Journal articles: 'Instrumentation for life-sciences'

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Patou, François, Maria Dimaki, Anja Maier, Winnie E. Svendsen, and Jan Madsen. "Model-based systems engineering for life-sciences instrumentation development." Systems Engineering 22, no. 2 (March 14, 2018): 98–113. http://dx.doi.org/10.1002/sys.21429.

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Griffin, Philippa C., Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, et al. "Best practice data life cycle approaches for the life sciences." F1000Research 6 (August 31, 2017): 1618. http://dx.doi.org/10.12688/f1000research.12344.1.

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Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.

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Griffin, Philippa C., Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, et al. "Best practice data life cycle approaches for the life sciences." F1000Research 6 (June 4, 2018): 1618. http://dx.doi.org/10.12688/f1000research.12344.2.

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Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a ‘life cycle’ view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain. Here we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on ‘omics’ datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.

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Sadrozinski, Hartmut F. W. "Radiation effects in life sciences." Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 514, no. 1-3 (November 2003): 224–29. http://dx.doi.org/10.1016/j.nima.2003.08.109.

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Leapman, RD. "Nanoscale Elemental Analysis by EELS in the Life Sciences." Microscopy and Microanalysis 14, S2 (August 2008): 1378–79. http://dx.doi.org/10.1017/s143192760808238x.

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Borst, Jan Willem, and Antonie J. W. G. Visser. "Fluorescence lifetime imaging microscopy in life sciences." Measurement Science and Technology 21, no. 10 (September 14, 2010): 102002. http://dx.doi.org/10.1088/0957-0233/21/10/102002.

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Williams, Robert E. A., David W. McComb, and Sriram Subramaniam. "Cryo-electron microscopy instrumentation and techniques for life sciences and materials science." MRS Bulletin 44, no. 12 (December 2019): 929–34. http://dx.doi.org/10.1557/mrs.2019.286.

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Kano, Hideaki, Hiroki Segawa, Masanari Okuno, Philippe Leproux, and Vincent Couderc. "Hyperspectral coherent Raman imaging - principle, theory, instrumentation, and applications to life sciences." Journal of Raman Spectroscopy 47, no. 1 (December 8, 2015): 116–23. http://dx.doi.org/10.1002/jrs.4853.

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Jakůbek, J. "Semiconductor Pixel detectors and their applications in life sciences." Journal of Instrumentation 4, no. 03 (March 17, 2009): P03013. http://dx.doi.org/10.1088/1748-0221/4/03/p03013.

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Mancuso, Joel, Kirk Czymmek, and Alexandra F. Elli. "Tools for 3D Electron in Life Sciences – Generate meaningful statistics from 3DEM Data Microscopy." Microscopy and Microanalysis 25, S2 (August 2019): 2676–77. http://dx.doi.org/10.1017/s1431927619014119.

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Digilio, F. Anna, Antonella Lanati, Antonella Bongiovanni, Anna Mascia, Marta Di Carlo, Adriano Barra, Anna Maria Cirafici, et al. "Quality-based model for Life Sciences research guidelines." Accreditation and Quality Assurance 21, no. 3 (April 25, 2016): 221–30. http://dx.doi.org/10.1007/s00769-016-1205-0.

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Tsakanov, V. M., R. M. Aroutiounian, G. A. Amatuni, L. R. Aloyan, L. G. Aslanyan, V. Sh Avagyan, N. S. Babayan, et al. "AREAL low energy electron beam applications in life and materials sciences." Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 829 (September 2016): 248–53. http://dx.doi.org/10.1016/j.nima.2016.02.028.

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Tsuda, Tetsuya, and Susumu Kuwabata. "Electron microscopy using ionic liquids for life and materials sciences." Microscopy 69, no. 4 (April 7, 2020): 183–95. http://dx.doi.org/10.1093/jmicro/dfaa013.

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Abstract An ionic liquid (IL) is a salt consisting of only cations and anions, which exists in the liquid state at room temperature. Interestingly ILs combine various favorable physicochemical properties, such as negligible vapor pressure, flame resistance, relatively high ionic conductivity, wide electrochemical window, etc. To take advantage of two specific features of ILs, viz. their nonvolatile and antistatic nature, in 2006, Kuwabata, Torimoto et al. reported a milestone study led to current IL-based electron microscopy techniques. Thereafter, several IL-based electron microscopy techniques have been proposed for life science and materials science applications, e.g. pretreatment of hydrous and/or non-electron conductive specimens and in situ/operando observation of chemical reactions occurring in ILs. In this review, the fundamental approaches for making full use of these techniques and their impact on science and technology are introduced.

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Mohanty, Sumit, Islam S. M. Khalil, and Sarthak Misra. "Contactless acoustic micro/nano manipulation: a paradigm for next generation applications in life sciences." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 476, no. 2243 (November 2020): 20200621. http://dx.doi.org/10.1098/rspa.2020.0621.

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Acoustic actuation techniques offer a promising tool for contactless manipulation of both synthetic and biological micro/nano agents that encompass different length scales. The traditional usage of sound waves has steadily progressed from mid-air manipulation of salt grains to sophisticated techniques that employ nanoparticle flow in microfluidic networks. State-of-the-art in microfabrication and instrumentation have further expanded the outreach of these actuation techniques to autonomous propulsion of micro-agents. In this review article, we provide a universal perspective of the known acoustic micromanipulation technologies in terms of their applications and governing physics. Hereby, we survey these technologies and classify them with regards to passive and active manipulation of agents. These manipulation methods account for both intelligent devices adept at dexterous non-contact handling of micro-agents, and acoustically induced mechanisms for self-propulsion of micro-robots. Moreover, owing to the clinical compliance of ultrasound, we provide future considerations of acoustic manipulation techniques to be fruitfully employed in biological applications that range from label-free drug testing to minimally invasive clinical interventions.

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Bessonov, E. G., M. V. Gorbunkov, P. V. Kostryukov, Yu Ya Maslova, V. G. Tunkin, A. A. Postnov, A. A. Mikhailichenko, V. I. Shvedunov, B. S. Ishkhanov, and A. V. Vinogradov. "Design study of compact Laser-Electron X-ray Generator for material and life sciences applications." Journal of Instrumentation 4, no. 07 (July 28, 2009): P07017. http://dx.doi.org/10.1088/1748-0221/4/07/p07017.

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Missing, P. R., R. C. Hennig, and H. M. Dyson. "Latest Developments in Tools for Life and Materials Sciences: Quorum Technologies Ltd Recent Improvements to existing Coater Instrumentation." Microscopy and Microanalysis 19, S2 (August 2013): 1340–41. http://dx.doi.org/10.1017/s1431927613008696.

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Lovric, Jelena, Jean-Nicolas Audinot, and Tom Wirtz. "In situ Correlative Helium Ion Microscopy and Secondary Ion Mass Spectrometry for High-Resolution Nano-Analytics in Life Sciences." Microscopy and Microanalysis 25, S2 (August 2019): 1026–27. http://dx.doi.org/10.1017/s1431927619005865.

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Lyman, Charles E. "Editorial." Microscopy and Microanalysis 11, no. 1 (January 28, 2005): 1. http://dx.doi.org/10.1017/s1431927605050269.

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With this issue, Microscopy and Microanalysis begins its eleventh year of publication. Our journal is getting better year-by-year. In 2004 this journal published more scientific articles than in any previous year. The first biological special issue, on parasites, increased the prominence of the life sciences within these pages. The growing popularity of the journal is also indicated by several letters to the editor about matters arising in certain articles. Such scientific exchanges highlight for our readership the subtleties of interpretation regarding advances in science, instrumentation, technique, and theory.

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Dixon, Andrew. "New Developments in Optical Microscopy for Biological Applications." Australian Journal of Physics 51, no. 4 (1998): 729. http://dx.doi.org/10.1071/p98024.

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In the past ten years a quiet revolution has been taking place in optical microscopy. So quiet indeed that if one has not been working in life sciences research one may have seen little or no evidence of it. Yet what has been going on is an excellent example of how developments in physical instrumentation drive research and research in turn drives further developments in instrumentation. In this paper I will briefly review these developments in optical microscopy and, in particular, show how processes originally proposed 65 years ago as esoteric theoretical solutions to Dirac’s equation are now used in practice for some of the most adventurous biological microscopy yet attempted.

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Stadtländer, Christian T. K. H. "Letter to the Editor." Microscopy and Microanalysis 9, no. 4 (August 2003): 269–71. http://dx.doi.org/10.1017/s1431927603030538.

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Over the years, I have read with great interest several articles and book chapters about historical aspects of electron microscopy. The report by F. Haguenau et al. about the key events in the history of electron microscopy (Microscopy and Microanalysis, Vol. 9, No. 2, April 2003, pp. 96–138) is, to my knowledge, by far the most comprehensive article ever published. The authors did a superb job in first listing chronologically the development of electron optics and instrumentation for the years from 1897 to 2002, and then describing major applications in physics and materials science, as well as life sciences.

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Caria, Mario. "Measurement Analysis: An Introduction to the Statistical Analysis of Laboratory Data in Physics, Chemistry and the Life Sciences." Measurement Science and Technology 12, no. 9 (August 16, 2001): 1610. http://dx.doi.org/10.1088/0957-0233/12/9/710.

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Sherman, Debby. "Equipment Funding Opportunities and Strategies for Success (Part 1)." Microscopy Today 20, no. 4 (July 2012): 54–56. http://dx.doi.org/10.1017/s155192951200048x.

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I think most of you probably know me. I tend to be rather vocal about things, whether it be on the Microscopy Listserver or through the years on problems of facility management, so I'm going to very briefly go over some of my experiences. I direct a core facility that has independent users, has a service component, is basically life sciences, but we do imaging for everybody. They can be from civil engineering, vet school, aeronautics, chemistry…who knows what will come in the door. So, some of the challenge has been to obtain major instrumentation that is versatile enough to handle a broad, broad range of users, but is initially justified based on a critical core research group. This is integral for obtaining any type of federal funding. So, we need new instrumentation for numerous reasons.

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Russin, William. "Scanning Electron Microscopy for the Life Sciences. Heide Schatten (Ed.). Cambridge University Press, Cambridge, UK, 2013, 261 pages. ISBN: 978-0-521-19599-7 (Hardcover)." Microscopy and Microanalysis 20, no. 1 (February 2014): 313. http://dx.doi.org/10.1017/s1431927613014062.

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Alves de Matos, A. P. "Introduction: Portuguese Society for Microscopy." Microscopy and Microanalysis 19, no. 5 (September 4, 2013): 1109. http://dx.doi.org/10.1017/s1431927613013378.

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SPMicros was founded in 1966 as Sociedade Portuguesa de Microscopia and since then has promoted Congresses dedicated to microscopy each year. For many of us this was the place where we delivered our first communications and received feedback by a panel of senior scientists devoted to the promotion of scientific quality; the Society was thus crucial to the rise of more than one generation of microscopists. In 2005 the Society's designation was changed to the “Portuguese Society for Microscopy” aka SPMicros, and incorporated a strong and growing group dedicated to materials science as well as to the life sciences.

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Morawski, Roman Z. "Measurement in the context of technoscientific research methodology." tm - Technisches Messen 87, no. 4 (April 26, 2020): 294–301. http://dx.doi.org/10.1515/teme-2019-0109.

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AbstractTechnoscience is a result of integration of technology with empirical sciences, including not only physical sciences, but also life sciences, social sciences and cognitive sciences. Further development of technoscience is unthinkable without extensive use of measurement and mathematical modelling, being two interrelated operations used for acquisition and representation of knowledge. Measurement fundamentals must, therefore, belong to the core of methodological instruction of young researchers in the domain of technoscience. This paper provides an outline of a sought-for discipline-independent programme of such formation, including a conceptual analysis of the key elements of the scientific method, with particular emphasis on the dialectical relationship between measurement and mathematical modelling, on the role of measurement in scientific prediction and explanation, on the role of measurement in the context of discovery and in the context of justification, as well as on the role of measurement in mitigating uncertainty of scientific knowledge.

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Rodgers, John R., and Pierre Villars. "Trends in Advanced Materials Data: Regularities and Predictions." MRS Bulletin 18, no. 2 (February 1993): 27–30. http://dx.doi.org/10.1557/s0883769400043608.

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Recently, there have been a number of reports identifying technologies of strategic importance. These technologies, which reflect the full range of national critical technology needs, are: materials, manufacturing, informatics and computing, biotechnology/life sciences, aeronautics/surface transport and energy/environment. In support of these technologies there has been much discussion on their research infrastructure, e.g., instrumentation, telecommunication networks, and supercomputing facilities. With the exception of biotechnology/life sciences, however, there has been little discussion on the uses of evaluated numeric and factual databases at the research level. The uses of databases are more advanced in biotechnology and life science research than in other fields, and this has been driven by the needs of genetic research, protein engineering, and drug design, where researchers need data and models for the design of new products. The needs of databases and their manipulation tools in materials science research are also essential in developing an intelligent research infrastructure. Given the present financial constraints, there is a need to use existing funds more efficiently and effectively. One way to achieve this is to use all available experimental data from various intersecting disciplines and bind them together with knowledge which will aid in the design of new materials.

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Schneckenburger, Herbert, and Verena Richter. "Laser Scanning versus Wide-Field—Choosing the Appropriate Microscope in Life Sciences." Applied Sciences 11, no. 2 (January 13, 2021): 733. http://dx.doi.org/10.3390/app11020733.

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Methods and applications of light microscopy in the life sciences are compared with respect to 3D imaging, resolution, light exposure, sensitivity, and recording time. While conventional wide-field or laser scanning microscopy appear appropriate for smaller samples of only a few micrometers in size with a limited number of light exposures, light sheet microscopy appears to be an optimal method for larger 3D cell cultures, biopsies, or small organisms if multiple exposures or long measuring periods are desired. Super-resolution techniques should be considered in the context of high light exposure possibly causing photobleaching and photo-toxicity to living specimens.

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Malis, Tom. "The Basics of Microtomy for Materials Science Microscopy." Microscopy and Microanalysis 4, S2 (July 1998): 874–75. http://dx.doi.org/10.1017/s1431927600024491.

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The common theme of most forms of thin specimen preparation for the physical sciences has been the controlled, gradual removal of material, whether by electrolytic dissolution, ion bombardment, careful mechanical dimpling or step-by-step tripod polishing. It is somewhat ironic that a “brute force” method, wherein the material is forced at a high rate against an atomically sharp diamond wedge so that an ultrathin slice, or section, is sheared, or fractured, from a ‘block’ of the material, should be viewed not only as acceptable, but with growing enthusiasm in the last several years. This process, known as ultramicrotomy, originated in life science TEM, but has been modified by materials scientists and applied to an impressive array of materials as illustrated in Table 1, culminating, perhaps, with the recent successful sectioning of diamond film.

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Gjelten, Herdis M., Øyvind Nordli, Arne A. Grimenes, and Elin Lundstad. "The Ås Temperature Series in Southern Norway–Homogeneity Testing And Climate Analysis." Bulletin of Geography. Physical Geography Series 7, no. 1 (December 1, 2014): 7–26. http://dx.doi.org/10.2478/bgeo-2014-0001.

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Abstract Homogeneity is important when analyzing climatic long-term time series. This is to ensure that the variability in the time series is not affected by changes such as station relocations, instrumentation changes and changes in the surroundings. The subject of this study is a long-term temperature series from the Norwegian University of Life Sciences at Ås in Southern Norway, located in a rural area about 30 km south of Oslo. Different methods for calculation of monthly mean temperature were studied and new monthly means were calculated before the homogeneity testing was performed. The statistical method used for the testing was the Standard Normal Homogeneity Test (SNHT) by Hans Alexandersson. Five breaks caused by relocations and changes in instrumentation were identified. The seasonal adjustments of the breaks lay between -0.4°C and +0.5°C. Comparison with two other homogenized temperature series in the Oslo fjord region showed similar linear trends, which suggests that the long-term linear temperature trends in the Oslo fjord region are not much affected by spatial climate variation.

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Malecki, Marek, Lea Tiongco, Annie Hsu, and Nina Takeuchi. "SCFV-6HIS Bioengineered for High Fidelity Labeling." Microscopy and Microanalysis 6, S2 (August 2000): 338–39. http://dx.doi.org/10.1017/s1431927600034188.

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In life sciences, the essential part of the functional molecular analysis is the unambiguous identification of biochemical composition of the observed structures. This analysis is expected to create a bridge between functional data pouring from biochemistry and molecular biology laboratories with the molecular architecture data available from ultrastructural images. This goal can be attained by application of various ultrastructural tags (See: Albrecht et al. 1992).A new promising approach for high fidelity labeling is offered by molecular cloning and expression of molecules containing metal binding sites making them suitable for electron spectroscopic imaging (ESI) (Malecki 1995). A truly enormous potential of ESI relies in its ability for mapping of various elements within the same sample. Interactions of electrons with an atom result in the electrons specific energy loss. Based upon these energy losses distribution of the elements within the sample can be mapped.

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Giovannucci, David. "Meeting Report: Microscopy & Microanalysis 2011." Microscopy Today 20, no. 1 (January 2012): 46. http://dx.doi.org/10.1017/s1551929511001386.

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Like that nourishing Music City confection, this year's Microscopy & Microanalysis Meeting, held August 7–11 in Nashville, was a GooGoo Cluster of top-notch science and networking. M&M is the annual meeting for the Microscopy Society of America, the Microanalysis Society, and the International Metallographic Society. It is the premier conference for microscopists working in the physical, life, and analytical sciences. This year's conference attracted 1,607 scientific attendees from 35 countries; the total number of attendees was 2,629. The perennially successful exhibitors' floor was again noteworthy with 113 companies providing the opportunity to wander 362 booths (9% more than the previous year) occupying 36,200 square feet with state-of-the-art instrumentation and publications.

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Mansfield, John F., and Brett L. Pennington. "X-Ray Energy Dispersive Spectroscopy in the Environmental Scanning Electron Microscope." Microscopy and Microanalysis 4, S2 (July 1998): 182–83. http://dx.doi.org/10.1017/s1431927600021036.

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The environmental scanning electron microscope (Environmental SEM) has proved to be a powerful tool in both materials science and the life sciences. Full characterization of materials in the environmental SEM often requires chemical analysis by X-ray energy dispersive spectroscopy (XEDS). However, the spatial resolution of the XEDS signal can be severely degraded by the gaseous environment in the sample chamber. At an operating pressure of 5Torr a significant fraction of the primary electron beam is scattered after it passes through the final pressure limiting aperture and before it strikes the sample. Bolon and Griffin have both published data that illustrates this effect very well. Bolon revealed that 45% of the primary electron beam was scattered by more than 25 μm in an Environmental SEM operating at an accelerating voltage of 30kV, with a water vapor pressure of 3Torr and a working distance of 15mm.

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Lyman, Charles E. "Editorial." Microscopy and Microanalysis 9, no. 2 (March 14, 2003): 95. http://dx.doi.org/10.1017/s1431927603030411.

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Microscopy and Microanalysis has made significant strides forward over the past year, and I would like to comment on two of these. First, the Institute for Scientific Information (ISI) ranked this journal third among the nine microscopy journals it indexes. The ranking was in terms of ISI's Impact Factor, which tracks the number of citations to papers published in the journal. A strong Impact Factor indicates that information in the journal is of interest to other workers in the field. Second, the National Library of Medicine (NLM) has selected Microscopy and Microanalysis to be indexed in MEDLINE (PubMed), beginning with the first issue of 2003. As any biologist will tell you, this listing is essential for the electronic visibility of papers in the fast-moving world of life sciences research. I thank Editorial Board member Dave Piston for his efforts in writing the initial letter of application to the NLM.

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Joy, David C. "The Low Voltage Scanning Electron Microscope." Microscopy and Microanalysis 3, S2 (August 1997): 1213–14. http://dx.doi.org/10.1017/s1431927600012952.

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A majority of the scanning electron microscopes (SEMs) now in use are probably employed as low voltage SEMs (LVSEMs), that is to say they are operated to produce beams with energies below 5keV. This trend away from the more conventional mode of operation at 20 or 30keV has gathered momentum over the past decade and has been driven by both theoretical and practical considera-tions.Firstly, the distance travelled by an electron falls rapidly (in fact as about E1.6 ) as the incident ener-gy E is reduced. Images generated by low energy electron beams therefore contain enhanced surface information compared to those images recorded at higher energies. Since surfaces are of great inter-est in both the life sciences and in materials science this has been a persuasive factor. Secondly, both the secondary and the backscattered electrons now come from essentially the same interaction volume, rather than from volumes which are widely different in size and shape.

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Lipski, Adam, and Dariusz Boroński. "Use of Thermography for the Analysis of Strength Properties of Mini-Specimens." Materials Science Forum 726 (August 2012): 156–61. http://dx.doi.org/10.4028/www.scientific.net/msf.726.156.

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This paper presents sample applications of passive infrared thermography for research on temperature changes of mini-specimens resulting from monotonously increasing or cyclically variable mechanical load. The MFS system developed in the Department of Machine Design at the University of Technology and Life Sciences in Bydgoszcz (Poland) and designed for testing mechanical properties of microelements were used for tests. The MFS system ensures nanometric measurement accuracy of many static and fatigue-related material properties, including, i.a., static tension curves, cyclic strain curves, fatigue life curves as a function of force, stress and strain. Measurements of the mini-specimens temperature were performed using thermographic camera equipped with microscope lens. The tests have shown that research on the passive infrared thermography may be successfully applied for determining strength properties of materials in micro scale. The used research instrumentation is characterized by sufficient sensitivity and resolution (camera with the microscope lens), while the MFS system ensures accurate load and position control.

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Kiefer, Johannes, Julia Bartels, Stephen Kroll, and Kurosch Rezwan. "Vibrational Spectroscopy as a Promising Toolbox for Analyzing Functionalized Ceramic Membranes." Applied Spectroscopy 72, no. 6 (April 18, 2018): 947–55. http://dx.doi.org/10.1177/0003702818769479.

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Ceramic materials find use in many fields including the life sciences and environmental engineering. For example, ceramic membranes have shown to be promising filters for water treatment and virus retention. The analysis of such materials, however, remains challenging. In the present study, the potential of three vibrational spectroscopic methods for characterizing functionalized ceramic membranes for water treatment is evaluated. For this purpose, Raman scattering, infrared (IR) absorption, and solvent infrared spectroscopy (SIRS) were employed. The data were analyzed with respect to spectral changes as well as using principal component analysis (PCA). The Raman spectra allow an unambiguous discrimination of the sample types. The IR spectra do not change systematically with functionalization state of the material. Solvent infrared spectroscopy allows a systematic distinction and enables studying the molecular interactions between the membrane surface and the solvent.

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Hofer, Ferdinand, Gerald Kothleitner, and Peter Warbichler. "Compositional Mapping with Energy Filtering TEM: The Present Status." Microscopy and Microanalysis 7, S2 (August 2001): 1136–37. http://dx.doi.org/10.1017/s1431927600031755.

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Energy filtering transmission electron microscopy (EFTEM) has matured into an important nanoanalytical technique in both materials and life sciences. One of the technique′s main advantages stems from the possibility to quickly form images that contain two-dimensional elemental information for most elements (Li to Pu) from relatively large specimen areas with nanometer resolution. Over the last years numerous and wide-ranging applications have demonstrated its almost unrivalled power for assessing typical materials science questions.Both in-column or post-column filter microscopes have reached a high performance level, but future improvements are still desirable, in particular with respect to increased transmissivity, improved isochromaticity and higher detection efficiency. Current instruments allow to acquire elemental maps with 1-5 nm spatial resolution limited mainly by the aberrations of the microscope and by the quality of the specimen. As recently shown 0.4 nm resolution is feasible.One major practical problem of EFTEM compositional mapping is the poor signal-to-noise ratio, which means that experimental parameters have to be chosen very carefully in order to optimize this ratio.

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Washington, Peter, Karina G. Samuel-Gama, Shirish Goyal, Ashwin Ramaswami, and Ingmar H. Riedel-Kruse. "Interactive programming paradigm for real-time experimentation with remote living matter." Proceedings of the National Academy of Sciences 116, no. 12 (March 1, 2019): 5411–19. http://dx.doi.org/10.1073/pnas.1815367116.

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Recent advancements in life-science instrumentation and automation enable entirely new modes of human interaction with microbiological processes and corresponding applications for science and education through biology cloud laboratories. A critical barrier for remote and on-site life-science experimentation (for both experts and nonexperts alike) is the absence of suitable abstractions and interfaces for programming living matter. To this end we conceptualize a programming paradigm that provides stimulus and sensor control functions for real-time manipulation of physical biological matter. Additionally, a simulation mode facilitates higher user throughput, program debugging, and biophysical modeling. To evaluate this paradigm, we implemented a JavaScript-based web toolkit, “Bioty,” that supports real-time interaction with swarms of phototacticEuglenacells hosted on a cloud laboratory. Studies with remote and on-site users demonstrate that individuals with little to no biology knowledge and intermediate programming knowledge were able to successfully create and use scientific applications and games. This work informs the design of programming environments for controlling living matter in general, for living material microfabrication and swarm robotics applications, and for lowering the access barriers to the life sciences for professional and citizen scientists, learners, and the lay public.

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Bijelić, Nikola, Tatjana Belovari, Dunja Stolnik, Ivana Lovrić, and Mirela Baus Lončar. "Histomorphometric Parameters of the Growth Plate and Trabecular Bone in Wild-Type and Trefoil Factor Family 3 (Tff3)-Deficient Mice Analyzed by Free and Open-Source Image Processing Software." Microscopy and Microanalysis 23, no. 4 (June 15, 2017): 818–25. http://dx.doi.org/10.1017/s1431927617000630.

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AbstractTrefoil factor family 3 (Tff3) peptide is present during intrauterine endochondral ossification in mice, and its deficiency affects cancellous bone quality in secondary ossification centers of mouse tibiae. The aim of this study was to quantitatively analyze parameters describing the growth plate and primary ossification centers in tibiae of 1-month-old wild-type and Tff3 knock-out mice (n=5 per genotype) by using free and open-source software. Digital photographs of the growth plates and trabecular bone were processed by open-source computer programs GIMP and FIJI. Histomorphometric parameters were calculated using measurements made with FIJI. Tff3 knock-out mice had significantly smaller trabecular number and significantly larger trabecular separation. Trabecular bone volume, trabecular bone surface, and trabecular thickness showed no significant difference between the two groups. Although such histomorphological differences were found in the cancellous bone structure, no significant differences were found in the epiphyseal plate histomorphology. Tff3 peptide probably has an effect on the formation and quality of the cancellous bone in the primary ossification centers, but not through disrupting the epiphyseal plate morphology. This work emphasizes the benefits of using free and open-source programs for morphological studies in life sciences.

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Hainfeld, James F., Richard D. Powell, Joshua K. Stein, Gerhard W. Hacker, Cornelia Hauser-Kronberger, Annie L. M. Cheung, and Christian Schöfer. "Gold-Based Autometallography." Microscopy and Microanalysis 5, S2 (August 1999): 486–87. http://dx.doi.org/10.1017/s1431927600015750.

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Gold labels such as Nanogold® and colloidal gold are enlarged and visualized in the electron microscope or optically by the selective deposition of silver onto their surfaces. This process, known as autometallography (AMG), silver amplification or silver enhancement, is initiated by exposing the particles to a solution containing silver (I) ions and a reducing agent such as hydroquinone or npropyl gallate. Particles may be enlarged to between 30 and 100 nm in diameter, giving a distinctive black, punctate staining in the light microscope. Nanogold® labeling with silver amplification is one of the most sensitive methods available for histopathology applications such as in situ hybridization. With Catalyzed Reporter Deposition (CARD; also called Tyramide Signal Amplification, or TSA® ; NEN Life Sciences, Boston MA), it has been used to detect as few as 1-2 copies of viral DNA or RNA per cell. However, its uses are restricted by reactions of silver (I) with halides and other elements in tissues. Also, after signal development, self-nucleation and non-specific background deposition begin quickly, which can make end-point selection difficult or prevent incorporation into automated procedures.

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Powell, Richard D., Vishwas N. Joshi, Carol M. R. Halsey, James F. Hainfeld, Gerhard W. Hacker, Cornelia Hauser-Kronberger, Wolfgang H. Muss, and Peter M. Takvorian. "Combined Cy3 / Nanogold Conjugates for ImmunocytoChemistry and in Situ Hybridization." Microscopy and Microanalysis 5, S2 (August 1999): 478–79. http://dx.doi.org/10.1017/s1431927600015713.

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Fluorescein and the 1.4 nm Nanogold® gold cluster label may be incorporated into a single Fab’ immunoprobe by separate cross-linking reactions, to give a probe which labels antigenic sites in a single step for correlative fluorescence and electron microscope visualization. These probes show high labeling density, labeling a pre-mRNA splicing factor in the HeLa cell nucleus; Microtubules were also densely labeled using fluorescence, other optical modalities, and electron microscopy; in a parallel experiment, a 5 nm colloidal gold probe gave only occasional labeling. We now describe Fab’ and streptavidin probes containing both Nanogold® and the fluorescent cyanine dye, Cy3.F(ab’)2 Goat anti-Mouse IgG and F(ab’)2 goat anti-rabbit IgG fragments were reductively cleaved to Fab’ fragments using dithiothreitol (DTT) or mercaptoethylamine hydrochloride (MEA), which selectively reduce the F(ab’)2 hinge disulfide bonds, with 5 mm EDTA to prevent reoxidation. Fab’ fragments were isolated by gel filtration (coarse gel: GH25, Amicon) then labeled with Monomaleimido- Nanogold® which reacts site-specifically with thiols. Streptavidin was labeled using Mono- Sulfo-NHS-Nanogold® at pH 7.5. Nanogold® conjugates were isolated by gel filtration (Superose-12 column, Pharmacia), then reacted with excess Cy3 monofunctional NHS ester (labeling kit, Amersham Life Sciences) at pH 7.5; dual-labeled conjugates were isolated by gel filtration (Superose-12).

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Malecki, Marek, Angel Sun, Lynn Wohlwend, and Annie Hsu. "Molecular Bioengineering of Multifuctional Markers for Energy Filtering Transmission Electron Microscopy (EFTEM) Correlative with Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI)." Microscopy and Microanalysis 7, S2 (August 2001): 1036–37. http://dx.doi.org/10.1017/s1431927600031251.

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Molecular immunolabeling allows us to recognize location of molecules within complex biomolecular assemblies, cells, and organs. This technology helps us to facilitate correlations of the data available from biochemistry, molecular biology, pathology, and molecular imaging laboratories concerned with the gene expression as well as location and functions of its products. in this sense, molecular imaging serves as an integrative factor for life sciences endeavors (Albrecht et al. 1992, Bazett-Jones et al. 1996, Hainfeld and Powell 2000, Malecki et al. 1998, Robinson et al. 2000, Malecki 2000). Nevertheless, the essential requirement for pursuit of those projects is availability of molecular markers, which are detectable with various imaging instruments (Malecki 1996). Correlations between positron emission tomography (PET) providing metabolic information, magnetic resonance imaging (MRI) delineating precise anatomical location, and energy filtering transmission electron microscopy (EFTEM) expanding insights into the molecular level are particularly powerful. We have designed three main strategies for pursuit of this project: (a) expression of fusion proteins containing amplified metal binding sites (Malecki et al. 1998), (b) expression of recombinant single chain variable fragment (scFv) antibodies containing elemental recipient (Malecki et al. 2000), and (c) covalent coupling of IgG and Fab with organometallic clusters (Malecki 1996). Herewith, we report the results obtained through imaging of organometallic clusters inserted into the recombinant single chain variable fragment (scFv) antibodies.

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Leite, E. A., J. M. C. Vilela, V. C. F. Mosqueira, and M. Spangler Andrade. "Poly-Caprolactone Nanocapsules Morphological Features by Atomic Force Microscopy." Microscopy and Microanalysis 11, S03 (December 2005): 48–51. http://dx.doi.org/10.1017/s1431927605050865.

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Polymeric nanoparticles containing an oily core, named nanocapsules (NCs), have been widely studied in the life sciences field due to their therapeutic potentialities of drug targeting in the body accompanied also by its larger stability in the biological fluids compared to other colloidal carriers. Many studies have shown different applications of nanocapsules for therapeutic use concerning their properties [1] of loading poorly water-soluble drugs, protection drugs from inactivation in the gastro-intestinal tract [2], gastric mucosal toxicity protection [3,4], increased drug permeation through mucous epithelium [5,6] and prolongation of drugs in blood circulation for surface modified nanocapsules [7]. The characterization of the nanocapsules is frequently performed by mean size, surface charge of the particles (zeta potential), hydrophobicity, drug loading yield and release kinetic [8]. These features are of great importance for biodistribution profile and interactions with the cells of mononuclear phagocyte system of any injected particles by intravenous route [1]. However, few data on structural organization of the nanocapsules constituents are available in literature and several hypotheses only suggest the presence of an oil "capsular" structure surrounded by a polymeric envelope. Recently, atomic force microscope (AFM) has been used as a method for imaging the surfaces of colloidal systems, such as liposomes [9,10] and nanospheres [11], supplying high resolution information in nanoscaled dimension. In the present work, unloaded nanocapsules were deposited on mica in order to analyze by AFM the diameter, height, particles polydispersion, and topographic characteristics of nanocapsule surface.

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Valasek, Mark A., and Joyce J. Repa. "The power of real-time PCR." Advances in Physiology Education 29, no. 3 (September 2005): 151–59. http://dx.doi.org/10.1152/advan.00019.2005.

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In recent years, real-time polymerase chain reaction (PCR) has emerged as a robust and widely used methodology for biological investigation because it can detect and quantify very small amounts of specific nucleic acid sequences. As a research tool, a major application of this technology is the rapid and accurate assessment of changes in gene expression as a result of physiology, pathophysiology, or development. This method can be applied to model systems to measure responses to experimental stimuli and to gain insight into potential changes in protein level and function. Thus physiology can be correlated with molecular events to gain a better understanding of biological processes. For clinical molecular diagnostics, real-time PCR can be used to measure viral or bacterial loads or evaluate cancer status. Here, we discuss the basic concepts, chemistries, and instrumentation of real-time PCR and include present applications and future perspectives for this technology in biomedical sciences and in life science education.

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Hwu, Yeukuang, and Giorgio Margaritondo. "Synchrotron radiation and X-ray free-electron lasers (X-FELs) explained to all users, active and potential." Journal of Synchrotron Radiation 28, no. 3 (April 27, 2021): 1014–29. http://dx.doi.org/10.1107/s1600577521003325.

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Synchrotron radiation evolved over one-half century into a gigantic worldwide enterprise involving tens of thousands of researchers. Initially, almost all users were physicists. But now they belong to a variety of disciplines: chemistry, materials science, the life sciences, medical research, ecology, cultural heritage and others. This poses a challenge: explaining synchrotron sources without requiring a sophisticated background in theoretical physics. Here this challenge is met with an innovative approach that only involves elementary notions, commonly possessed by scientists of all domains.

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Lühl, Lars, Konstantin Andrianov, Hanna Dierks, Andreas Haidl, Aurelie Dehlinger, Markus Heine, Jörg Heeren, Thomas Nisius, Thomas Wilhein, and Birgit Kanngießer. "Scanning transmission X-ray microscopy with efficient X-ray fluorescence detection (STXM-XRF) for biomedical applications in the soft and tender energy range." Journal of Synchrotron Radiation 26, no. 2 (January 21, 2019): 430–38. http://dx.doi.org/10.1107/s1600577518016879.

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Scanning transmission X-ray microscopy, especially in combination with X-ray fluorescence detection (STXM-XRF) in the soft X-ray energy range, is becoming an increasingly important tool for life sciences. Using X-ray fluorescence detection, the study of biochemical mechanisms becomes accessible. As biological matrices generally have a low fluorescence yield and thus a low fluorescence signal, high detector efficiency (e.g. large solid angle) is indispensable for avoiding long measurement times and radiation damage. Here, the new AnImaX STXM-XRF microscope equipped with a large solid angle of detection enabling fast scans and the first proof-of-principle measurements on biomedical samples are described. In addition, characterization measurements for future quantitative elemental imaging are presented.

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Boehm, Daniela, and Cristina Canal. "Application of Plasma Technology in Bioscience and Biomedicine." Applied Sciences 11, no. 16 (August 4, 2021): 7203. http://dx.doi.org/10.3390/app11167203.

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Plasma technology has been an integral part of research in life sciences for decades through its role in the manufacture and modification of material surface characteristics of many common laboratory consumables, and it is still of interest in many fields, including the treatment of biomaterials and implants [...]

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Fürst, Josef, Hans Peter Nachtnebel, Josef Gasch, Reinhard Nolz, Michael Paul Stockinger, Christine Stumpp, and Karsten Schulz. "Rosalia: an experimental research site to study hydrological processes in a forest catchment." Earth System Science Data 13, no. 8 (August 19, 2021): 4019–34. http://dx.doi.org/10.5194/essd-13-4019-2021.

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Abstract. Experimental watersheds have a long tradition as research sites in hydrology and have been used since the late nineteenth and early twentieth centuries. The University of Natural Resources and Life Sciences Vienna (BOKU) recently extended its experimental research forest site “Rosalia” with an area of 950 ha towards the creation of a full ecological-hydrological experimental watershed. The overall objective is to implement a multi-scale, multi-disciplinary observation system that facilitates the study of water, energy and solute transport processes in the soil–plant–atmosphere continuum. This article describes the characteristics of the site and the monitoring network and its instrumentation that has been installed since 2015, as well as the datasets. The network includes four discharge gauging stations and seven rain gauges along with observations of air and water temperature, relative humidity, and electrical conductivity. In four profiles, soil water content and temperature are recorded at different depths. In addition, since 2018, nitrate, TOC and turbidity have been monitored at one gauging station. In 2019, a programme to collect isotopic data in precipitation and discharge was initiated. All data collected since 2015, including, in total, 56 high-resolution time series (with 10 min sampling intervals), are provided to the scientific community on a publicly accessible repository. The datasets are available at https://doi.org/10.5281/zenodo.3997140 (Fürst et al., 2020).

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Campi, Gaetano, and Antonio Bianconi. "Evolution of Complexity in Out-of-Equilibrium Systems by Time-Resolved or Space-Resolved Synchrotron Radiation Techniques." Condensed Matter 4, no. 1 (March 14, 2019): 32. http://dx.doi.org/10.3390/condmat4010032.

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Out-of-equilibrium phenomena are attracting high interest in physics, materials science, chemistry and life sciences. In this state, the study of structural fluctuations at different length scales in time and space are necessary to achieve significant advances in the understanding of the structure-functionality relationship. The visualization of patterns arising from spatiotemporal fluctuations is nowadays possible thanks to new advances in X-ray instrumentation development that combine high-resolution both in space and in time. We present novel experimental approaches using high brilliance synchrotron radiation sources, fast detectors and focusing optics, joint with advanced data analysis based on automated statistical, mathematical and imaging processing tools. This approach has been used to investigate structural fluctuations in out-of-equilibrium systems in the novel field of inhomogeneous quantum complex matter at the crossing point of technology, physics and biology. In particular, we discuss how nanoscale complexity controls the emergence of high-temperature superconductivity (HTS), myelin functionality and formation of hybrid organic-inorganic supramolecular assembly. The emergent complex geometries, opening novel venues to quantum technology and to the development of quantum physics of living systems, are discussed.

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Abu-Hatab, Nahla A., Joshy F. John, Jenny M. Oran, and Michael J. Sepaniak. "Multiplexed Microfluidic Surface-Enhanced Raman Spectroscopy." Applied Spectroscopy 61, no. 10 (October 2007): 1116–22. http://dx.doi.org/10.1366/000370207782217842.

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Over the past few decades, surface-enhanced Raman spectroscopy (SERS) has garnered respect as an analytical technique with significant chemical and biological applications. SERS is important for the life sciences because it can provide trace level detection, a high level of structural information, and enhanced chemical detection. However, creating and successfully implementing a sensitive, reproducible, and robust SERS active substrate continues to be a challenging task. Herein, we report a novel method for SERS that is based upon using multiplexed microfluidics (MMFs) in a polydimethylsiloxane platform to perform parallel, high throughput, and sensitive detection/identification of single or various analytes under easily manipulated conditions. A facile passive pumping method is used to deliver Ag colloids and analytes into the channels where SERS measurements are done under nondestructive flowing conditions. With this approach, SERS signal reproducibility is found to be better than 7%. Utilizing a very high numerical aperture microscope objective with a confocal-based Raman spectrometer, high sensitivity is achieved. Moreover, the long working distance of this objective coupled with an appreciable channel depth obviates normal alignment issues expected with translational multiplexing. Rapid evaluation of the effects of anion activators and the type of colloid employed on SERS performance are used to demonstrate the efficiency and applicability of the MMF approach. SERS spectra of various pesticides were also obtained. Calibration curves of crystal violet (non-resonant enhanced) and Mitoxantrone (resonant enhanced) were generated, and the major SERS bands of these analytes were observable down to concentrations in the low nM and sub-pM ranges, respectively. While conventional random morphology colloids were used in most of these studies, unique cubic nanoparticles of silver were synthesized with different sizes and studied using visible wavelength optical extinction spectrometry, scanning electron microscopy, and the MMF-SERS approach.

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Journal articles on the topic 'Instrumentation for life-sciences'

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