretreatment method in biological, environmental and clinical research. However, lacking of experimental predictability and unsharpness of extraction mechanism limit the development of this promising method. Herein, this work tries to establish theoretical-based experimental designs for extraction of trace analytes from complex samples using magnetic mixed hemimicelles solid-phase extraction. We selected three categories and six sub-types of compounds for systematic comparative study of extraction mechanism, and comprehensively illustrated the roles of different force (hydrophobic interaction, π-π stacking interactions, hydrogen-bonding interaction, electrostatic interaction) for the first time. What’s more, the application guidelines for supporting materials, surfactants and sample matrix were also summarized. The extraction mechanism and platform established in the study render its future promising for foreseeable and efficient pretreatment under theoretical based experimental design for trace analytes from environmental, biological and clinical samples. PMID:27924944

Multi and mixed 3D-printing of graphene-hydroxyapatite hybrid materials for complex tissue engineering.

PubMed

Jakus, Adam E; Shah, Ramille N

2017-01-01

With the emergence of three-dimensional (3D)-printing (3DP) as a vital tool in tissue engineering and medicine, there is an ever growing need to develop new biomaterials that can be 3D-printed and also emulate the compositional, structural, and functional complexities of human tissues and organs. In this work, we probe the 3D-printable biomaterials spectrum by combining two recently established functional 3D-printable particle-laden biomaterial inks: one that contains hydroxyapatite microspheres (hyperelastic bone, HB) and another that contains graphene nanoflakes (3D-graphene, 3DG). We demonstrate that not only can these distinct, osteogenic, and neurogenic inks be co-3D-printed to create complex, multimaterial constructs, but that composite inks of HB and 3DG can also be synthesized. Specifically, the printability, microstructural, mechanical, electrical, and biological properties of a hybrid material comprised of 1:1 HA:graphene by volume is investigated. The resulting HB-3DG hybrid exhibits mixed characteristics of the two distinct systems, while maintaining 3D-printability, electrical conductivity, and flexibility. In vitro assessment of HB-3DG using mesenchymal stem cells demonstrates the hybrid material supports cell viability and proliferation, as well as significantly upregulates both osteogenic and neurogenic gene expression over 14 days. This work ultimately demonstrates a significant step forward towards being able to 3D-print graded, multicompositional, and multifunctional constructs from hybrid inks for complex composite tissue engineering. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 105A: 274-283, 2017. © 2016 Wiley Periodicals, Inc.

Biologically-Inspired Concepts for Self-Management of Complexity

NASA Technical Reports Server (NTRS)

Sterritt, Roy; Hinchey, G.

2006-01-01

Inherent complexity in large-scale applications may be impossible to eliminate or even ameliorate despite a number of promising advances. In such cases, the complexity must be tolerated and managed. Such management may be beyond the abilities of humans, or require such overhead as to make management by humans unrealistic. A number of initiatives inspired by concepts in biology have arisen for self-management of complex systems. We present some ideas and techniques we have been experimenting with, inspired by lesser-known concepts in biology that show promise in protecting complex systems and represent a step towards self-management of complexity.

Chromatin immunoprecipitation with fixed animal tissues and preparation for high-throughput sequencing.

PubMed

Cotney, Justin L; Noonan, James P

2015-02-02

Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) is a powerful method used to identify genome-wide binding patterns of transcription factors and distribution of various histone modifications associated with different chromatin states. In most published studies, ChIP-Seq has been performed on cultured cells grown under controlled conditions, allowing generation of large amounts of material in a homogeneous biological state. Although such studies have provided great insight into the dynamic landscapes of animal genomes, they do not allow the examination of transcription factor binding and chromatin states in adult tissues, developing embryonic structures, or tumors. Such knowledge is critical to understanding the information required to create and maintain a complex biological tissue and to identify noncoding regions of the genome directly involved in tissues affected by complex diseases such as autism. Studying these tissue types with ChIP-Seq can be challenging due to the limited availability of tissues and the lack of complex biological states able to be achieved in culture. These inherent differences require alterations of standard cross-linking and chromatin extraction typically used in cell culture. Here we describe a general approach for using small amounts of animal tissue to perform ChIP-Seq directed at histone modifications and transcription factors. Tissue is homogenized before treatment with formaldehyde to ensure proper cross-linking, and a two-step nuclear isolation is performed to increase extraction of soluble chromatin. Small amounts of soluble chromatin are then used for immunoprecipitation (IP) and prepared for multiplexed high-throughput sequencing. © 2015 Cold Spring Harbor Laboratory Press.

Biomedical surface analysis: Evolution and future directions (Review)

PubMed Central

Castner, David G.

2017-01-01

This review describes some of the major advances made in biomedical surface analysis over the past 30–40 years. Starting from a single technique analysis of homogeneous surfaces, it has been developed into a complementary, multitechnique approach for obtaining detailed, comprehensive information about a wide range of surfaces and interfaces of interest to the biomedical community. Significant advances have been made in each surface analysis technique, as well as how the techniques are combined to provide detailed information about biological surfaces and interfaces. The driving force for these advances has been that the surface of a biomaterial is the interface between the biological environment and the biomaterial, and so, the state-of-the-art in instrumentation, experimental protocols, and data analysis methods need to be developed so that the detailed surface structure and composition of biomedical devices can be determined and related to their biological performance. Examples of these advances, as well as areas for future developments, are described for immobilized proteins, complex biomedical surfaces, nanoparticles, and 2D/3D imaging of biological materials. PMID:28438024

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

PubMed

Yuan, Bing

2016-12-01

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

Miniaturized soft bio-hybrid robotics: a step forward into healthcare applications.

PubMed

Patino, T; Mestre, R; Sánchez, S

2016-10-07

Soft robotics is an emerging discipline that employs soft flexible materials such as fluids, gels and elastomers in order to enhance the use of robotics in healthcare applications. Compared to their rigid counterparts, soft robotic systems have flexible and rheological properties that are closely related to biological systems, thus allowing the development of adaptive and flexible interactions with complex dynamic environments. With new technologies arising in bioengineering, the integration of living cells into soft robotic systems offers the possibility of accomplishing multiple complex functions such as sensing and actuating upon external stimuli. These emerging bio-hybrid systems are showing promising outcomes and opening up new avenues in the field of soft robotics for applications in healthcare and other fields.

Peptide aptamer-assisted immobilization of green fluorescent protein for creating biomolecule-complexed carbon nanotube device

NASA Astrophysics Data System (ADS)

Nii, Daisuke; Nozawa, Yosuke; Miyachi, Mariko; Yamanoi, Yoshinori; Nishihara, Hiroshi; Tomo, Tatsuya; Shimada, Yuichiro

2017-10-01

Carbon nanotubes are a novel material for next-generation applications. In this study, we generated carbon nanotube and green fluorescent protein (GFP) conjugates using affinity binding peptides. The carbon nanotube-binding motif was introduced into the N-terminus of the GFP through molecular biology methods. Multiple GFPs were successfully aligned on a single-walled carbon nanotube via the molecular recognition function of the peptide aptamer, which was confirmed through transmission electron microscopy and optical analysis. Fluorescence spectral analysis results also suggested that the carbon nanotube-GFP complex was autonomously formed with orientation and without causing protein denaturation during immobilization. This simple process has a widespread potential for fabricating carbon nanotube-biomolecule hybrid devices.

Link between the dielectric properties of mesomorphic and biological materials

NASA Astrophysics Data System (ADS)

Szwajczak, Elzbieta; Szymanski, Aleksander B.

2002-06-01

An application of liquid crystalline materials as a model materials for the use in dielectric spectroscopy of the artificial biological materials and the tissues is discussed. It is shown that an application of the standard electrochemical concepts may break in the case of liquid crystalline materials as well as biological materials. The presence of space charge regions as well as electrical non- linearities of the sample may suggest some special possibility of the time domain technique application.

BIOZON: a system for unification, management and analysis of heterogeneous biological data.

PubMed

Birkland, Aaron; Yona, Golan

2006-02-15

Integration of heterogeneous data types is a challenging problem, especially in biology, where the number of databases and data types increase rapidly. Amongst the problems that one has to face are integrity, consistency, redundancy, connectivity, expressiveness and updatability. Here we present a system (Biozon) that addresses these problems, and offers biologists a new knowledge resource to navigate through and explore. Biozon unifies multiple biological databases consisting of a variety of data types (such as DNA sequences, proteins, interactions and cellular pathways). It is fundamentally different from previous efforts as it uses a single extensive and tightly connected graph schema wrapped with hierarchical ontology of documents and relations. Beyond warehousing existing data, Biozon computes and stores novel derived data, such as similarity relationships and functional predictions. The integration of similarity data allows propagation of knowledge through inference and fuzzy searches. Sophisticated methods of query that span multiple data types were implemented and first-of-a-kind biological ranking systems were explored and integrated. The Biozon system is an extensive knowledge resource of heterogeneous biological data. Currently, it holds more than 100 million biological documents and 6.5 billion relations between them. The database is accessible through an advanced web interface that supports complex queries, "fuzzy" searches, data materialization and more, online at http://biozon.org.

Ultrafast dynamics and Raman imaging of metal complexes of tetrasulphonated phthalocyanines in human cancerous and noncancerous breast tissues

NASA Astrophysics Data System (ADS)

Abramczyk, H.; Jarota, A.; Brozek-Pluska, B.; Tondusson, M.; Freysz, E.; Musial, J.; Kordek, R.

2013-03-01

A promising material in medicine, electronics, optoelectronics, electrochemistry, catalysis and photophysics, Al(III) phthalocyanine chloride tetrasulfonic acid (AlPcS4) is investigated at biological interfaces of human breast tissue by means of time-resolved spectroscopy. The nature of fast processes and pathways of the competing relaxation mechanisms from the initially excited electronic states of a photosensitizer at biological interfaces have been studied. Comparison between the results in the biological environment of the breast tissues and in aqueous solutions demonstrates that the photochemical mechanisms become dramatically different. The presented results provide a basis for a substantial revision of the commonly accepted assumption that photochemistry of the bulk properties of photosensitizers in solutions can be translated to the interfacial region. First, in solution the dynamics of the photosensitizer is much slower than that at the biological interface. Second, the dynamics of the photosensitizer in the cancerous tissue is dramatically slower than that in noncancerous tissue. Our results provide evidence that molecular structures responsible for harvesting of the light energy in biological tissue find their ways for a recovery through some special features of the potential energy surfaces such as conical intersections, which facilitate the rate of radiationless transitions and maintain the photostability in the biological systems.

A highly compliant serpentine shaped polyimide interconnect for front-end strain relief in chronic neural implants.

PubMed

Sankar, Viswanath; Sanchez, Justin C; McCumiskey, Edward; Brown, Nagid; Taylor, Curtis R; Ehlert, Gregory J; Sodano, Henry A; Nishida, Toshikazu

2013-01-01

While the signal quality of recording neural electrodes is observed to degrade over time, the degradation mechanisms are complex and less easily observable. Recording microelectrodes failures are attributed to different biological factors such as tissue encapsulation, immune response, and disruption of blood-brain barrier (BBB) and non-biological factors such as strain due to micromotion, insulation delamination, corrosion, and surface roughness on the recording site (1-4). Strain due to brain micromotion is considered to be one of the important abiotic factors contributing to the failure of the neural implants. To reduce the forces exerted by the electrode on the brain, a high compliance 2D serpentine shaped electrode cable was designed, simulated, and measured using polyimide as the substrate material. Serpentine electrode cables were fabricated using MEMS microfabrication techniques, and the prototypes were subjected to load tests to experimentally measure the compliance. The compliance of the serpentine cable was numerically modeled and quantitatively measured to be up to 10 times higher than the compliance of a straight cable of same dimensions and material.

Enrichment of Glycoproteins using Nano-scale Chelating Con A Monolithic Capillary Chromatography

PubMed Central

Feng, Shun; Yang, Na; Pennathur, Subramaniam; Goodison, Steve; Lubman, David M.

2009-01-01

Immobilized lectin chromatography can be employed for glycoprotein enrichment, but commonly used columns have limitations of yield and resolution. In order to improve efficiency and to make the technique applicable to minimal sample material, we have developed a nano-scale chelating Concanavalin A (Con A) monolithic capillary prepared using GMA-EDMA (glycidyl methacrylate–co-ethylene dimethacrylate) as polymeric support. Con A was immobilized on Cu(II)-charged iminodiacetic acid (IDA) regenerable sorbents by forming a IDA:Cu(II):Con A sandwich affinity structure that has high column capacity as well as stability. When compared with conventional Con A lectin chromatography, the monolithic capillary enabled the better reproducible detection of over double the number of unique N-glycoproteins in human urine samples. Utility for analysis of minimal biological samples was confirmed by the successful elucidation of glycoprotein profiles in mouse urine samples at the microliter scale. The improved efficiency of the nano-scale monolithic capillary will impact the analysis of glycoproteins in complex biological samples, especially where only limited material may be available. PMID:19366252

A Highly Compliant Serpentine Shaped Polyimide Interconnect for Front-End Strain Relief in Chronic Neural Implants

PubMed Central

Sankar, Viswanath; Sanchez, Justin C.; McCumiskey, Edward; Brown, Nagid; Taylor, Curtis R.; Ehlert, Gregory J.; Sodano, Henry A.; Nishida, Toshikazu

2013-01-01

While the signal quality of recording neural electrodes is observed to degrade over time, the degradation mechanisms are complex and less easily observable. Recording microelectrodes failures are attributed to different biological factors such as tissue encapsulation, immune response, and disruption of blood-brain barrier (BBB) and non-biological factors such as strain due to micromotion, insulation delamination, corrosion, and surface roughness on the recording site (1–4). Strain due to brain micromotion is considered to be one of the important abiotic factors contributing to the failure of the neural implants. To reduce the forces exerted by the electrode on the brain, a high compliance 2D serpentine shaped electrode cable was designed, simulated, and measured using polyimide as the substrate material. Serpentine electrode cables were fabricated using MEMS microfabrication techniques, and the prototypes were subjected to load tests to experimentally measure the compliance. The compliance of the serpentine cable was numerically modeled and quantitatively measured to be up to 10 times higher than the compliance of a straight cable of same dimensions and material. PMID:24062716

From Mendel to epigenetics: History of genetics.

PubMed

Gayon, Jean

2016-01-01

The origins of genetics are to be found in Gregor Mendel's memoir on plant hybridization (1865). However, the word 'genetics' was only coined in 1906, to designate the new science of heredity. Founded upon the Mendelian method for analyzing the products of crosses, this science is distinguished by its explicit purpose of being a general 'science of heredity', and by the introduction of totally new biological concepts (in particular those of gene, genotype, and phenotype). In the 1910s, Mendelian genetics fused with the chromosomal theory of inheritance, giving rise to what is still called 'classical genetics'. Within this framework, the gene is simultaneously a unit of function and transmission, a unit of recombination, and of mutation. Until the early 1950s, these concepts of the gene coincided. But when DNA was found to be the material basis of inheritance, this congruence dissolved. Then began the venture of molecular biology, which has never stopped revealing the complexity of the way in which hereditary material functions. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

DNA-controlled dynamic colloidal nanoparticle systems for mediating cellular interaction

NASA Astrophysics Data System (ADS)

Ohta, Seiichi; Glancy, Dylan; Chan, Warren C. W.

2016-02-01

Precise control of biosystems requires development of materials that can dynamically change physicochemical properties. Inspired by the ability of proteins to alter their conformation to mediate function, we explored the use of DNA as molecular keys to assemble and transform colloidal nanoparticle systems. The systems consist of a core nanoparticle surrounded by small satellites, the conformation of which can be transformed in response to DNA via a toe-hold displacement mechanism. The conformational changes can alter the optical properties and biological interactions of the assembled nanosystem. Photoluminescent signal is altered by changes in fluorophore-modified particle distance, whereas cellular targeting efficiency is increased 2.5 times by changing the surface display of targeting ligands. These concepts provide strategies for engineering dynamic nanotechnology systems for navigating complex biological environments.

Biology Teacher and Expert Opinions about Computer Assisted Biology Instruction Materials: A Software Entitled Nucleic Acids and Protein Synthesis

ERIC Educational Resources Information Center

Hasenekoglu, Ismet; Timucin, Melih

2007-01-01

The aim of this study is to collect and evaluate opinions of CAI experts and biology teachers about a high school level Computer Assisted Biology Instruction Material presenting computer-made modelling and simulations. It is a case study. A material covering "Nucleic Acids and Protein Synthesis" topic was developed as the…

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-structure-function relationship of the biological concept generators as well as the bio-inspired metal foams was achieved, on deeper hierarchical levels and overarching different levels.

[Synthetic biology and rearrangements of microbial genetic material].

PubMed

Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

2011-10-01

As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

A new mixed-ligand copper(II) complex of (E)-N";-(2-hydroxybenzylidene) acetohydrazide: Synthesis, characterization, NLO behavior, DFT calculation and biological activities

NASA Astrophysics Data System (ADS)

Yousef Ebrahimipour, S.; Sheikhshoaie, Iran; Crochet, Aurelien; Khaleghi, Moj; Fromm, Katharina M.

2014-08-01

A tridentate hydrazone Schiff base ligand, (E)-N";-(2-hydroxybenzylidene)acetohydrazide [HL], and its mixed-ligand Cu(II) complex [CuL(phen)], have been synthesized and characterized by elemental analyses, FT-IR, molar conductivity, UV-Vis spectroscopy. The structure of the complex has been determined by X-ray diffraction. This complex has square pyramidal geometry and the positions around central atom are occupied with donor atoms of Schiff base ligand and two nitrogens of 1,10-phenanthroline. Computational studies of compounds were performed by using DFT calculations. The linear polarizabilities and first hyperpolarizabilities of the studied molecules indicate that these compounds can be good candidates of nonlinear optical materials. It is in accordance with experimental data. In addition, invitro antimicrobial results show that these compounds specially [CuL(phen)] have great potential of antibacterial activity against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Listeria monocytogenes bacteria and antifungal activity against Candida Albicans in comparison to some standard drugs.

Coherent multi-dimensional spectroscopy at optical frequencies in a single beam with optical readout

NASA Astrophysics Data System (ADS)

Seiler, Hélène; Palato, Samuel; Kambhampati, Patanjali

2017-09-01

Ultrafast coherent multi-dimensional spectroscopies form a powerful set of techniques to unravel complex processes, ranging from light-harvesting, chemical exchange in biological systems to many-body interactions in quantum-confined materials. Yet these spectroscopies remain complex to implement at the high frequencies of vibrational and electronic transitions, thereby limiting their widespread use. Here we demonstrate the feasibility of two-dimensional spectroscopy at optical frequencies in a single beam. Femtosecond optical pulses are spectrally broadened to a relevant bandwidth and subsequently shaped into phase coherent pulse trains. By suitably modulating the phases of the pulses within the beam, we show that it is possible to directly read out the relevant optical signals. This work shows that one needs neither complex beam geometries nor complex detection schemes in order to measure two-dimensional spectra at optical frequencies. Our setup provides not only a simplified experimental design over standard two-dimensional spectrometers but its optical readout also enables novel applications in microscopy.

Guiding principles for peptide nanotechnology through directed discovery.

PubMed

Lampel, A; Ulijn, R V; Tuttle, T

2018-05-21

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

Methods of staining target chromosomal DNA employing high complexity nucleic acid probes

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Ol'li-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2006-10-03

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Single-stranded DNA and RNA origami.

PubMed

Han, Dongran; Qi, Xiaodong; Myhrvold, Cameron; Wang, Bei; Dai, Mingjie; Jiang, Shuoxing; Bates, Maxwell; Liu, Yan; An, Byoungkwon; Zhang, Fei; Yan, Hao; Yin, Peng

2017-12-15

Self-folding of an information-carrying polymer into a defined structure is foundational to biology and offers attractive potential as a synthetic strategy. Although multicomponent self-assembly has produced complex synthetic nanostructures, unimolecular folding has seen limited progress. We describe a framework to design and synthesize a single DNA or RNA strand to self-fold into a complex yet unknotted structure that approximates an arbitrary user-prescribed shape. We experimentally construct diverse multikilobase single-stranded structures, including a ~10,000-nucleotide (nt) DNA structure and a ~6000-nt RNA structure. We demonstrate facile replication of the strand in vitro and in living cells. The work here thus establishes unimolecular folding as a general strategy for constructing complex and replicable nucleic acid nanostructures, and expands the design space and material scalability for bottom-up nanotechnology. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Compiler-aided systematic construction of large-scale DNA strand displacement circuits using unpurified components

NASA Astrophysics Data System (ADS)

Thubagere, Anupama J.; Thachuk, Chris; Berleant, Joseph; Johnson, Robert F.; Ardelean, Diana A.; Cherry, Kevin M.; Qian, Lulu

2017-02-01

Biochemical circuits made of rationally designed DNA molecules are proofs of concept for embedding control within complex molecular environments. They hold promise for transforming the current technologies in chemistry, biology, medicine and material science by introducing programmable and responsive behaviour to diverse molecular systems. As the transformative power of a technology depends on its accessibility, two main challenges are an automated design process and simple experimental procedures. Here we demonstrate the use of circuit design software, combined with the use of unpurified strands and simplified experimental procedures, for creating a complex DNA strand displacement circuit that consists of 78 distinct species. We develop a systematic procedure for overcoming the challenges involved in using unpurified DNA strands. We also develop a model that takes synthesis errors into consideration and semi-quantitatively reproduces the experimental data. Our methods now enable even novice researchers to successfully design and construct complex DNA strand displacement circuits.

Biomechanical validation of an artificial tooth–periodontal ligament–bone complex for in vitro orthodontic load measurement

PubMed Central

Xia, Zeyang; Chen, Jie

2014-01-01

Objectives To develop an artificial tooth–periodontal ligament (PDL)–bone complex (ATPBC) that simulates clinical crown displacement. Material and Methods An ATPBC was created. It had a socket hosting a tooth with a thin layer of silicon mixture in between for simulating the PDL. The complex was attached to a device that allows applying a controlled force to the crown and measuring the resulting crown displacement. Crown displacements were compared to previously published data for validation. Results The ATPBC that had a PDL made of two types of silicones, 50% gasket sealant No. 2 and 50% RTV 587 silicone, with a thickness of 0.3 mm, simulated the PDL well. The mechanical behaviors (1) force-displacement relationship, (2) stress relaxation, (3) creep, and (4) hysteresis were validated by the published results. Conclusion The ATPBC simulated the crown displacement behavior reported from biological studies well. PMID:22970752

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

Nguyen, Thao D.; Grazier, John Mark; Boyce, Brad Lee

Biological tissues are uniquely structured materials with technologically appealing properties. Soft tissues such as skin, are constructed from a composite of strong fibrils and fluid-like matrix components. This was the first coordinated experimental/modeling project at Sandia or in the open literature to consider the mechanics of micromechanically-based anisotropy and viscoelasticity of soft biological tissues. We have exploited and applied Sandia's expertise in experimentation and mechanics modeling to better elucidate the behavior of collagen fibril-reinforced soft tissues. The purpose of this project was to provide a detailed understanding of the deformation of ocular tissues, specifically the highly structured skin-like tissue inmore » the cornea. This discovery improved our knowledge of soft/complex materials testing and modeling. It also provided insight into the way that cornea tissue is bio-engineered such that under physiologically-relevant conditions it has a unique set of properties which enhance functionality. These results also provide insight into how non-physiologic loading conditions, such as corrective surgeries, may push the cornea outside of its natural design window, resulting in unexpected non-linear responses. Furthermore, this project created a clearer understanding of the mechanics of soft tissues that could lead to bio-inspired materials, such as highly supple and impact resistant body armor, and improve our design of human-machine interfaces, such as micro-electrical-mechanical (MEMS) based prosthetics.« less

Traumatic eye injuries as a result of blunt impact: computational issues

NASA Astrophysics Data System (ADS)

Clemente, C.; Esposito, L.; Bonora, N.; Limido, J.; Lacome, J. L.; Rossi, T.

2014-05-01

The detachment or tearing of the retina in the human eye as a result of a collision is a phenomenon that occurs very often. Reliable numerical simulations of eye impact can be very useful tools to understand the physical mechanisms responsible for traumatic eye injuries accompanying blunt impact. The complexity and variability of the physical and mechanical properties of the biological materials, the lack of agreement on their related experimental data as well as the unsuitability of specific numerical codes and models are only some of the difficulties when dealing with this matter. All these challenging issues must be solved to obtain accurate numerical analyses involving dynamic behavior of biological soft tissues. To this purpose, a numerical and experimental investigation of the dynamic response of the eye during an impact event was performed. Numerical simulations were performed with IMPETUS-AFEA, a new general non-linear finite element (FE) software which offers non uniform rational B-splines (NURBS) FE technology for the simulation of large deformation and fracture in materials. IMPETUS code was selected in order to solve hourglass and locking problems typical of nearly incompressible materials like eye tissues. Computational results were compared with the experimental results on fresh enucleated porcine eyes impacted with airsoft pellets.

Design and Printing Strategies in 3D Bioprinting of Cell-Hydrogels: A Review.

PubMed

Lee, Jia Min; Yeong, Wai Yee

2016-11-01

Bioprinting is an emerging technology that allows the assembling of both living and non-living biological materials into an ideal complex layout for further tissue maturation. Bioprinting aims to produce engineered tissue or organ in a mechanized, organized, and optimized manner. Various biomaterials and techniques have been utilized to bioprint biological constructs in different shapes, sizes and resolutions. There is a need to systematically discuss and analyze the reported strategies employed to fabricate these constructs. We identified and discussed important design factors in bioprinting, namely shape and resolution, material heterogeneity, and cellular-material remodeling dynamism. Each design factors are represented by the corresponding process capabilities and printing parameters. The process-design map will inspire future biomaterials research in these aspects. Design considerations such as data processing, bio-ink formulation and process selection are discussed. Various printing and crosslinking strategies, with relevant applications, are also systematically reviewed. We categorized them into 5 general bioprinting strategies, including direct bioprinting, in-process crosslinking, post-process crosslinking, indirect bioprinting and hybrid bioprinting. The opportunities and outlook in 3D bioprinting are highlighted. This review article will serve as a framework to advance computer-aided design in bioprinting technologies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Graphene Oxide Directed One-Step Synthesis of Flowerlike Graphene@HKUST-1 for Enzyme-Free Detection of Hydrogen Peroxide in Biological Samples.

PubMed

Wang, Qingxiang; Yang, Yizhen; Gao, Feng; Ni, Jiancong; Zhang, Yanhui; Lin, Zhenyu

2016-11-30

A novel metal-organic framework (MOF)-based electroactive nanocomposite containing graphene fragments and HKUST-1 was synthesized via a facile one-step solvothermal method using graphene oxide (GO), benzene-1,3,5-tricarboxylic acid (BTC), and copper nitrate (Cu(NO 3 ) 2 ) as the raw materials. The morphology and structure characterization revealed that the GO could induce the transformation of HKUST-1 from octahedral structure to the hierarchical flower shape as an effective structure-directing agent. Also, it is interesting to find out that the GO was torn into small fragments to participate in the formation of HKUST-1 and then transformed into the reduction form during the solvothermal reaction process, which dramatically increased the surface area, electronic conductivity, and redox-activity of the material. Electrochemical assays showed that the synergy of graphene and HKUST-1 in the nanocomposite leaded to high electrocatalysis, fast response, and excellent selectivity toward the reduction of hydrogen peroxide (H 2 O 2 ). Based on these remarkable advantages, satisfactory results were obtained when the nanocomposite was used as a sensing material for electrochemical determination of H 2 O 2 in the complex biological samples such as human serum and living Raw 264.7 cell fluids.

Cell-based composite materials with programmed structures and functions

DOEpatents

None

2016-03-01

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

Cell-based composite materials with programmed structures and functions

DOEpatents

Kaehr, Bryan J.; Brinker, C. Jeffrey; Townson, Jason L.

2018-05-15

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

[Applications of synthetic biology in materials science].

PubMed

Zhao, Tianxin; Zhong, Chao

2017-03-25

Materials are the basis for human being survival and social development. To keep abreast with the increasing needs from all aspects of human society, there are huge needs in the development of advanced materials as well as high-efficiency but low-cost manufacturing strategies that are both sustainable and tunable. Synthetic biology, a new engineering principle taking gene regulation and engineering design as the core, greatly promotes the development of life sciences. This discipline has also contributed to the development of material sciences and will continuously bring new ideas to future new material design. In this paper, we review recent advances in applications of synthetic biology in material sciences, with the focus on how synthetic biology could enable synthesis of new polymeric biomaterials and inorganic materials, phage display and directed evolution of proteins relevant to materials development, living functional materials, engineered bacteria-regulated artificial photosynthesis system as well as applications of gene circuits for material sciences.

Inverse Algorithm Optimization for Determining Optical Properties of Biological Materials from Spatially-Resolved Diffuse Reflectance

USDA-ARS?s Scientific Manuscript database

Optical characterization of biological materials is useful in many scientific and industrial applications like biomedical diagnosis and nondestructive quality evaluation of food and agricultural products. However, accurate determination of the optical properties from intact biological materials base...

Digital and analog chemical evolution.

PubMed

Goodwin, Jay T; Mehta, Anil K; Lynn, David G

2012-12-18

Living matter is the most elaborate, elegant, and complex hierarchical material known and is consequently the natural target for an ever-expanding scientific and technological effort to unlock and deconvolute its marvelous forms and functions. Our current understanding suggests that biological materials are derived from a bottom-up process, a spontaneous emergence of molecular networks in the course of chemical evolution. Polymer cooperation, so beautifully manifested in the ribosome, appeared in these dynamic networks, and the special physicochemical properties of the nucleic and amino acid polymers made possible the critical threshold for the emergence of extant cellular life. These properties include the precise and geometrically discrete hydrogen bonding patterns that dominate the complementary interactions of nucleic acid base-pairing that guide replication and ensure replication fidelity. In contrast, complex and highly context-dependent sets of intra- and intermolecular interactions guide protein folding. These diverse interactions allow the more analog environmental chemical potential fluctuations to dictate conformational template-directed propagation. When these two different strategies converged in the remarkable synergistic ribonucleoprotein that is the ribosome, this resulting molecular digital-to-analog converter achieved the capacity for both persistent information storage and adaptive responses to an ever-changing environment. The ancestral chemical networks that preceded the Central Dogma of Earth's biology must reflect the dynamic chemical evolutionary landscapes that allowed for selection, propagation, and diversification and ultimately the demarcation and specialization of function that modern biopolymers manifest. Not only should modern biopolymers contain molecular fossils of this earlier age, but it should be possible to use this information to reinvent these dynamic functional networks. In this Account, we review the first dynamic network created by modification of a nucleic acid backbone and show how it has exploited the digital-like base pairing for reversible polymer construction and information transfer. We further review how these lessons have been extended to the complex folding landscapes of templated peptide assembly. These insights have allowed for the construction of molecular hybrids of each biopolymer class and made possible the reimagining of chemical evolution. Such elaboration of biopolymer chimeras has already led to applications in therapeutics and diagnostics, to the construction of novel nanostructured materials, and toward orthogonal biochemical pathways that expand the evolution of existing biochemical systems. The ability to look beyond the primordial emergence of the ribosome may allow us to better define the origins of chemical evolution, to extend its horizons beyond the biology of today and ask whether evolution is an inherent property of matter unbounded by physical limitations imposed by our planet's diverse environments.

Incorporating microorganisms into polymer layers provides bioinspired functional living materials

PubMed Central

Gerber, Lukas C.; Koehler, Fabian M.; Grass, Robert N.; Stark, Wendelin J.

2012-01-01

Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus Penicillium roqueforti to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart materials with capability for evolutionary adaptation. This allows realization of most complex responses to environmental stimuli. As a conceptual design, we prepared a material surface with self-cleaning capability when subjected to standardized food spill. Fungal growth and reproduction were observed in between two specifically adapted polymer layers. Gas exchange for breathing and transport of nutrient through a nano-porous top layer allowed selective intake of food whilst limiting the microorganism to dwell exclusively in between a confined, well-enclosed area of the material. We demonstrated a design of such living materials and showed both active (eating) and waiting (dormant, hibernation) states with additional recovery for reinitiation of a new active state by observing the metabolic activity over two full nutrition cycles of the living material (active, hibernation, reactivation). This novel class of living materials can be expected to provide nonclassical solutions in consumer goods such as packaging, indoor surfaces, and in biotechnology. PMID:22198770

Integrative Biological Analysis For Neuropsychopharmacology

PubMed Central

Emmett, Mark R; Kroes, Roger A; Moskal, Joseph R; Conrad, Charles A; Priebe, Waldemar; Laezza, Fernanda; Meyer-Baese, Anke; Nilsson, Carol L

2014-01-01

Although advances in psychotherapy have been made in recent years, drug discovery for brain diseases such as schizophrenia and mood disorders has stagnated. The need for new biomarkers and validated therapeutic targets in the field of neuropsychopharmacology is widely unmet. The brain is the most complex part of human anatomy from the standpoint of number and types of cells, their interconnections, and circuitry. To better meet patient needs, improved methods to approach brain studies by understanding functional networks that interact with the genome are being developed. The integrated biological approaches—proteomics, transcriptomics, metabolomics, and glycomics—have a strong record in several areas of biomedicine, including neurochemistry and neuro-oncology. Published applications of an integrated approach to projects of neurological, psychiatric, and pharmacological natures are still few but show promise to provide deep biological knowledge derived from cells, animal models, and clinical materials. Future studes that yield insights based on integrated analyses promise to deliver new therapeutic targets and biomarkers for personalized medicine. PMID:23800968

IMPROVED TECHNNOLOGY TO PREVENT ILLICIT TRAFFICKING IN NUCLEAR MATERIALS

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

Richardson, J H

2005-07-20

The proliferation of nuclear, chemical, and biological weapons (collectively known as weapons of mass destruction, or WMD) and the potential acquisition and use of WMD against the world by terrorists are extremely serious threats to international security. These threats are complex and interrelated. There are myriad routes to weapons of mass destruction--many different starting materials, material sources, and production processes. There are many possible proliferators--threshold countries, rogue states, state-sponsored or transnational terrorists groups, domestic terrorists, and even international crime organizations. Motives for acquiring and using WMD are similarly wide ranging--from a desire to change the regional power balance, deny accessmore » to a strategic area, or alter international policy to extortion, revenge, or hate. Because of the complexity of this threat landscape, no single program, technology, or capability--no silver bullet--can solve the WMD proliferation and terrorism problem. An integrated program is needed that addresses the WMD proliferation and terrorism problem from end to end, from prevention to detection, reversal, and response, while avoiding surprise at all stages, with different activities directed specifically at different types of WMD and proliferators. Radiation detection technologies are an important tool in the prevention of proliferation. A variety of new developments have enabled enhanced performance in terms of energy resolution, spatial resolution, predictive modeling and simulation, active interrogation, and ease of operation and deployment in the field. The radiation properties of nuclear materials, particularly highly enriched uranium (HEU), make the detection of smuggled nuclear materials technically difficult. A number of efforts are under way to devise improved detector materials and instruments and to identify novel signatures that could be detected. Key applications of this work include monitoring for radioactive materials at choke points, searching for nuclear materials, and developing instruments for response personnel.« less

Tandem Repeat Proteins Inspired By Squid Ring Teeth

NASA Astrophysics Data System (ADS)

Pena-Francesch, Abdon

Proteins are large biomolecules consisting of long chains of amino acids that hierarchically assemble into complex structures, and provide a variety of building blocks for biological materials. The repetition of structural building blocks is a natural evolutionary strategy for increasing the complexity and stability of protein structures. However, the relationship between amino acid sequence, structure, and material properties of protein systems remains unclear due to the lack of control over the protein sequence and the intricacies of the assembly process. In order to investigate the repetition of protein building blocks, a recently discovered protein from squids is examined as an ideal protein system. Squid ring teeth are predatory appendages located inside the suction cups that provide a strong grasp of prey, and are solely composed of a group of proteins with tandem repetition of building blocks. The objective of this thesis is the understanding of sequence, structure and property relationship in repetitive protein materials inspired in squid ring teeth for the first time. Specifically, this work focuses on squid-inspired structural proteins with tandem repeat units in their sequence (i.e., repetition of alternating building blocks) that are physically cross-linked via beta-sheet structures. The research work presented here tests the hypothesis that, in these systems, increasing the number of building blocks in the polypeptide chain decreases the protein network defects and improves the material properties. Hence, the sequence, nanostructure, and properties (thermal, mechanical, and conducting) of tandem repeat squid-inspired protein materials are examined. Spectroscopic structural analysis, advanced materials characterization, and entropic elasticity theory are combined to elucidate the structure and material properties of these repetitive proteins. This approach is applied not only to native squid proteins but also to squid-inspired synthetic polypeptides that allow for a fine control of the sequence and network morphology. The results provided in this work establish a clear dependence between the repetitive building blocks, the network morphology, and the properties of squid-inspired repetitive protein materials. Increasing the number of tandem repeat units in SRT-inspired proteins led to more effective protein networks with superior properties. Through increasing tandem repetition and optimization of network morphology, highly efficient protein materials capable of withstanding deformations up to 400% of their original length, with MPa-GPa modulus, high energy absorption (50 MJ m-3), peak proton conductivity of 3.7 mS cm-1 (at pH 7, highest reported to date for biological materials), and peak thermal conductivity of 1.4 W m-1 K -1 (which exceeds that of most polymer materials) were developed. These findings introduce new design rules in the engineering of proteins based on tandem repetition and morphology control, and provide a novel framework for tailoring and optimizing the properties of protein-based materials.

Trends in United States Biological Materials Oversight and Institutional Biosafety Committees

ERIC Educational Resources Information Center

Jenkins, Chris

2014-01-01

Biological materials oversight in life sciences research in the United States is a challenging endeavor for institutions and the scientific, regulatory compliance, and federal communities. In order to assess biological materials oversight at Institutional Biosafety Committees (IBCs) registered with the United States National Institutes of Health,…

Comparative study of P19 EC stem cell differentiation in between conventional hanging drop and the zebrafish chorion as a bio-derived material.

PubMed

Dae Seok Na; Lee, Hwang; Sun Uk Kim; Chang Nam Hwang; Sang Ho Lee; Ji Yoon Kang; Jai Kyeong Kim; James Jungho Pak

2008-07-01

Various materials including glass and polymers have been widely used for stem cell culture due to their biocompatibility. However, the roles of these materials are fundamentally limited because they cannot realize or imitate the complex biological functions of living tissues, except in very simple cases. Here, the development of a bio-derived material suitable for stem cell culture and improvement of differentiation efficiency to specific cell lineages with no stimulating agents by using a chorion obtained from a fertilized zebrafish egg through the removal of the yolk and embryonic cell mass from the egg is reported. Mouse P19 EC stem cells introduced into the empty chorion form a uniform embryoid body (EB) without addition of any inducing agent. It is demonstrated that the zebrafish chorion with nanopores improves efficiencies greatly in the EB formation, cell proliferation, and lineage-specific differentiations compared to those of the conventional hanging drop culture method.

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

PubMed

Wang, Yong

2017-03-25

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

Biological conversion system

DOEpatents

Scott, C.D.

A system for bioconversion of organic material comprises a primary bioreactor column wherein a biological active agent (zymomonas mobilis) converts the organic material (sugar) to a product (alcohol), a rejuvenator column wherein the biological activity of said biological active agent is enhanced, and means for circulating said biological active agent between said primary bioreactor column and said rejuvenator column.

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 communication (OFC) and optical computing. The SEM image of the copper(II) complex implies that the size of the particles is 1 μm.

Agricultural waste material as potential adsorbent for sequestering heavy metal ions from aqueous solutions - a review.

PubMed

Sud, Dhiraj; Mahajan, Garima; Kaur, M P

2008-09-01

Heavy metal remediation of aqueous streams is of special concern due to recalcitrant and persistency of heavy metals in environment. Conventional treatment technologies for the removal of these toxic heavy metals are not economical and further generate huge quantity of toxic chemical sludge. Biosorption is emerging as a potential alternative to the existing conventional technologies for the removal and/or recovery of metal ions from aqueous solutions. The major advantages of biosorption over conventional treatment methods include: low cost, high efficiency, minimization of chemical or biological sludge, regeneration of biosorbents and possibility of metal recovery. Cellulosic agricultural waste materials are an abundant source for significant metal biosorption. The functional groups present in agricultural waste biomass viz. acetamido, alcoholic, carbonyl, phenolic, amido, amino, sulphydryl groups etc. have affinity for heavy metal ions to form metal complexes or chelates. The mechanism of biosorption process includes chemisorption, complexation, adsorption on surface, diffusion through pores and ion exchange etc. The purpose of this review article is to provide the scattered available information on various aspects of utilization of the agricultural waste materials for heavy metal removal. Agricultural waste material being highly efficient, low cost and renewable source of biomass can be exploited for heavy metal remediation. Further these biosorbents can be modified for better efficiency and multiple reuses to enhance their applicability at industrial scale.

Composites comprising biologically-synthesized nanomaterials

DOEpatents

Curran, Seamus; Dias, Sampath; Blau, Werner; Wang, Jun; Oremland, Ronald S; Baesman, Shaun

2013-04-30

The present disclosure describes composite materials containing a polymer material and a nanoscale material dispersed in the polymer material. The nanoscale materials may be biologically synthesized, such as tellurium nanorods synthesized by Bacillus selenitireducens. Composite materials of the present disclosure may have optical limiting properties and find use in optical limiting devices.

KSC-06pd1686

NASA Image and Video Library

2006-07-28

KENNEDY SPACE CENTER, FLA. - In the Space Station Processing Facility, processing continues on the Japanese Experiment Module (JEM) for its flight to the International Space Station (ISS). The JEM, developed by the Japan Aerospace Exploration Agency (JAXA) for installation on the ISS, is named Kibo -- which means "hope" in Japanese -- and will enhance the unique research capabilities of the orbiting complex by providing an additional environment for astronauts to conduct science experiments. Research conducted in Kibo will focus on space medicine, biology, Earth observations, material production, biotechnology and communications. Photo credit: NASA/Amanda Diller

Regulatory considerations for pluripotent stem cell therapies.

PubMed

Carpenter, Melissa K

2017-01-01

The development of pluripotent stem cell (PSC) therapies is rapidly advancing, and a number of PSC-derived cell products are currently being tested in clinical trials. The biological complexity of these therapies results in specific challenges in complying with regulatory guidelines. This includes the choice of starting material, reproducible and consistent manufacturing, and preclinical safety and efficacy assessment of the PSC-derived product. This review discusses current US cell therapy regulations and strategies for compliance with these regulations when developing PSC-derived products. © 2017 Elsevier B.V. All rights reserved.

Luminescent Rhenium(I) and Iridium(III) Polypyridine Complexes as Biological Probes, Imaging Reagents, and Photocytotoxic Agents.

PubMed

Lo, Kenneth Kam-Wing

2015-12-15

Although the interactions of transition metal complexes with biological molecules have been extensively studied, the use of luminescent transition metal complexes as intracellular sensors and bioimaging reagents has not been a focus of research until recently. The main advantages of luminescent transition metal complexes are their high photostability, long-lived phosphorescence that allows time-resolved detection, and large Stokes shifts that can minimize the possible self-quenching effect. Also, by the use of transition metal complexes, the degree of cellular uptake can be readily determined using inductively coupled plasma mass spectrometry. For more than a decade, we have been interested in the development of luminescent transition metal complexes as covalent labels and noncovalent probes for biological molecules. We argue that many transition metal polypyridine complexes display triplet charge transfer ((3)CT) emission that is highly sensitive to the local environment of the complexes. Hence, the biological labeling and binding interactions can be readily reflected by changes in the photophysical properties of the complexes. In this laboratory, we have modified luminescent tricarbonylrhenium(I) and bis-cyclometalated iridium(III) polypyridine complexes of general formula [Re(bpy-R(1))(CO)3(py-R(2))](+) and [Ir(ppy-R(3))2(bpy-R(4))](+), respectively, with reactive functional groups and used them to label the amine and sulfhydryl groups of biomolecules such as oligonucleotides, amino acids, peptides, and proteins. Additionally, using a range of biological substrates such as biotin, estradiol, and indole, we have designed luminescent rhenium(I) and iridium(III) polypyridine complexes as noncovalent probes for biological receptors. The interesting results generated from these studies have prompted us to investigate the possible applications of luminescent transition metal complexes in intracellular systems. Thus, in the past few years, we have developed an interest in the cytotoxic activity, cellular uptake, and bioimaging applications of these complexes. Additionally, we and other research groups have demonstrated that many transition metal complexes have facile cellular uptake and organelle-localization properties and that their cytotoxic activity can be readily controlled. For example, complexes that can target the nucleus, nucleolus, mitochondria, lysosomes, endoplasmic reticulum, and Golgi apparatus have been identified. We anticipate that this selective localization property can be utilized in the development of intracellular sensors and bioimaging reagents. Thus, we have functionalized luminescent rhenium(I) and iridium(III) polypyridine complexes with various pendants, including molecule-binding moieties, sugar molecules, bioorthogonal functional groups, and polymeric chains such as poly(ethylene glycol) and polyethylenimine, and examined their potentials as biological reagents. This Account describes our design of luminescent rhenium(I) and iridium(III) polypyridine complexes and explains how they can serve as a new generation of biological reagents for diagnostic and therapeutic applications.

On the relationship between indentation hardness and modulus, and the damage resistance of biological materials.

PubMed

Labonte, David; Lenz, Anne-Kristin; Oyen, Michelle L

2017-07-15

The remarkable mechanical performance of biological materials is based on intricate structure-function relationships. Nanoindentation has become the primary tool for characterising biological materials, as it allows to relate structural changes to variations in mechanical properties on small scales. However, the respective theoretical background and associated interpretation of the parameters measured via indentation derives largely from research on 'traditional' engineering materials such as metals or ceramics. Here, we discuss the functional relevance of indentation hardness in biological materials by presenting a meta-analysis of its relationship with indentation modulus. Across seven orders of magnitude, indentation hardness was directly proportional to indentation modulus. Using a lumped parameter model to deconvolute indentation hardness into components arising from reversible and irreversible deformation, we establish criteria which allow to interpret differences in indentation hardness across or within biological materials. The ratio between hardness and modulus arises as a key parameter, which is related to the ratio between irreversible and reversible deformation during indentation, the material's yield strength, and the resistance to irreversible deformation, a material property which represents the energy required to create a unit volume of purely irreversible deformation. Indentation hardness generally increases upon material dehydration, however to a larger extent than expected from accompanying changes in indentation modulus, indicating that water acts as a 'plasticiser'. A detailed discussion of the role of indentation hardness, modulus and toughness in damage control during sharp or blunt indentation yields comprehensive guidelines for a performance-based ranking of biological materials, and suggests that quasi-plastic deformation is a frequent yet poorly understood damage mode, highlighting an important area of future research. Instrumented indentation is a widespread tool for characterising the mechanical properties of biological materials. Here, we show that the ratio between indentation hardness and modulus is approximately constant in biological materials. A simple elastic-plastic series deformation model is employed to rationalise part of this correlation, and criteria for a meaningful comparison of indentation hardness across biological materials are proposed. The ratio between indentation hardness and modulus emerges as the key parameter characterising the relative amount of irreversible deformation during indentation. Despite their comparatively high hardness to modulus ratio, biological materials are susceptible to quasiplastic deformation, due to their high toughness: quasi-plastic deformation is hence hypothesised to be a frequent yet poorly understood phenomenon, highlighting an important area of future research. Copyright © 2017 Acta Materialia Inc. All rights reserved.

Biological response to prosthetic debris

PubMed Central

Bitar, Diana; Parvizi, Javad

2015-01-01

Joint arthroplasty had revolutionized the outcome of orthopaedic surgery. Extensive and collaborative work of many innovator surgeons had led to the development of durable bearing surfaces, yet no single material is considered absolutely perfect. Generation of wear debris from any part of the prosthesis is unavoidable. Implant loosening secondary to osteolysis is the most common mode of failure of arthroplasty. Osteolysis is the resultant of complex contribution of the generated wear debris and the mechanical instability of the prosthetic components. Roughly speaking, all orthopedic biomaterials may induce a universal biologic host response to generated wear débris with little specific characteristics for each material; but some debris has been shown to be more cytotoxic than others. Prosthetic wear debris induces an extensive biological cascade of adverse cellular responses, where macrophages are the main cellular type involved in this hostile inflammatory process. Macrophages cause osteolysis indirectly by releasing numerous chemotactic inflammatory mediators, and directly by resorbing bone with their membrane microstructures. The bio-reactivity of wear particles depends on two major elements: particle characteristics (size, concentration and composition) and host characteristics. While any particle type may enhance hostile cellular reaction, cytological examination demonstrated that more than 70% of the debris burden is constituted of polyethylene particles. Comprehensive understanding of the intricate process of osteolysis is of utmost importance for future development of therapeutic modalities that may delay or prevent the disease progression. PMID:25793158

New bioproduction systems: from molecular circuits to novel reactor concepts in cell-free biotechnology.

PubMed

Rupp, Steffen

2013-01-01

: The last decades witnessed a strong growth in several areas of biotechnology, especially in fields related to health, as well as in industrial biotechnology. Advances in molecular engineering now enable biotechnologists to design more efficient pathways in order to convert a larger spectrum of renewable resources into industrially used biofuels and chemicals as well as into new pharmaceuticals and therapeutic proteins. In addition material sciences advanced significantly making it more and more possible to integrate biology and engineering. One of the key questions currently is how to develop new ways of engineering biological systems to cope with the complexity and limitations given by the cell. The options to integrate biology with classical engineering advanced cell free technologies in the recent years significantly. Cell free protein production using cellular extracts is now a well-established universal technology for production of proteins derived from many organisms even at the milligram scale. Among other applications it has the potential to supply the demand for a multitude of enzymes and enzyme variants facilitating in vitro metabolic engineering. This review will briefly address the recent achievements and limitations of cell free conversions. Especially, the requirements for reactor systems in cell free biotechnology, a currently underdeveloped field, are reviewed and some perspectives are given on how material sciences and biotechnology might be able to advance these new developments in the future.

New Materials for Biological Fuel Cells

DTIC Science & Technology

2012-04-01

polymer electrolyte membrane ( PEM ), to the membrane-less biological fuel cell (center figure) where the two electrodes are submerged in the same... PEM . MT15_4p166_173.indd 171 4/10/2012 3:46:31 PM REVIEW New materials for biological fuel cells APRIL 2012 | VOLUME 15 | NUMBER 4172 These...ISSN:1369 7021 © Elsevier Ltd 2012APRIL 2012 | VOLUME 15 | NUMBER 4166 New materials for biological fuel cells Over the last decade, there has

Kirigami design and fabrication for biomimetic robotics

NASA Astrophysics Data System (ADS)

Rossiter, Jonathan; Sareh, Sina

2014-03-01

Biomimetics faces a continual challenge of how to bridge the gap between what Nature has so effectively evolved and the current tools and materials that engineers and scientists can exploit. Kirigami, from the Japanese `cut' and `paper', is a method of design where laminar materials are cut and then forced out-of-plane to yield 3D structures. Kirimimetic design provides a convenient and relatively closed design space within which to replicate some of the most interesting niche biological mechanisms. These include complex flexing organelles such as cilia in algae, energy storage and buckled structures in plants, and organic appendages that actuate out-of-plane such as the myoneme of the Vorticella protozoa. Where traditional kirigami employs passive materials which must be forced to transition to higher dimensions, we can exploit planar smart actuators and artificial muscles to create self-actuating kirigami structures. Here we review biomimetics with respect to the kirigami design and fabrication methods and examine how smart materials, including electroactive polymers and shape memory polymers, can be used to realise effective biomimetic components for robotic, deployable structures and engineering systems. One-way actuation, for example using shape memory polymers, can yield complete self-deploying structures. Bi-directional actuation, in contrast, can be exploited to mimic fundamental biological mechanisms such as thrust generation and fluid control. We present recent examples of kirigami robotic mechanisms and actuators and discuss planar fabrication methods, including rapid prototyping and 3D printing, and how current technologies, and their limitations, affect Kirigami robotics.

Reversibly immobilized biological materials in monolayer films on electrodes

DOEpatents

Weaver, P.F.; Frank, A.J.

1993-05-04

Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

Reversibly immobilized biological materials in monolayer films on electrodes

DOEpatents

Weaver, Paul F.; Frank, Arthur J.

1993-01-01

Methods and techniques are described for reversibly binding charged biological particles in a fluid medium to an electrode surface. The methods are useful in a variety of applications. The biological materials may include microbes, proteins, and viruses. The electrode surface may consist of reversibly electroactive materials such as polyvinylferrocene, silicon-linked ferrocene or quinone.

Preparation and Characterization of Biofunctionalized Inorganic Substrates.

PubMed

Dugger, Jason W; Webb, Lauren J

2015-09-29

Integrating the function of biological molecules into traditional inorganic materials and substrates couples biologically relevant function to synthetic devices and generates new materials and capabilities by combining biological and inorganic functions. At this so-called "bio/abio interface," basic biological functions such as ligand binding and catalysis can be co-opted to detect analytes with exceptional sensitivity or to generate useful molecules with chiral specificity under entirely benign reaction conditions. Proteins function in dynamic, complex, and crowded environments (the living cell) and are therefore appropriate for integrating into multistep, multiscale, multimaterial devices such as integrated circuits and heterogeneous catalysts. However, the goal of reproducing the highly specific activities of biomolecules in the perturbed chemical and electrostatic environment at an inorganic interface while maintaining their native conformations is challenging to achieve. Moreover, characterizing protein structure and function at a surface is often difficult, particularly if one wishes to compare the activity of the protein to that of the dilute, aqueous solution phase. Our laboratory has developed a general strategy to address this challenge by taking advantage of the structural and chemical properties of alkanethiol self-assembled monolayers (SAMs) on gold surfaces that are functionalized with covalently tethered peptides. These surface-bound peptides then act as the chemical recognition element for a target protein, generating a biomimetic surface in which protein orientation, structure, density, and function are controlled and variable. Herein we discuss current research and future directions related to generating a chemically tunable biofunctionalization strategy that has potential to successfully incorporate the highly specialized functions of proteins onto inorganic substrates.

Biomedical and Catalytic Opportunities of Virus-Like Particles in Nanotechnology.

PubMed

Schwarz, B; Uchida, M; Douglas, T

2017-01-01

Within biology, molecules are arranged in hierarchical structures that coordinate and control the many processes that allow for complex organisms to exist. Proteins and other functional macromolecules are often studied outside their natural nanostructural context because it remains difficult to create controlled arrangements of proteins at this size scale. Viruses are elegantly simple nanosystems that exist at the interface of living organisms and nonliving biological machines. Studied and viewed primarily as pathogens to be combatted, viruses have emerged as models of structural efficiency at the nanoscale and have spurred the development of biomimetic nanoparticle systems. Virus-like particles (VLPs) are noninfectious protein cages derived from viruses or other cage-forming systems. VLPs provide incredibly regular scaffolds for building at the nanoscale. Composed of self-assembling protein subunits, VLPs provide both a model for studying materials' assembly at the nanoscale and useful building blocks for materials design. The robustness and degree of understanding of many VLP structures allow for the ready use of these systems as versatile nanoparticle platforms for the conjugation of active molecules or as scaffolds for the structural organization of chemical processes. Lastly the prevalence of viruses in all domains of life has led to unique activities of VLPs in biological systems most notably the immune system. Here we discuss recent efforts to apply VLPs in a wide variety of applications with the aim of highlighting how the common structural elements of VLPs have led to their emergence as paradigms for the understanding and design of biological nanomaterials. © 2017 Elsevier Inc. All rights reserved.

Synthesis and studies on Cu(II), Co(II), Ni(II) complexes of Knoevenagel β-diketone ligands.

PubMed

Sumathi, S; Tharmaraj, P; Sheela, C D; Anitha, C

2012-11-01

Transition metal complexes of various acetylacetone based ligands of the type ML [where M=Cu(II), Ni(II), Co(II); L=3-(aryl)-pentane-2,4-dione] have been synthesized. The structural features have been derived from their elemental analysis, magnetic susceptibility, molar conductance, IR, UV-Vis, (1)H NMR, Mass and ESR spectral studies. Conductivity measurements reveal that all the complexes are non-electrolytic in nature. Spectroscopic and other analytical data of the complexes suggest octahedral geometry for other metal(II) complexes. The redox behavior of the copper(II) complexes have been studied by cyclic voltammetry. The free ligands and their metal complexes have been screened for their in vitro biological activities against the bacteria Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus as well as the fungus Candida albicans by well diffusion method. The zone of inhibition value indicates that the most of the metal(II) complexes are found to possess increased activities compared to those of the free ligands. All synthesized compounds may serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The second harmonic generation (SHG) efficiency of the ligands (L1-L3) was found to be considerable effect than that of urea and KDP (potassium dihydrogen phosphate). Copyright © 2012 Elsevier B.V. All rights reserved.

Synthesis and studies on Cu(II), Co(II), Ni(II) complexes of Knoevenagel β-diketone ligands

NASA Astrophysics Data System (ADS)

Sumathi, S.; Tharmaraj, P.; Sheela, C. D.; Anitha, C.

2012-11-01

Transition metal complexes of various acetylacetone based ligands of the type ML [where M = Cu(II), Ni(II), Co(II); L = 3-(aryl)-pentane-2,4-dione] have been synthesized. The structural features have been derived from their elemental analysis, magnetic susceptibility, molar conductance, IR, UV-Vis, 1H NMR, Mass and ESR spectral studies. Conductivity measurements reveal that all the complexes are non-electrolytic in nature. Spectroscopic and other analytical data of the complexes suggest octahedral geometry for other metal(II) complexes. The redox behavior of the copper(II) complexes have been studied by cyclic voltammetry. The free ligands and their metal complexes have been screened for their in vitro biological activities against the bacteria Pseudomonas aeruginosa, Escherichia coli and Staphylococcus aureus as well as the fungus Candida albicans by well diffusion method. The zone of inhibition value indicates that the most of the metal(II) complexes are found to possess increased activities compared to those of the free ligands. All synthesized compounds may serve as potential photoactive materials as indicated from their characteristic fluorescence properties. The second harmonic generation (SHG) efficiency of the ligands (L1-L3) was found to be considerable effect than that of urea and KDP (potassium dihydrogen phosphate).

Arbuscular mycorrhizal fungi make a complex contribution to soil aggregation

NASA Astrophysics Data System (ADS)

McGee, Peter; Daynes, Cathal; Damien, Field

2013-04-01

Soil aggregates contain solid and fluid components. Aggregates develop as a consequence of the organic materials, plants and hyphae of arbuscular mycorrhizal (AM) fungi acting on the solid phase. Various correlative studies indicate hyphae of AM fungi enmesh soil particles, but their impact on the pore space is poorly understood. Hyphae may penetrate between particles, remove water from interstitial spaces, and otherwise re-arrange the solid phase. Thus we might predict that AM fungi also change the pore architecture of aggregates. Direct observations of pore architecture of soil, such as by computer-aided tomography (CT), is difficult. The refractive natures of solid and biological material are similar. The plant-available water in various treatments allows us to infer changes in pore architecture. Our experimental studies indicate AM fungi have a complex role in the formation and development of aggregates. Soils formed from compost and coarse subsoil materials were planted with mycorrhizal or non-mycorrhizal seedlings and the resultant soils compared after 6 or 14 months in separate experiments. As well as enmeshing particles, AM fungi were associated with the development of a complex pore space and greater pore volume. Even though AM fungi add organic matter to soil, the modification of pore space is not correlated with organic carbon. In a separate study, we visualised hyphae of AM fungi in a coarse material using CT. In this study, hyphae appeared to grow close to the surfaces of particles with limited ramification across the pore spaces. Hyphae of AM fungi appear to utilise soil moisture for their growth and development of mycelium. The strong correlation between moisture and hyphae has profound implications for soil aggregation, plant utilisation of soil water, and the distribution of water as water availability declines.

Real-time, haptics-enabled simulator for probing ex vivo liver tissue.

PubMed

Lister, Kevin; Gao, Zhan; Desai, Jaydev P

2009-01-01

The advent of complex surgical procedures has driven the need for realistic surgical training simulators. Comprehensive simulators that provide realistic visual and haptic feedback during surgical tasks are required to familiarize surgeons with the procedures they are to perform. Complex organ geometry inherent to biological tissues and intricate material properties drive the need for finite element methods to assure accurate tissue displacement and force calculations. Advances in real-time finite element methods have not reached the state where they are applicable to soft tissue surgical simulation. Therefore a real-time, haptics-enabled simulator for probing of soft tissue has been developed which utilizes preprocessed finite element data (derived from accurate constitutive model of the soft-tissue obtained from carefully collected experimental data) to accurately replicate the probing task in real-time.

Ice Shaping Properties, Similar to That of Antifreeze Proteins, of a Zirconium Acetate Complex

PubMed Central

Deville, Sylvain; Viazzi, Céline; Leloup, Jérôme; Lasalle, Audrey; Guizard, Christian; Maire, Eric; Adrien, Jérôme; Gremillard, Laurent

2011-01-01

The control of the growth morphologies of ice crystals is a critical issue in fields as diverse as biomineralization, medicine, biology, civil or food engineering. Such control can be achieved through the ice-shaping properties of specific compounds. The development of synthetic ice-shaping compounds is inspired by the natural occurrence of such properties exhibited by antifreeze proteins. We reveal how a particular zirconium acetate complex is exhibiting ice-shaping properties very similar to that of antifreeze proteins, albeit being a radically different compound. We use these properties as a bioinspired approach to template unique faceted pores in cellular materials. These results suggest that ice-structuring properties are not exclusive to long organic molecules and should broaden the field of investigations and applications of such substances. PMID:22028886

Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour.

PubMed

Land, Sander; Gurev, Viatcheslav; Arens, Sander; Augustin, Christoph M; Baron, Lukas; Blake, Robert; Bradley, Chris; Castro, Sebastian; Crozier, Andrew; Favino, Marco; Fastl, Thomas E; Fritz, Thomas; Gao, Hao; Gizzi, Alessio; Griffith, Boyce E; Hurtado, Daniel E; Krause, Rolf; Luo, Xiaoyu; Nash, Martyn P; Pezzuto, Simone; Plank, Gernot; Rossi, Simone; Ruprecht, Daniel; Seemann, Gunnar; Smith, Nicolas P; Sundnes, Joakim; Rice, J Jeremy; Trayanova, Natalia; Wang, Dafang; Jenny Wang, Zhinuo; Niederer, Steven A

2015-12-08

Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.

Physico-Chemical Alternatives in Lignocellulosic Materials in Relation to the Kind of Component for Fermenting Purposes

PubMed Central

Coz, Alberto; Llano, Tamara; Cifrián, Eva; Viguri, Javier; Maican, Edmond; Sixta, Herbert

2016-01-01

The complete bioconversion of the carbohydrate fraction is of great importance for a lignocellulosic-based biorefinery. However, due to the structure of the lignocellulosic materials, and depending basically on the main parameters within the pretreatment steps, numerous byproducts are generated and they act as inhibitors in the fermentation operations. In this sense, the impact of inhibitory compounds derived from lignocellulosic materials is one of the major challenges for a sustainable biomass-to-biofuel and -bioproduct industry. In order to minimise the negative effects of these compounds, numerous methodologies have been tested including physical, chemical, and biological processes. The main physical and chemical treatments have been studied in this work in relation to the lignocellulosic material and the inhibitor in order to point out the best mechanisms for fermenting purposes. In addition, special attention has been made in the case of lignocellulosic hydrolysates obtained by chemical processes with SO2, due to the complex matrix of these materials and the increase in these methodologies in future biorefinery markets. Recommendations of different detoxification methods have been given. PMID:28773700

Method And System For Examining Biological Materials Using Low Power Cw Excitation Raman Spectroscopy.

DOEpatents

Alfano, Robert R.; Wang, Wubao

2000-11-21

A method and system for examining biological materials using low-power cw excitation Raman spectroscopy. In accordance with the teachings of the invention, a low-power continuous wave (cw) pump laser beam and a low-power cw Stokes (or anti-Stokes) probe laser beam simultaneously illuminate a biological material and traverse the biological material in collinearity. The pump beam, whose frequency is varied, is used to induce Raman emission from the biological material. The intensity of the probe beam, whose frequency is kept constant, is monitored as it leaves the biological material. When the difference between the pump and probe excitation frequencies is equal to a Raman vibrational mode frequency of the biological material, the weak probe signal becomes amplified by one or more orders of magnitude (typically up to about 10.sup.4 -10.sup.6) due to the Raman emission from the pump beam. In this manner, by monitoring the intensity of the probe beam emitted from the biological material as the pump beam is varied in frequency, one can obtain an excitation Raman spectrum for the biological material tested. The present invention may be applied to in the in vivo and/or in vitro diagnosis of diabetes, heart disease, hepatitis, cancers and other diseases by measuring the characteristic excitation Raman lines of blood glucose, cholesterol, serum glutamic oxalacetic transaminase (SGOT)/serum glutamic pyruvic tansaminase (SGPT), tissues and other corresponding Raman-active body constituents, respectively. For example, it may also be used to diagnose diseases associated with the concentration of Raman-active constituents in urine, lymph and saliva It may be used to identify cancer in the breast, cervix, uterus, ovaries and the like by measuring the fingerprint excitation Raman spectra of these tissues. It may also be used to reveal the growing of tumors or cancers by measuring the levels of nitric oxide in tissue.

Designing Biomimetic Materials from Marine Organisms.

PubMed

Nichols, William T

2015-01-01

Two biomimetic design approaches that apply biological solutions to engineering problems are discussed. In the first case, motivation comes from an engineering problem and the key challenge is to find analogous biological functions and map them into engineering materials. We illustrate with an example of water pollution remediation through appropriate design of a biomimetic sponge. In the second case, a biological function is already known and the challenge is to identify the appropriate engineering problem. We demonstrate the biological approach with marine diatoms that control energy and materials at their surface providing inspiration for a number of engineering applications. In both cases, it is essential to select materials and structures at the nanoscale to control energy and materials flows at interfaces.

A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6gc01147k Click here for additional data file.

PubMed Central

Grimm, Fabian A.; Iwata, Yasuhiro; Sirenko, Oksana; Chappell, Grace A.; Wright, Fred A.; Reif, David M.; Braisted, John; Gerhold, David L.; Yeakley, Joanne M.; Shepard, Peter; Seligmann, Bruce; Roy, Tim; Boogaard, Peter J.; Ketelslegers, Hans B.; Rohde, Arlean M.

2016-01-01

Comparative assessment of potential human health impacts is a critical step in evaluating both chemical alternatives and existing products on the market. Most alternatives assessments are conducted on a chemical-by-chemical basis and it is seldom acknowledged that humans are exposed to complex products, not individual substances. Indeed, substances of Unknown or Variable composition, Complex reaction products, and Biological materials (UVCBs) are ubiquitous in commerce yet they present a major challenge for registration and health assessments. Here, we present a comprehensive experimental and computational approach to categorize UVCBs according to global similarities in their bioactivity using a suite of in vitro models. We used petroleum substances, an important group of UVCBs which are grouped for regulatory approval and read-across primarily on physico-chemical properties and the manufacturing process, and only partially based on toxicity data, as a case study. We exposed induced pluripotent stem cell-derived cardiomyocytes and hepatocytes to DMSO-soluble extracts of 21 petroleum substances from five product groups. Concentration-response data from high-content imaging in cardiomyocytes and hepatocytes, as well as targeted high-throughput transcriptomic analysis of the hepatocytes, revealed distinct groups of petroleum substances. Data integration showed that bioactivity profiling affords clustering of petroleum substances in a manner similar to the manufacturing process-based categories. Moreover, we observed a high degree of correlation between bioactivity profiles and physico-chemical properties, as well as improved groupings when chemical and biological data were combined. Altogether, we demonstrate how novel in vitro screening approaches can be effectively utilized in combination with physico-chemical characteristics to group complex substances and enable read-across. This approach allows for rapid and scientifically-informed evaluation of health impacts of both existing substances and their chemical alternatives. PMID:28035192

Predicting clinical biological responses to dental materials.

PubMed

Wataha, John C

2012-01-01

Methods used to measure and predict clinical biological responses to dental materials remain controversial, confusing, and to some extent, unsuccessful. The current paper reviews significant issues surrounding how we assess the biological safety of materials, with a historical summary and critical look at the biocompatibility literature. The review frames these issues from a U.S. perspective to some degree, but emphasizes their global nature and universal importance. The PubMed database and information from the U.S. Food and Drug Administration, International Standards Organization, and American National Standards Institute were searched for prominent literature addressing the definition of biocompatibility, types of biological tests employed, regulatory and standardization issues, and how biological tests are used together to establish the biological safety of materials. The search encompassed articles published in English from approximately 1965-2011. The review does not comprehensively review the literature, but highlights significant issues that confront the field. Years ago, tests for biological safety sought to establish material inertness as the measure of safety, a criterion that is now deemed naive; the definition of biocompatibility has broadened along with the roles for materials in patient oral health care. Controversies persist about how in vitro or animal tests should be used to evaluate the biological safety of materials for clinical use. Controlled clinical trials remain the single best measure of the clinical response to materials, but even these tests have significant limitations and are less useful to identify mechanisms that shape material performance. Practice-based research networks and practitioner databases are emerging as important supplements to controlled clinical trials, but their final utility remains to be determined. Today we ask materials to play increasingly sophisticated structural and therapeutic roles in patient treatment. To accommodate these roles, strategies to assess, predict, and monitor material safety need to evolve. This evolution will be driven not only by researchers and manufacturers, but also by patients and practitioners, who want to use novel materials in new ways to treat oral disease. Copyright © 2011 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Major structural components in freshwater dissolved organic matter.

PubMed

Lam, Buuan; Baer, Andrew; Alaee, Mehran; Lefebvre, Brent; Moser, Arvin; Williams, Antony; Simpson, André J

2007-12-15

Dissolved organic matter (DOM) contains a complex array of chemical components that are intimately linked to many environmental processes, including the global carbon cycle, and the fate and transport of chemical pollutants. Despite its importance, fundamental aspects, such as the structural components in DOM remain elusive, due in part to the molecular complexity of the material. Here, we utilize multidimensional nuclear magnetic resonance spectroscopy to demonstrate the major structural components in Lake Ontario DOM. These include carboxyl-rich alicyclic molecules (CRAM), heteropolysaccharides, and aromatic compounds, which are consistent with components recently identified in marine dissolved organic matter. In addition, long-range proton-carbon correlations are obtained for DOM, which support the existence of material derived from linear terpenoids (MDLT). It is tentatively suggested that the bulk of freshwater dissolved organic matter is aliphatic in nature, with CRAM derived from cyclic terpenoids, and MDLT derived from linear terpenoids. This is in agreement with previous reports which indicate terpenoids as major precursors of DOM. At this time it is not clear in Lake Ontario whether these precursors are of terrestrial or aquatic origin or whether transformations proceed via biological and/ or photochemical processes.

Programming Cells for Dynamic Assembly of Inorganic Nano-Objects with Spatiotemporal Control.

PubMed

Wang, Xinyu; Pu, Jiahua; An, Bolin; Li, Yingfeng; Shang, Yuequn; Ning, Zhijun; Liu, Yi; Ba, Fang; Zhang, Jiaming; Zhong, Chao

2018-04-01

Programming living cells to organize inorganic nano-objects (NOs) in a spatiotemporally precise fashion would advance new techniques for creating ordered ensembles of NOs and new bio-abiotic hybrid materials with emerging functionalities. Bacterial cells often grow in cellular communities called biofilms. Here, a strategy is reported for programming dynamic biofilm formation for the synchronized assembly of discrete NOs or hetero-nanostructures on diverse interfaces in a dynamic, scalable, and hierarchical fashion. By engineering Escherichia coli to sense blue light and respond by producing biofilm curli fibers, biofilm formation is spatially controlled and the patterned NOs' assembly is simultaneously achieved. Diverse and complex fluorescent quantum dot patterns with a minimum patterning resolution of 100 µm are demonstrated. By temporally controlling the sequential addition of NOs into the culture, multilayered heterostructured thin films are fabricated through autonomous layer-by-layer assembly. It is demonstrated that biologically dynamic self-assembly can be used to advance a new repertoire of nanotechnologies and materials with increasing complexity that would be otherwise challenging to produce. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fiber optic-based biosensor

NASA Technical Reports Server (NTRS)

Ligler, Frances S.

1991-01-01

The NRL fiber optic biosensor is a device which measures the formation of a fluorescent complex at the surface of an optical fiber. Antibodies and DNA binding proteins provide the mechanism for recognizing an analyze and immobilizing a fluorescent complex on the fiber surface. The fiber optic biosensor is fast, sensitive, and permits analysis of hazardous materials remote from the instrumentation. The fiber optic biosensor is described in terms of the device configuration, chemistry for protein immobilization, and assay development. A lab version is being used for assay development and performance characterization while a portable device is under development. Antibodies coated on the fiber are stable for up to two years of storage prior to use. The fiber optic biosensor was used to measure concentration of toxins in the parts per billion (ng/ml) range in under a minute. Immunoassays for small molecules and whole bacteria are under development. Assays using DNA probes as the detection element can also be used with the fiber optic sensor, which is currently being developed to detect biological warfare agents, explosives, pathogens, and toxic materials which pollute the environment.

Smart Actuators and Adhesives for Reconfigurable Matter.

PubMed

Ko, Hyunhyub; Javey, Ali

2017-04-18

Biological systems found in nature provide excellent stimuli-responsive functions. The camouflage adaptation of cephalopods (octopus, cuttlefish), rapid stiffness change of sea cucumbers, opening of pine cones in response to humidity, and rapid closure of Venus flytraps upon insect touch are some examples of nature's smart systems. Although current technologies are still premature to mimic these sophisticated structures and functions in smart biological systems, recent work on stimuli-responsive programmable matter has shown great progress. Stimuli-responsive materials based on hydrogels, responsive nanocomposites, hybrid structures, shape memory polymers, and liquid crystal elastomers have demonstrated excellent responsivities to various stimuli such as temperature, light, pH, and electric field. However, the technologies in these stimuli-responsive materials are still not sophisticated enough to demonstrate the ultimate attributes of an ideal programmable matter: fast and reversible reconfiguration of programmable matter into complex and robust shapes. Recently, reconfigurable (or programmable) matter that reversibly changes its structure/shape or physical/chemical properties in response to external stimuli has attracted great interest for applications in sensors, actuators, robotics, and smart systems. In particular, key attributes of programmable matter including fast and reversible reconfiguration into complex and robust 2D and 3D shapes have been demonstrated by various approaches. In this Account, we review focused areas of smart materials with special emphasis on the material and device structure designs to enhance the response time, reversibility, multistimuli responsiveness, and smart adhesion for efficient shape transformation and functional actuations. First, the capability of fast reconfiguration of 2D and 3D structures in a reversible way is a critical requirement for programmable matter. For the fast and reversible reconfiguration, various approaches based on enhanced solvent diffusion rate through the porous or structured hydrogel materials, electrostatic repulsion between cofacial electrolyte nanosheets, and photothermal actuation are discussed. Second, the ability to reconfigure programmable matters into a variety of complex structures is beneficial for the use of reconfigurable matter in diverse applications. For the reconfiguration of planar 2D structures into complex 3D structures, asymmetric and multidirectional stress should be applied. In this regard, local hinges with stimuli-responsive stiffness, multilayer laminations with different responsiveness in individual layers, and origami and kirigami assembly approaches are reviewed. Third, multistimuli responsiveness will be required for the efficient reconfiguration of complex programmable matter in response to user-defined stimulus under different chemical and physical environments. In addition, with multistimuli responsiveness, the reconfigured shape can be temporarily affixed by one signal and disassembled by another signal at a user-defined location and time. Photoactuation depending on the chirality of carbon nanotubes and composite gels with different responsiveness will be discussed. Finally, the development of smart adhesives with on-demand adhesion strength is critically required to maintain the robust reconfigurable shapes and for the switching on/off of the binding between components or with target objects. Among various connectors and adhesives, thermoresponsive nanowire connectors, octopus-inspired smart adhesives, and elastomeric tiles with soft joints are described due to their potential applications in joints of deformable 3D structures and smart gripping systems.

Advances in three-dimensional rapid prototyping of microfluidic devices for biological applications

PubMed Central

O'Neill, P. F.; Ben Azouz, A.; Vázquez, M.; Liu, J.; Marczak, S.; Slouka, Z.; Chang, H. C.; Diamond, D.; Brabazon, D.

2014-01-01

The capability of 3D printing technologies for direct production of complex 3D structures in a single step has recently attracted an ever increasing interest within the field of microfluidics. Recently, ultrafast lasers have also allowed developing new methods for production of internal microfluidic channels within the bulk of glass and polymer materials by direct internal 3D laser writing. This review critically summarizes the latest advances in the production of microfluidic 3D structures by using 3D printing technologies and direct internal 3D laser writing fabrication methods. Current applications of these rapid prototyped microfluidic platforms in biology will be also discussed. These include imaging of cells and living organisms, electrochemical detection of viruses and neurotransmitters, and studies in drug transport and induced-release of adenosine triphosphate from erythrocytes. PMID:25538804

Crystallization Pathways in Biomineralization

NASA Astrophysics Data System (ADS)

Weiner, Steve; Addadi, Lia

2011-08-01

A crystallization pathway describes the movement of ions from their source to the final product. Cells are intimately involved in biological crystallization pathways. In many pathways the cells utilize a unique strategy: They temporarily concentrate ions in intracellular membrane-bound vesicles in the form of a highly disordered solid phase. This phase is then transported to the final mineralization site, where it is destabilized and crystallizes. We present four case studies, each of which demonstrates specific aspects of biological crystallization pathways: seawater uptake by foraminifera, calcite spicule formation by sea urchin larvae, goethite formation in the teeth of limpets, and guanine crystal formation in fish skin and spider cuticles. Three representative crystallization pathways are described, and aspects of the different stages of crystallization are discussed. An in-depth understanding of these complex processes can lead to new ideas for synthetic crystallization processes of interest to materials science.

Numerical FEM modeling in dental implantology

NASA Astrophysics Data System (ADS)

Roateşi, Iulia; Roateşi, Simona

2016-06-01

This paper is devoted to a numerical approach of the stress and displacement calculation of a system made up of dental implant, ceramic crown and surrounding bone. This is the simulation of a clinical situation involving both biological - the bone tissue, and non-biological - the implant and the crown, materials. On the other hand this problem deals with quite fine technical structure details - the threads, tapers, etc with a great impact in masticatory force transmission. Modeling the contact between the implant and the bone tissue is important to a proper bone-implant interface model and implant design. The authors proposed a three-dimensional numerical model to assess the biomechanical behaviour of this complex structure in order to evaluate its stability by determining the risk zones. A comparison between this numerical analysis and clinical cases is performed and a good agreement is obtained.

Describing the complexity of systems: multivariable "set complexity" and the information basis of systems biology.

PubMed

Galas, David J; Sakhanenko, Nikita A; Skupin, Alexander; Ignac, Tomasz

2014-02-01

Context dependence is central to the description of complexity. Keying on the pairwise definition of "set complexity," we use an information theory approach to formulate general measures of systems complexity. We examine the properties of multivariable dependency starting with the concept of interaction information. We then present a new measure for unbiased detection of multivariable dependency, "differential interaction information." This quantity for two variables reduces to the pairwise "set complexity" previously proposed as a context-dependent measure of information in biological systems. We generalize it here to an arbitrary number of variables. Critical limiting properties of the "differential interaction information" are key to the generalization. This measure extends previous ideas about biological information and provides a more sophisticated basis for the study of complexity. The properties of "differential interaction information" also suggest new approaches to data analysis. Given a data set of system measurements, differential interaction information can provide a measure of collective dependence, which can be represented in hypergraphs describing complex system interaction patterns. We investigate this kind of analysis using simulated data sets. The conjoining of a generalized set complexity measure, multivariable dependency analysis, and hypergraphs is our central result. While our focus is on complex biological systems, our results are applicable to any complex system.

Issues In Space Radiation Protection: Galactic Cosmic Rays

NASA Technical Reports Server (NTRS)

Wilson, J. W.; Kim, M.; Schimmerling, W.; Badavi, F. F.; Thibeault, S. A.; Cucinotta, F. A.; Shinn, J. L.; Kiefer, R.

1995-01-01

When shielding from cosmic heavy ions, one is faced with limited knowledge about the physical properties and biological responses of these radiations. Herein, the current health is discussed in terms of conventional protection practice and a test biological response model. The impact of biological response on optimum materials selection for cosmic ray shielding is presented in terms of the transmission characteristics of the shield material. Although liquid hydrogen is an optimum shield material, evaluation of the effectiveness of polymeric structural materials must await improvement in our knowledge of both the biological response and the nuclear processes.

Hidden biodiversity in entomological collections: The overlooked co-occurrence of dipteran and hymenopteran ant parasitoids in stored biological material

PubMed Central

Pérez-Lachaud, Gabriela

2017-01-01

Biological collections around the world are the repository of biodiversity on Earth; they also hold a large quantity of unsorted, unidentified, or misidentified material and can house behavioral information on species that are difficult to access or no longer available to science. Among the unsorted, alcohol-preserved material stored in the Formicidae Collection of the ‘El Colegio de la Frontera Sur’ Research Center (Chetumal, Mexico), we found nine colonies of the ponerine ant Neoponera villosa, that had been collected in bromeliads at Calakmul (Campeche, Mexico) in 1999. Ants and their brood were revised for the presence of any sign of parasitism. Cocoons were dissected and their content examined under a stereomicroscope. Six N. villosa prepupae had been attacked by the ectoparasitoid syrphid fly Hypselosyrphus trigonus Hull (Syrphidae: Microdontinae), to date the only known dipteran species of the Microdontinae with a parasitoid lifestyle. In addition, six male pupae from three colonies contained gregarious endoparasitoid wasps. These were specialized in parasitizing this specific host caste as no gyne or worker pupae displayed signs of having been attacked. Only immature stages (larvae and pupae) of the wasp could be obtained. Due to the long storage period, DNA amplification failed; however, based on biological and morphological data, pupae were placed in the Encyrtidae family. This is the first record of an encyrtid wasp parasitizing N. villosa, and the second example of an encyrtid as a primary parasitoid of ants. Furthermore, it is also the first record of co-occurrence of a dipteran ectoparasitoid and a hymenopteran endoparasitoid living in sympatry within the same population of host ants. Our findings highlight the importance of biological collections as reservoirs of hidden biodiversity, not only at the taxonomic level, but also at the behavioral level, revealing complex living networks. They also highlight the need for funding in order to carry out biodiversity inventories and manage existing collections. PMID:28926617

Hidden biodiversity in entomological collections: The overlooked co-occurrence of dipteran and hymenopteran ant parasitoids in stored biological material.

PubMed

Pérez-Lachaud, Gabriela; Lachaud, Jean-Paul

2017-01-01

Biological collections around the world are the repository of biodiversity on Earth; they also hold a large quantity of unsorted, unidentified, or misidentified material and can house behavioral information on species that are difficult to access or no longer available to science. Among the unsorted, alcohol-preserved material stored in the Formicidae Collection of the 'El Colegio de la Frontera Sur' Research Center (Chetumal, Mexico), we found nine colonies of the ponerine ant Neoponera villosa, that had been collected in bromeliads at Calakmul (Campeche, Mexico) in 1999. Ants and their brood were revised for the presence of any sign of parasitism. Cocoons were dissected and their content examined under a stereomicroscope. Six N. villosa prepupae had been attacked by the ectoparasitoid syrphid fly Hypselosyrphus trigonus Hull (Syrphidae: Microdontinae), to date the only known dipteran species of the Microdontinae with a parasitoid lifestyle. In addition, six male pupae from three colonies contained gregarious endoparasitoid wasps. These were specialized in parasitizing this specific host caste as no gyne or worker pupae displayed signs of having been attacked. Only immature stages (larvae and pupae) of the wasp could be obtained. Due to the long storage period, DNA amplification failed; however, based on biological and morphological data, pupae were placed in the Encyrtidae family. This is the first record of an encyrtid wasp parasitizing N. villosa, and the second example of an encyrtid as a primary parasitoid of ants. Furthermore, it is also the first record of co-occurrence of a dipteran ectoparasitoid and a hymenopteran endoparasitoid living in sympatry within the same population of host ants. Our findings highlight the importance of biological collections as reservoirs of hidden biodiversity, not only at the taxonomic level, but also at the behavioral level, revealing complex living networks. They also highlight the need for funding in order to carry out biodiversity inventories and manage existing collections.

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

Atom Probe Tomographic Analysis of Biological Systems Enabled by Advanced Specimen Preparation Approaches

NASA Astrophysics Data System (ADS)

Perea, D. E.; Evans, J. E.

2017-12-01

The ability to image biointerfaces over nanometer to micrometer length scales is fundamental to correlating biological composition and structure to physiological function, and is aided by a multimodal approach using advanced complementary microscopic and spectroscopic characterization techniques. Atom Probe Tomography (APT) is a rapidly expanding technique for atomic-scale three-dimensional structural and chemical analysis. However, the regular application of APT to soft biological materials is lacking in large part due to difficulties in specimen preparation and inabilities to yield meaningful tomographic reconstructions that produce atomic scale compositional distributions as no other technique currently can. Here we describe the atomic-scale tomographic analysis of biological materials using APT that is facilitated by an advanced focused ion beam based approach. A novel specimen preparation strategy is used in the analysis of horse spleen ferritin protein embedded in an organic polymer resin which provides chemical contrast to distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell of the ferritin protein. One-dimensional composition profiles directly reveal an enhanced concentration of P and Na at the surface of the ferrihydrite mineral core. We will also describe the development of a unique multifunctional environmental transfer hub allowing controlled cryogenic transfer of specimens under vacuum pressure conditions between an Atom Probe and cryo-FIB/SEM. The utility of the environmental transfer hub is demonstrated through the acquisition of previously unavailable mass spectral analysis of an intact organometallic molecule made possible via controlled cryogenic transfer. The results demonstrate a viable application of APT analysis to study complex biological organic/inorganic interfaces relevant to energy and the environment. References D.E. Perea et al. An environmental transfer hub for multimodal atom probe tomography, Adv. Struct. Chem. Imag, 2017, 3:12 The research was performed at the Environmental Molecular Sciences Laboratory; a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research located at Pacific Northwest National Laboratory.

Anal Sphincter Augmentation Using Biological Material.

PubMed

Alam, Nasra N; Narang, Sunil K; Köckerling, Ferdinand; Daniels, Ian R; Smart, Neil J

2015-01-01

The aim of this review is to provide an overview of the use of biological materials in the augmentation of the anal sphincter either as part of an overlapping sphincter repair (OSR) or anal bulking procedure. A systematic search of PubMed was conducted using the search terms "anal bulking agents," "anal sphincter repair," or "overlapping sphincter repair." Five studies using biological material as part of an overlapping sphincter repair (OSR) or as an anal bulking agent were identified. 122 patients underwent anal bulking with a biological material. Anorectal physiology was conducted in 27 patients and demonstrated deterioration in maximum resting pressure, and no significant change in maximum squeeze increment. Quality of life scores (QoLs) demonstrated improvements at 6 weeks and 6 months, but this had deteriorated at 12 months of follow up. Biological material was used in 23 patients to carry out an anal encirclement procedure. Improvements in QoLs were observed in patients undergoing OSR as well as anal encirclement using biological material. Incontinence episodes decreased to an average of one per week from 8 to 10 preoperatively. Sphincter encirclement with biological material has demonstrated improvements in continence and QoLs in the short term compared to traditional repair alone. Long-term studies are necessary to determine if this effect is sustained. As an anal bulking agent the benefits are short-term.

Structure and mechanics of aegagropilae fiber network.

PubMed

Verhille, Gautier; Moulinet, Sébastien; Vandenberghe, Nicolas; Adda-Bedia, Mokhtar; Le Gal, Patrice

2017-05-02

Fiber networks encompass a wide range of natural and manmade materials. The threads or filaments from which they are formed span a wide range of length scales: from nanometers, as in biological tissues and bundles of carbon nanotubes, to millimeters, as in paper and insulation materials. The mechanical and thermal behavior of these complex structures depends on both the individual response of the constituent fibers and the density and degree of entanglement of the network. A question of paramount importance is how to control the formation of a given fiber network to optimize a desired function. The study of fiber clustering of natural flocs could be useful for improving fabrication processes, such as in the paper and textile industries. Here, we use the example of aegagropilae that are the remains of a seagrass ( Posidonia oceanica ) found on Mediterranean beaches. First, we characterize different aspects of their structure and mechanical response, and second, we draw conclusions on their formation process. We show that these natural aggregates are formed in open sea by random aggregation and compaction of fibers held together by friction forces. Although formed in a natural environment, thus under relatively unconstrained conditions, the geometrical and mechanical properties of the resulting fiber aggregates are quite robust. This study opens perspectives for manufacturing complex fiber network materials.

Low temperature hydrothermal oil and associated biological precursors in serpentinites from Mid-Ocean Ridge

NASA Astrophysics Data System (ADS)

Pasini, Valerio; Brunelli, Daniele; Dumas, Paul; Sandt, Christophe; Frederick, Joni; Benzerara, Karim; Bernard, Sylvain; Ménez, Bénédicte

2013-09-01

The origin of light hydrocarbons discovered at serpentinite-hosted mid-ocean hydrothermal fields is generally attributed to the abiogenic reduction of carbon (di)oxide by molecular hydrogen released during the progressive hydration of mantle-derived peridotites. These serpentinization by-products represent a valuable source of carbon and energy and are known to support deep microbial ecosystems unrelated to photosynthesis. In addition, the pool of subsurface organic compounds could also include materials derived from the thermal degradation of biological material. We re-investigate the recently described relics of deep microbial ecosystems hosted in serpentinites of the Mid-Atlantic Ridge (4-6°N) in order to study the ageing and (hydro)thermal degradation of the preserved biomass. An integrated set of high resolution micro-imaging techniques (Scanning Electron Microscopy, High Resolution Transmission Electron Microscopy, Raman and Fourier Transform Infra-Red microspectroscopy, Confocal Laser Scanning Microscopy, and Scanning Transmission X-ray Microscopy at the carbon K-edge) has been applied to map the distribution of the different organic components at the micrometer scale and to characterize their speciation and structure. We show that biologically-derived material, containing aliphatic groups, along with carbonyl and amide functional groups, has experienced hydrothermal degradation and slight aromatization. In addition, aliphatic compounds up to C6-C10 with associated carboxylic functional groups wet the host bastite and the late serpentine veins crosscutting the rock. These compounds represent a light soluble organic fraction expelled after biomass degradation through oxidation and thermal cracking. The detected complex organic matter distribution recalls a typical petroleum system, where fossil organic matter of biological origin maturates, expelling the soluble fraction which then migrates from the source to the reservoir. Ecosystem-hosting serpentinites can thus be seen as source rocks generating a net transfer of hydrocarbons and/or fatty acids issued from oxidative processes and primary cracking reactions, then migrating upward through the serpentine vein network. This finally suggests that deep thermogenic organic compounds of biological origin can be a significant contributor to the organic carbon balance at and far below peridotite-hosted hydrothermal fields.

Supramolecular Biofunctional Materials

PubMed Central

Zhou, Jie; Li, Jie; Du, Xuewen; Xu, Bing

2017-01-01

This review discusses supramolecular biofunctional materials, a novel class of biomaterials formed by small molecules that are held together via noncovalent interactions. The complexity of biology and relevant biomedical problems not only inspire, but also demand effective molecular design for functional materials. Supramolecular biofunctional materials offer (almost) unlimited possibilities and opportunities to address challenging biomedical problems. Rational molecular design of supramolecular biofunctional materials exploit powerful and versatile noncovalent interactions, which offer many advantages, such as responsiveness, reversibility, tunability, biomimicry, modularity, predictability, and, most importantly, adaptiveness. In this review, besides elaborating on the merits of supramolecular biofunctional materials (mainly in the form of hydrogels and/or nanoscale assemblies) resulting from noncovalent interactions, we also discuss the advantages of small peptides as a prevalent molecular platform to generate a wide range of supramolecular biofunctional materials for the applications in drug delivery, tissue engineering, immunology, cancer therapy, fluorescent imaging, and stem cell regulation. This review aims to provide a brief synopsis of recent achievements at the intersection of supramolecular chemistry and biomedical science in hope of contributing to the multidisciplinary research on supramolecular biofunctional materials for a wide range of applications. We envision that supramolecular biofunctional materials will contribute to the development of new therapies that will ultimately lead to a paradigm shift for developing next generation biomaterials for medicine. PMID:28319779

Supramolecular biofunctional materials.

PubMed

Zhou, Jie; Li, Jie; Du, Xuewen; Xu, Bing

2017-06-01

This review discusses supramolecular biofunctional materials, a novel class of biomaterials formed by small molecules that are held together via noncovalent interactions. The complexity of biology and relevant biomedical problems not only inspire, but also demand effective molecular design for functional materials. Supramolecular biofunctional materials offer (almost) unlimited possibilities and opportunities to address challenging biomedical problems. Rational molecular design of supramolecular biofunctional materials exploit powerful and versatile noncovalent interactions, which offer many advantages, such as responsiveness, reversibility, tunability, biomimicry, modularity, predictability, and, most importantly, adaptiveness. In this review, besides elaborating on the merits of supramolecular biofunctional materials (mainly in the form of hydrogels and/or nanoscale assemblies) resulting from noncovalent interactions, we also discuss the advantages of small peptides as a prevalent molecular platform to generate a wide range of supramolecular biofunctional materials for the applications in drug delivery, tissue engineering, immunology, cancer therapy, fluorescent imaging, and stem cell regulation. This review aims to provide a brief synopsis of recent achievements at the intersection of supramolecular chemistry and biomedical science in hope of contributing to the multidisciplinary research on supramolecular biofunctional materials for a wide range of applications. We envision that supramolecular biofunctional materials will contribute to the development of new therapies that will ultimately lead to a paradigm shift for developing next generation biomaterials for medicine. Copyright © 2017 Elsevier Ltd. All rights reserved.

An outlook review: mechanochromic materials and their potential for biological and healthcare applications.

PubMed

Jiang, Ying

2014-12-01

Macroscopic mechanical perturbations have been observed to result in optical changes for certain compounds and composite materials. This phenomenon could originate from chemical and physical changes across various length scales, from the rearrangement of chemical bonds to alteration of molecular domains on the order of several hundred nanometers. This review classifies the mechanisms and surveys of how each class of mechanochromic materials has been, and can potentially be applied in biological and healthcare innovations. The study of cellular and molecular responses to mechanical forces in biological systems is an emerging field; there is potential in applying mechanochromic principles and material systems for probing biological systems. On the other hand, application of mechanochromic materials for medical and healthcare consumer products has been described in a wide variety of concepts and inventions. It is hopeful that further understanding of mechanochromism and material innovations would initiate concrete, impactful studies in biological systems soon. Copyright © 2014 Elsevier B.V. All rights reserved.

Near-Infrared Fluorescent Materials for Sensing of Biological Targets

PubMed Central

Amiot, Carrie L.; Xu, Shuping; Liang, Song; Pan, Lingyun; Zhao, Julia Xiaojun

2008-01-01

Near-infrared fluorescent (NIRF) materials are promising labeling reagents for sensitive determination and imaging of biological targets. In the near-infrared region biological samples have low background fluorescence signals, providing high signal to noise ratio. Meanwhile, near-infrared radiation can penetrate into sample matrices deeply due to low light scattering. Thus, in vivo and in vitro imaging of biological samples can be achieved by employing the NIRF probes. To take full advantage of NIRF materials in the biological and biomedical field, one of the key issues is to develop intense and biocompatible NIRF probes. In this review, a number of NIRF materials are discussed including traditional NIRF dye molecules, newly developed NIRF quantum dots and single-walled carbon nanotubes, as well as rare earth metal compounds. The use of some NIRF materials in various nanostructures is illustrated. The enhancement of NIRF using metal nanostructures is covered as well. The fluorescence mechanism and bioapplications of each type of the NIRF materials are discussed in details. PMID:27879867

Connecting drug delivery reality to smart materials design.

PubMed

Grainger, David W

2013-09-15

Inflated claims to both design and mechanistic novelty in drug delivery and imaging systems, including most nanotechnologies, are not supported by the generally poor translation of these systems to clinical efficacy. The "form begets function" design paradigm is seductive but perhaps over-simplistic in translation to pharmaceutical efficacy. Most innovations show few clinically important distinctions in their therapeutic benefits in relevant preclinical disease and delivery models, despite frequent claims to the contrary. Long-standing challenges in drug delivery issues must enlist more realistic, back-to-basics approaches to address fundamental materials properties in complex biological systems, preclinical test beds, and analytical methods to more reliably determine fundamental pharmaceutical figures of merit, including drug carrier purity and batch-batch variability, agent biodistribution, therapeutic index (safety), and efficacy. Copyright © 2013 Elsevier B.V. All rights reserved.

[Ru(bipy)3]2+ nanoparticle-incorporate dental light cure resin to promote photobiomodulation therapy for enhanced vital pulp tissue repair

NASA Astrophysics Data System (ADS)

Mosca, Rodrigo C.; Young, Nicholas; Zeituni, Carlos A.; Arany, Praveen R.

2018-02-01

The use of nanoparticle on dental light cure resin is not new, currently several compounds (nanoadditives) are used to promote better communication between the restorative material and biological tissues. The interest for this application is growing up to enhance mechanical proprieties to dental tissue cells regeneration. Bioactive nanoparticles and complex compounds with multiple functions are the major target for optimizing the restorative materials. In this work, we incorporate [Ru(bipy)3]2+ nanoparticles, that absorbs energy at 450 nm (blue-light) and emits strongly at 620 nm (red-light), in PLGA Microspheres and insert it in Dental Light Cure Resin to promote the Photobiomodulation Therapy (PBM) effects to accelerate dental pulp repair by in vitro using cytotoxicity and proliferation assay.

Self-Assembly of Hierarchical DNA Nanotube Architectures with Well-Defined Geometries.

PubMed

Jorgenson, Tyler D; Mohammed, Abdul M; Agrawal, Deepak K; Schulman, Rebecca

2017-02-28

An essential motif for the assembly of biological materials such as actin at the scale of hundreds of nanometers and beyond is a network of one-dimensional fibers with well-defined geometry. Here, we demonstrate the programmed organization of DNA filaments into micron-scale architectures where component filaments are oriented at preprogrammed angles. We assemble L-, T-, and Y-shaped DNA origami junctions that nucleate two or three micron length DNA nanotubes at high yields. The angles between the nanotubes mirror the angles between the templates on the junctions, demonstrating that nanoscale structures can control precisely how micron-scale architectures form. The ability to precisely program filament orientation could allow the assembly of complex filament architectures in two and three dimensions, including circuit structures, bundles, and extended materials.

Recent advances in pericentriolar material organization: ordered layers and scaffolding gels.

PubMed

Fry, Andrew M; Sampson, Josephina; Shak, Caroline; Shackleton, Sue

2017-01-01

The centrosome is an unusual organelle that lacks a surrounding membrane, raising the question of what limits its size and shape. Moreover, while electron microscopy (EM) has provided a detailed view of centriole architecture, there has been limited understanding of how the second major component of centrosomes, the pericentriolar material (PCM), is organized. Here, we summarize exciting recent findings from super-resolution fluorescence imaging, structural biology, and biochemical reconstitution that together reveal the presence of ordered layers and complex gel-like scaffolds in the PCM. Moreover, we discuss how this is leading to a better understanding of the process of microtubule nucleation, how alterations in PCM size are regulated in cycling and differentiated cells, and why mutations in PCM components lead to specific human pathologies.

Recent advances in pericentriolar material organization: ordered layers and scaffolding gels

PubMed Central

Fry, Andrew M.; Sampson, Josephina; Shak, Caroline; Shackleton, Sue

2017-01-01

The centrosome is an unusual organelle that lacks a surrounding membrane, raising the question of what limits its size and shape. Moreover, while electron microscopy (EM) has provided a detailed view of centriole architecture, there has been limited understanding of how the second major component of centrosomes, the pericentriolar material (PCM), is organized. Here, we summarize exciting recent findings from super-resolution fluorescence imaging, structural biology, and biochemical reconstitution that together reveal the presence of ordered layers and complex gel-like scaffolds in the PCM. Moreover, we discuss how this is leading to a better understanding of the process of microtubule nucleation, how alterations in PCM size are regulated in cycling and differentiated cells, and why mutations in PCM components lead to specific human pathologies. PMID:29026530

Physicochemical characterization of modified clay based composites obtained by a novel method

NASA Astrophysics Data System (ADS)

Kalra, Swati; Dudi, D.; Singh, G. P.; Verma, S. K.; Bhojak, N.

2018-05-01

Material science is one of the important fields where, absorption spectra of lanthanide ions have been a subject of several investigations because of their possible use as laser materials, diagnostic tools and sensors. Study of absorption spectra in visible and near infrared regions yields useful information regarding energy and intensity parameters, and nature and probabilities of transitions. Chemical physics provides fundamental tool to develop lanthanide chemistry, which has been increasingly significant in the last few years due to the wide variety of potential applications of their complexes in many important areas of biology and medicines. The present work describes the development of a novel method of composite preparation based on clay and its physiochemical characterization. Simultaneous measurement of some thermal properties has made study more useful. Results match with accepted models.

Deciphering the Complex Chemistry of Deep-Ocean Particles Using Complementary Synchrotron X-ray Microscope and Microprobe Instruments.

PubMed

Toner, Brandy M; German, Christopher R; Dick, Gregory J; Breier, John A

2016-01-19

The reactivity and mobility of natural particles in aquatic systems have wide ranging implications for the functioning of Earth surface systems. Particles in the ocean are biologically and chemically reactive, mobile, and complex in composition. The chemical composition of marine particles is thought to be central to understanding processes that convert globally relevant elements, such as C and Fe, among forms with varying bioavailability and mobility in the ocean. The analytical tools needed to measure the complex chemistry of natural particles are the subject of this Account. We describe how a suite of complementary synchrotron radiation instruments with nano- and micrometer focusing, and X-ray absorption spectroscopy (XAS) and X-ray diffraction (XRD) capabilities are changing our understanding of deep-ocean chemistry and life. Submarine venting along mid-ocean ridges creates hydrothermal plumes where dynamic particle-forming reactions occur as vent fluids mix with deep-ocean waters. Whether plumes are net sources or sinks of elements in ocean budgets depends in large part on particle formation, reactivity, and transport properties. Hydrothermal plume particles have been shown to host microbial communities and exhibit complex size distributions, aggregation behavior, and composition. X-ray microscope and microprobe instruments can address particle size and aggregation, but their true strength is in measuring chemical composition. Plume particles comprise a stunning array of inorganic and organic phases, from single-crystal sulfides to poorly ordered nanophases and polymeric organic matrices to microbial cells. X-ray microscopes and X-ray microprobes with elemental imaging, XAS, and XRD capabilities are ideal for investigating these complex materials because they can (1) measure the chemistry of organic and inorganic constituents in complex matrices, usually within the same particle or aggregate, (2) provide strong signal-to-noise data with exceedingly small amounts of material, (3) simplify the chemical complexity of particles or sets of particles with a focused-beam, providing spatial resolution over 6 orders of magnitude (nanometer to millimeter), (4) provide elemental specificity for elements in the soft-, tender-, and hard-X-ray energies, (5) switch rapidly among elements of interest, and (6) function in the presence of water and gases. Synchrotron derived data sets are discussed in the context of important advances in deep-ocean technology, sample handling and preservation, molecular microbiology, and coupled physical-chemical-biological modeling. Particle chemistry, size, and morphology are all important in determining whether particles are reactive with dissolved constituents, provide substrates for microbial respiration and growth, and are delivered to marine sediments or dispersed by deep-ocean currents.

The DNA Triangle and Its Application to Learning Meiosis

PubMed Central

Wright, L. Kate; Catavero, Christina M.; Newman, Dina L.

2017-01-01

Although instruction on meiosis is repeated many times during the undergraduate curriculum, many students show poor comprehension even as upper-level biology majors. We propose that the difficulty lies in the complexity of understanding DNA, which we explain through a new model, the DNA triangle. The DNA triangle integrates three distinct scales at which one can think about DNA: chromosomal, molecular, and informational. Through analysis of interview and survey data from biology faculty and students through the lens of the DNA triangle, we illustrate important differences in how novices and experts are able to explain the concepts of ploidy, homology, and mechanism of homologous pairing. Similarly, analysis of passages from 16 different biology textbooks shows a large divide between introductory and advanced material, with introductory books omitting explanations of meiosis-linked concepts at the molecular level of DNA. Finally, backed by textbook findings and feedback from biology experts, we show that the DNA triangle can be applied to teaching and learning meiosis. By applying the DNA triangle to topics on meiosis we present a new framework for educators and researchers that ties concepts of ploidy, homology, and mechanism of homologous pairing to knowledge about DNA on the chromosomal, molecular, and informational levels. PMID:28798212

Radiation effects in concrete for nuclear power plants Part I: Quantification of radiation exposure and radiation effects

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

Field, Kevin G; Pape, Yann Le; Remec, Igor

A large fraction of light water reactor (LWR) construction utilizes concrete, including safety-related structures such as the biological shielding and containment building. Concrete is an inherently complex material, with the properties of concrete structures changing over their lifetime due to the intrinsic nature of concrete and influences from local environment. As concrete structures within LWRs age, the total neutron fluence exposure of the components, in particular the biological shield, can increase to levels where deleterious effects are introduced as a result of neutron irradiation. This work summarizes the current state of the art on irradiated concrete, including a review ofmore » the current literature and estimates the total neutron fluence expected in biological shields in typical LWR configurations. It was found a first-order mechanism for loss of mechanical properties of irradiated concrete is due to radiation-induced swelling of aggregates, which leads to volumetric expansion of the concrete. This phenomena is estimated to occur near the end of life of biological shield components in LWRs based on calculations of estimated peak neutron fluence in the shield after 80 years of operation.« less

Functionalized apertures for the detection of chemical and biological materials

DOEpatents

Letant, Sonia E.; van Buuren, Anthony W.; Terminello, Louis J.; Thelen, Michael P.; Hope-Weeks, Louisa J.; Hart, Bradley R.

2010-12-14

Disclosed are nanometer to micron scale functionalized apertures constructed on a substrate made of glass, carbon, semiconductors or polymeric materials that allow for the real time detection of biological materials or chemical moieties. Many apertures can exist on one substrate allowing for the simultaneous detection of numerous chemical and biological molecules. One embodiment features a macrocyclic ring attached to cross-linkers, wherein the macrocyclic ring has a biological or chemical probe extending through the aperture. Another embodiment achieves functionalization by attaching chemical or biological anchors directly to the walls of the apertures via cross-linkers.

Integrative Bioengineering Institute

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

Eddington, David; Magin,L,Richard; Hetling, John

2009-01-09

Microfabrication enables many exciting experimental possibilities for medicine and biology that are not attainable through traditional methods. However, in order for microfabricated devices to have an impact they must not only provide a robust solution to a current unmet need, but also be simple enough to seamlessly integrate into standard protocols. Broad dissemination of bioMEMS has been stymied by the common aim of replacing established and well accepted protocols with equally or more complex devices, methods, or materials. The marriage of a complex, difficult to fabricate bioMEMS device with a highly variable biological system is rarely successful. Instead, the designmore » philosophy of my lab aims to leverage a beneficial microscale phenomena (e.g. fast diffusion at the microscale) within a bioMEMS device and adapt to established methods (e.g. multiwell plate cell culture) and demonstrate a new paradigm for the field (adapt instead of replace). In order for the field of bioMEMS to mature beyond novel proof-of-concept demonstrations, researchers must focus on developing systems leveraging these phenomena and integrating into standard labs, which have largely been ignored. Towards this aim, the Integrative Bioengineering Institute has been established.« less

Contributions of 3D Cell Cultures for Cancer Research.

PubMed

Ravi, Maddaly; Ramesh, Aarthi; Pattabhi, Aishwarya

2017-10-01

Cancer cell lines have contributed immensely in understanding the complex physiology of cancers. They are excellent material for studies as they offer homogenous samples without individual variations and can be utilised with ease and flexibility. Also, the number of assays and end-points one can study is almost limitless; with the advantage of improvising, modifying or altering several variables and methods. Literally, a new dimension to cancer research has been achieved by the advent of 3Dimensional (3D) cell culture techniques. This approach increased many folds the ways in which cancer cell lines can be utilised for understanding complex cancer biology. 3D cell culture techniques are now the preferred way of using cancer cell lines to bridge the gap between the 'absolute in vitro' and 'true in vivo'. The aspects of cancer biology that 3D cell culture systems have contributed include morphology, microenvironment, gene and protein expression, invasion/migration/metastasis, angiogenesis, tumour metabolism and drug discovery, testing chemotherapeutic agents, adaptive responses and cancer stem cells. We present here, a comprehensive review on the applications of 3D cell culture systems for these aspects of cancers. J. Cell. Physiol. 232: 2679-2697, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Change in Stripes for Cholesteric Shells via Anchoring in Moderation

NASA Astrophysics Data System (ADS)

Tran, Lisa; Lavrentovich, Maxim O.; Durey, Guillaume; Darmon, Alexandre; Haase, Martin F.; Li, Ningwei; Lee, Daeyeon; Stebe, Kathleen J.; Kamien, Randall D.; Lopez-Leon, Teresa

2017-10-01

Chirality, ubiquitous in complex biological systems, can be controlled and quantified in synthetic materials such as cholesteric liquid crystal (CLC) systems. In this work, we study spherical shells of CLC under weak anchoring conditions. We induce anchoring transitions at the inner and outer boundaries using two independent methods: by changing the surfactant concentration or by raising the temperature close to the clearing point. The shell confinement leads to new states and associated surface structures: a state where large stripes on the shell can be filled with smaller, perpendicular substripes, and a focal conic domain (FCD) state, where thin stripes wrap into at least two, topologically required, double spirals. Focusing on the latter state, we use a Landau-de Gennes model of the CLC to simulate its detailed configurations as a function of anchoring strength. By abruptly changing the topological constraints on the shell, we are able to study the interconversion between director defects and pitch defects, a phenomenon usually restricted by the complexity of the cholesteric phase. This work extends the knowledge of cholesteric patterns, structures that not only have potential for use as intricate, self-assembly blueprints but are also pervasive in biological systems.

Chromatographic analysis of tryptophan metabolites

PubMed Central

Sadok, Ilona; Gamian, Andrzej

2017-01-01

The kynurenine pathway generates multiple tryptophan metabolites called collectively kynurenines and leads to formation of the enzyme cofactor nicotinamide adenine dinucleotide. The first step in this pathway is tryptophan degradation, initiated by the rate‐limiting enzymes indoleamine 2,3‐dioxygenase, or tryptophan 2,3‐dioxygenase, depending on the tissue. The balanced kynurenine metabolism, which has been a subject of multiple studies in last decades, plays an important role in several physiological and pathological conditions such as infections, autoimmunity, neurological disorders, cancer, cataracts, as well as pregnancy. Understanding the regulation of tryptophan depletion provide novel diagnostic and treatment opportunities, however it requires reliable methods for quantification of kynurenines in biological samples with complex composition (body fluids, tissues, or cells). Trace concentrations, interference of sample components, and instability of some tryptophan metabolites need to be addressed using analytical methods. The novel separation approaches and optimized extraction protocols help to overcome difficulties in analyzing kynurenines within the complex tissue material. Recent developments in chromatography coupled with mass spectrometry provide new opportunity for quantification of tryptophan and its degradation products in various biological samples. In this review, we present current accomplishments in the chromatographic methodologies proposed for detection of tryptophan metabolites and provide a guide for choosing the optimal approach. PMID:28590049

Profile of High School Students’ Propositional Network Representation when Interpreting Convention Diagrams

NASA Astrophysics Data System (ADS)

Fatiha, M.; Rahmat, A.; Solihat, R.

2017-09-01

The delivery of concepts in studying Biology often represented through a diagram to easily makes student understand about Biology material. One way to knowing the students’ understanding about diagram can be seen from causal relationship that is constructed by student in the propositional network representation form. This research reveal the trend of students’ propositional network representation patterns when confronted with convention diagram. This descriptive research involved 32 students at one of senior high school in Bandung. The research data was acquired by worksheet that was filled by diagram and it was developed according on information processing standards. The result of this research revealed three propositional network representation patterns are linear relationship, simple reciprocal relationship, and complex reciprocal relationship. The dominating pattern is linear form that is simply connect some information components in diagram by 59,4% students, the reciprocal relationship form with medium level by 28,1% students while the complex reciprocal relationship by only 3,1% and the rest was students who failed to connect information components by 9,4%. Based on results, most of student only able to connect information components on the picture in linear form and a few student constructing reciprocal relationship between information components on convention diagram.

Biological and nonbiological complex drugs for multiple sclerosis in Latin America: regulations and risk management.

PubMed

Carrá, Adriana; Macías Islas, Miguel Angel; Tarulla, Adriana; Bichuetti, Denis Bernardi; Finkelsztejn, Alessandro; Fragoso, Yara Dadalti; Árcega-Revilla, Raul; Cárcamo Rodríguez, Claudia; Durán, Juan Carlos; Bonitto, Juan García; León, Rosalba; Oehninger Gatti, Carlos; Orozco, Geraldine; Vizcarra Escobar, Darwin

2015-06-01

Biological drugs and nonbiological complex drugs with expired patents are followed by biosimilars and follow-on drugs that are supposedly similar and comparable with the reference product in terms of quality, safety and efficacy. Unlike simple molecules that can be copied and reproduced, biosimilars and follow-on complex drugs are heterogeneous and need specific regulations from health and pharmacovigilance agencies. A panel of 14 Latin American experts on multiple sclerosis from nine different countries met to discuss the recommendations regarding biosimilars and follow-on complex drugs for treating multiple sclerosis. Specific measures relating to manufacturing, therapeutic equivalence assessment and pharmacovigilance reports need to be implemented before commercialization. Physical, chemical, biological and immunogenic characterizations of the new product need to be available before clinical trials start. The new product must maintain the same immunogenicity as the original. Automatic substitution of biological and complex drugs poses unacceptable risks to the patient.

Evolutionary analyses of non-genealogical bonds produced by introgressive descent.

PubMed

Bapteste, Eric; Lopez, Philippe; Bouchard, Frédéric; Baquero, Fernando; McInerney, James O; Burian, Richard M

2012-11-06

All evolutionary biologists are familiar with evolutionary units that evolve by vertical descent in a tree-like fashion in single lineages. However, many other kinds of processes contribute to evolutionary diversity. In vertical descent, the genetic material of a particular evolutionary unit is propagated by replication inside its own lineage. In what we call introgressive descent, the genetic material of a particular evolutionary unit propagates into different host structures and is replicated within these host structures. Thus, introgressive descent generates a variety of evolutionary units and leaves recognizable patterns in resemblance networks. We characterize six kinds of evolutionary units, of which five involve mosaic lineages generated by introgressive descent. To facilitate detection of these units in resemblance networks, we introduce terminology based on two notions, P3s (subgraphs of three nodes: A, B, and C) and mosaic P3s, and suggest an apparatus for systematic detection of introgressive descent. Mosaic P3s correspond to a distinct type of evolutionary bond that is orthogonal to the bonds of kinship and genealogy usually examined by evolutionary biologists. We argue that recognition of these evolutionary bonds stimulates radical rethinking of key questions in evolutionary biology (e.g., the relations among evolutionary players in very early phases of evolutionary history, the origin and emergence of novelties, and the production of new lineages). This line of research will expand the study of biological complexity beyond the usual genealogical bonds, revealing additional sources of biodiversity. It provides an important step to a more realistic pluralist treatment of evolutionary complexity.

[Preparation of cysteine-click maltose modified silica as a hydrophilic interaction liquid chromatography material for the enrichment of glycopeptides].

PubMed

Sun, Xudong; Zhang, Lingyi; Zhang, Weibing

2017-07-08

Because of the low abundance of glycoprotein and glycopeptide in complex biological samples, it is urgent to develop an efficient method for glycopeptide enrichment in comprehensive and in-depth glycoproteomes research. Herein, a novel hydrophilic silica was developed through surface modification with cysteine-click maltose (Cys-Mal@SiO 2 ). The developed hydrophilic silica was packed into a solid phase extraction (SPE) column, and applied to the highly selective enrichment and identification of N -linked glycopeptides. The Cys-Mal@SiO 2 demonstrated better identification capability over Cys@SiO 2 , Mal@SiO 2 and commercial hydrophilic interaction liquid chromatography (HILIC) in glycopeptide enrichment due to the synergistic effect of the two kinds of hydrophilic molecules. In the selective enrichment of tryptic digest from human immunoglobulin G, glycopeptides with higher signal-to-noises were detected by Cys-Mal@SiO 2 . In addition, 1551 unique glycopeptides with 906 N -glycosylation sites from 466 different N -linked glycoproteins were identified from the proteins extracted from mouse liver after the enrichment with Cys-Mal@SiO 2 . In contrast, the numbers of identified glycopeptides, glycoproteins and N -glycosylation sites identified by Cys@SiO 2 were 211, 67, 127 respectively less than by Cys-Mal@SiO 2 , and the corresponding numbers were 289, 76, 193 by Mal@SiO 2 . These results showed that the developed Cys-Mal@SiO 2 is a promising affinity material for N -glycoproteomics research of real complex biological samples.