Imaging multicellular specimens with real-time optimized tiling light-sheet selective plane illumination microscopy

PubMed Central

Fu, Qinyi; Martin, Benjamin L.; Matus, David Q.; Gao, Liang

2016-01-01

Despite the progress made in selective plane illumination microscopy, high-resolution 3D live imaging of multicellular specimens remains challenging. Tiling light-sheet selective plane illumination microscopy (TLS-SPIM) with real-time light-sheet optimization was developed to respond to the challenge. It improves the 3D imaging ability of SPIM in resolving complex structures and optimizes SPIM live imaging performance by using a real-time adjustable tiling light sheet and creating a flexible compromise between spatial and temporal resolution. We demonstrate the 3D live imaging ability of TLS-SPIM by imaging cellular and subcellular behaviours in live C. elegans and zebrafish embryos, and show how TLS-SPIM can facilitate cell biology research in multicellular specimens by studying left-right symmetry breaking behaviour of C. elegans embryos. PMID:27004937

Apparatus for automated testing of biological specimens

DOEpatents

Layne, Scott P.; Beugelsdijk, Tony J.

1999-01-01

An apparatus for performing automated testing of infections biological specimens is disclosed. The apparatus comprise a process controller for translating user commands into test instrument suite commands, and a test instrument suite comprising a means to treat the specimen to manifest an observable result, and a detector for measuring the observable result to generate specimen test results.

High resolution IVEM tomography of biological specimens

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

Sedat, J.W.; Agard, D.A.

Electron tomography is a powerful tool for elucidating the three-dimensional architecture of large biological complexes and subcellular organelles. The introduction of intermediate voltage electron microscopes further extended the technique by providing the means to examine very large and non-symmetrical subcellular organelles, at resolutions beyond what would be possible using light microscopy. Recent studies using electron tomography on a variety of cellular organelles and assemblies such as centrosomes, kinetochores, and chromatin have clearly demonstrated the power of this technique for obtaining 3D structural information on non-symmetric cell components. When combined with biochemical and molecular observations, these 3D reconstructions have provided significantmore » new insights into biological function.« less

Reaction-based small-molecule fluorescent probes for chemoselective bioimaging

PubMed Central

Chan, Jefferson; Dodani, Sheel C.; Chang, Christopher J.

2014-01-01

The dynamic chemical diversity of elements, ions and molecules that form the basis of life offers both a challenge and an opportunity for study. Small-molecule fluorescent probes can make use of selective, bioorthogonal chemistries to report on specific analytes in cells and in more complex biological specimens. These probes offer powerful reagents to interrogate the physiology and pathology of reactive chemical species in their native environments with minimal perturbation to living systems. This Review presents a survey of tools and tactics for using such probes to detect biologically important chemical analytes. We highlight design criteria for effective chemical tools for use in biological applications as well as gaps for future exploration. PMID:23174976

Scanning transmission ion micro-tomography (STIM-T) of biological specimens.

PubMed

Schwertner, Micheal; Sakellariou, Arthur; Reinert, Tilo; Butz, Tilman

2006-05-01

Computed tomography (CT) was applied to sets of Scanning Transmission Ion Microscopy (STIM) projections recorded at the LIPSION ion beam laboratory (Leipzig) in order to visualize the 3D-mass distribution in several specimens. Examples for a test structure (copper grid) and for biological specimens (cartilage cells, cygospore) are shown. Scanning Transmission Micro-Tomography (STIM-T) at a resolution of 260 nm was demonstrated for the first time. Sub-micron features of the Cu-grid specimen were verified by scanning electron microscopy. The ion energy loss measured during a STIM-T experiment is related to the mass density of the specimen. Typically, biological specimens can be analysed without staining. Only shock freezing and freeze-drying is required to preserve the ultra-structure of the specimen. The radiation damage to the specimen during the experiment can be neglected. This is an advantage compared to other techniques like X-ray micro-tomography. At present, the spatial resolution is limited by beam position fluctuations and specimen vibrations.

Cryo-FIB specimen preparation for use in a cartridge-type cryo-TEM.

PubMed

He, Jie; Hsieh, Chyongere; Wu, Yongping; Schmelzer, Thomas; Wang, Pan; Lin, Ying; Marko, Michael; Sui, Haixin

2017-08-01

Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET. Commercial cryosystems are available for cryo-FIB specimen preparation, however re-engineering and additional fixtures are often essential for reliable results with a particular cryo-FIB and cryo-transmission electron microscope (cryo-TEM). Here, we describe our optimized protocol and modified instrumentation for cryo-FIB milling to produce thin lamellae and subsequent damage-free cryotransfer of the lamellae into our cartridge-type cryo-TEM. Published by Elsevier Inc.

Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

PubMed Central

Cope, Julia; Heumann, John; Hoenger, Andreas

2011-01-01

Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

Finding the patterns in complex specimens by improving the acquisition and analysis of x-ray spectromicroscopy data

NASA Astrophysics Data System (ADS)

Lerotic, Mirna

Soft x-ray spectromicroscopy provides spectral data on the chemical speciation of light elements at sub-100 nanometer spatial resolution. The high resolution imaging places a strong demand on the microscope stability and on the reproducibility of the scanned image field, and the volume of data necessitates the need for improved data analysis methods. This dissertation concerns two developments in extending the capability of soft x-ray transmission microscopes to carry out studies of chemical speciation at high spatial resolution. One development involves an improvement in x-ray microscope instrumentation: a new Stony Brook scanning transmission x-ray microscope which incorporates laser interferometer feedback in scanning stage positions. The interferometer is used to control the position between the sample and focusing optics, and thus improve the stability of the system. A second development concerns new analysis methods for the study of chemical speciation of complex specimens, such as those in biological and environmental science studies. When all chemical species in a specimen are known and separately characterized, existing approaches can be used to measure the concentration of each component at each pixel. In other cases (such as often occur in biology or environmental science), where the specimen may be too complicated or provide at least some unknown spectral signatures, other approaches must be used. We describe here an approach that uses principal component analysis (similar to factor analysis) to orthogonalize and noise-filter spectromicroscopy data. We then use cluster analysis (a form of unsupervised pattern matching) to classify pixels according to spectral similarity, to extract representative, cluster-averaged spectra with good signal-to-noise ratio, and to obtain gradations of concentration of these representative spectra at each pixel. The method is illustrated with a simulated data set of organic compounds, and a mixture of lutetium in hematite used to understand colloidal transport properties of radionuclides. Also, we describe here an extension of that work employing an angle distance measure; this measure provides better classification based on spectral signatures alone in specimens with significant thickness variations. The method is illustrated using simulated data, and also to examine sporulation in the bacterium Clostridium sp.

Biological imaging by soft X-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Shapiro, David

We have developed a microscope for soft x-ray diffraction imaging of dry or frozen hydrated biological specimens. This lensless imaging system does not suffer from the resolution or specimen thickness limitations that other short wavelength microscopes experience. The microscope, currently situated at beamline 9.0.1 of the Advanced Light Source, can collect diffraction data to 12 nm resolution with 750 eV photons and 17 nm resolution with 520 eV photons. The specimen can be rotated with a precision goniometer through an angle of 160 degrees allowing for the collection of nearly complete three-dimensional diffraction data. The microscope is fully computer controlled through a graphical user interface and a scripting language automates the collection of both two-dimensional and three-dimensional data. Diffraction data from a freeze-dried dwarf yeast cell, Saccharomyces cerevisiae carrying the CLN3-1 mutation, was collected to 12 run resolution from 8 specimen orientations spanning a total rotation of 8 degrees. The diffraction data was phased using the difference map algorithm and the reconstructions provide real space images of the cell to 30 nm resolution from each of the orientations. The agreement of the different reconstructions provides confidence in the recovered, and previously unknown, structure and indicates the three dimensionality of the cell. This work represents the first imaging of the natural complex refractive contrast from a whole unstained cell by the diffraction microscopy method and has achieved a resolution superior to lens based x-ray tomographic reconstructions of similar specimens. Studies of the effects of exposure to large radiation doses were also carried out. It was determined that the freeze-dried cell suffers from an initial collapse, which is followed by a uniform, but slow, shrinkage. This structural damage to the cell is not accompanied by a diminished ability to see small features in the specimen. Preliminary measurements on frozen-hydrated yeast indicate that the frozen specimens do not exhibit these changes even with doses as high as 5 x 109 Gray.

Five task clusters that enable efficient and effective digitization of biological collections

PubMed Central

Nelson, Gil; Paul, Deborah; Riccardi, Gregory; Mast, Austin R.

2012-01-01

Abstract This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation’s National Resource for Advancing Digitization of Biological Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) pre-digitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs. PMID:22859876

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

PubMed Central

Kusber, W.-H.; Tschöpe, O.; Güntsch, A.; Berendsohn, W. G.

2017-01-01

Abstract Biological research collections holding billions of specimens world-wide provide the most important baseline information for systematic biodiversity research. Increasingly, specimen data records become available in virtual herbaria and data portals. The traditional (physical) annotation procedure fails here, so that an important pathway of research documentation and data quality control is broken. In order to create an online annotation system, we analysed, modeled and adapted traditional specimen annotation workflows. The AnnoSys system accesses collection data from either conventional web resources or the Biological Collection Access Service (BioCASe) and accepts XML-based data standards like ABCD or DarwinCore. It comprises a searchable annotation data repository, a user interface, and a subscription based message system. We describe the main components of AnnoSys and its current and planned interoperability with biodiversity data portals and networks. Details are given on the underlying architectural model, which implements the W3C OpenAnnotation model and allows the adaptation of AnnoSys to different problem domains. Advantages and disadvantages of different digital annotation and feedback approaches are discussed. For the biodiversity domain, AnnoSys proposes best practice procedures for digital annotations of complex records. Database URL: https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys PMID:28365735

TASI: A software tool for spatial-temporal quantification of tumor spheroid dynamics.

PubMed

Hou, Yue; Konen, Jessica; Brat, Daniel J; Marcus, Adam I; Cooper, Lee A D

2018-05-08

Spheroid cultures derived from explanted cancer specimens are an increasingly utilized resource for studying complex biological processes like tumor cell invasion and metastasis, representing an important bridge between the simplicity and practicality of 2-dimensional monolayer cultures and the complexity and realism of in vivo animal models. Temporal imaging of spheroids can capture the dynamics of cell behaviors and microenvironments, and when combined with quantitative image analysis methods, enables deep interrogation of biological mechanisms. This paper presents a comprehensive open-source software framework for Temporal Analysis of Spheroid Imaging (TASI) that allows investigators to objectively characterize spheroid growth and invasion dynamics. TASI performs spatiotemporal segmentation of spheroid cultures, extraction of features describing spheroid morpho-phenotypes, mathematical modeling of spheroid dynamics, and statistical comparisons of experimental conditions. We demonstrate the utility of this tool in an analysis of non-small cell lung cancer spheroids that exhibit variability in metastatic and proliferative behaviors.

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language.

PubMed

Metlagel, Zoltan; Kikkawa, Yayoi S; Kikkawa, Masahide

2007-01-01

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.

Total rate imaging with x-rays (TRIX)--a simple method of forming a non-projection x-ray image in the SEM using an energy dispersive detector and its application to biological specimens.

PubMed

Ingram, P; Shelburne, J D

1980-01-01

X-ray images can be formed in a conventional scanning electron microscope equipped with a Si(Li) energy dispersive spectrometer. All the x-ray events generated in the electron beam scanning process are synchronously displayed in the same manner as for dot maps. The quasi-digital image formed using Total Rate Imaging with X-rays (TRIX) exhibits good gray scale contrast and is dependent on topography, orientation and atomic number. Although this latter dependence is complex, it has been found useful in locating several types of inclusions in lung tissue (silicosis), human alveolar macrophages and cigarette smoke condensate. This is because of the greater depth of penetration of x-rays than backscattered electrons (BSE) usually used for such localizations in a matrix, and the negligible sensitivity of the Si(Li) detector to x-rays from an organic biological matrix. The optimum procedure is to use a combination of TRIX and BSE to investigate such specimens.

Introduction to electron crystallography.

PubMed

Kühlbrandt, Werner

2013-01-01

From the earliest work on regular arrays in negative stain, electron crystallography has contributed greatly to our understanding of the structure and function of biological macromolecules. The development of electron cryo-microscopy (cryo-EM) then lead to the first groundbreaking atomic models of the membrane proteins bacteriorhodopsin and light harvesting complex II within lipid bilayers. Key contributions towards cryo-EM and electron crystallography methods included specimen preparation and vitrification, liquid-helium cooling, data collection, and image processing. These methods are now applied almost routinely to both membrane and soluble proteins. Here we outline the advances and the breakthroughs that paved the way towards high-resolution structures by electron crystallography, both in terms of methods development and biological milestones.

Assessing the Biological Safety Profession's Evaluation and Control of Risks Associated with the Field Collection of Potentially Infectious Specimens.

PubMed

Patlovich, Scott J; Emery, Robert J; Whitehead, Lawrence W; Brown, Eric L; Flores, Rene

2015-03-01

Because the origins of the biological safety profession are rooted in the control and prevention of laboratory-associated infections, the vocation focuses primarily on the safe handling of specimens within the laboratory. But in many cases, the specimens and samples handled in the lab are originally collected in the field where a broader set of possible exposure considerations may be present, each with varying degrees of controllability. The failure to adequately control the risks associated with collecting biological specimens in the field may result in illness or injury, and could have a direct impact on laboratory safety, if infectious specimens were packaged or transported inappropriately, for example. This study developed a web-based survey distributed to practicing biological safety professionals to determine the prevalence of and extent to which biological safety programs consider and evaluate field collection activities. In cases where such issues were considered, the data collected characterize the types of controls and methods of oversight at the institutional level that are employed. Sixty-one percent (61%) of the survey respondents indicated that research involving the field collection of biological specimens is conducted at their institutions. A majority (79%) of these field collection activities occur at academic institutions. Twenty-seven percent (27%) of respondents indicated that their safety committees do not consider issues related to biological specimens collected in the field, and only 25% with an oversight committee charged to review field collection protocols have generated a field research-specific risk assessment form to facilitate the assembly of pertinent information for a project risk assessment review. The results also indicated that most biosafety professionals (73% overall; 71% from institutions conducting field collection activities) have not been formally trained on the topic, but many (64% overall; 87% from institutions conducting field collection activities) indicated that training on field research safety issues would be helpful, and even more (71% overall; 93% from institutions conducting field collection activities) would consider participation in such a training course. Results obtained from this study can be used to develop a field research safety toolkit and associated training curricula specifically targeted to biological safety professionals.

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

Space Science

NASA Image and Video Library

2003-06-01

NASA’s Virtual Glovebox (VGX) was developed to allow astronauts on Earth to train for complex biology research tasks in space. The astronauts may reach into the virtual environment, naturally manipulating specimens, tools, equipment, and accessories in a simulated microgravity environment as they would do in space. Such virtual reality technology also provides engineers and space operations staff with rapid prototyping, planning, and human performance modeling capabilities. Other Earth based applications being explored for this technology include biomedical procedural training and training for disarming bio-terrorism weapons.

Virtual Glovebox (VGX) Aids Astronauts in Pre-Flight Training

NASA Technical Reports Server (NTRS)

2003-01-01

NASA's Virtual Glovebox (VGX) was developed to allow astronauts on Earth to train for complex biology research tasks in space. The astronauts may reach into the virtual environment, naturally manipulating specimens, tools, equipment, and accessories in a simulated microgravity environment as they would do in space. Such virtual reality technology also provides engineers and space operations staff with rapid prototyping, planning, and human performance modeling capabilities. Other Earth based applications being explored for this technology include biomedical procedural training and training for disarming bio-terrorism weapons.

Fundamental Technical Elements of Freeze-fracture/Freeze-etch in Biological Electron Microscopy

EPA Science Inventory

Freeze-fracture/freeze-etch describes a process whereby specimens, typically biological or nanomaterial in nature, are frozen, fractured, and replicated to generate a carbon/platinum "cast" intended for examination by transmission electron microscopy. Specimens are subjected to u...

Imaging fully hydrated whole cells by coherent x-ray diffraction microscopy.

PubMed

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Naitow, Hisashi; Kunishima, Naoki; Yoshida, Takashi; Ishikawa, Tetsuya; Song, Changyong

2013-03-01

Nanoscale imaging of biological specimens in their native condition is of long-standing interest, in particular with direct, high resolution views of internal structures of intact specimens, though as yet progress has been limited. Here we introduce wet coherent x-ray diffraction microscopy capable of imaging fully hydrated and unstained biological specimens. Whole cell morphologies and internal structures better than 25 nm can be clearly visualized without contrast degradation.

New and unconventional approaches for advancing resolution in biological transmission electron microscopy by improving macromolecular specimen preparation and preservation.

PubMed

Massover, William H

2011-02-01

Resolution in transmission electron microscopy (TEM) now is limited by the properties of specimens, rather than by those of instrumentation. The long-standing difficulties in obtaining truly high-resolution structure from biological macromolecules with TEM demand the development, testing, and application of new ideas and unconventional approaches. This review concisely describes some new concepts and innovative methodologies for TEM that deal with unsolved problems in the preparation and preservation of macromolecular specimens. The selected topics include use of better support films, a more protective multi-component matrix surrounding specimens for cryo-TEM and negative staining, and, several quite different changes in microscopy and micrography that should decrease the effects of electron radiation damage; all these practical approaches are non-traditional, but have promise to advance resolution for specimens of biological macromolecules beyond its present level of 3-10 Å (0.3-1.0 nm). The result of achieving truly high resolution will be a fulfillment of the still unrealized potential of transmission electron microscopy for directly revealing the structure of biological macromolecules down to the atomic level. Published by Elsevier Ltd.

[Establishment and Management of Multiple Myeloma Specimen Bank Applied for Molecular Biological Researches].

PubMed

Li, Han-Qing; Mei, Jian-Gang; Cao, Hong-Qin; Shao, Liang-Jing; Zhai, Yong-Ping

2017-12-01

To establish a multiple myeloma specimen bank applied for molecular biological researches and to explore the methods of specimen collection, transportation, storage, quality control and the management of specimen bank. Bone marrow and blood samples were collected from multiple myeloma patients, plasma cell sorting were operated after the separation of mononuclear cells from bone marrow specimens. The plasma cells were divided into 2 parts, one was added with proper amount of TRIzol and then kept in -80 °C refrigerator for subsequent RNA extraction, the other was added with proper amount of calf serum cell frozen liquid and then kept in -80 °C refrigerator for subsequent cryopreservation of DNA extraction after numbered respectively. Serum and plasma were separated from peripheral blood, specimens of serum and plasma were then stored at -80 °C refrigerator after registration. Meantime, the myeloma specimen information management system was established, managed and maintained by specially-assigned persons and continuous modification and improvement in the process of use as to facilitate the rapid collection, management, query of the effective samples and clinical data. A total of 244 portions plasma cells, 564 portions of serum, and 1005 portions of plasma were collected, clinical characters were documented. A multiple myeloma specimen bank have been established initially, which can provide quality samples and related clinical information for molecular biological research on multiple myeloma.

Studies on the Biology of Hypogeococcus pungens (sensu stricto) (Hemiptera: Pseudococcidae) in Argentina to Aid the Identification of the Mealybug Pest of Cactaceae in Puerto Rico

PubMed Central

Aguirre, M. B.; Diaz-Soltero, H.; Claps, L. E.; Saracho Bottero, A.; Triapitsyn, S.; Hasson, E.; Logarzo, G. A.

2016-01-01

Hypogeococcus pungens Granara de Willink, sensu stricto, is a serious pest of cacti in Puerto Rico threating many Caribbean islands. A classical biological control program for H. pungens was initiated for Puerto Rico in 2010 with a survey for natural enemies of H. pungens in its native range of Argentina. Biological differences were observed between populations of H. pungens sampled on Amaranthaceae and Cactaceae. Molecular studies suggested that H. pungens populations from different host plant families are likely a complex of species. Our objective was to study the biology of H. pungens sensu stricto on specimens collected in the same locality and host plant as the holotype [Tucumán Province, Argentina; Alternanthera pungens Kunth (Amaranthaceae)]. We were interested in the reproductive biology of females, longevity and survival of adults, the effect of temperature on the development, and nymph performance (survival and development) on five Cactaceae species. We found that H. pungens s.s. showed marked biological differences from the populations collected on Cactaceae and exported to Australia for the biological control of the cactus Harrisia spp. The main differences were the presence of deuterotoky parthenogenesis and the fact that H. pungens did not attack Cactaceae in the laboratory. Our results provide biological evidence that H. pungens is a species complex. We propose that the population introduced to Australia is neither Hypogeococcus festerianus Lizer y Trelles nor H. pungens, but an undescribed species with three circuli, and that the Hypogeococcus pest of cacti in Puerto Rico is not H. pungens. PMID:27324585

Investigations in space-related molecular biology. [cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens

NASA Technical Reports Server (NTRS)

Fernandez-Moran, H.; Pritzker, A. N.

1974-01-01

Improved instrumentation and preparation techniques for high resolution, high voltage cryo-electron microscopic and diffraction studies on terrestrial and extraterrestrial specimens are reported. Computer correlated ultrastructural and biochemical work on hydrated and dried cell membranes and related biological systems provided information on membrane organization, ice crystal formation and ordered water, RNA virus linked to cancer, lunar rock samples, and organometallic superconducting compounds. Apollo 11, 12, 14, and 15 specimens were analyzed

DETERMINATION OF INDUCED RADIOACTIVITY IN THE SECOND COSMIC SPACESHIP

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

Matveev, V.V.; Sokolov, A.D.

1961-01-01

The residual gamma activity in a biological specimen on board the second Soviet cosmic spaceship was determined. The biological specimens were in the form of cylinders (3.8-cm dia., 4-cm long) with a total weight of 86 g. The activity of the specimens was measured after return to earth, and it was found that if there was a residual gamma activity 15 days after the return to earth it did not exceed 10-/sup 10/ g equivalents of Ra. (OTS)

Centrifuge-operated specimen staining method and apparatus

NASA Technical Reports Server (NTRS)

Feeback, Daniel L. (Inventor); Clarke, Mark S. F. (Inventor)

1999-01-01

A method of staining preselected, mounted specimens of either biological or nonbiological material enclosed within a staining chamber where the liquid staining reagents are applied and removed from the staining chamber using hypergravity as the propelling force. In the preferred embodiment, a spacecraft-operated centrifuge and method of diagnosing biological specimens while in orbit, characterized by hermetically sealing a shell assembly. The assembly contains slide stain apparatus with computer control therefor, the operative effect of which is to overcome microgravity, for example on board an International Space Station.

Molecular profiling of single cancer cells and clinical tissue specimens with semiconductor quantum dots

PubMed Central

Xing, Yun; Smith, Andrew M; Agrawal, Amit; Ruan, Gang; Nie, Shuming

2006-01-01

Semiconductor quantum dots (QDs) are a new class of fluorescent labels with broad applications in biomedical imaging, disease diagnostics, and molecular and cell biology. In comparison with organic dyes and fluorescent proteins, quantum dots have unique optical and electronic properties such as size-tunable light emission, improved signal brightness, resistance against photobleaching, and simultaneous excitation of multiple fluorescence colors. Recent advances have led to multifunctional nanoparticle probes that are highly bright and stable under complex in vitro and in vivo conditions. New designs involve encapsulating luminescent QDs with amphiphilic block copolymers, and linking the polymer coating to tumor-targeting ligands and drug-delivery functionalities. These improved QDs have opened new possibilities for real-time imaging and tracking of molecular targets in living cells, for multiplexed analysis of biomolecular markers in clinical tissue specimens, and for ultrasensitive imaging of malignant tumors in living animal models. In this article, we briefly discuss recent developments in bioaffinity QD probes and their applications in molecular profiling of individual cancer cells and clinical tissue specimens. PMID:17722280

WATER QUALITY, MERCURY, AND HEAVY METAL DEPOSITION STUDIES IN BIOLOGICAL SPECIMENS AND SEDIMENTS FOR ECOLOGICAL BASELINE DATA IN THE ISLAND PARK WATERWAYS SYSTEM, 1973

EPA Science Inventory

The water quality, mercury, and heavy metal deposition in biological specimens from the Island Park waterways (17040202) were measured to establish ecological baseline data. Neutron activation analysis was used to identify quantitatively and qualitatively approximately 20 differ...

Measurement of specimen-induced aberrations of biological samples using phase stepping interferometry.

PubMed

Schwertner, M; Booth, M J; Neil, M A A; Wilson, T

2004-01-01

Confocal or multiphoton microscopes, which deliver optical sections and three-dimensional (3D) images of thick specimens, are widely used in biology. These techniques, however, are sensitive to aberrations that may originate from the refractive index structure of the specimen itself. The aberrations cause reduced signal intensity and the 3D resolution of the instrument is compromised. It has been suggested to correct for aberrations in confocal microscopes using adaptive optics. In order to define the design specifications for such adaptive optics systems, one has to know the amount of aberrations present for typical applications such as with biological samples. We have built a phase stepping interferometer microscope that directly measures the aberration of the wavefront. The modal content of the wavefront is extracted by employing Zernike mode decomposition. Results for typical biological specimens are presented. It was found for all samples investigated that higher order Zernike modes give only a small contribution to the overall aberration. Therefore, these higher order modes can be neglected in future adaptive optics sensing and correction schemes implemented into confocal or multiphoton microscopes, leading to more efficient designs.

Orthotopic Patient-Derived Glioblastoma Xenografts in Mice.

PubMed

Xu, Zhongye; Kader, Michael; Sen, Rajeev; Placantonakis, Dimitris G

2018-01-01

Patient-derived xenografts (PDX) provide in vivo glioblastoma (GBM) models that recapitulate actual tumors. Orthotopic tumor xenografts within the mouse brain are obtained by injection of GBM stem-like cells derived from fresh surgical specimens. These xenografts reproduce GBM's histologic complexity and hallmark biological behaviors, such as brain invasion, angiogenesis, and resistance to therapy. This method has become essential for analyzing mechanisms of tumorigenesis and testing the therapeutic effect of candidate agents in the preclinical setting. Here, we describe a protocol for establishing orthotopic tumor xenografts in the mouse brain with human GBM cells.

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

Flash for Biological Dosimetry Experiments- A BEXUS 16 Project

NASA Astrophysics Data System (ADS)

Bigge, K.; Cermak, D.; Schuberg, V.; Guerin, E. A.; Blessenohl, M. A.; Passenberg, F.; Bach, M.; Hausmann, M.; Hildenbrand, G.

2015-09-01

The effects of low dose radiation on living organisms are still topic of current research and radiation protection. Complex compound radiation, such as of cosmic origin, is of special interest, since it is of pivotal significance for human space flight and, in the long run, cancer research. Fluid LAb in the StratospHere (FLASH) is a Heidelberg University student project that transported specimens of living cells of human origin into the stratosphere to investigate the effects of cosmic radiation on the 3D chromatin nanostructure of their genome. Since, owing to its complexity, cosmic radiation is extremely difficult to replicate on the ground, the FLASH project took part in the BEXUS (Balloon Experiments for University Students) program of the German Aerospace Center (DLR) and the Swedish National Space Board (SNSB) to use a balloon to get better access to cosmic radiation over several hours. To keep the cells alive and allow for in-flight fixation after given radiation exposure times in order to prevent restorative processes, a compact and fully automated fluid lab suited for low-pressure environments was designed and built. Challenges included fluid exchange of specimen buffers and temperature control, as well as low-budget insulating mounting. After the flight, the specimens fixed during the flight were subjected to further analysis. After antibody labeling specific against heterochromatin, Spectral Precision Distance Microscopy (SPDM) (an embodiment of super-resolution localization microscopy) was used, which is a new approach for the sensitive detection and analysis of structure modifying irradiation effects on organisms. This technique allows light resolution on the order of tens of nanometers. Preliminary evaluation of the data indicated reasonable differences in chromatin conformation compared to control specimen data.

Process for measuring low cadmium levels in blood and other biological specimens

DOEpatents

Peterson, David P.; Huff, Edmund A.; Bhattacharyya, Maryka H.

1994-01-01

A process for measuring low levels of cadmium in blood and other biological specimens is provided without interference from high levels of alkali metal contaminants by forming an aqueous solution and without contamination by environmental cadmium absent the proteins from the specimen, selectively removing cadmium from the aqueous solution on an anion exchange resin, thereby removing the alkali metal contaminants, resolubilizing cadmium from the resin to form a second solution and analyzing the second solution for cadmium, the process being carried out in a cadmium-free environment.

Process for measuring low cadmium levels in blood and other biological specimens

DOEpatents

Peterson, David P.; Huff, Edmund A.; Bhattacharyya, Maryka H.

1994-05-03

A process for measuring low levels of cadmium in blood and other biological specimens is provided without interference from high levels of alkali metal contaminants by forming an aqueous solution and without contamination by environmental cadmium absent the proteins from the specimen, selectively removing cadmium from the aqueous solution on an anion exchange resin, thereby removing the alkali metal contaminants, resolubilizing cadmium from the resin to form a second solution and analyzing the second solution for cadmium, the process being carried out in a cadmium-free environment.

A Study of Sandy Beach Zonation.

ERIC Educational Resources Information Center

Alexander, Steve K.

1991-01-01

Describes the study of sandy beach zonations as a seashore activity for either high school or lower-level college courses in biology, ecology, or marine biology. Students first draw a profile of a beach scene and then collect specimens from the zones of the shore. In a laboratory, students identify their specimens and relate them to the beach…

Endoscopic ultrasound-guided fine-needle aspiration with liquid-based cytologic preparation in the diagnosis of primary pancreatic lymphoma.

PubMed

Rossi, Esther Diana; Larghi, Alberto; Verna, Elizabeth C; Martini, Maurizio; Galasso, Domenico; Carnuccio, Antonella; Larocca, Luigi Maria; Costamagna, Guido; Fadda, Guido

2010-11-01

The diagnosis subtyping of lymphoma on specimens collected by endoscopic ultrasound fine-needle aspiration (EUS-FNA) can be extremely difficult. When a cytopathologist is available for the on-site evaluation, the diagnosis may be achieved by applying flow cytometric techniques. We describe our experience with immunocytochemistry (ICC) and molecular biology studies applied on EUS-FNA specimens processed with a liquid-based cytologic (LBC) preparation for the diagnosis of primary pancreatic lymphoma (PPL). Three patients with a pancreatic mass underwent EUS-FNA. The collected specimens were processed with the ThinPrep method for the cytologic diagnosis and eventual additional investigations. A morphologic picture consistent with PPL was found on the LBC specimens of the 3 patients. Subsequent ICC and molecular biology studies for immunoglobulin heavy chain gene rearrangement established the diagnosis of pancreatic large B-cell non-Hodgkin lymphoma in 2 patients and a non-Hodgkin lymphoma with plasmoblastic/immunoblastic differentiation in the remaining one. An LBC preparation can be used to diagnose and subtype PPL by applying ICC and molecular biology techniques to specimens collected with EUS-FNA. This method can be an additional processing method for EUS-FNA specimens in centers where on-site cytopathologist expertise is not available.

A Characterization of the Oral Microbiome in Allogeneic Stem Cell Transplant Patients

PubMed Central

Ames, Nancy J.; Sulima, Pawel; Ngo, Thoi; Barb, Jennifer; Munson, Peter J.; Paster, Bruce J.; Hart, Thomas C.

2012-01-01

Background The mouth is a complex biological structure inhabited by diverse bacterial communities. The purpose of this study is to describe the effects of allogeneic stem cell transplantation on the oral microbiota and to examine differences among those patients who acquired respiratory complications after transplantation. Methodology/Principal Findings All patients were consented at the National Institutes of Health, Clinical Center. Bacterial DNA was analyzed from patients' oral specimens using the Human Oral Microbe Identification Microarray. The specimens were collected from four oral sites in 45 allogeneic transplantation patients. Specimens were collected at baseline prior to transplantation, after transplantation at the nadir of the neutrophil count and after myeloid engraftment. If respiratory signs and symptoms developed, additional specimens were obtained. Patients were followed for 100 days post transplantation. Eleven patients' specimens were subjected to further statistical analysis. Many common bacterial genera, such as Streptococcus, Veillonella, Gemella, Granulicatella and Camplyobacter were identified as being present before and after transplantation. Five of 11 patients developed respiratory complications following transplantation and there was preliminary evidence that the oral microbiome changed in their oral specimens. Cluster analysis and principal component analysis revealed this change in the oral microbiota. Conclusions/Significance After allogeneic transplantation, the oral bacterial community's response to a new immune system was not apparent and many of the most common core oral taxa remained unaffected. However, the oral microbiome was affected in patients who developed respiratory signs and symptoms after transplantation. The association related to the change in the oral microbiota and respiratory complications after transplantation will be validated by future studies using high throughput molecular methods. PMID:23144704

21 CFR 58.195 - Retention of records.

Code of Federal Regulations, 2010 CFR

2010-04-01

... specimens (except those specimens obtained from mutagenicity tests and wet specimens of blood, urine, feces, and biological fluids), samples of test or control articles, and specially prepared material, which are relatively fragile and differ markedly in stability and quality during storage, shall be retained...

Studies on the Biology of Hypogeococcus pungens (sensu stricto) (Hemiptera: Pseudococcidae) in Argentina to Aid the Identification of the Mealybug Pest of Cactaceae in Puerto Rico.

PubMed

Aguirre, M B; Diaz-Soltero, H; Claps, L E; Saracho Bottero, A; Triapitsyn, S; Hasson, E; Logarzo, G A

2016-01-01

Hypogeococcus pungens Granara de Willink, sensu stricto, is a serious pest of cacti in Puerto Rico threating many Caribbean islands. A classical biological control program for H. pungens was initiated for Puerto Rico in 2010 with a survey for natural enemies of H. pungens in its native range of Argentina. Biological differences were observed between populations of H. pungens sampled on Amaranthaceae and Cactaceae. Molecular studies suggested that H. pungens populations from different host plant families are likely a complex of species. Our objective was to study the biology of H. pungens sensu stricto on specimens collected in the same locality and host plant as the holotype [Tucumán Province, Argentina; Alternanthera pungens Kunth (Amaranthaceae)]. We were interested in the reproductive biology of females, longevity and survival of adults, the effect of temperature on the development, and nymph performance (survival and development) on five Cactaceae species. We found that H. pungens s.s showed marked biological differences from the populations collected on Cactaceae and exported to Australia for the biological control of the cactus Harrisia spp. The main differences were the presence of deuterotoky parthenogenesis and the fact that H. pungens did not attack Cactaceae in the laboratory. Our results provide biological evidence that H. pungens is a species complex. We propose that the population introduced to Australia is neither Hypogeococcus festerianus Lizer y Trelles nor H. pungens, but an undescribed species with three circuli, and that the Hypogeococcus pest of cacti in Puerto Rico is not H. pungens. © The Authors 2016. Published by Oxford University Press on behalf of Entomological Society of America.

Life Sciences Research in the Centrifuge Accommodation Module of the International Space Station

NASA Technical Reports Server (NTRS)

Dalton, Bonnie P.; Plaut, Karen; Meeker, Gabrielle B.; Sun, Sid (Technical Monitor)

2000-01-01

The Centrifuge Accommodation Module (CAM) will be the home of the fundamental biology research facilities on the International Space Station (ISS). These facilities are being built by the Biological Research Project (BRP), whose goal is to oversee development of a wide variety of habitats and host systems to support life sciences research on the ISS. The habitats and host systems are designed to provide life support for a variety of specimens including cells, bacteria, yeast, plants, fish, rodents, eggs (e.g., quail), and insects. Each habitat contains specimen chambers that allow for easy manipulation of specimens and alteration of sample numbers. All habitats are capable of sustaining life support for 90 days and have automated as well as full telescience capabilities for sending habitat parameters data to investigator homesite laboratories. The habitats provide all basic life support capabilities including temperature control, humidity monitoring and control, waste management, food, media and water delivery as well as adjustable lighting. All habitats will have either an internal centrifuge or are fitted to the 2.5-meter diameter centrifuge allowing for variable centrifugation up to 2 g. Specimen chambers are removable so that the specimens can be handled in the life sciences glovebox. Laboratory support equipment is provided for handling the specimens. This includes a compound and dissecting microscope with advanced video imaging, mass measuring devices, refrigerated centrifuge for processing biological samples, pH meter, fixation and complete cryogenic storage capabilities. The research capabilities provided by the fundamental biology facilities will allow for flexibility and efficiency for long term research on the International Space Station.

Comparison of CT numbers of organs before and after plastination using standard S-10 technique.

PubMed

Shanthi, Pauline; Singh, Rabi Raja; Gibikote, Sridhar; Rabi, Suganthy

2015-05-01

Plastination is the art of preserving biological tissues with curable polymers. Imaging with plastinates offers a unique opportunity for radiographic, anatomical, pathological correlation to elucidate complex anatomical relationships. The aim of this study was to make plastinates from cadavers using the standard S-10 plastination technique and to compare the radiological properties of the tissue before and afterwards to examine the suitability of plastinates as phantoms for planning radiotherapy treatment. An above-diaphragm and a below-diaphragm specimen were obtained from a male and a female cadaver, respectively, and subjected to the standard S-10 plastination technique. CT images were obtained before and after plastination and were compared using Treatment Planning System for anatomical accuracy, volume of organs, and CT numbers. The plastinated specimens obtained were dry, robust, and durable. CT imaging of the plastinated specimens showed better anatomical detail of the organs than the preplastinate. Organ volumes were estimated by contouring the organs' outline in the CT images of the preplastinated and postplastinated specimens, revealing an average shrinkage of 25%. CT numbers were higher in the plastinated specimens except in bones and air-filled cavities such as the maxillary air sinus. Although plastination by the standard S-10 technique preserves anatomical accuracy, it increases the CT numbers of the organs because of the density of silicone, making it unsuitable for radiation dosimetry. Further improvements of the technique could yield more suitable plastinated phantoms. © 2015 Wiley Periodicals, Inc.

Efficiently Maintaining a National Resource of Historical and Contemporary Biological Collections: The NHLBI Biorepository Model.

PubMed

Shea, Katheryn E; Wagner, Elizabeth L; Marchesani, Leah; Meagher, Kevin; Giffen, Carol

2017-02-01

Reducing costs by improving storage efficiency has been a focus of the National Heart, Lung, and Blood Institute (NHLBI) Biologic Specimen Repository (Biorepository) and Biologic Specimen and Data Repositories Information Coordinating Center (BioLINCC) programs for several years. Study specimen profiles were compiled using the BioLINCC collection catalog. Cost assessments and calculations on the return on investments to consolidate or reduce a collection, were developed and implemented. Over the course of 8 months, the NHLBI Biorepository evaluated 35 collections that consisted of 1.8 million biospecimens. A total of 23 collections were selected for consolidation, with a total of 1.2 million specimens located in 21,355 storage boxes. The consolidation resulted in a savings of 4055 boxes of various sizes and 10.2 mechanical freezers (∼275 cubic feet) worth of space. As storage costs in a biorepository increase over time, the development and use of information technology tools to assess the potential advantage and feasiblity of vial consolidation can reduce maintenance expenses.

Robust analysis method for acoustic properties of biological specimens measured by acoustic microscopy

NASA Astrophysics Data System (ADS)

Arakawa, Mototaka; Mori, Shohei; Kanai, Hiroshi; Nagaoka, Ryo; Horie, Miki; Kobayashi, Kazuto; Saijo, Yoshifumi

2018-07-01

We proposed a robust analysis method for the acoustic properties of biological specimens measured by acoustic microscopy. Reflected pulse signals from the substrate and specimen were converted into frequency domains to obtain sound speed and thickness. To obtain the average acoustic properties of the specimen, parabolic approximation was performed to determine the frequency at which the amplitude of the normalized spectrum became maximum or minimum, considering the sound speed and thickness of the specimens and the operating frequency of the ultrasonic device used. The proposed method was demonstrated for a specimen of malignant melanoma of the skin by using acoustic microscopy attaching a concave transducer with a center frequency of 80 MHz. The variations in sound speed and thickness analyzed by the proposed method were markedly smaller than those analyzed by the method based on an autoregressive model. The proposed method is useful for the analysis of the acoustic properties of bilogical tissues or cells.

National Aeronautics and Space Administration Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, Kathleen A.; Pietrzyk, Robert a.; Johnson, Mary Anne

2008-01-01

The National Aeronautics and Space Administration Biological Specimen Repository (Repository) is a storage bank that is used to maintain biological specimens over extended periods of time and under well-controlled conditions. Samples from the International Space Station (ISS), including blood and urine, will be collected, processed and archived during the preflight, inflight and postflight phases of ISS missions. This investigation has been developed to archive biosamples for use as a resource for future space flight related research. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can study space flight related changes and investigate physiological markers. The development of the National Aeronautics and Space Administration Biological Specimen Repository will allow for the collection, processing, storage, maintenance, and ethical distribution of biosamples to meet goals of scientific and programmatic relevance to the space program. Archiving of the biosamples will provide future research opportunities including investigating patterns of physiological changes, analysis of components unknown at this time or analyses performed by new methodologies.

An Automated Peak Identification/Calibration Procedure for High-Dimensional Protein Measures From Mass Spectrometers.

PubMed

Yasui, Yutaka; McLerran, Dale; Adam, Bao-Ling; Winget, Marcy; Thornquist, Mark; Feng, Ziding

2003-01-01

Discovery of "signature" protein profiles that distinguish disease states (eg, malignant, benign, and normal) is a key step towards translating recent advancements in proteomic technologies into clinical utilities. Protein data generated from mass spectrometers are, however, large in size and have complex features due to complexities in both biological specimens and interfering biochemical/physical processes of the measurement procedure. Making sense out of such high-dimensional complex data is challenging and necessitates the use of a systematic data analytic strategy. We propose here a data processing strategy for two major issues in the analysis of such mass-spectrometry-generated proteomic data: (1) separation of protein "signals" from background "noise" in protein intensity measurements and (2) calibration of protein mass/charge measurements across samples. We illustrate the two issues and the utility of the proposed strategy using data from a prostate cancer biomarker discovery project as an example.

Anti-contamination device for cryogenic soft X-ray diffraction microscopy

DOE PAGES

Huang, Xiaojing; Miao, Huijie; Nelson, Johanna; ...

2011-05-01

Cryogenic microscopy allows one to view frozen hydrated biological and soft matter specimens with good structural preservation and a high degree of stability against radiation damage. We describe a liquid nitrogen-cooled anti-contamination device for cryogenic X-ray diffraction microscopy. The anti-contaminator greatly reduces the buildup of ice layers on the specimen due to condensation of residual water vapor in the experimental vacuum chamber. We show by coherent X-ray diffraction measurements that this leads to fivefold reduction of background scattering, which is important for far-field X-ray diffraction microscopy of biological specimens.

Expansion Mini-Microscopy: An Enabling Alternative in Point-of-Care Diagnostics

PubMed Central

Zhang, Yu Shrike; Santiago, Grissel Trujillo-de; Alvarez, Mario Moisés; Schiff, Steven J.; Boyden, Edward S.; Khademhosseini, Ali

2017-01-01

Diagnostics play a significant role in health care. In the developing world and low-resource regions the utility for point-of-care (POC) diagnostics becomes even greater. This need has long been recognized, and diagnostic technology has seen tremendous progress with the development of portable instrumentation such as miniature imagers featuring low complexity and cost. However, such inexpensive devices have not been able to achieve a resolution sufficient for POC detection of pathogens at very small scales, such as single-cell parasites, bacteria, fungi, and viruses. To this end, expansion microscopy (ExM) is a recently developed technique that, by physically expanding preserved biological specimens through a chemical process, enables super-resolution imaging on conventional microscopes and improves imaging resolution of a given microscope without the need to modify the existing microscope hardware. Here we review recent advances in ExM and portable imagers, respectively, and discuss the rational combination of the two technologies, that we term expansion mini-microscopy (ExMM). In ExMM, the physical expansion of a biological sample followed by imaging on a mini-microscope achieves a resolution as high as that attainable by conventional high-end microscopes imaging non-expanded samples, at significant reduction in cost. We believe that this newly developed ExMM technique is likely to find widespread applications in POC diagnostics in resource-limited and remote regions by expanded-scale imaging of biological specimens that are otherwise not resolvable using low-cost imagers. PMID:29062977

Probing the Potential of Neutron Imaging for Biomedical and Biological Applications

NASA Astrophysics Data System (ADS)

Watkin, K. L.; Bilheux, H. Z.; Ankner, J. F.

Neutron imaging of biological specimens began soon after the discovery of the neutron by Chadwick in 1932. The first samples included tumors in tissues, internal organs in rats, and bones. These studies mainly employed thermal neutrons and were often compared with X-ray images of the same or equivalent samples. Although neutron scattering is widely used in biological studies, neutron imaging has yet to be exploited to its full capability in this area. This chapter summarizes past and current research efforts to apply neutron radiography to the study of biological specimens, in the expectation that clinical and medical research, as well as forensic science, may benefit from it.

Electron microprobe analysis program for biological specimens: BIOMAP

NASA Technical Reports Server (NTRS)

Edwards, B. F.

1972-01-01

BIOMAP is a Univac 1108 compatible program which facilitates the electron probe microanalysis of biological specimens. Input data are X-ray intensity data from biological samples, the X-ray intensity and composition data from a standard sample and the electron probe operating parameters. Outputs are estimates of the weight percentages of the analyzed elements, the distribution of these estimates for sets of red blood cells and the probabilities for correlation between elemental concentrations. An optional feature statistically estimates the X-ray intensity and residual background of a principal standard relative to a series of standards.

Identification of host response signatures of infection.

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

Branda, Steven S.; Sinha, Anupama; Bent, Zachary

2013-02-01

Biological weapons of mass destruction and emerging infectious diseases represent a serious and growing threat to our national security. Effective response to a bioattack or disease outbreak critically depends upon efficient and reliable distinguishing between infected vs healthy individuals, to enable rational use of scarce, invasive, and/or costly countermeasures (diagnostics, therapies, quarantine). Screening based on direct detection of the causative pathogen can be problematic, because culture- and probe-based assays are confounded by unanticipated pathogens (e.g., deeply diverged, engineered), and readily-accessible specimens (e.g., blood) often contain little or no pathogen, particularly at pre-symptomatic stages of disease. Thus, in addition to themore » pathogen itself, one would like to detect infection-specific host response signatures in the specimen, preferably ones comprised of nucleic acids (NA), which can be recovered and amplified from tiny specimens (e.g., fingerstick draws). Proof-of-concept studies have not been definitive, however, largely due to use of sub-optimal sample preparation and detection technologies. For purposes of pathogen detection, Sandia has developed novel molecular biology methods that enable selective isolation of NA unique to, or shared between, complex samples, followed by identification and quantitation via Second Generation Sequencing (SGS). The central hypothesis of the current study is that variations on this approach will support efficient identification and verification of NA-based host response signatures of infectious disease. To test this hypothesis, we re-engineered Sandia's sophisticated sample preparation pipelines, and developed new SGS data analysis tools and strategies, in order to pioneer use of SGS for identification of host NA correlating with infection. Proof-of-concept studies were carried out using specimens drawn from pathogen-infected non-human primates (NHP). This work provides a strong foundation for large-scale, highly-efficient efforts to identify and verify infection-specific host NA signatures in human populations.« less

Functional Inference of Complex Anatomical Tendinous Networks at a Macroscopic Scale via Sparse Experimentation

PubMed Central

Saxena, Anupam; Lipson, Hod; Valero-Cuevas, Francisco J.

2012-01-01

In systems and computational biology, much effort is devoted to functional identification of systems and networks at the molecular-or cellular scale. However, similarly important networks exist at anatomical scales such as the tendon network of human fingers: the complex array of collagen fibers that transmits and distributes muscle forces to finger joints. This network is critical to the versatility of the human hand, and its function has been debated since at least the 16th century. Here, we experimentally infer the structure (both topology and parameter values) of this network through sparse interrogation with force inputs. A population of models representing this structure co-evolves in simulation with a population of informative future force inputs via the predator-prey estimation-exploration algorithm. Model fitness depends on their ability to explain experimental data, while the fitness of future force inputs depends on causing maximal functional discrepancy among current models. We validate our approach by inferring two known synthetic Latex networks, and one anatomical tendon network harvested from a cadaver's middle finger. We find that functionally similar but structurally diverse models can exist within a narrow range of the training set and cross-validation errors. For the Latex networks, models with low training set error [<4%] and resembling the known network have the smallest cross-validation errors [∼5%]. The low training set [<4%] and cross validation [<7.2%] errors for models for the cadaveric specimen demonstrate what, to our knowledge, is the first experimental inference of the functional structure of complex anatomical networks. This work expands current bioinformatics inference approaches by demonstrating that sparse, yet informative interrogation of biological specimens holds significant computational advantages in accurate and efficient inference over random testing, or assuming model topology and only inferring parameters values. These findings also hold clues to both our evolutionary history and the development of versatile machines. PMID:23144601

Functional inference of complex anatomical tendinous networks at a macroscopic scale via sparse experimentation.

PubMed

Saxena, Anupam; Lipson, Hod; Valero-Cuevas, Francisco J

2012-01-01

In systems and computational biology, much effort is devoted to functional identification of systems and networks at the molecular-or cellular scale. However, similarly important networks exist at anatomical scales such as the tendon network of human fingers: the complex array of collagen fibers that transmits and distributes muscle forces to finger joints. This network is critical to the versatility of the human hand, and its function has been debated since at least the 16(th) century. Here, we experimentally infer the structure (both topology and parameter values) of this network through sparse interrogation with force inputs. A population of models representing this structure co-evolves in simulation with a population of informative future force inputs via the predator-prey estimation-exploration algorithm. Model fitness depends on their ability to explain experimental data, while the fitness of future force inputs depends on causing maximal functional discrepancy among current models. We validate our approach by inferring two known synthetic Latex networks, and one anatomical tendon network harvested from a cadaver's middle finger. We find that functionally similar but structurally diverse models can exist within a narrow range of the training set and cross-validation errors. For the Latex networks, models with low training set error [<4%] and resembling the known network have the smallest cross-validation errors [∼5%]. The low training set [<4%] and cross validation [<7.2%] errors for models for the cadaveric specimen demonstrate what, to our knowledge, is the first experimental inference of the functional structure of complex anatomical networks. This work expands current bioinformatics inference approaches by demonstrating that sparse, yet informative interrogation of biological specimens holds significant computational advantages in accurate and efficient inference over random testing, or assuming model topology and only inferring parameters values. These findings also hold clues to both our evolutionary history and the development of versatile machines.

High-performance serial block-face SEM of nonconductive biological samples enabled by focal gas injection-based charge compensation.

PubMed

Deerinck, T J; Shone, T M; Bushong, E A; Ramachandra, R; Peltier, S T; Ellisman, M H

2018-05-01

A longstanding limitation of imaging with serial block-face scanning electron microscopy is specimen surface charging. This charging is largely due to the difficulties in making biological specimens and the resins in which they are embedded sufficiently conductive. Local accumulation of charge on the specimen surface can result in poor image quality and distortions. Even minor charging can lead to misalignments between sequential images of the block-face due to image jitter. Typically, variable-pressure SEM is used to reduce specimen charging, but this results in a significant reduction to spatial resolution, signal-to-noise ratio and overall image quality. Here we show the development and application of a simple system that effectively mitigates specimen charging by using focal gas injection of nitrogen over the sample block-face during imaging. A standard gas injection valve is paired with a precisely positioned but retractable application nozzle, which is mechanically coupled to the reciprocating action of the serial block-face ultramicrotome. This system enables the application of nitrogen gas precisely over the block-face during imaging while allowing the specimen chamber to be maintained under high vacuum to maximise achievable SEM image resolution. The action of the ultramicrotome drives the nozzle retraction, automatically moving it away from the specimen area during the cutting cycle of the knife. The device described was added to a Gatan 3View system with minimal modifications, allowing high-resolution block-face imaging of even the most charge prone of epoxy-embedded biological samples. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Depth-resolved dual-beamlet vibrometry based on Fourier domain low coherence interferometry

PubMed Central

Choudhury, Niloy; Chen, Fangyi; Wang, Ruikang K.; Jacques, Steven L.; Nuttall, Alfred L.

2013-01-01

Abstract. We present an optical vibrometer based on delay-encoded, dual-beamlet phase-sensitive Fourier domain interferometric system to provide depth-resolved subnanometer scale vibration information from scattering biological specimens. System characterization, calibration, and preliminary vibrometry with biological specimens were performed. The proposed system has the potential to provide both amplitude and direction of vibration of tissue microstructures on a single two-dimensional plane. PMID:23455961

Characteristics of coated copper wire specimens using high frequency ultrasonic complex vibration welding equipments.

PubMed

Tsujino, J; Ihara, S; Harada, Y; Kasahara, K; Sakamaki, N

2004-04-01

Welding characteristic of thin coated copper wires were studied using 40, 60, 100 kHz ultrasonic complex vibration welding equipments with elliptical to circular vibration locus. The complex vibration systems consisted of a longitudinal-torsional vibration converter and a driving longitudinal vibration system. Polyurethane coated copper wires of 0.036 mm outer diameter and copper plates of 0.3 mm thickness and the other dimension wires were used as welding specimens. The copper wire part is completely welded on the copper substrate and the insulated coating material is driven from welded area to outsides of the wire specimens by high frequency complex vibration.

The use of museum specimens with high-throughput DNA sequencers

PubMed Central

Burrell, Andrew S.; Disotell, Todd R.; Bergey, Christina M.

2015-01-01

Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists’ ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials. PMID:25532801

Maximizing Modern Distribution of Complex Anatomical Spatial Information: 3D Reconstruction and Rapid Prototype Production of Anatomical Corrosion Casts of Human Specimens

ERIC Educational Resources Information Center

Li, Jianyi; Nie, Lanying; Li, Zeyu; Lin, Lijun; Tang, Lei; Ouyang, Jun

2012-01-01

Anatomical corrosion casts of human specimens are useful teaching aids. However, their use is limited due to ethical dilemmas associated with their production, their lack of perfect reproducibility, and their consumption of original specimens in the process of casting. In this study, new approaches with modern distribution of complex anatomical…

Functional protease profiling for diagnosis of malignant disease.

PubMed

Findeisen, Peter; Neumaier, Michael

2012-01-01

Clinical proteomic profiling by mass spectrometry (MS) aims at uncovering specific alterations within mass profiles of clinical specimens that are of diagnostic value for the detection and classification of various diseases including cancer. However, despite substantial progress in the field, the clinical proteomic profiling approaches have not matured into routine diagnostic applications so far. Their limitations are mainly related to high-abundance proteins and their complex processing by a multitude of endogenous proteases thus making rigorous standardization difficult. MS is biased towards the detection of low-molecular-weight peptides. Specifically, in serum specimens, the particular fragments of proteolytically degraded proteins are amenable to MS analysis. Proteases are known to be involved in tumour progression and tumour-specific proteases are released into the blood stream presumably as a result of invasive progression and metastasis. Thus, the determination of protease activity in clinical specimens from patients with malignant disease can offer diagnostic and also therapeutic options. The identification of specific substrates for tumour proteases in complex biological samples is challenging, but proteomic screens for proteases/substrate interactions are currently experiencing impressive progress. Such proteomic screens include peptide-based libraries, differential isotope labelling in combination with MS, quantitative degradomic analysis of proteolytically generated neo-N-termini, monitoring the degradation of exogenous reporter peptides with MS, and activity-based protein profiling. In the present article, we summarize and discuss the current status of proteomic techniques to identify tumour-specific protease-substrate interactions for functional protease profiling. Thereby, we focus on the potential diagnostic use of the respective approaches. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Endoprotease profiling with double-tagged peptide substrates: a new diagnostic approach in oncology.

PubMed

Peccerella, Teresa; Lukan, Nadine; Hofheinz, Ralf; Schadendorf, Dirk; Kostrezewa, Markus; Neumaier, Michael; Findeisen, Peter

2010-02-01

The measurement of disease-related proteolytic activity in complex biological matrices like serum is of emerging interest to improve the diagnosis of malignant diseases. We developed a mass spectrometry (MS)-based functional proteomic profiling approach that tracks degradation of artificial endoprotease substrates in serum specimens. The synthetic reporter peptides that are cleaved by tumor-associated endopeptidases were systematically optimized with regard to flanking affinity tags, linkers, and stabilizing elements. Serum specimens were incubated with reporter peptides under standardized conditions and the peptides subsequently extracted with affinity chromatography before MS. In a pilot study an optimized reporter peptide with the cleavage motif WKPYDAADL was added to serum specimens from colorectal tumor patients (n = 50) and healthy controls (n = 50). This reporter peptide comprised a known cleavage site for the cysteine-endopeptidase "cancer procoagulant." Serial affinity chromatography using biotin- and 6xHis tags was superior to the single affinity enrichment using only 6xHis tags. Furthermore, protease-resistant stop elements ensured signal accumulation after prolonged incubation. In contrast, signals from reporter peptides without stop elements vanished completely after prolonged incubation owing to their total degradation. Reporter-peptide spiking showed good reproducibility, and the difference in proteolytic activity between serum specimens from cancer patients and controls was highly significant (P < 0.001). The introduction of a few structural key elements (affinity tags, linkers, d-amino acids) into synthetic reporter peptides increases the diagnostic sensitivity for MS-based protease profiling of serum specimens. This new approach might lead to functional MS-based protease profiling for improved disease classification.

Immunological Insights into the Life and Times of the Extinct Tasmanian Tiger (Thylacinus cynocephalus).

PubMed

Old, Julie M

2015-01-01

The thylacine (Thylacinus cynocephalus) was Australia's largest marsupial carnivore until its extinction within the last century. There remains considerable interest and debate regarding the biology of this species. Studies of thylacine biology are now limited to preserved specimens, and parts thereof, as well as written historical accounts of its biology. This study describes the development of the immune tissues of a pouch young thylacine, one of only eleven in existence, and the only specimen to be histologically sectioned. The appearance of the immune tissue of the developing pouch young thylacine is compared to the immune tissues of extant marsupials, providing insights into the immunity, biology and ecology of the extinct thylacine.

Soft x-ray holographic tomography for biological specimens

NASA Astrophysics Data System (ADS)

Gao, Hongyi; Chen, Jianwen; Xie, Honglan; Li, Ruxin; Xu, Zhizhan; Jiang, Shiping; Zhang, Yuxuan

2003-10-01

In this paper, we present some experimental results on X -ray holography, holographic tomography, and a new holographic tomography method called pre-amplified holographic tomography is proposed. Due to the shorter wavelength and the larger penetration depths, X-rays provide the potential of higher resolution in imaging techniques, and have the ability to image intact, living, hydrated cells w ithout slicing, dehydration, chemical fixation or stain. Recently, using X-ray source in National Synchrotron Radiation Laboratory in Hefei, we have successfully performed some soft X-ray holography experiments on biological specimen. The specimens used in the experiments was the garlic clove epidermis, we got their X-ray hologram, and then reconstructed them by computer programs, the feature of the cell walls, the nuclei and some cytoplasm were clearly resolved. However, there still exist some problems in realization of practical 3D microscopic imaging due to the near-unity refractive index of the matter. There is no X-ray optics having a sufficient high numerical aperture to achieve a depth resolution that is comparable to the transverse resolution. On the other hand, computer tomography needs a record of hundreds of views of the test object at different angles for high resolution. This is because the number of views required for a densely packed object is equal to the object radius divided by the desired depth resolution. Clearly, it is impractical for a radiation-sensitive biological specimen. Moreover, the X-ray diffraction effect makes projection data blur, this badly degrades the resolution of the reconstructed image. In order to observe 3D structure of the biological specimens, McNulty proposed a new method for 3D imaging called "holographic tomography (HT)" in which several holograms of the specimen are recorded from various illumination directions and combined in the reconstruction step. This permits the specimens to be sampled over a wide range of spatial frequencies to improve the depth resolution. In NSRL, we performed soft X-ray holographic tomography experiments. The specimen was the spider filaments and PM M A as recording medium. By 3D CT reconstruction of the projection data, three dimensional density distribution of the specimen was obtained. Also, we developed a new X-ray holographic tomography m ethod called pre-amplified holographic tomography. The method permits a digital real-time 3D reconstruction with high-resolution and a simple and compact experimental setup as well.

Iterative expansion microscopy.

PubMed

Chang, Jae-Byum; Chen, Fei; Yoon, Young-Gyu; Jung, Erica E; Babcock, Hazen; Kang, Jeong Seuk; Asano, Shoh; Suk, Ho-Jun; Pak, Nikita; Tillberg, Paul W; Wassie, Asmamaw T; Cai, Dawen; Boyden, Edward S

2017-06-01

We recently developed a method called expansion microscopy, in which preserved biological specimens are physically magnified by embedding them in a densely crosslinked polyelectrolyte gel, anchoring key labels or biomolecules to the gel, mechanically homogenizing the specimen, and then swelling the gel-specimen composite by ∼4.5× in linear dimension. Here we describe iterative expansion microscopy (iExM), in which a sample is expanded ∼20×. After preliminary expansion a second swellable polymer mesh is formed in the space newly opened up by the first expansion, and the sample is expanded again. iExM expands biological specimens ∼4.5 × 4.5, or ∼20×, and enables ∼25-nm-resolution imaging of cells and tissues on conventional microscopes. We used iExM to visualize synaptic proteins, as well as the detailed architecture of dendritic spines, in mouse brain circuitry.

Iterative expansion microscopy

PubMed Central

Chang, Jae-Byum; Chen, Fei; Yoon, Young-Gyu; Jung, Erica E.; Babcock, Hazen; Kang, Jeong Seuk; Asano, Shoh; Suk, Ho-Jun; Pak, Nikita; Tillberg, Paul W.; Wassie, Asmamaw; Cai, Dawen; Boyden, Edward S.

2017-01-01

We recently discovered it was possible to physically magnify preserved biological specimens by embedding them in a densely crosslinked polyelectrolyte gel, anchoring key labels or biomolecules to the gel, mechanically homogenizing the specimen, and then swelling the gel-specimen composite by ~4.5x in linear dimension, a process we call expansion microscopy (ExM). Here we describe iterative expansion microscopy (iExM), in which a sample is expanded, then a second swellable polymer mesh is formed in the space newly opened up by the first expansion, and finally the sample is expanded again. iExM expands biological specimens ~4.5 × 4.5 or ~20x, and enables ~25 nm resolution imaging of cells and tissues on conventional microscopes. We used iExM to visualize synaptic proteins, as well as the detailed architecture of dendritic spines, in mouse brain circuitry. PMID:28417997

Specimen preparation for NanoSIMS analysis of biological materials

NASA Astrophysics Data System (ADS)

Grovenor, C. R. M.; Smart, K. E.; Kilburn, M. R.; Shore, B.; Dilworth, J. R.; Martin, B.; Hawes, C.; Rickaby, R. E. M.

2006-07-01

In order to achieve reliable and reproducible analysis of biological materials by SIMS, it is critical both that the chosen specimen preparation method does not modify substantially the in vivo chemistry that is the focus of the study and that any chemical information obtained can be calibrated accurately by selection of appropriate standards. In Oxford, we have been working with our new Cameca NanoSIMS50 on two very distinct classes of biological materials; the first where the sample preparation problems are relatively undemanding - human hair - but calibration for trace metal analysis is a critical issue and, the second, marine coccoliths and hyperaccumulator plants where reliable specimen preparation by rapid freezing and controlled drying to preserve the distribution of diffusible species is the first and most demanding requirement, but worthwhile experiments on tracking key elements can still be undertaken even when it is clear that some redistribution of the most diffusible ions has occurred.

A universal fluid cell for the imaging of biological specimens in the atomic force microscope.

PubMed

Kasas, Sandor; Radotic, Ksenja; Longo, Giovanni; Saha, Bashkar; Alonso-Sarduy, Livan; Dietler, Giovanni; Roduit, Charles

2013-04-01

Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set-up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Copyright © 2013 Wiley Periodicals, Inc.

A combined method for correlative 3D imaging of biological samples from macro to nano scale

NASA Astrophysics Data System (ADS)

Kellner, Manuela; Heidrich, Marko; Lorbeer, Raoul-Amadeus; Antonopoulos, Georgios C.; Knudsen, Lars; Wrede, Christoph; Izykowski, Nicole; Grothausmann, Roman; Jonigk, Danny; Ochs, Matthias; Ripken, Tammo; Kühnel, Mark P.; Meyer, Heiko

2016-10-01

Correlative analysis requires examination of a specimen from macro to nano scale as well as applicability of analytical methods ranging from morphological to molecular. Accomplishing this with one and the same sample is laborious at best, due to deformation and biodegradation during measurements or intermediary preparation steps. Furthermore, data alignment using differing imaging techniques turns out to be a complex task, which considerably complicates the interconnection of results. We present correlative imaging of the accessory rat lung lobe by combining a modified Scanning Laser Optical Tomography (SLOT) setup with a specially developed sample preparation method (CRISTAL). CRISTAL is a resin-based embedding method that optically clears the specimen while allowing sectioning and preventing degradation. We applied and correlated SLOT with Multi Photon Microscopy, histological and immunofluorescence analysis as well as Transmission Electron Microscopy, all in the same sample. Thus, combining CRISTAL with SLOT enables the correlative utilization of a vast variety of imaging techniques.

Mammals of the Braulio Carrillo- La Selva Complex, Costa Rica

USGS Publications Warehouse

Timm, Robert M.; Wilson, Don E.; Clauson, Barbara L.; LaVal, Richard K.; Vaughan, Christopher S.

1989-01-01

Costa Rica's La Selva-Braulio Carrillo complex encompasses a 60-km protected corridor of Caribbean rain and cloud forest extending from 30 m at the La Selva Biological Station to 2,906 m at the top of Volcán Barva. The 52,000-ha complex covers four life zones and two transitional zones, including tropical wet forest, tropical wet forest cool-transition, tropical premontane wet-transition rain forest, tropical premontane rain forest, lower montane rain forest, and montane rain forest. Located in the northeastern part of the country, the area is representative of Central American Caribbean slope forests that extend from Mexico to Panama. The extensive elevational gradient of the complex provides protected habitat for a variety of altitudinal migrants. With support from the National Geographic Society and Rice Foundation, the Organization for Tropical Studies organized a biological survey of the complex in early 1986. The mammal team worked at six sites along the elevational transect established by the expedition: 300 m, 700 m, 1,000 m, 1,500 m, 2,050 m, and 2,600 m. We supplemented our collecting records with unpublished records made available by colleagues, records in the published literature, and specimens in museum collections. In addition, observations recorded by a variety of observers at the La Selva Biological Station are summarized. The mammal fauna of the complex comprises 142 species including 79 bats, 23 rodents, 15 carnivores, 7 marsupials, 6 edentates, 4 artiodactyls, 3 primates, 2 rabbits, 2 shrews, and 1 perissodactyl. At least 10 additional species are likely to occur there. The only species of mammal likely to have been extirpated from the area is the giant anteater. Recognizing the importance of the area to wildlife and to mankind in general, the government of Costa Rica added 13,500 ha to the complex on 13 April 1986. This area, previously known as the “Zona Protectora,” provided the mid-elevational link between the lowlands of the La Selva Biological Station and the montane forests of Braulio Carrillo National Park. Unfortunately, destruction of the rain forests surrounding the complex will soon render it an isolated island of protected forest. Thus, the area will become increasingly valuable as a refuge for many species with home ranges that require extensive tracts of undisturbed habitat.

Learning About Bird Species on the Primary Level

NASA Astrophysics Data System (ADS)

Randler, Christoph

2009-04-01

Animal species identification is often emphasized as a basic prerequisite for an understanding of ecology because ecological interactions are based on interactions between species at least as it is taught on the school level. Therefore, training identification skills or using identification books seems a worthwhile task in biology education, and should already start on the primary level. On the primary level, however, complex interactions could not be taught but pupils are often interested in basic knowledge about species. We developed a hands-on, group-based and self-determined learning phase organized in workstations. About 138 pupils (2nd-4th graders) participated in this study. The two groups received an identification treatment with six different bird species. These were presented either as soft toys or as taxidermy specimen. Both groups scored similar prior and after the treatment (posttest 1) and with a delay of 6-8 weeks (posttest 2). More complex general linear modeling revealed a significant influence of prior knowledge, treatment and of grade (2nd, 3rd or 4th grade) on the first posttest while in the retention test gender differences emerged. We suggest that soft toys may be of equal value for teaching species identification on the primary level compared to natural taxidermic specimen, especially when considering pricing, insensitivity to handling, and contamination with agents used for preservation.

Soft x-ray contact imaging of biological specimens using a laser-produced plasma as an x-ray source

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

Cheng, P.C.

The use of a laser-produced plasma as an x-ray source provides significant advantages over other types of sources for x-ray microradiography of, particularly, living biological specimens. The pulsed nature of the x-rays enables imaging of the specimen in a living state, and the small source size minimizes penumbral blurring. This makes it possible to make an exposure close to the source, thereby increasing the x-ray intensity. In this article, we will demonstrate the applications of x-ray contact microradiography in structural and developmental botany such as the localization of silica deposition and the floral morphologenesis of maize.

Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope

PubMed Central

Wu, J.S.; Kim, A. M.; Bleher, R.; Myers, B.D.; Marvin, R. G.; Inada, H.; Nakamura, K.; Zhang, X.F.; Roth, E.; Li, S.Y.; Woodruff, T. K.; O'Halloran, T. V.; Dravid, Vinayak P.

2013-01-01

A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room- and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. PMID:23500508

Correlative Instrumental Neutron Activation Analysis, Light Microscopy, Transmission Electron Microscopy, and X-ray Microanalysis for Qualitative and Quantitative Detection of Colloidal Gold Spheres in Biological Specimens

NASA Astrophysics Data System (ADS)

Hillyer, Julián F.; Albrecht, Ralph M.

1998-10-01

: Colloidal gold, conjugated to ligands or antibodies, is routinely used as a label for the detection of cell structures by light (LM) and electron microscopy (EM). To date, several methods to count the number of colloidal gold labels have been employed with limited success. Instrumental neutron activation analysis (INAA), a physical method for the analysis of the elemental composition of materials, can be used to provide a quantitative index of gold accumulation in bulk specimens. Given that gold is not naturally found in biological specimens in any substantial amount and that colloidal gold and ligand conjugates can be prepared to yield uniform bead sizes, the amount of label can be calculated in bulk biological samples by INAA. Here we describe the use of INAA, LM, transmission EM, and X-ray microanalysis (EDX) in a model to determine both distribution (localization) and amount of colloidal gold at the organ, tissue, cellular, and ultrastructural levels in whole animal systems following administration. In addition, the sensitivity for gold in biological specimens by INAA is compared with that of inductively coupled plasma mass spectrometry (ICP-MS). The correlative use of INAA, LM, TEM, and EDX can be useful, for example, in the quantitative and qualitative tracking of various labeled molecular species following administration in vivo.

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT)

PubMed Central

Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

2016-01-01

Abstract Background During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. New information The Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices. PMID:27956848

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT).

PubMed

Keklikoglou, Kleoniki; Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

2016-01-01

During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CT vlab ) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. The Micro-CT vlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CT vlab can be accessed either on a normal computer or through a dedicated version for mobile devices.

Laser-induced breakdown spectroscopy (LIBS): an overview of recent progress and future potential for biomedical applications.

PubMed

Rehse, S J; Salimnia, H; Miziolek, A W

2012-02-01

The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind.

Immunological Insights into the Life and Times of the Extinct Tasmanian Tiger (Thylacinus cynocephalus)

PubMed Central

Old, Julie M.

2015-01-01

The thylacine (Thylacinus cynocephalus) was Australia’s largest marsupial carnivore until its extinction within the last century. There remains considerable interest and debate regarding the biology of this species. Studies of thylacine biology are now limited to preserved specimens, and parts thereof, as well as written historical accounts of its biology. This study describes the development of the immune tissues of a pouch young thylacine, one of only eleven in existence, and the only specimen to be histologically sectioned. The appearance of the immune tissue of the developing pouch young thylacine is compared to the immune tissues of extant marsupials, providing insights into the immunity, biology and ecology of the extinct thylacine. PMID:26655868

Mechanical properties of biological specimens explored by atomic force microscopy

NASA Astrophysics Data System (ADS)

Kasas, S.; Longo, G.; Dietler, G.

2013-04-01

The atomic force microscope is a widely used surface scanning apparatus capable of reconstructing at a nanometric scale resolution the 3D morphology of biological samples. Due to its unique sensitivity, it is now increasingly used as a force sensor, to characterize the mechanical properties of specimens with a similar lateral resolution. This unique capability has produced, in the last years, a vast increase in the number of groups that have exploited the versatility and sensitivity of the instrument to explore the nanomechanics of various samples in the fields of biology, microbiology and medicine. In this review we outline the state of the art in this field, reporting the most interesting recent works involving the exploration of the nanomechanical properties of various biological samples.

DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation.

PubMed

Koroiva, Ricardo; Pepinelli, Mateus; Rodrigues, Marciel Elio; Roque, Fabio de Oliveira; Lorenz-Lemke, Aline Pedroso; Kvist, Sebastian

2017-01-01

We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of "Cerrado" and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0-2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation.

Impregnation of soft biological specimens with thermosetting resins and elastomers.

PubMed

von Hagens, G

1979-06-01

A new method for impregnation of biological specimens with thermosetting resins and elastomers is described. The method has the advantage that the original relief of the surface is retained. The impregnation is carried out by utilizing the difference between the high vapor tension of the intermedium (e.g., methylene chloride) and the low vapor tension of the solution to be polymerized. After impregnation, the specimen is subject to polymerization conditions without surrounding embedding material. The optical and mechanical properties can be selected by proper choice from various kinds of resins and different procedures, for example, by complete or incomplete impregnation. Acrylic resins, polyester resins, epoxy resins, polyurethanes and silicone rubber have been found suitable for the method. Excellent results have been obtained using transparent silicone rubber since after treatment the specimens are still flexible and resilient, and have retained their natural appearance.

Ultrastable gold substrates: Properties of a support for high-resolution electron cryomicroscopy of biological specimens

PubMed Central

Russo, Christopher J.; Passmore, Lori A.

2016-01-01

Electron cryomicroscopy (cryo-EM) allows structure determination of a wide range of biological molecules and specimens. All-gold supports improve cryo-EM images by reducing radiation-induced motion and image blurring. Here we compare the mechanical and electrical properties of all-gold supports to amorphous carbon foils. Gold supports are more conductive, and have suspended foils that are not compressed by differential contraction when cooled to liquid nitrogen temperatures. These measurements show how the choice of support material and geometry can reduce specimen movement by more than an order of magnitude during low-dose imaging. We provide methods for fabrication of all-gold supports and preparation of vitrified specimens. We also analyse illumination geometry for optimal collection of high resolution, low-dose data. Together, the support structures and methods herein can improve the resolution and quality of images from any electron cryomicroscope. PMID:26592474

Performance characteristics of the new Abbott Real Time MTB assay for detection of Mycobacterium tuberculosis complex in respiratory specimens.

PubMed

Vinuesa, Víctor; Navarro, David; Poujois, Sandrine; Zaragoza, Susana; Borrás, Rafael

2016-03-01

The performance of the Abbott Real Time MTB assay for detection of Mycobacterium tuberculosis complex in respiratory specimens was evaluated using a standard culture as the reference. The overall concordance between both methods was 0.95. The assay displayed an excellent sensitivity (100% for smear-positive/92.3% for smear-negative specimens) and specificity (100%). Copyright © 2015 Elsevier Inc. All rights reserved.

Integrated light-sheet imaging and flow-based enquiry (iLIFE) system for 3D in-vivo imaging of multicellular organism

NASA Astrophysics Data System (ADS)

Rasmi, Chelur K.; Padmanabhan, Sreedevi; Shirlekar, Kalyanee; Rajan, Kanhirodan; Manjithaya, Ravi; Singh, Varsha; Mondal, Partha Pratim

2017-12-01

We propose and demonstrate a light-sheet-based 3D interrogation system on a microfluidic platform for screening biological specimens during flow. To achieve this, a diffraction-limited light-sheet (with a large field-of-view) is employed to optically section the specimens flowing through the microfluidic channel. This necessitates optimization of the parameters for the illumination sub-system (illumination intensity, light-sheet width, and thickness), microfluidic specimen platform (channel-width and flow-rate), and detection sub-system (camera exposure time and frame rate). Once optimized, these parameters facilitate cross-sectional imaging and 3D reconstruction of biological specimens. The proposed integrated light-sheet imaging and flow-based enquiry (iLIFE) imaging technique enables single-shot sectional imaging of a range of specimens of varying dimensions, ranging from a single cell (HeLa cell) to a multicellular organism (C. elegans). 3D reconstruction of the entire C. elegans is achieved in real-time and with an exposure time of few hundred micro-seconds. A maximum likelihood technique is developed and optimized for the iLIFE imaging system. We observed an intracellular resolution for mitochondria-labeled HeLa cells, which demonstrates the dynamic resolution of the iLIFE system. The proposed technique is a step towards achieving flow-based 3D imaging. We expect potential applications in diverse fields such as structural biology and biophysics.

The joint US-USSR biological satellite program

NASA Technical Reports Server (NTRS)

Souza, K. A.

1979-01-01

The joint US-USSR biological satellite missions carried out in 1975 and 1977 using Cosmos 782 and Cosmos 936 spacecraft, respectively, is reviewed. The experimental equipment and the biological specimens aboard the aircraft are considered, and it is noted that Cosmos 782, unlike Cosmos 936, carried no centrifuges for rats, although it did contain a centrifuge where a variety of biological specimens, including carrot tissue and fruit flies, were subjected to artificial gravity during space flight. The ground control groups, designed for biological experiments under simulated space-conditions, are taken into account. The U.S. experiments aboard the aircraft are described, with attention given to the experiments with rats, fish embryos, plants, and insects. Results of the experiments are noted, including the finding that space flight factors, especially weightlessness, have a measurable effect on the erythropoietic and musculoskeletal systems of rats

New specimen of Archaeopteryx provides insights into the evolution of pennaceous feathers.

PubMed

Foth, Christian; Tischlinger, Helmut; Rauhut, Oliver W M

2014-07-03

Discoveries of bird-like theropod dinosaurs and basal avialans in recent decades have helped to put the iconic 'Urvogel' Archaeopteryx into context and have yielded important new data on the origin and early evolution of feathers. However, the biological context under which pennaceous feathers evolved is still debated. Here we describe a new specimen of Archaeopteryx with extensive feather preservation, not only on the wings and tail, but also on the body and legs. The new specimen shows that the entire body was covered in pennaceous feathers, and that the hindlimbs had long, symmetrical feathers along the tibiotarsus but short feathers on the tarsometatarsus. Furthermore, the wing plumage demonstrates that several recent interpretations are problematic. An analysis of the phylogenetic distribution of pennaceous feathers on the tail, hindlimb and arms of advanced maniraptorans and basal avialans strongly indicates that these structures evolved in a functional context other than flight, most probably in relation to display, as suggested by some previous studies. Pennaceous feathers thus represented an exaptation and were later, in several lineages and following different patterns, recruited for aerodynamic functions. This indicates that the origin of flight in avialans was more complex than previously thought and might have involved several convergent achievements of aerial abilities.

High resolution quantitative phase imaging of live cells with constrained optimization approach

NASA Astrophysics Data System (ADS)

Pandiyan, Vimal Prabhu; Khare, Kedar; John, Renu

2016-03-01

Quantitative phase imaging (QPI) aims at studying weakly scattering and absorbing biological specimens with subwavelength accuracy without any external staining mechanisms. Use of a reference beam at an angle is one of the necessary criteria for recording of high resolution holograms in most of the interferometric methods used for quantitative phase imaging. The spatial separation of the dc and twin images is decided by the reference beam angle and Fourier-filtered reconstructed image will have a very poor resolution if hologram is recorded below a minimum reference angle condition. However, it is always inconvenient to have a large reference beam angle while performing high resolution microscopy of live cells and biological specimens with nanometric features. In this paper, we treat reconstruction of digital holographic microscopy images as a constrained optimization problem with smoothness constraint in order to recover only complex object field in hologram plane even with overlapping dc and twin image terms. We solve this optimization problem by gradient descent approach iteratively and the smoothness constraint is implemented by spatial averaging with appropriate size. This approach will give excellent high resolution image recovery compared to Fourier filtering while keeping a very small reference angle. We demonstrate this approach on digital holographic microscopy of live cells by recovering the quantitative phase of live cells from a hologram recorded with nearly zero reference angle.

High-contrast 3D microscopic imaging of deep layers in a biological medium

NASA Astrophysics Data System (ADS)

Faridian, Ahmad; Pedrini, Giancarlo; Osten, Wolfgang

2014-03-01

Multilayer imaging of biological specimens is a demanding field of research, but scattering is one of the major obstacles in imaging the internal layers of a specimen. Although in many studies the biological object is assumed to be a weak scatterer, this condition is hardly satisfied for sub-millimeter sized organisms. The scattering medium is inhomogeneously distributed inside the specimen. Therefore, the scattering which occurs in the upper layers of a given internal layer of interest is different from the lower layers. That results in a different amount of collectable information for a specific point in the layer from each view. An opposed view dark-field digital holographic microscope (DHM) has been implemented in this work to collect the information concurrently from both views and increase the image quality. Implementing a DHM system gives the possibility to perform digital refocusing process and obtain multilayer images from each side without depth scanning of the object. The results have been presented and discussed here for a Drosophila embryo.

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

Ogura, Toshihiko, E-mail: t-ogura@aist.go.jp

Highlights: • We developed a high-sensitive frequency transmission electric-field (FTE) system. • The output signal was highly enhanced by applying voltage to a metal layer on SiN. • The spatial resolution of new FTE method is 41 nm. • New FTE system enables observation of the intact bacteria and virus in water. - Abstract: The high-resolution structural analysis of biological specimens by scanning electron microscopy (SEM) presents several advantages. Until now, wet bacterial specimens have been examined using atmospheric sample holders. However, images of unstained specimens in water using these holders exhibit very poor contrast and heavy radiation damage. Recently,more » we developed the frequency transmission electric-field (FTE) method, which facilitates the SEM observation of biological specimens in water without radiation damage. However, the signal detection system presents low sensitivity. Therefore, a high EB current is required to generate clear images, and thus reducing spatial resolution and inducing thermal damage to the samples. Here a high-sensitivity detection system is developed for the FTE method, which enhances the output signal amplitude by hundredfold. The detection signal was highly enhanced when voltage was applied to the metal layer on silicon nitride thin film. This enhancement reduced the EB current and improved the spatial resolution as well as the signal-to-noise ratio. The spatial resolution of a high-sensitive FTE system is 41 nm, which is considerably higher than previous FTE system. New FTE system can easily be utilised to examine various unstained biological specimens in water, such as living bacteria and viruses.« less

Apparatus for X-ray diffraction microscopy and tomography of cryo specimens

DOE PAGES

Beetz, T.; Howells, M. R.; Jacobsen, C.; ...

2005-03-14

An apparatus for diffraction microscopy of biological and materials science specimens is described. In this system, a coherent soft X-ray beam is selected with a pinhole, and the illuminated specimen is followed by an adjustable beamstop and CCD camera to record diffraction data from non-crystalline specimens. In addition, a Fresnel zone plate can be inserted to allow for direct imaging. The system makes use of a cryogenic specimen holder with cryotransfer capabilities to allow frozen hydrated specimens to be loaded. The specimen can be tilted over a range of ± 80 ° degrees for three-dimensional imaging; this is done bymore » computer-controlled motors, enabling automated alignment of the specimen through a tilt series. The system is now in use for experiments in soft X-ray diffraction microscopy.« less

Infrared Microtransmission And Microreflectance Of Biological Systems

NASA Astrophysics Data System (ADS)

Hill, Steve L.; Krishnan, K.; Powell, Jay R.

1989-12-01

The infrared microsampling technique has been successfully applied to a variety of biological systems. A microtomed tissue section may be prepared to permit both visual and infrared discrimination. Infrared structural information may be obtained for a single cell, and computer-enhanced images of tissue specimens may be calculated from spectral map data sets. An analysis of a tissue section anomaly may gg suest eitherprotein compositional differences or a localized concentration of foreign matterp. Opaque biological materials such as teeth, gallstones, and kidney stones may be analyzed by microreflectance spectroscop. Absorption anomalies due to specular dispersion are corrected with the Kraymers-Kronig transformation. Corrected microreflectance spectra may contribute to compositional analysis and correlate diseased-related spectral differences to visual specimen anomalies.

DNA barcoding of human-biting black flies (Diptera: Simuliidae) in Thailand.

PubMed

Pramual, Pairot; Thaijarern, Jiraporn; Wongpakam, Komgrit

2016-12-01

Black flies (Diptera: Simuliidae) are important insect vectors and pests of humans and animals. Accurate identification, therefore, is important for control and management. In this study, we used mitochondrial cytochrome oxidase I (COI) barcoding sequences to test the efficiency of species identification for the human-biting black flies in Thailand. We used human-biting specimens because they enabled us to link information with previous studies involving the immature stages. Three black fly taxa, Simulium nodosum, S. nigrogilvum and S. doipuiense complex, were collected. The S. doipuiense complex was confirmed for the first time as having human-biting habits. The COI sequences revealed considerable genetic diversity in all three species. Comparisons to a COI sequence library of black flies in Thailand and in a public database indicated a high efficiency for specimen identification for S. nodosum and S. nigrogilvum, but this method was not successful for the S. doipuiense complex. Phylogenetic analyses revealed two divergent lineages in the S. doipuiense complex. Human-biting specimens formed a separate clade from other members of this complex. The results are consistent with the Barcoding Index Number System (BINs) analysis that found six BINs in the S. doipuiense complex. Further taxonomic work is needed to clarify the species status of these human-biting specimens. Copyright © 2016 Elsevier B.V. All rights reserved.

Biomarker discovery in biological specimens (plasma, hair, liver and kidney) of diabetic mice based upon metabolite profiling using ultra-performance liquid chromatography with electrospray ionization time-of-flight mass spectrometry.

PubMed

Tsutsui, Haruhito; Maeda, Toshio; Min, Jun Zhe; Inagaki, Shinsuke; Higashi, Tatsuya; Kagawa, Yoshiyuki; Toyo'oka, Toshimasa

2011-05-12

The number of diabetic patients has recently been increasing worldwide. Diabetes is a multifactorial disorder based on environmental factors and genetic background. In many cases, diabetes is asymptomatic for a long period and the patient is not aware of the disease. Therefore, the potential biomarker(s), leading to the early detection and/or prevention of diabetes mellitus, are strongly required. However, the diagnosis of the prediabetic state in humans is a very difficult issue, because the lifestyle is variable in each person. Although the development of a diagnosis method in humans is the goal of our research, the extraction and structural identification of biomarker candidates in several biological specimens (i.e., plasma, hair, liver and kidney) of ddY strain mice, which undergo naturally occurring diabetes along with aging, were carried out based upon a metabolite profiling study. The low-molecular-mass compounds including metabolites in the biological specimens of diabetic mice (ddY-H) and normal mice (ddY-L) were globally separated by ultra-performance liquid chromatography (UPLC) using different reversed-phase columns (i.e., T3-C18 and HS-F5) and detected by electrospray ionization time-of-flight mass spectrometry (ESI-TOF-MS). The biomarker candidates related to diabetes mellitus were extracted from a multivariate statistical analysis, such as an orthogonal partial least-squares-discriminant analysis (OPLS-DA), followed by a database search, such as ChemSpider, KEGG and HMDB. Many metabolites and unknown compounds in each biological specimen were detected as the biomarker candidates related to diabetic mellitus. Among them, the elucidation of the chemical structures of several possible metabolites, including more than two biological specimens, was carried out along with the comparison of the tandem MS/MS analyses using authentic compounds. One metabolite was clearly identified as N-acetyl-L-leucine based upon the MS/MS spectra and the retention time on the chromatograms. N-acetyl-L-leucine is an endogenous compound included in all biological specimens (plasma, hair, liver and kidney). Therefore, this metabolite appears to be a potential biomarker candidate related to diabetes. Although the structures of other biomarker candidates have still not yet determined, the present approach based upon a metabolite profiling study using UPLC-ESI-TOF-MS could be helpful for understanding the abnormal state of various diseases. Copyright © 2010 Elsevier B.V. All rights reserved.

Neutron scattering for the analysis of biological structures. Brookhaven symposia in biology. Number 27

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

Schoenborn, B P

1976-01-01

Sessions were included on neutron scattering and biological structure analysis, protein crystallography, neutron scattering from oriented systems, solution scattering, preparation of deuterated specimens, inelastic scattering, data analysis, experimental techniques, and instrumentation. Separate entries were made for the individual papers.

Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope.

PubMed

Wu, J S; Kim, A M; Bleher, R; Myers, B D; Marvin, R G; Inada, H; Nakamura, K; Zhang, X F; Roth, E; Li, S Y; Woodruff, T K; O'Halloran, T V; Dravid, Vinayak P

2013-05-01

A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems. Copyright © 2013 Elsevier B.V. All rights reserved.

Phase-contrast x-ray computed tomography for observing biological specimens and organic materials

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji

1995-02-01

A novel three-dimensional x-ray imaging method has been developed by combining a phase-contrast x-ray imaging technique with x-ray computed tomography. This phase-contrast x-ray computed tomography (PCX-CT) provides sectional images of organic specimens that would produce absorption-contrast x-ray CT images with little contrast. Comparing PCX-CT images of rat cerebellum and cancerous rabbit liver specimens with corresponding absorption-contrast CT images shows that PCX-CT is much more sensitive to the internal structure of organic specimens.

Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens

PubMed Central

Loreille, Odile; Ratnayake, Shashikala; Stockwell, Timothy B.; Mallick, Swapan; Skoglund, Pontus; Onorato, Anthony J.; Bergman, Nicholas H.; Reich, David; Irwin, Jodi A.

2018-01-01

High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens. PMID:29494531

LBL Whole Frog Project

Science.gov Websites

specimens), X-ray CT imaging (industrial imaging of non-biological objects), and direct generation from experimental study unit for biology was developed with the assistance of several high school teachers, and

A Chemoenzymatic Histology Method for O-GlcNAc Detection.

PubMed

Aguilar, Aime Lopez; Hou, Xiaomeng; Wen, Liuqing; Wang, Peng G; Wu, Peng

2017-12-14

Modification of nuclear and cytoplasmic proteins by the addition or removal of O-GlcNAc dynamically impacts multiple biological processes. Here, we present the development of a chemoenzymatic histology method for the detection of O-GlcNAc in tissue specimens. We applied this method to screen murine organs, uncovering specific O-GlcNAc distribution patterns in different tissue structures. We then utilized our histology method for O-GlcNAc detection in human brain specimens from healthy donors and donors with Alzheimer's disease and found higher levels of O-GlcNAc in specimens from healthy donors. We also performed an analysis using a multiple cancer tissue array, uncovering different O-GlcNAc levels between healthy and cancerous tissues, as well as different O-GlcNAc cellular distributions within certain tissue specimens. This chemoenzymatic histology method therefore holds great potential for revealing the biology of O-GlcNAc in physiopathological processes. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation

PubMed Central

Pepinelli, Mateus; Rodrigues, Marciel Elio; Roque, Fabio de Oliveira; Lorenz-Lemke, Aline Pedroso; Kvist, Sebastian

2017-01-01

We present a DNA barcoding study of Neotropical odonates from the Upper Plata basin, Brazil. A total of 38 species were collected in a transition region of “Cerrado” and Atlantic Forest, both regarded as biological hotspots, and 130 cytochrome c oxidase subunit I (COI) barcodes were generated for the collected specimens. The distinct gap between intraspecific (0–2%) and interspecific variation (15% and above) in COI, and resulting separation of Barcode Index Numbers (BIN), allowed for successful identification of specimens in 94% of cases. The 6% fail rate was due to a shared BIN between two separate nominal species. DNA barcoding, based on COI, thus seems to be a reliable and efficient tool for identifying Neotropical odonate specimens down to the species level. These results underscore the utility of DNA barcoding to aid specimen identification in diverse biological hotspots, areas that require urgent action regarding taxonomic surveys and biodiversity conservation. PMID:28763495

Automatic system for 3D reconstruction of the chick eye based on digital photographs.

PubMed

Wong, Alexander; Genest, Reno; Chandrashekar, Naveen; Choh, Vivian; Irving, Elizabeth L

2012-01-01

The geometry of anatomical specimens is very complex and accurate 3D reconstruction is important for morphological studies, finite element analysis (FEA) and rapid prototyping. Although magnetic resonance imaging, computed tomography and laser scanners can be used for reconstructing biological structures, the cost of the equipment is fairly high and specialised technicians are required to operate the equipment, making such approaches limiting in terms of accessibility. In this paper, a novel automatic system for 3D surface reconstruction of the chick eye from digital photographs of a serially sectioned specimen is presented as a potential cost-effective and practical alternative. The system is designed to allow for automatic detection of the external surface of the chick eye. Automatic alignment of the photographs is performed using a combination of coloured markers and an algorithm based on complex phase order likelihood that is robust to noise and illumination variations. Automatic segmentation of the external boundaries of the eye from the aligned photographs is performed using a novel level-set segmentation approach based on a complex phase order energy functional. The extracted boundaries are sampled to construct a 3D point cloud, and a combination of Delaunay triangulation and subdivision surfaces is employed to construct the final triangular mesh. Experimental results using digital photographs of the chick eye show that the proposed system is capable of producing accurate 3D reconstructions of the external surface of the eye. The 3D model geometry is similar to a real chick eye and could be used for morphological studies and FEA.

Allometry and Ecology of the Bilaterian Gut Microbiome

PubMed Central

Sherrill-Mix, Scott; McCormick, Kevin; Lauder, Abigail; Bailey, Aubrey; Zimmerman, Laurie; Li, Yingying; Django, Jean-Bosco N.; Bertolani, Paco; Colin, Christelle; Hart, John A.; Hart, Terese B.; Georgiev, Alexander V.; Sanz, Crickette M.; Morgan, David B.; Atencia, Rebeca; Cox, Debby; Muller, Martin N.; Sommer, Volker; Piel, Alexander K.; Stewart, Fiona A.; Speede, Sheri; Roman, Joe; Wu, Gary; Taylor, Josh; Bohm, Rudolf; Rose, Heather M.; Carlson, John; Mjungu, Deus; Schmidt, Paul; Gaughan, Celeste; Bushman, Joyslin I.; Schmidt, Ella; Bittinger, Kyle; Collman, Ronald G.; Hahn, Beatrice H.

2018-01-01

ABSTRACT Classical ecology provides principles for construction and function of biological communities, but to what extent these apply to the animal-associated microbiota is just beginning to be assessed. Here, we investigated the influence of several well-known ecological principles on animal-associated microbiota by characterizing gut microbial specimens from bilaterally symmetrical animals (Bilateria) ranging from flies to whales. A rigorously vetted sample set containing 265 specimens from 64 species was assembled. Bacterial lineages were characterized by 16S rRNA gene sequencing. Previously published samples were also compared, allowing analysis of over 1,098 samples in total. A restricted number of bacterial phyla was found to account for the great majority of gut colonists. Gut microbial composition was associated with host phylogeny and diet. We identified numerous gut bacterial 16S rRNA gene sequences that diverged deeply from previously studied taxa, identifying opportunities to discover new bacterial types. The number of bacterial lineages per gut sample was positively associated with animal mass, paralleling known species-area relationships from island biogeography and implicating body size as a determinant of community stability and niche complexity. Samples from larger animals harbored greater numbers of anaerobic communities, specifying a mechanism for generating more-complex microbial environments. Predictions for species/abundance relationships from models of neutral colonization did not match the data set, pointing to alternative mechanisms such as selection of specific colonists by environmental niche. Taken together, the data suggest that niche complexity increases with gut size and that niche selection forces dominate gut community construction. PMID:29588401

Hybrid label-free multiphoton and optoacoustic microscopy (MPOM)

NASA Astrophysics Data System (ADS)

Soliman, Dominik; Tserevelakis, George J.; Omar, Murad; Ntziachristos, Vasilis

2015-07-01

Many biological applications require a simultaneous observation of different anatomical features. However, unless potentially harmful staining of the specimens is employed, individual microscopy techniques do generally not provide multi-contrast capabilities. We present a hybrid microscope integrating optoacoustic microscopy and multiphoton microscopy, including second-harmonic generation, into a single device. This combined multiphoton and optoacoustic microscope (MPOM) offers visualization of a broad range of structures by employing different contrast mechanisms and at the same time enables pure label-free imaging of biological systems. We investigate the relative performance of the two microscopy modalities and demonstrate their multi-contrast abilities through the label-free imaging of a zebrafish larva ex vivo, simultaneously visualizing muscles and pigments. This hybrid microscopy application bears great potential for developmental biology studies, enabling more comprehensive information to be obtained from biological specimens without the necessity of staining.

The phantom leaf effect: a replication, part 1.

PubMed

Hubacher, John

2015-02-01

To replicate the phantom leaf effect and demonstrate a possible means to directly observe properties of the biological field. Thirty percent to 60% of plant leaves were amputated, and the remaining leaf sections were photographed with corona discharge imaging. All leaves were cut before placement on film. A total of 137 leaves were used. Plant leaves of 14 different species. Ninety-six phantom leaf specimens were successfully obtained; 41 specimens did not yield the phantom leaf effect. A normally undetected phantom "structure," possibly evidence of the biological field, can persist in the area of an amputated leaf section, and corona discharge can occur from this invisible structure. This protocol may suggest a testable method to study properties of conductivity and other parameters through direct observation of the complete biological field in plant leaves, with broad implications for biology and physics.

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

Berenguer de la Cuesta, Felisa; Wenger, Marco P.E.; Bean, Richard J.

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patternsmore » from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60-70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the 'speckled' nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques.« less

Coherent X-ray diffraction from collagenous soft tissues

PubMed Central

Berenguer de la Cuesta, Felisa; Wenger, Marco P. E.; Bean, Richard J.; Bozec, Laurent; Horton, Michael A.; Robinson, Ian K.

2009-01-01

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60–70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the ‘speckled’ nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques. PMID:19706395

Coherent X-ray diffraction from collagenous soft tissues.

PubMed

Berenguer de la Cuesta, Felisa; Wenger, Marco P E; Bean, Richard J; Bozec, Laurent; Horton, Michael A; Robinson, Ian K

2009-09-08

Coherent X-ray diffraction has been applied in the imaging of inorganic materials with great success. However, its application to biological specimens has been limited to some notable exceptions, due to the induced radiation damage and the extended nature of biological samples, the last limiting the application of most part of the phasing algorithms. X-ray ptychography, still under development, is a good candidate to overcome such difficulties and become a powerful imaging method for biology. We describe herein the feasibility of applying ptychography to the imaging of biological specimens, in particular collagen rich samples. We report here speckles in diffraction patterns from soft animal tissue, obtained with an optimized small angle X-ray setup that exploits the natural coherence of the beam. By phasing these patterns, dark field images of collagen within tendon, skin, bone, or cornea will eventually be obtained with a resolution of 60-70 nm. We present simulations of the contrast mechanism in collagen based on atomic force microscope images of the samples. Simulations confirmed the 'speckled' nature of the obtained diffraction patterns. Once inverted, the patterns will show the disposition and orientation of the fibers within the tissue, by enhancing the phase contrast between protein and no protein regions of the sample. Our work affords the application of the most innovative coherent X-ray diffraction tools to the study of biological specimens, and this approach will have a significant impact in biology and medicine because it overcomes many of the limits of current microscopy techniques.

Specimen Sample Preservation for Cell and Tissue Cultures

NASA Technical Reports Server (NTRS)

Meeker, Gabrielle; Ronzana, Karolyn; Schibner, Karen; Evans, Robert

1996-01-01

The era of the International Space Station with its longer duration missions will pose unique challenges to microgravity life sciences research. The Space Station Biological Research Project (SSBRP) is responsible for addressing these challenges and defining the science requirements necessary to conduct life science research on-board the International Space Station. Space Station will support a wide range of cell and tissue culture experiments for durations of 1 to 30 days. Space Shuttle flights to bring experimental samples back to Earth for analyses will only occur every 90 days. Therefore, samples may have to be retained for periods up to 60 days. This presents a new challenge in fresh specimen sample storage for cell biology. Fresh specimen samples are defined as samples that are preserved by means other than fixation and cryopreservation. The challenge of long-term storage of fresh specimen samples includes the need to suspend or inhibit proliferation and metabolism pending return to Earth-based laboratories. With this challenge being unique to space research, there have not been any ground based studies performed to address this issue. It was decided hy SSBRP that experiment support studies to address the following issues were needed: Fixative Solution Management; Media Storage Conditions; Fresh Specimen Sample Storage of Mammalian Cell/Tissue Cultures; Fresh Specimen Sample Storage of Plant Cell/Tissue Cultures; Fresh Specimen Sample Storage of Aquatic Cell/Tissue Cultures; and Fresh Specimen Sample Storage of Microbial Cell/Tissue Cultures. The objective of these studies was to derive a set of conditions and recommendations that can be used in a long duration microgravity environment such as Space Station that will permit extended storage of cell and tissue culture specimens in a state consistent with zero or minimal growth, while at the same time maintaining their stability and viability.

Integrated dual-tomography for refractive index analysis of free-floating single living cell with isotropic superresolution.

PubMed

B, Vinoth; Lai, Xin-Ji; Lin, Yu-Chih; Tu, Han-Yen; Cheng, Chau-Jern

2018-04-13

Digital holographic microtomography is a promising technique for three-dimensional (3D) measurement of the refractive index (RI) profiles of biological specimens. Measurement of the RI distribution of a free-floating single living cell with an isotropic superresolution had not previously been accomplished. To the best of our knowledge, this is the first study focusing on the development of an integrated dual-tomographic (IDT) imaging system for RI measurement of an unlabelled free-floating single living cell with an isotropic superresolution by combining the spatial frequencies of full-angle specimen rotation with those of beam rotation. A novel 'UFO' (unidentified flying object) like shaped coherent transfer function is obtained. The IDT imaging system does not require any complex image-processing algorithm for 3D reconstruction. The working principle was successfully demonstrated and a 3D RI profile of a single living cell, Candida rugosa, was obtained with an isotropic superresolution. This technology is expected to set a benchmark for free-floating single live sample measurements without labeling or any special sample preparations for the experiments.

Zachsia zenkewitschi (Teredinidae), a Rare and Unusual Seagrass Boring Bivalve Revisited and Redescribed.

PubMed

Shipway, J R; O'Connor, R; Stein, D; Cragg, S M; Korshunova, T; Martynov, A; Haga, T; Distel, D L

2016-01-01

The sea-grass borer Zachsia zenkewitschi belongs to a group of economically and ecologically important bivalves, commonly referred to as shipworms. The sole recognized representative of the genus Zachsia, this species displays an unusual life history and reproductive strategy that is now understood to include: environmental sex determination of free swimming larvae, extreme sexual and size dimorphism between males and females, internal fertilization, maintenance of often large harems of male dwarfs within a specialized cavity of the female mantle, and complex maternal care of larvae in specialized brood pouches within the gill. It is also the only shipworm species known to burrow in sea grass rhizomes rather than terrestrial wood. Although Z. zenkewitschi is rare and little studied, understanding of its biology and anatomy has evolved substantially, rendering some aspects of its original description inaccurate. Moreover, no existing type specimens are known for this species. In light of these facts, we designate a neotype from among specimens recently collected at the type location, and undertake a re-description of this species, accounting for recent reinterpretation of its life history and functional anatomy.

Cytotoxicity Test and Mass Spectrometry of IPMC

NASA Astrophysics Data System (ADS)

Takashima, Kazuto; Kamamichi, Norihiro; Yagi, Tohru; Asaka, Kinji; Mukai, Toshiharu

Ionic polymer-metal composite (IPMC) is a promising material in biomedical actuators and sensors because IPMC is soft and flexible, leading to the safety of the device itself. The purpose of this study is to investigate the biocompatibility of IPMC by in vitro experiments, in order to evaluate the applicability in biomedical fields. In addition to an IPMC specimen prepared by the conventional “impregnation-reduction method” using cationic gold complexes and reducing agents, two specimens were prepared by processes in addition to that used for the conventional IPMC specimen. One specimen was reduced in Na2SO3 solution and another specimen was cleaned in H2O2 solution. Colony-forming test using Chinese hamster V79 cells shows high cytotoxicity of all IPMC specimens. Examination of direct inlet mass spectrometry (DI-MS) revealed that the peak intensity of gold complex (particularly, m/z=180) was different from that of Nafion film. Monitoring the peak at m/z=180 showed a remnant with the structure of phenanthroline in IPMC specimens which were not cleaned in H2O2 solution.

Tropical Biological Drawings with Notes.

ERIC Educational Resources Information Center

Mitchelmore, June A.

The annotated illustrations of biological specimens useful for illustrating the "tropical" topics dealt with in African secondary school biology courses are designed to serve a two-fold purpose. The diagrams are intended to show the pupil the structures he should be looking for in his laboratory work, with the textual material being an…

X-ray microscopy with high-resolution zone plates: recent developments

NASA Astrophysics Data System (ADS)

Schneider, Gerd; Wilhein, Thomas; Niemann, Bastian; Guttman, P.; Schliebe, T.; Lehr, J.; Aschoff, H.; Thieme, Juergen; Rudolph, Dietbert M.; Schmahl, Guenther A.

1995-09-01

In order to expand the applications of x-ray microscopy, developments in the fields of zone plate technology, specimen preparation and imaging techniques have been made. A new cross- linked polymer chain electron beam resist allows us to record zone plate pattern down to 19 nm outermost zone width. High resolution zone plates in germanium with outermost zone widths down to 19 nm have been developed. In addition, phase zone plates in nickel down to 30 nm zone width have been made by electroplating. In order to enhance the image contrast for weak absorbing objects, the phase contrast method for x-ray microscopy was developed and implemented on the Gottingen x-ray microscope at BESSY. The effects of x ray absorption on the structure of biological specimen limits the maximum applicable radiation dose and therefore the achievable signal to noise ratio for an artifact-free x-ray image. To improve the stability especially of biological specimen, a cryogenic object chamber has been developed and tested. It turns out that at the operating temperature T less than or equal to 130 K unfixed biological specimen can be exposed to a radiation dose of 109 - 1010 Gy without any observable structural changes. A multiple-angle viewing stage allows us to take stereoscopic images with the x-ray microscope, giving a 3D-impression of the object. As an example for the applications of x-ray microscopy in biology, erythrocytes infected by malaria parasite have been examined. Studies of the aggregation of hematite by sodium sulfate gives an example for the application of x-ray microscopy in the field of colloid research.

Proposed BioRepository platform solution for the ALS research community.

PubMed

Sherman, Alex; Bowser, Robert; Grasso, Daniela; Power, Breen; Milligan, Carol; Jaffa, Matthew; Cudkowicz, Merit

2011-01-01

ALS is a rare disorder whose cause and pathogenesis is largely unknown ( 1 ). There is a recognized need to develop biomarkers for ALS to better understand the disease, expedite diagnosis and to facilitate therapy development. Collaboration is essential to obtain a sufficient number of samples to allow statistically meaningful studies. The availability of high quality biological specimens for research purposes requires the development of standardized methods for collection, long-term storage, retrieval and distribution of specimens. The value of biological samples to scientists and clinicians correlates with the completeness and relevance of phenotypical and clinical information associated with the samples ( 2 , 3 ). While developing a secure Web-based system to manage an inventory of multi-site BioRepositories, algorithms were implemented to facilitate ad hoc parametric searches across heterogeneous data sources that contain data from clinical trials and research studies. A flexible schema for a barcode label was introduced to allow association of samples to these data. The ALSBank™ BioRepository platform solution for managing biological samples and associated data is currently deployed by the Northeast ALS Consortium (NEALS). The NEALS Consortium and the Massachusetts General Hospital (MGH) Neurology Clinical Trials Unit (NCTU) support a network of multiple BioBanks, thus allowing researchers to take advantage of a larger specimen collection than they might have at an individual institution. Standard operating procedures are utilized at all collection sites to promote common practices for biological sample integrity, quality control and associated clinical data. Utilizing this platform, we have created one of the largest virtual collections of ALS-related specimens available to investigators studying ALS.

40 CFR 792.195 - Retention of records.

Code of Federal Regulations, 2011 CFR

2011-07-01

... mutagenicity tests, specimens of soil, water, and plants, and wet specimens of blood, urine, feces, biological... 40 Protection of Environment 32 2011-07-01 2011-07-01 false Retention of records. 792.195 Section... ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Records and Reports § 792.195 Retention of records...

40 CFR 792.195 - Retention of records.

Code of Federal Regulations, 2014 CFR

2014-07-01

... mutagenicity tests, specimens of soil, water, and plants, and wet specimens of blood, urine, feces, biological... 40 Protection of Environment 32 2014-07-01 2014-07-01 false Retention of records. 792.195 Section... ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Records and Reports § 792.195 Retention of records...

40 CFR 792.195 - Retention of records.

Code of Federal Regulations, 2012 CFR

2012-07-01

... mutagenicity tests, specimens of soil, water, and plants, and wet specimens of blood, urine, feces, biological... 40 Protection of Environment 33 2012-07-01 2012-07-01 false Retention of records. 792.195 Section... ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Records and Reports § 792.195 Retention of records...

40 CFR 792.195 - Retention of records.

Code of Federal Regulations, 2013 CFR

2013-07-01

... mutagenicity tests, specimens of soil, water, and plants, and wet specimens of blood, urine, feces, biological... 40 Protection of Environment 33 2013-07-01 2013-07-01 false Retention of records. 792.195 Section... ACT (CONTINUED) GOOD LABORATORY PRACTICE STANDARDS Records and Reports § 792.195 Retention of records...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2013 CFR

2013-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2012 CFR

2012-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2010 CFR

2010-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

50 CFR 23.36 - What are the requirements for an export permit?

Code of Federal Regulations, 2011 CFR

2011-10-01

... Ginseng Appendix-I Plants Artificially Propagated for Commercial Purposes Biological Specimens Captive... noncommercial purposes. (See § 23.46 for the export of specimens that originated at a commercial breeding... IMPORTATION OF WILDLIFE AND PLANTS (CONTINUED) CONVENTION ON INTERNATIONAL TRADE IN ENDANGERED SPECIES OF WILD...

Apparatus for generating x-ray holograms

DOEpatents

Rhodes, C.K.; Boyer, K.; Solem, J.C.; Haddad, W.S.

1990-09-11

Apparatus for x-ray microholography of living biological materials. A Fourier transform holographic configuration is described as being most suitable for the 3-dimensional recording of the physical characteristics of biological specimens. The use of a spherical scatterer as a reference and a charge-coupled device two-dimensional detector array placed in the forward direction relative to the incident x-radiation for viewing electromagnetic radiation simultaneously scattered from both the specimen and the reference scatterer permits the ready reconstruction of the details of the specimen from the fringe pattern detected by the charge-coupled device. For example, by using a nickel reference scatter at 4.5 nm, sufficient reference illumination is provided over a wide enough angle to allow similar resolution in both transverse and longitudinal directions. Both laser and synchrotron radiation sources are feasible for generating microholographs. Operation in the water window (2.4 to 4.5 nm) should provide maximum contrast for features of the specimen and spatial resolution on the order of the wavelength of x-radiation should be possible in all three dimensions, which is sufficient for the visualization of many biological features. It is anticipated that the present apparatus will find utility in other areas as well where microscopic physical details of a specimen are important. A computational procedure which enables the holographic data collected by the detector to be used to correct for misalignments introduced by inexact knowledge of the relative positions of the spherical reference scatterer and the sample under investigation has been developed. If the correction is performed prior to reconstruction, full compensation can be achieved and a faithfully reconstructed image produced. 7 figs.

Apparatus for generating x-ray holograms

DOEpatents

Rhodes, Charles K.; Boyer, Keith; Solem, Johndale C.; Haddad, Waleed S.

1990-01-01

Apparatus for x-ray microholography of living biological materials. A Fourier transform holographic configuration is described as being most suitable for the 3-dimensional recording of the physical characteristics of biological specimens. The use of a spherical scatterer as a reference and a charge-coupled device two-dimensional detector array placed in the forward direction relative to the incident x-radiation for viewing electromagnetic radiation simultaneously scattered from both the specimen and the reference scatterer permits the ready reconstruction of the details of the specimen from the fringe pattern detected by the charge-coupled device. For example, by using a nickel reference scatter at 4.5 nm, sufficient reference illumination is provided over a wide enough angle to allow similar resolution in both transverse and longitudinal directions. Both laser and synchrotron radiation sources are feasible for generating microholographs. Operation in the water window (2.4 to 4.5 nm) should provide maximum contrast for features of the specimen and spatial resolution on the order of the wavelength of x-radiation should be possible in all three dimensions, which is sufficient for the visualization of many biological features. It is anticipated that the present apparatus will find utility in other areas as well where microscopic physical details of a specimen are important. A computational procedure which enables the holographic data collected by the detector to be used to correct for misalignments introduced by inexact knowledge of the relative positions of the spherical reference scatterer and the sample under investigation has been developed. If the correction is performed prior to reconstruction, full compensation can be achieved and a faithfully reconstructed image produced.

Soft x-ray holography and microscopy of biological cells

NASA Astrophysics Data System (ADS)

Chen, Jianwen; Gao, Hongyi; Xie, Honglan; Li, Ruxin; Xu, Zhizhan

2003-10-01

Some experimental results on soft X-ray microscopy and holography imaging of biological specimens are presented in the paper. As we know, due to diffraction effects, there exists a resolution limit determined by wavelength λ and numerical aperture NA in conventional optical microscopy. In order to improve resolution, the num erical aperture should be made as large as possible and the wavelength as short as possible. Owing to the shorter wavelength, X-rays provide the potential of higher resolution in X-ray microscopy, holography image and allow for exam ination the interior structures of thicker specimens. In the experiments, we used synchrotron radiation source in Hefei as light source. Soft X-rays come from a bending magnet in 800 M eV electron storage ring with characteristic wavelength of 2.4 nm. The continuous X-ray spectrums are monochromatized by a zone-plate and a pinhole with 300 m diameter. The experimental set-up is typical contact microscopic system, its main advantage is simplicity and no special optical element is needed. The specimens used in the experiments of microscopic imaging are the colibacillus, the gingko vascular hundle and the fritillaries ovary karyon. The specimen for holographic imaging is the spider filam ents. The basic structures of plant cells such as the cell walls, the cytoplasm and the karyon especially the joint structures between the cells are observed clearly. An experimental study on a thick biological specimen that is a whole sporule w ith the thickness of about 30 μm is performed. In the holographic experiments, the experimental setup is typical Gabor in-line holography. The specimen is placed in line with X-ray source, which provides both the reference w aves and specimen illum ination. The specimen is some spider filament, which adhere to a Si3N4 film. The recording medium is PM M A, which is placed at recording distance of about 400 μm from the specimen. The hologram s were reconstructed by digital method with 300 nm resolutions. A novel method for recording in-line hologram is proposed which is called X-ray in-line holography with zone-plate magnification in this paper. The magnification factor of the micro zone plate imaging is about 103. The transverse resolution can be 48 nm in this method.

Biological markers of intermediate outcomes in studies of indoor air and other complex mixtures.

PubMed Central

Wilcosky, T C

1993-01-01

Biological markers of intermediate health outcomes sometimes provide a superior alternative to traditional measures of pollutant-related disease. Some opportunities and methodologic issues associated with using markers are discussed in the context of exposures to four complex mixtures: environmental tobacco smoke and nitrogen dioxide, acid aerosols and oxidant outdoor pollution, environmental tobacco smoke and radon, and volatile organic compounds. For markers of intermediate health outcomes, the most important property is the positive predictive value for clinical outcomes of interest. Unless the marker has a known relationship with disease, a marker response conveys no information about disease risk. Most markers are nonspecific in that various exposures cause the same marker response. Although nonspecificity can be an asset in studies of complex mixtures, it leads to problems with confounding and dilution of exposure-response associations in the presence of other exposures. The timing of a marker's measurement in relation to the occurrence of exposure influences the ability to detect a response; measurements made too early or too late may underestimate the response's magnitude. Noninvasive markers, such as those measured in urine, blood, or nasal lavage fluid, are generally more useful for field studies than are invasive markers. However, invasive markers, such as those measured in bronchoalveolar lavage fluid or lung specimens from autopsies, provide the most direct evidence of pulmonary damage from exposure to air pollutants. Unfortunately, the lack of basic information about marker properties (e.g., sensitivity, variability, statistical link with disease) currently precludes the effective use of most markers in studies of complex mixtures. PMID:8206030

Operational considerations for the Space Station Life Science Glovebox

NASA Technical Reports Server (NTRS)

Rasmussen, Daryl N.; Bosley, John J.; Vogelsong, Kristofer; Schnepp, Tery A.; Phillips, Robert W.

1988-01-01

The U.S. Laboratory (USL) module on Space Station will house a biological research facility for multidisciplinary research using living plant and animal specimens. Environmentally closed chambers isolate the specimen habitats, but specimens must be removed from these chambers during research procedures as well as while the chambers are being cleaned. An enclosed, sealed Life Science Glovebox (LSG) is the only locale in the USL where specimens can be accessed by crew members. This paper discusses the key science, engineering and operational considerations and constraints involving the LSG, such as bioisolation, accessibility, and functional versatility.

Fundamental technical elements of freeze-fracture/freeze-etch in biological electron microscopy.

PubMed

Carson, Johnny L

2014-09-11

Freeze-fracture/freeze-etch describes a process whereby specimens, typically biological or nanomaterial in nature, are frozen, fractured, and replicated to generate a carbon/platinum "cast" intended for examination by transmission electron microscopy. Specimens are subjected to ultrarapid freezing rates, often in the presence of cryoprotective agents to limit ice crystal formation, with subsequent fracturing of the specimen at liquid nitrogen cooled temperatures under high vacuum. The resultant fractured surface is replicated and stabilized by evaporation of carbon and platinum from an angle that confers surface three-dimensional detail to the cast. This technique has proved particularly enlightening for the investigation of cell membranes and their specializations and has contributed considerably to the understanding of cellular form to related cell function. In this report, we survey the instrument requirements and technical protocol for performing freeze-fracture, the associated nomenclature and characteristics of fracture planes, variations on the conventional procedure, and criteria for interpretation of freeze-fracture images. This technique has been widely used for ultrastructural investigation in many areas of cell biology and holds promise as an emerging imaging technique for molecular, nanotechnology, and materials science studies.

Space Station Biological Research Project Habitat: Incubator

NASA Technical Reports Server (NTRS)

Nakamura, G. J.; Kirven-Brooks, M.; Scheller, N. M.

2001-01-01

Developed as part of the suite of Space Station Biological Research Project (SSBRP) hardware to support research aboard the International Space Station (ISS), the Incubator is a temperature-controlled chamber, for conducting life science research with small animal, plant and microbial specimens. The Incubator is designed for use only on the ISS and is transported to/from the ISS, unpowered and without specimens, in the Multi-Purpose Logistics Module (MPLM) of the Shuttle. The Incubator interfaces with the three SSBRP Host Systems; the Habitat Holding Racks (HHR), the Life Sciences Glovebox (LSG) and the 2.5 m Centrifuge Rotor (CR), providing investigators with the ability to conduct research in microgravity and at variable gravity levels of up to 2-g. The temperature within the Specimen Chamber can be controlled between 4 and 45 C. Cabin air is recirculated within the Specimen Chamber and can be exchanged with the ISS cabin at a rate of approximately equal 50 cc/min. The humidity of the Specimen Chamber is monitored. The Specimen Chamber has a usable volume of approximately equal 19 liters and contains two (2) connectors at 28v dc, (60W) for science equipment; 5 dedicated thermometers for science; ports to support analog and digital signals from experiment unique sensors or other equipment; an Ethernet port; and a video port. It is currently manifested for UF-3 and will be launched integrated within the first SSBRP Habitat Holding Rack.

Chemical variation in Piper aduncum and biological properties of its dillapiole-rich essential oil.

PubMed

de Almeida, Roseli R P; Souto, Raimundo N P; Bastos, Cleber N; da Silva, Milton H L; Maia, José G S

2009-09-01

The essential oils of the specimens of Piper aduncum that occur in deforested areas of Brazilian Amazon, North Brazil, are rich in dillapiole (35-90%), a derivative of phenylpropene, to which are attributed biological properties. On the other hand, the oils of the specimens with occurrence in the Atlantic Forest, and Northeastern and Southeastern Brazil, do not contain dillapiole, but only terpene compounds such as (E)-nerolidol and linalool. One specimen existing in the Amazon was hydrodistilled. The obtained oil was fractioned on a silica chromatographic column, resulting in fractions rich in dillapiole (95.0-98.9%) utilized for analyses by GC and GC/MS, structural characterization by NMR, confirmation of their biological properties, and to obtain the isomer isodillapiole. Dillapiole showed a fungicide action against the fungus Clinipellis perniciosa (witches' broom) by inhibition of its basidiospores, in concentrations ranging from 0.6 to 1.0 ppm. The larvicide and insecticide actions of dillapiole were tested against the larvae and the adult insects of Anopheles marajoara and Aedes aegypti (malaria and dengue mosquitoes), resulting in mortality of the larvae (48 h, 100%) at a concentration of 100 ppm, and mortality of the insects (30 min, 100%) at a concentration of 600 ppm. The isomeric isodillapiole showed no significant activity in the same biological tests.

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA.

PubMed

Kobayashi, Amane; Sekiguchi, Yuki; Takayama, Yuki; Oroguchi, Tomotaka; Shirahama, Keiya; Torizuka, Yasufumi; Manoda, Masahiro; Nakasako, Masayoshi; Yamamoto, Masaki

2016-05-01

Coherent X-ray diffraction imaging (CXDI) is a technique for structure analyses of non-crystalline particles with dimensions ranging from micrometer to sub-micrometer. We have developed a diffraction apparatus named TAKASAGO-6 for use in single-shot CXDI experiments of frozen-hydrated non-crystalline biological particles at cryogenic temperature with X-ray free electron laser pulses provided at a repetition rate of 30 Hz from the SPring-8 Angstrom Compact free-electron LAser. Specimen particles are flash-cooled after being dispersed on thin membranes supported by specially designed disks. The apparatus is equipped with a high-speed translation stage with a cryogenic pot for raster-scanning of the disks at a speed higher than 25 μm/33 ms. In addition, we use devices assisting the easy transfer of cooled specimens from liquid-nitrogen storages to the cryogenic pot. In the current experimental procedure, more than 20 000 diffraction patterns can be collected within 1 h. Here we report the key components and performance of the diffraction apparatus. Based on the efficiency of the diffraction data collection and the structure analyses of metal particles, biological cells, and cellular organelles, we discuss the future application of this diffraction apparatus for structure analyses of biological specimens.

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS

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

Gritsenko, Marina A.; Xu, Zhe; Liu, Tao

Comprehensive, quantitative information on abundances of proteins and their post-translational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labelling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification andmore » quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples, and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.« less

A mass spectrometry primer for mass spectrometry imaging

PubMed Central

Rubakhin, Stanislav S.; Sweedler, Jonathan V.

2011-01-01

Mass spectrometry imaging (MSI), a rapidly growing subfield of chemical imaging, employs mass spectrometry (MS) technologies to create single- and multi-dimensional localization maps for a variety of atoms and molecules. Complimentary to other imaging approaches, MSI provides high chemical specificity and broad analyte coverage. This powerful analytical toolset is capable of measuring the distribution of many classes of inorganics, metabolites, proteins and pharmaceuticals in chemically and structurally complex biological specimens in vivo, in vitro, and in situ. The MSI approaches highlighted in this Methods in Molecular Biology volume provide flexibility of detection, characterization, and identification of multiple known and unknown analytes. The goal of this chapter is to introduce investigators who may be unfamiliar with MS to the basic principles of the mass spectrometric approaches as used in MSI. In addition to guidelines for choosing the most suitable MSI method for specific investigations, cross-references are provided to the chapters in this volume that describe the appropriate experimental protocols. PMID:20680583

Large-Scale and Deep Quantitative Proteome Profiling Using Isobaric Labeling Coupled with Two-Dimensional LC-MS/MS.

PubMed

Gritsenko, Marina A; Xu, Zhe; Liu, Tao; Smith, Richard D

2016-01-01

Comprehensive, quantitative information on abundances of proteins and their posttranslational modifications (PTMs) can potentially provide novel biological insights into diseases pathogenesis and therapeutic intervention. Herein, we introduce a quantitative strategy utilizing isobaric stable isotope-labeling techniques combined with two-dimensional liquid chromatography-tandem mass spectrometry (2D-LC-MS/MS) for large-scale, deep quantitative proteome profiling of biological samples or clinical specimens such as tumor tissues. The workflow includes isobaric labeling of tryptic peptides for multiplexed and accurate quantitative analysis, basic reversed-phase LC fractionation and concatenation for reduced sample complexity, and nano-LC coupled to high resolution and high mass accuracy MS analysis for high confidence identification and quantification of proteins. This proteomic analysis strategy has been successfully applied for in-depth quantitative proteomic analysis of tumor samples and can also be used for integrated proteome and PTM characterization, as well as comprehensive quantitative proteomic analysis across samples from large clinical cohorts.

Metabolome analysis for discovering biomarkers of gastroenterological cancer.

PubMed

Suzuki, Makoto; Nishiumi, Shin; Matsubara, Atsuki; Azuma, Takeshi; Yoshida, Masaru

2014-09-01

Improvements in analytical technologies have made it possible to rapidly determine the concentrations of thousands of metabolites in any biological sample, which has resulted in metabolome analysis being applied to various types of research, such as clinical, cell biology, and plant/food science studies. The metabolome represents all of the end products and by-products of the numerous complex metabolic pathways operating in a biological system. Thus, metabolome analysis allows one to survey the global changes in an organism's metabolic profile and gain a holistic understanding of the changes that occur in organisms during various biological processes, e.g., during disease development. In clinical metabolomic studies, there is a strong possibility that differences in the metabolic profiles of human specimens reflect disease-specific states. Recently, metabolome analysis of biofluids, e.g., blood, urine, or saliva, has been increasingly used for biomarker discovery and disease diagnosis. Mass spectrometry-based techniques have been extensively used for metabolome analysis because they exhibit high selectivity and sensitivity during the identification and quantification of metabolites. Here, we describe metabolome analysis using liquid chromatography-mass spectrometry, gas chromatography-mass spectrometry, and capillary electrophoresis-mass spectrometry. Furthermore, the findings of studies that attempted to discover biomarkers of gastroenterological cancer are also outlined. Finally, we discuss metabolome analysis-based disease diagnosis. Copyright © 2014 Elsevier B.V. All rights reserved.

Complex colony-level organization of the deep-sea siphonophore Bargmannia elongata (Cnidaria, Hydrozoa) is directionally asymmetric and arises by the subdivision of pro-buds.

PubMed

Dunn, Casey W

2005-12-01

Siphonophores are free-swimming colonial hydrozoans (Cnidaria) composed of asexually produced multicellular zooids. These zooids, which are homologous to solitary animals, are functionally specialized and arranged in complex species-specific patterns. The coloniality of siphonophores provides an opportunity to study the major transitions in evolution that give rise to new levels of biological organization, but siphonophores are poorly known because they are fragile and live in the open ocean. The organization and development of the deep-sea siphonophore Bargmannia elongata is described here using specimens collected with a remotely operated underwater vehicle. Each bud gives rise to a precise, directionally asymmetric sequence of zooids through a stereotypical series of subdivisions, rather than to a single zooid as in most other hydrozoans. This initial description of development in a deep-sea siphonophore provides an example of how precise colony-level organization can arise, and illustrates that the morphological complexity of cnidarians is greater than is often assumed. Copyright 2005 Wiley-Liss, Inc.

Detection of Mycobacterium tuberculosis complex by nested polymerase chain reaction in pulmonary and extrapulmonary specimens* ,**

PubMed Central

Furini, Adriana Antônia da Cruz; Pedro, Heloisa da Silveira Paro; Rodrigues, Jean Francisco; Montenegro, Lilian Maria Lapa; Machado, Ricardo Luiz Dantas; Franco, Célia; Schindler, Haiana Charifker; Batista, Ida Maria Foschiani Dias; Rossit, Andrea Regina Baptista

2013-01-01

OBJECTIVE: To compare the performance of nested polymerase chain reaction (NPCR) with that of cultures in the detection of the Mycobacterium tuberculosis complex in pulmonary and extrapulmonary specimens. METHODS: We analyzed 20 and 78 pulmonary and extrapulmonary specimens, respectively, of 67 hospitalized patients suspected of having tuberculosis. An automated microbial system was used for the identification of Mycobacterium spp. cultures, and M. tuberculosis IS6110 was used as the target sequence in the NPCR. The kappa statistic was used in order to assess the level of agreement among the results. RESULTS: Among the 67 patients, 6 and 5, respectively, were diagnosed with pulmonary and extrapulmonary tuberculosis, and the NPCR was positive in all of the cases. Among the 98 clinical specimens, smear microscopy, culture, and NPCR were positive in 6.00%, 8.16%, and 13.26%, respectively. Comparing the results of NPCR with those of cultures (the gold standard), we found that NPCR had a sensitivity and specificity of 100% and 83%, respectively, in pulmonary specimens, compared with 83% and 96%, respectively, in extrapulmonary specimens, with good concordance between the tests (kappa, 0.50 and 0.6867, respectively). CONCLUSIONS: Although NPCR proved to be a very useful tool for the detection of M. tuberculosis complex, clinical, epidemiological, and other laboratory data should also be considered in the diagnosis and treatment of pulmonary and extrapulmonary tuberculosis. PMID:24473765

Comparison of oligosaccharides in milk specimens from humans and twelve other species.

PubMed

Warren, C D; Chaturvedi, P; Newburg, A R; Oftedal, O T; Tilden, C D; Newburg, D S

2001-01-01

Human milk contains large amounts of many oligosaccharides, most of which are fucosylated; several inhibit pathogenic bacteria, viruses, and toxins that cause disease in humans. Although bovine milk is known to have much less and many fewer types of oligosaccharides, no studies heretofore have indicated whether the amount or complexity of human milk oligosaccharides is unique to our species. Toward this end, a comparison was made of the major individual oligosaccharides in milk specimens from a variety of species, including the great apes. The neutral compounds, which represent the bulk of oligosaccharides in human milk, were isolated, perbenzoylated, resolved by high performance liquid chromatography (HPLC), and detected at 229nm. Ambiguous structures were determined by mass spectrometry. All milk specimens contained lactose, although levels were quite low in bear and kangaroo milk. The types of oligosaccharides in milk specimens from the primates resembled those of human milk, but the amounts, especially of the larger molecules, were markedly lower. The relative amounts of oligosaccharides in the bonobo changed over the course of lactation, as they do in humans. Marine mammals generally had few oligosaccharides in their milk other than 2'-fucosyllactose. Grizzly and black bear milk specimens contained a wide range of oligosaccharides, many of which had novel, fucosylated structures. Milk specimens from humans, bears, and marsupials had the greatest quantity of, and the most complex, neutral oligosaccharides. Although human milk contained more oligosaccharide than did milk specimens from the other species studied, the presence of appreciable amounts of complex oligosaccharides was not unique to humans. This finding suggests that in animal milk specimens, as in human milk, neutral fucosylated oligosaccharides potentially offer protection from pathogens to offspring with immature immune systems.

The copolymer P(HEMA-co-SS) binds gluten and reduces immune response in gluten-sensitized mice and human tissues.

PubMed

Pinier, Maud; Fuhrmann, Gregor; Galipeau, Heather J; Rivard, Nathalie; Murray, Joseph A; David, Chella S; Drasarova, Hana; Tuckova, Ludmila; Leroux, Jean-Christophe; Verdu, Elena F

2012-02-01

Copolymers of hydroxyethyl methacrylate and styrene sulfonate complex with isolated gliadin (the toxic fraction of gluten) and prevent damage to the intestinal barrier in HLA-HCD4/DQ8 mice. We studied the activity toward gluten and hordein digestion and biologic effects of poly(hydroxyethyl methacrylate-co-styrene sulfonate (P(HEMA-co-SS)). We also investigated the effect of gliadin complex formation in intestinal biopsy specimens from patients with celiac disease. We studied the ability of P(HEMA-co-SS) to reduce digestion of wheat gluten and barley hordein into immunotoxic peptides using liquid chromatography-mass spectrometry. The biodistribution and pharmacokinetic profile of orally administered P(HEMA-co-SS) was established in rodents using tritium-labeled polymer. We assessed the capacity of P(HEMA-co-SS) to prevent the immunologic and intestinal effects induced by a gluten-food mixture in gluten-sensitized HLA-HCD4/DQ8 mice after short-term and long-term administration. We measured the effects of gliadin complex formation on cytokine release ex vivo using intestinal biopsy specimens from patients with celiac disease. P(HEMA-co-SS) reduced digestion of wheat gluten and barley hordein in vitro, thereby decreasing formation of toxic peptides associated with celiac disease. After oral administration to rodents, P(HEMA-co-SS) was predominantly excreted in feces, even in the presence of low-grade mucosal inflammation and increased intestinal permeability. In gluten-sensitized mice, P(HEMA-co-SS) reduced paracellular permeability, normalized anti-gliadin immunoglobulin A in intestinal washes, and modulated the systemic immune response to gluten in a food mixture. Furthermore, incubation of P(HEMA-co-SS) with mucosal biopsy specimens from patients with celiac disease showed that secretion of tumor necrosis factor-α was reduced in the presence of partially digested gliadin. The copolymer P(HEMA-co-SS) reduced digestion of wheat gluten and barley hordein and attenuated the immune response to gluten in a food mixture in rodents. It might be developed to prevent or reduce gluten-induced disorders in humans. Copyright © 2012 AGA Institute. Published by Elsevier Inc. All rights reserved.

[Evaluation of Xpert® MTB/RIF technique for Mycobacterium tuberculosis complex detection in extra-respiratory specimens].

PubMed

García, Patricia; Balcells, M Elvira; Castillo, Claudia; Miranda, Carolina; Geoffroy, Enrique; Román, Juan C; Wozniak, Aniela

2017-08-01

Extra-pulmonary tuberculosis (TB) represents the 26.2% of total TB cases in Chile. Culture is the gold standard method, but the process is extremely slow. Xpert®MTB/RIF technique detects Mycobacterium tuberculosis complex (MTBc) through real time PCR in less than 3 h. However, it has been validated only for respiratory specimens. We aimed to determine the performance of Xpert®MTB/RIF test in detecting MTBc in extra-respiratory specimens compared with a combined gold standard consisting in a positive (liquid and solid) mycobacterial culture and/or a positive validated molecular method (q-RPC, Cobas®TaqMan®-MTB). Fifty extra-respiratory specimens were analyzed, from which 25 were positive and 25 negative for MTBc based on the combined gold standard. The 25 positive specimens had a positive result by Xpert®MTB/RIF; from the 25 negative specimens, 24 had a negative result and one had a positive result. We obtained an overall concordance of 98% between Xpert®MTB/RIF and the combined gold standard. Xpert®MTB/RIF test was able to detect 12 smear-negative specimens and 3 culture-negative specimens, all of them corresponding to extra-pulmonary TB cases. Xpert®MTB/RIF showed similar sensitivity to q-RPC in detecting MTBc in extra-respiratory specimens. This procedure allowed a substantial reduction in the time of diagnosis.

Conceptual design of a biological specimen holding facility. [Life Science Laboratory for Space Shuttle

NASA Technical Reports Server (NTRS)

Jackson, J. K.; Yakut, M. M.

1976-01-01

An all-important first step in the development of the Spacelab Life Science Laboratory is the design of the Biological Specimen Holding Facility (BSHF) which will provide accommodation for living specimens for life science research in orbit. As a useful tool in the understanding of physiological and biomedical changes produced in the weightless environment, the BSHF will enable biomedical researchers to conduct in-orbit investigations utilizing techniques that may be impossible to perform on human subjects. The results of a comprehensive study for defining the BSHF, description of its experiment support capabilities, and the planning required for its development are presented. Conceptual designs of the facility, its subsystems and interfaces with the Orbiter and Spacelab are included. Environmental control, life support and data management systems are provided. Interface and support equipment required for specimen transfer, surgical research, and food, water and waste storage is defined. New and optimized concepts are presented for waste collection, feces and urine separation and sampling, environmental control, feeding and watering, lighting, data management and other support subsystems.

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

PubMed Central

Quammen, Cory W.; Richardson, Alvin C.; Haase, Julian; Harrison, Benjamin D.; Taylor, Russell M.; Bloom, Kerry S.

2010-01-01

Fluorescence microscopy provides a powerful method for localization of structures in biological specimens. However, aspects of the image formation process such as noise and blur from the microscope's point-spread function combine to produce an unintuitive image transformation on the true structure of the fluorescing molecules in the specimen, hindering qualitative and quantitative analysis of even simple structures in unprocessed images. We introduce FluoroSim, an interactive fluorescence microscope simulator that can be used to train scientists who use fluorescence microscopy to understand the artifacts that arise from the image formation process, to determine the appropriateness of fluorescence microscopy as an imaging modality in an experiment, and to test and refine hypotheses of model specimens by comparing the output of the simulator to experimental data. FluoroSim renders synthetic fluorescence images from arbitrary geometric models represented as triangle meshes. We describe three rendering algorithms on graphics processing units for computing the convolution of the specimen model with a microscope's point-spread function and report on their performance. We also discuss several cases where the microscope simulator has been used to solve real problems in biology. PMID:20431698

The multiBac protein complex production platform at the EMBL.

PubMed

Berger, Imre; Garzoni, Frederic; Chaillet, Maxime; Haffke, Matthias; Gupta, Kapil; Aubert, Alice

2013-07-11

Proteomics research revealed the impressive complexity of eukaryotic proteomes in unprecedented detail. It is now a commonly accepted notion that proteins in cells mostly exist not as isolated entities but exert their biological activity in association with many other proteins, in humans ten or more, forming assembly lines in the cell for most if not all vital functions.(1,2) Knowledge of the function and architecture of these multiprotein assemblies requires their provision in superior quality and sufficient quantity for detailed analysis. The paucity of many protein complexes in cells, in particular in eukaryotes, prohibits their extraction from native sources, and necessitates recombinant production. The baculovirus expression vector system (BEVS) has proven to be particularly useful for producing eukaryotic proteins, the activity of which often relies on post-translational processing that other commonly used expression systems often cannot support.(3) BEVS use a recombinant baculovirus into which the gene of interest was inserted to infect insect cell cultures which in turn produce the protein of choice. MultiBac is a BEVS that has been particularly tailored for the production of eukaryotic protein complexes that contain many subunits.(4) A vital prerequisite for efficient production of proteins and their complexes are robust protocols for all steps involved in an expression experiment that ideally can be implemented as standard operating procedures (SOPs) and followed also by non-specialist users with comparative ease. The MultiBac platform at the European Molecular Biology Laboratory (EMBL) uses SOPs for all steps involved in a multiprotein complex expression experiment, starting from insertion of the genes into an engineered baculoviral genome optimized for heterologous protein production properties to small-scale analysis of the protein specimens produced.(5-8) The platform is installed in an open-access mode at EMBL Grenoble and has supported many scientists from academia and industry to accelerate protein complex research projects.

Harvestmen of the BOS Arthropod Collection of the University of Oviedo (Spain) (Arachnida, Opiliones).

PubMed

Merino-Sáinz, Izaskun; Anadón, Araceli; Torralba-Burrial, Antonio

2013-01-01

There are significant gaps in accessible knowledge about the distribution and phenology of Iberian harvestmen (Arachnida: Opiliones). Harvestmen accessible datasets in Iberian Peninsula are unknown, an only two other datasets available in GBIF are composed exclusively of harvestmen records. Moreover, only a few harvestmen data from Iberian Peninsula are available in GBIF network (or in any network that allows public retrieval or use these data). This paper describes the data associated with the Opiliones kept in the BOS Arthropod Collection of the University of Oviedo, Spain (hosted in the Department of Biología de Organismos y Sistemas), filling some of those gaps. The specimens were mainly collected from the northern third of the Iberian Peninsula. The earliest specimen deposited in the collection, dating back to the early 20(th) century, belongs to the P. Franganillo Collection. The dataset documents the collection of 16,455 specimens, preserved in 3,772 vials. Approximately 38% of the specimens belong to the family Sclerosomatidae, and 26% to Phalangidae; six other families with fewer specimens are also included. Data quality control was incorporated at several steps of digitisation process to facilitate reuse and improve accuracy. The complete dataset is also provided in Darwin Core Archive format, allowing public retrieval, use and combination with other biological, biodiversity of geographical variables datasets.

In Vitro Analysis of Fibronectin-Modified Titanium Surfaces

PubMed Central

Chang, Yu-Chi; Lee, Wei-Fang; Feng, Sheng-Wei; Huang, Haw-Ming; Lin, Che-Tong; Teng, Nai-Chia; Chang, Wei Jen

2016-01-01

Background Glow discharge plasma (GDP) procedure is an effective method for grafting various proteins, including albumin, type I collagen, and fibronectin, onto a titanium surface. However, the behavior and impact of titanium (Ti) surface modification is yet to be unraveled. Purpose The purpose of this study is to evaluate and analyze the biological properties of fibronectin-grafted Ti surfaces treated by GDP. Materials and Methods Grade II Ti discs were initially cleaned and autoclaved to obtain original specimens. Subsequently, the specimens were GDP treated and grafted with fibronectin to form Ar-GDP (Argon GDP treatment only) and GDP-fib (fibronectin coating following GDP treatment) groups. Blood coagulation test and MG-63 cell culture were performed to evaluate the biological effects on the specimen. Results There was no significant difference between Ar-GDP and GDP-fib groups in blood compatibility analysis. While in the MTT test, cellular proliferation was benefited from the presence of fibronectin coating. The numbers of cells on Ar-GDP and GDP-fib specimens were greater than those in the original specimens after 24 h of culturing. Conclusions GDP treatment combined with fibronectin grafting favored MG-63 cell adhesion, migration, and proliferation on titanium surfaces, which could be attributed to the improved surface properties. PMID:26731536

Future role of endoscopic ultrasound in personalized management of pancreatic cancer

PubMed Central

Ooi, Marie; Phan, An; Nguyen, Nam Q.

2017-01-01

Pancreatic ductal adenocarcinoma (PDAC) is aggressive and lethal with the majority of cases presenting with advanced unresectable disease due to delayed diagnosis. Despite improvement in surgery, chemotherapies, and intensive care medicine, the outcome of PDAC remains poor, which may relate to the tumor biology. Recent data suggest that PDAC is a “systemic cancer” with complex molecular or genomics derangement with marked heterogeneity. The ability to characterize the PDAC better by detailed evaluation of tissue biomarkers or genomics allows for improved prediction of prognosis and stratification of treatment, a concept known as “personalized cancer therapy.” Using tissue from resected PDAC specimens has several weaknesses and is only possible in 20% of patients with PDAC. Endoscopic ultrasound (EUS)-guided biopsy overcomes these weaknesses, and with recent advancements in needle technology, tissue can be obtained for personalized cancer therapy for all patients with PDAC. This review aims to outline our current understanding of the molecular biology of PDAC specifically focusing on how EUS-guided biopsy may play a fundamental role in tissue acquisition, allowing for assessment and stratify therapy according to the individual cancer biology as we move toward the era of precision medicine. PMID:29063873

[Biomechanical performance of different wires and cable fixation devices in posterior instrumentation for atlantoaxial instability].

PubMed

Liu, Tie-long; Yan, Wang-jun; Han, Yu; Ye, Xiao-jian; Jia, Lian-shun; Li, Jia-shun; Yuan, Wen

2010-05-01

To compare the biomechanical performances of different wires and cable fixation devices in posterior instrumentation for atlantoaxial instability, and test the effect of different fixation strengths and fixation approaches on the surgical outcomes. Six specimens of the atlantoaxial complex (C0-C3) were used to establish models of the normal complex, unstable complex (type II odontoid fracture) and fixed complex. On the wd-5 mechanical testing machine, the parameters including the strength and rigidity of anti-rotation, change and strength of stress, and stability were measured for the normal complex, atlantoaxial instability complex, the new type titanium cable fixation system, Atlas titanium cable, Songer titanium cable, and stainless wire. The strength and rigidity of anti-rotation, change and strength of stress, stability of flexion, extension and lateral bending of the unstable atlantoaxial complex fixed by the new double locking titanium cable fixation system were superior to those of the Songer or Atlas titanium cable (P<0.05) and medical stainless wire (P<0.05). Simultaneous cable fastening on both sides resulted in better fixation effect than successive cable fastening (P<0.05). Better fixation effect was achieved by fastening the specimen following a rest (P<0.05). The fixation effects can be enhanced by increased fastening strengths. The new type double locking titanium cable fixation system has better biomechanical performance than the conventional Songer and Atlas titanium cables. Fastening the unstable specimens after a rest following simultaneous fastening of the specimen on both sides produces better fixation effect.

Cryo-scanning transmission electron tomography of vitrified cells.

PubMed

Wolf, Sharon Grayer; Houben, Lothar; Elbaum, Michael

2014-04-01

Cryo-electron tomography (CET) of fully hydrated, vitrified biological specimens has emerged as a vital tool for biological research. For cellular studies, the conventional imaging modality of transmission electron microscopy places stringent constraints on sample thickness because of its dependence on phase coherence for contrast generation. Here we demonstrate the feasibility of using scanning transmission electron microscopy for cryo-tomography of unstained vitrified specimens (CSTET). We compare CSTET and CET for the imaging of whole bacteria and human tissue culture cells, finding favorable contrast and detail in the CSTET reconstructions. Particularly at high sample tilts, the CSTET signals contain more informative data than energy-filtered CET phase contrast images, resulting in improved depth resolution. Careful control over dose delivery permits relatively high cumulative exposures before the onset of observable beam damage. The increase in acceptable specimen thickness broadens the applicability of electron cryo-tomography.

Radioimmunoassays of hidden viral antigens

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

Neurath, A.R.; Strick, N.; Baker, L.

1982-07-01

Antigens corresponding to infectious agents may be present in biological specimens only in a cryptic form bound to antibodies and, thus, may elude detection. We describe a solid-phase technique for separation of antigens from antibodies. Immune complexes are precipitated from serum by polyethylene glycol, dissociated with NaSCN, and adsorbed onto nitrocellulose or polystyrene supports. Antigens remain topographically separated from antibodies after removal of NaSCN and can be detected with radiolabeled antibodies. Genomes from viruses immobilized on nitrocellulose can be identified by nucleic acid hybridization. Nanogram quantities of sequestered hepatitis B surface and core antigens and picogram amounts of hepatitis Bmore » virus DNA were detected. Antibody-bound adenovirus, herpesvirus, and measles virus antigens were discerned by the procedure.« less

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

2010-01-01

The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

Morphometric analyses of hominoid crania, probabilities of conspecificity and an approximation of a biological species constant.

PubMed

Thackeray, J F; Dykes, S

2016-02-01

Thackeray has previously explored the possibility of using a morphometric approach to quantify the "amount" of variation within species and to assess probabilities of conspecificity when two fossil specimens are compared, instead of "pigeon-holing" them into discrete species. In an attempt to obtain a statistical (probabilistic) definition of a species, Thackeray has recognized an approximation of a biological species constant (T=-1.61) based on the log-transformed standard error of the coefficient m (log sem) in regression analysis of cranial and other data from pairs of specimens of conspecific extant species, associated with regression equations of the form y=mx+c where m is the slope and c is the intercept, using measurements of any specimen A (x axis), and any specimen B of the same species (y axis). The log-transformed standard error of the co-efficient m (log sem) is a measure of the degree of similarity between pairs of specimens, and in this study shows central tendency around a mean value of -1.61 and standard deviation 0.10 for modern conspecific specimens. In this paper we focus attention on the need to take into account the range of difference in log sem values (Δlog sem or "delta log sem") obtained from comparisons when specimen A (x axis) is compared to B (y axis), and secondly when specimen A (y axis) is compared to B (x axis). Thackeray's approach can be refined to focus on high probabilities of conspecificity for pairs of specimens for which log sem is less than -1.61 and for which Δlog sem is less than 0.03. We appeal for the adoption of a concept here called "sigma taxonomy" (as opposed to "alpha taxonomy"), recognizing that boundaries between species are not always well defined. Copyright © 2015 Elsevier GmbH. All rights reserved.

An Information Storage and Retrieval System for Biological and Geological Data. Interim Report.

ERIC Educational Resources Information Center

Squires, Donald F.

A project is being conducted to test the feasibility of an information storage and retrieval system for museum specimen data, particularly for natural history museums. A pilot data processing system has been developed, with the specimen records from the national collections of birds, marine crustaceans, and rocks used as sample data. The research…

Maintaining respect and fairness in the usage of stored shared specimens

PubMed Central

2013-01-01

Background Every year, research specimens are shipped from one institution to another as well as across national boundaries. A significant proportion of specimens move from poor to rich countries. Concerns are always raised on the future usage of the stored specimens shipped to research insitutions from developing countries. Creating awareness of the processes is required in all sectors involved in biomedical research. To maintain fairness and respect in sharing biomedical specimens and reserch products requires safeguarding by Ethics Review Committees in both provider and recepient institutions. Training in basic ethical principles in research is required to all sectors involved in biomedical research so as to level up the research playing field. Discussion By agreeing to provide specimens, individuals and communities from whom samples are collected would have placed their trust and all ensuing up-keep of the specimens to the researchers. In most collaborative set-up, laid down material transfer agreements are negotiated and signed before the shipment of specimens. Researchers, research ethics committees (RECs) and institutions in the countries of origin are supposed to serve as overseers of the specimens. There is need to advocate for honesty in sample handling and sharing, and also need to oversee any written commitments by researchers, RECs and institutions at source as well as in recipient institution. Commitments from source RECs and Institutional Review Boards (IRBs) and in the receiving institution on overseeing the future usage of stored specimens are required; including the ultimate confirmation abiding by the agreement. Training in ethical issues pertaining to sample handling and biomedical research in general is essential at all levels of academic pursuit. While sharing of biological specimens and research data demands honesty and oversight by ethical regulatory agents from both institutions in developing country and recepient institutions in developed countries. Concluding summary Archiving of biological specimens requires reconsideration for the future of biomedical findings and scientific break-throughs. Biomedical ethical regulations still need to established clear viable regulations that have vision for the future of science through shared and archived samples. This discussion covers and proposes essential points that need to be considered in view of future generations and scientific break-throughs. The discussion is based on the experience of working in resource-limited settings, the local regulatory laws and the need to refine research regulations governing sharing and storage of specimens for the future of science. PMID:24565022

Maintaining respect and fairness in the usage of stored shared specimens.

PubMed

Mduluza, Takafira; Midzi, Nicholas; Duruza, Donold; Ndebele, Paul

2013-01-01

Every year, research specimens are shipped from one institution to another as well as across national boundaries. A significant proportion of specimens move from poor to rich countries. Concerns are always raised on the future usage of the stored specimens shipped to research institutions from developing countries. Creating awareness of the processes is required in all sectors involved in biomedical research. To maintain fairness and respect in sharing biomedical specimens and research products requires safeguarding by Ethics Review Committees in both provider and recipient institutions. Training in basic ethical principles in research is required to all sectors involved in biomedical research so as to level up the research playing field. By agreeing to provide specimens, individuals and communities from whom samples are collected would have placed their trust and all ensuing up-keep of the specimens to the researchers. In most collaborative set-up, laid down material transfer agreements are negotiated and signed before the shipment of specimens. Researchers, research ethics committees (RECs) and institutions in the countries of origin are supposed to serve as overseers of the specimens. There is need to advocate for honesty in sample handling and sharing, and also need to oversee any written commitments by researchers, RECs and institutions at source as well as in recipient institution. Commitments from source RECs and Institutional Review Boards (IRBs) and in the receiving institution on overseeing the future usage of stored specimens are required; including the ultimate confirmation abiding by the agreement. Training in ethical issues pertaining to sample handling and biomedical research in general is essential at all levels of academic pursuit. While sharing of biological specimens and research data demands honesty and oversight by ethical regulatory agents from both institutions in developing country and recipient institutions in developed countries. Archiving of biological specimens requires reconsideration for the future of biomedical findings and scientific break-throughs. Biomedical ethical regulations still need to established clear viable regulations that have vision for the future of science through shared and archived samples. This discussion covers and proposes essential points that need to be considered in view of future generations and scientific break-throughs. The discussion is based on the experience of working in resource-limited settings, the local regulatory laws and the need to refine research regulations governing sharing and storage of specimens for the future of science.

Optical Ptychographic Microscope for Quantitative Bio-Mechanical Imaging

NASA Astrophysics Data System (ADS)

Anthony, Nicholas; Cadenazzi, Guido; Nugent, Keith; Abbey, Brian

The role that mechanical forces play in biological processes such as cell movement and death is becoming of significant interest to further develop our understanding of the inner workings of cells. The most common method used to obtain stress information is photoelasticity which maps a samples birefringence, or its direction dependent refractive indices, using polarized light. However this method only provides qualitative data and for stress information to be useful quantitative data is required. Ptychography is a method for quantitatively determining the phase of a samples complex transmission function. The technique relies upon the collection of multiple overlapping coherent diffraction patterns from laterally displaced points on the sample. The overlap of measurement points provides complementary information that significantly aids in the reconstruction of the complex wavefield exiting the sample and allows for quantitative imaging of weakly interacting specimens. Here we describe recent advances at La Trobe University Melbourne on achieving quantitative birefringence mapping using polarized light ptychography with applications in cell mechanics. Australian Synchrotron, ARC Centre of Excellence for Advanced Molecular Imaging.

The biobank of the Norwegian mother and child cohort Study: A resource for the next 100 years

PubMed Central

Rønningen, Kjersti S.; Paltiel, Liv; Meltzer, Helle M.; Nordhagen, Rannveig; Lie, Kari K.; Hovengen, Ragnhild; Haugen, Margaretha; Nystad, Wenche; Magnus, Per; Hoppin, Jane A.

2007-01-01

Introduction Long-term storage of biological materials is a critical component of any epidemiological study. In designing specimen repositories, efforts need to balance future needs for samples with logistical constraints necessary to process and store samples in a timely fashion. Objectives In the Norwegian Mother and Child Cohort Study (MoBa), the Biobank was charged with long-term storage of more than 380,000 biological samples from pregnant women, their partners and their children for up to 100 years. Methods Biological specimens include whole blood, plasma, DNA and urine; samples are collected at 50 hospitals in Norway. All samples are sent via ordinary mail to the Biobank in Oslo where the samples are registered, aliquoted and DNA extracted. DNA is stored at −20 °C while whole blood, urine and plasma are stored at − 80 °C. Results As of July 2006, over 227,000 sample sets have been collected, processed and stored at the Biobank. Currently 250–300 sets are received daily. An important part of the Biobank is the quality control program. Conclusion With the unique combination of biological specimens and questionnaire data, the MoBa Study will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental factors on pregnancy outcome and on human morbidity, mortality and health in general. PMID:17031521

TAKASAGO-6 apparatus for cryogenic coherent X-ray diffraction imaging of biological non-crystalline particles using X-ray free electron laser at SACLA

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

Kobayashi, Amane; Sekiguchi, Yuki; Oroguchi, Tomotaka

Coherent X-ray diffraction imaging (CXDI) is a technique for structure analyses of non-crystalline particles with dimensions ranging from micrometer to sub-micrometer. We have developed a diffraction apparatus named TAKASAGO-6 for use in single-shot CXDI experiments of frozen-hydrated non-crystalline biological particles at cryogenic temperature with X-ray free electron laser pulses provided at a repetition rate of 30 Hz from the SPring-8 Angstrom Compact free-electron LAser. Specimen particles are flash-cooled after being dispersed on thin membranes supported by specially designed disks. The apparatus is equipped with a high-speed translation stage with a cryogenic pot for raster-scanning of the disks at a speedmore » higher than 25 μm/33 ms. In addition, we use devices assisting the easy transfer of cooled specimens from liquid-nitrogen storages to the cryogenic pot. In the current experimental procedure, more than 20 000 diffraction patterns can be collected within 1 h. Here we report the key components and performance of the diffraction apparatus. Based on the efficiency of the diffraction data collection and the structure analyses of metal particles, biological cells, and cellular organelles, we discuss the future application of this diffraction apparatus for structure analyses of biological specimens.« less

[Application of polyguanidine solution for fixation of biological and anatomical specimens].

PubMed

Anichkov, N M; Danilova, I A; Riabinin, I A; Kipenko, A V

2010-01-01

A new method for fixation of biological material is described, and its effectiveness is compared to that one of formalin fixation. As an embalming agent, polyhexamethylenguanidine (PHMG) hydrochloride was used. Using the proposed method of fixation, the anatomical and histological preparations of human organs and of chick embryos at developmental 12 days, were produced. The anatomical preparations obtained show the appearance, similar to that of the recently removed organs. Histological preparations were free from significant distortions of the microscopic characteristics of the specimens, which are typical to the material fixed with formalin. The results of the study suggest the possibility of PHMG application in the morphological studies.

Beam deceleration for block-face scanning electron microscopy of embedded biological tissue.

PubMed

Ohta, Keisuke; Sadayama, Shoji; Togo, Akinobu; Higashi, Ryuhei; Tanoue, Ryuichiro; Nakamura, Kei-ichiro

2012-04-01

The beam deceleration (BD) method for scanning electron microscopes (SEM) also referred to as "retarding" was applied to back-scattered electron (BSE) imaging of the flat block face of a resin embedded biological specimen under low accelerating voltage and low beam current conditions. BSE imaging was performed with 0-4 kV of BD on en bloc stained rat hepatocyte. BD drastically enhanced the compositional contrast of the specimen and also improved the resolution at low landing energy levels (1.5-3 keV) and a low beam current (10 pA). These effects also functioned in long working distance observation, however, stage tilting caused uncorrectable astigmatism in BD observation. Stage tilting is mechanically required for a FIB/SEM, so we designed a novel specimen holder to minimize the unfavorable tilting effect. The FIB/SEM 3D reconstruction using the new holder showed a reasonable contrast and resolution high enough to analyze individual cell organelles and also the mitochondrial cristae structures (~5 nm) of the hepatocyte. These results indicate the advantages of BD for block face imaging of biological materials such as cells and tissues under low-voltage and low beam current conditions. Copyright © 2011 Elsevier Ltd. All rights reserved.

Quantitative Cryo-Scanning Transmission Electron Microscopy of Biological Materials.

PubMed

Elbaum, Michael

2018-05-11

Electron tomography provides a detailed view into the 3D structure of biological cells and tissues. Physical fixation by vitrification of the aqueous medium provides the most faithful preservation of biological specimens in the native, fully hydrated state. Cryo-microscopy is challenging, however, because of the sensitivity to electron irradiation and due to the weak electron scattering of organic material. Tomography is even more challenging because of the dependence on multiple exposures of the same area. Tomographic imaging is typically performed in wide-field transmission electron microscopy (TEM) mode with phase contrast generated by defocus. Scanning transmission electron microscopy (STEM) is an alternative mode based on detection of scattering from a focused probe beam, without imaging optics following the specimen. While careful configuration of the illumination and detectors is required to generate useful contrast, STEM circumvents the major restrictions of phase contrast TEM to very thin specimens and provides a signal that is more simply interpreted in terms of local composition and density. STEM has gained popularity in recent years for materials science. The extension of STEM to cryomicroscopy and tomography of cells and macromolecules is summarized herein. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scanning transmission electron microscopy through-focal tilt-series on biological specimens.

PubMed

Trepout, Sylvain; Messaoudi, Cédric; Perrot, Sylvie; Bastin, Philippe; Marco, Sergio

2015-10-01

Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples. Copyright © 2015 Elsevier Ltd. All rights reserved.

The cutting of ultrathin sections with the thickness less than 20 nm from biological specimens embedded in resin blocks.

PubMed

Nebesářová, Jana; Hozák, Pavel; Frank, Luděk; Štěpan, Petr; Vancová, Marie

2016-06-01

Low voltage electron microscopes working in transmission mode, like LVEM5 (Delong Instruments, Czech Republic) working at accelerating voltage 5 kV or scanning electron microscope working in transmission mode with accelerating voltage below 1 kV, require ultrathin sections with the thickness below 20 nm. Decreasing of the primary electron energy leads to enhancement of image contrast, which is especially useful in the case of biological samples composed of elements with low atomic numbers. As a result treatments with heavy metals, like post-fixation with osmium tetroxide or ultrathin section staining, can by omitted. The disadvantage is reduced penetration ability of incident electrons influencing the usable thickness of the specimen resulting in the need of ultrathin sections of under 20 nm thickness. In this study we want to answer basic questions concerning the cutting of extremely ultrathin sections: Is it possible routinely and reproducibly to cut extremely thin sections of biological specimens embedded in commonly used resins with contemporary ultramicrotome techniques and under what conditions? Microsc. Res. Tech. 79:512-517, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Mosaicing of single plane illumination microscopy images using groupwise registration and fast content-based image fusion

NASA Astrophysics Data System (ADS)

Preibisch, Stephan; Rohlfing, Torsten; Hasak, Michael P.; Tomancak, Pavel

2008-03-01

Single Plane Illumination Microscopy (SPIM; Huisken et al., Nature 305(5686):1007-1009, 2004) is an emerging microscopic technique that enables live imaging of large biological specimens in their entirety. By imaging the living biological sample from multiple angles SPIM has the potential to achieve isotropic resolution throughout even relatively large biological specimens. For every angle, however, only a relatively shallow section of the specimen is imaged with high resolution, whereas deeper regions appear increasingly blurred. In order to produce a single, uniformly high resolution image, we propose here an image mosaicing algorithm that combines state of the art groupwise image registration for alignment with content-based image fusion to prevent degrading of the fused image due to regional blurring of the input images. For the registration stage, we introduce an application-specific groupwise transformation model that incorporates per-image as well as groupwise transformation parameters. We also propose a new fusion algorithm based on Gaussian filters, which is substantially faster than fusion based on local image entropy. We demonstrate the performance of our mosaicing method on data acquired from living embryos of the fruit fly, Drosophila, using four and eight angle acquisitions.

Systematics and biology of Xylocopa subgenus Schonnherria (Hymenoptera, Apidae) in Argentina

PubMed Central

Lucia, Mariano; Gonzalez, Victor H.; Abrahamovich, Alberto H.

2015-01-01

Abstract Biological information on the species of the large carpenter bee Xylocopa subgenus Schonnherria occurring in Argentina is revised. Based on the appraisal of museum specimens, the study of type material, and field surveys conducted across 15 provinces between 2007 and 2011, the following seven species are recognized for the country: Xylocopa bambusae Schrottky, Xylocopa chrysopoda Schrottky, Xylocopa macrops Lepeletier de Saint Fargeau, Xylocopa simillima Smith Xylocopa splendidula Lepeletier de Saint Fargeau, Xylocopa pulchra Smith, and Xylocopa viridis Smith. Previous literature records of Xylocopa dimidiata Latreille, Xylocopa subcyanea Pérez, and Xylocopa varians Smith for the province of Misiones appear to have been misidentified specimens, although the presence of these species in Argentina cannot be entirely ruled out given the proximity of this province to Brazil and Paraguay where they occur; Xylocopa boops Maidl was described from a male specimen with unusually enlarged eyes and is newly synonymized under Xylocopa macrops. Males and females of all species are diagnosed, described, and figured, including details of the male genitalia. Taxonomic comments, data on the geographical distribution and nesting substrates, and identification keys to all Argentinean species of Schonnherria are provided. The nesting biologies of Xylocopa splendidula and Xylocopa viridis are documented. PMID:26798288

Robust and automated three-dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines-of-Sight decomposition.

PubMed

Mathew, B; Schmitz, A; Muñoz-Descalzo, S; Ansari, N; Pampaloni, F; Stelzer, E H K; Fischer, S C

2015-06-08

Due to the large amount of data produced by advanced microscopy, automated image analysis is crucial in modern biology. Most applications require reliable cell nuclei segmentation. However, in many biological specimens cell nuclei are densely packed and appear to touch one another in the images. Therefore, a major difficulty of three-dimensional cell nuclei segmentation is the decomposition of cell nuclei that apparently touch each other. Current methods are highly adapted to a certain biological specimen or a specific microscope. They do not ensure similarly accurate segmentation performance, i.e. their robustness for different datasets is not guaranteed. Hence, these methods require elaborate adjustments to each dataset. We present an advanced three-dimensional cell nuclei segmentation algorithm that is accurate and robust. Our approach combines local adaptive pre-processing with decomposition based on Lines-of-Sight (LoS) to separate apparently touching cell nuclei into approximately convex parts. We demonstrate the superior performance of our algorithm using data from different specimens recorded with different microscopes. The three-dimensional images were recorded with confocal and light sheet-based fluorescence microscopes. The specimens are an early mouse embryo and two different cellular spheroids. We compared the segmentation accuracy of our algorithm with ground truth data for the test images and results from state-of-the-art methods. The analysis shows that our method is accurate throughout all test datasets (mean F-measure: 91%) whereas the other methods each failed for at least one dataset (F-measure≤69%). Furthermore, nuclei volume measurements are improved for LoS decomposition. The state-of-the-art methods required laborious adjustments of parameter values to achieve these results. Our LoS algorithm did not require parameter value adjustments. The accurate performance was achieved with one fixed set of parameter values. We developed a novel and fully automated three-dimensional cell nuclei segmentation method incorporating LoS decomposition. LoS are easily accessible features that ensure correct splitting of apparently touching cell nuclei independent of their shape, size or intensity. Our method showed superior performance compared to state-of-the-art methods, performing accurately for a variety of test images. Hence, our LoS approach can be readily applied to quantitative evaluation in drug testing, developmental and cell biology.

Anatomy of the interosseous region of the sacroiliac joint.

PubMed

Rosatelli, Alessandro L; Agur, Anne M; Chhaya, Sam

2006-04-01

Anatomical study of the interosseous region of the sacroiliac joint (SIJ) complex. To document and quantify the surface topography of the interosseous region of the SIJ. A review of the literature reveals that little consideration has been given to the interosseous region of the SIJ anatomically, biomechanically, and clinically. The interosseous region of 11 cadaveric specimens (9 formalin embalmed and 2 fresh frozen) were studied. Ten specimens were 55 years of age or older and 1 was 20 years old. To view the interosseous surfaces of the sacrum and ilium the specimens were either axially sectioned (1-cm slices) or disarticulated. One fresh-frozen and 6 embalmed specimens were disarticulated and the remainder axially sectioned. The topography (surface ridging and areas of ossification) of the interosseous region was documented in all specimens and in 2 specimens the surfaces were 3-dimensionally reconstructed using modeling and animation software (MAYA; Autodesk, Inc, San Rafael, CA). Surface characteristics of the SIJ complex observed in specimens 55 years of age or older included moderate to extensive ridging of the interosseous region of the sacrum and ilium in 100% of specimens and ossification of the central interosseous region of the sacroiliac (SI) ligament in 60% of specimens. Central region ossification of the interosseous SI ligament and the presence of ridges and depressions over the opposing interosseous surfaces of the sacrum and ilium are features common to specimens that are in or beyond their sixth decade. These findings further support the contention that there is little to no movement available at this joint in older individuals.

Biological implications of lab-on-a-chip devices fabricated using multi-jet modelling and stereolithography processes

NASA Astrophysics Data System (ADS)

Zhu, Feng; Macdonald, Niall; Skommer, Joanna; Wlodkowic, Donald

2015-06-01

Current microfabrication methods are often restricted to two-dimensional (2D) or two and a half dimensional (2.5D) structures. Those fabrication issues can be potentially addressed by emerging additive manufacturing technologies. Despite rapid growth of additive manufacturing technologies in tissue engineering, microfluidics has seen relatively little developments with regards to adopting 3D printing for rapid fabrication of complex chip-based devices. This has been due to two major factors: lack of sufficient resolution of current rapid-prototyping methods (usually >100 μm ) and optical transparency of polymers to allow in vitro imaging of specimens. We postulate that adopting innovative fabrication processes can provide effective solutions for prototyping and manufacturing of chip-based devices with high-aspect ratios (i.e. above ration of 20:1). This work provides a comprehensive investigation of commercially available additive manufacturing technologies as an alternative for rapid prototyping of complex monolithic Lab-on-a-Chip devices for biological applications. We explored both multi-jet modelling (MJM) and several stereolithography (SLA) processes with five different 3D printing resins. Compared with other rapid prototyping technologies such as PDMS soft lithography and infrared laser micromachining, we demonstrated that selected SLA technologies had superior resolution and feature quality. We also for the first time optimised the post-processing protocols and demonstrated polymer features under scanning electronic microscope (SEM). Finally we demonstrate that selected SLA polymers have optical properties enabling high-resolution biological imaging. A caution should be, however, exercised as more work is needed to develop fully bio-compatible and non-toxic polymer chemistries.

Biophysical and biological factors determining the ability to achieve long-term cryobiological preservation

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

Mazur, P.

1997-12-01

The BESTCapsule will maintain appropriate biological specimens for decades or centuries at cryogenic temperatures in the living state. Maintenance at temperatures below {approximately} {minus}140 C is not a problem. No ordinary chemical reactions in aqueous solutions can occur. The only source of damage will be the slow accumulation of physical damage to DNA from background ionizing radiation. But this source of damage should not become serious in less than a millennium. Rather, the main problem in cryopreservation is to devise procedures for cooling the biological specimens to {minus}196 C and returning them to normal temperatures without inflicting lethal injury. Regardlessmore » of the cell type, there are certain encompassing biophysical factors and constraints that determine whether they will survive or die during freezing and thawing. Superimposed on these may be special biological factors that apply to specific cell types. This paper will emphasize the former and give illustrative examples of the latter.« less

Scientific experiments in the flight of the 1977 biological satellite (draft plan)

NASA Technical Reports Server (NTRS)

1977-01-01

The physiological, biological, radiobiological and radiophysical experiments planned for the 1977 biological satellite are described. The biological experiments will involve rats, higher and lower plants, insects and other biological specimens carried on the biosatellite. The responses of these organisms to weightlessness, artificial gravity, cosmic radiation particles and general flight factors will be studied. The radiophysical experiments will investigate certain properties of cosmic radiation as well as the possibility of creating electrostatic and dielectric radiation shields under actual space-flight conditions.

Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics.

PubMed

M'Koma, Amosy E

2014-11-27

Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn's colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed.

Diagnosis of inflammatory bowel disease: Potential role of molecular biometrics

PubMed Central

M’Koma, Amosy E

2014-01-01

Accurate diagnosis of predominantly colonic inflammatory bowel disease (IBD) is not possible in 30% of patients. For decades, scientists have worked to find a solution to improve diagnostic accuracy for IBD, encompassing Crohn’s colitis and ulcerative colitis. Evaluating protein patterns in surgical pathology colectomy specimens of colonic mucosal and submucosal compartments, individually, has potential for diagnostic medicine by identifying integrally independent, phenotype-specific cellular and molecular characteristics. Mass spectrometry (MS) and imaging (I) MS are analytical technologies that directly measure molecular species in clinical specimens, contributing to the in-depth understanding of biological molecules. The biometric-system complexity and functional diversity is well suited to proteomic and diagnostic studies. The direct analysis of cells and tissues by Matrix-Assisted-Laser Desorption/Ionization (MALDI) MS/IMS has relevant medical diagnostic potential. MALDI-MS/IMS detection generates molecular signatures obtained from specific cell types within tissue sections. Herein discussed is a perspective on the use of MALDI-MS/IMS and bioinformatics technologies for detection of molecular-biometric patterns and identification of differentiating proteins. I also discuss a perspective on the global challenge of transferring technologies to clinical laboratories dealing with IBD issues. The significance of serologic-immunometric advances is also discussed. PMID:25429322

The Alaska Area Specimen Bank: a tribal-federal partnership to maintain and manage a resource for health research.

PubMed

Parkinson, Alan J; Hennessy, Thomas; Bulkow, Lisa; Smith, H Sally

2013-01-01

Banked biospecimens from a defined population are a valuable resource that can be used to assess early markers for illness or to determine the prevalence of a disease to aid the development of intervention strategies to reduce morbidity and mortality. The Alaska Area Specimen Bank (AASB) currently contains 266,353 residual biologic specimens (serum, plasma, whole blood, tissue, bacterial cultures) from 83,841 persons who participated in research studies, public health investigations and clinical testing conducted by the U.S. Public Health Service and Alaska Native tribal health organisations dating back to 1961. The majority (95.7%) are serum specimens, 77% were collected between 1981 and 1994 and 85% were collected from Alaska Native people. Oversight of the specimen bank is provided by a working group with representation from tribal, state and federal health organisations, the Alaska Area IRB and a specimen bank committee which ensures the specimens are used in accordance with policies and procedures developed by the working group.

Validation of RNA-based molecular clonotype analysis for virus-specific CD8+ T-cells in formaldehyde-fixed specimens isolated from peripheral blood

PubMed Central

van Bockel, David; Price, David A.; Asher, Tedi E.; Venturi, Vanessa; Suzuki, Kazuo; Warton, Kristina; Davenport, Miles P.; Cooper, David A.; Douek, Daniel C.; Kelleher, Anthony D.

2007-01-01

Recent advances in the field of molecular clonotype analysis have enabled detailed repertoire characterization of viably isolated antigen-specific T cell populations directly ex vivo. However, in the absence of a biologically contained FACS facility, peripheral blood mononuclear cell (PBMC) preparations derived from patients infected with agents such as HIV must be formaldehyde fixed to inactivate the pathogen; this procedure adversely affects nucleic acid template quality. Here, we developed and validated a method to amplify and sequence mRNA species derived from formaldehyde fixed PBMC specimens. Antigen-specific CD8+ cytotoxic T-lymphocyte populations were identified with standard fluorochrome-conjugated peptide-major histocompatibility complex class I tetramers refolded around synthetic peptides representing immunodominant epitopes from HIV p24 Gag (KRWII[M/L]GLNK/HLA B*2705) and CMV pp65 (NLVPMVATV/HLA A*0201 and TPRVTGGGAM/HLA B*0702), and acquired in separate laboratories with or without fixation. In the presence of proteinase K pre-treatment, the observed antigen-specific CD8+ T-cell repertoire determined by molecular clonotype analysis was statistically no different whether derived from fixed or unfixed PBMC. However, oligo-dT recovery methods were not suitable for use with fixed tissue as significant skewing of clonotypic representation was observed. Thus, we have developed a reliable RNA-based method for molecular clonotype analysis that is compatible with formaldehyde fixation and therefore suitable for use with primary human samples isolated by FACS outside the context of a biological safety level 3 containment facility. PMID:17716684

Revealing hidden clonal complexity in Mycobacterium tuberculosis infection by qualitative and quantitative improvement of sampling.

PubMed

Pérez-Lago, L; Palacios, J J; Herranz, M; Ruiz Serrano, M J; Bouza, E; García-de-Viedma, D

2015-02-01

The analysis of microevolution events, its functional relevance and impact on molecular epidemiology strategies, constitutes one of the most challenging aspects of the study of clonal complexity in infection by Mycobacterium tuberculosis. In this study, we retrospectively evaluated whether two improved sampling schemes could provide access to the clonal complexity that is undetected by the current standards (analysis of one isolate from one sputum). We evaluated in 48 patients the analysis by mycobacterial interspersed repetitive unit-variable number tandem repeat of M. tuberculosis isolates cultured from bronchial aspirate (BAS) or bronchoalveolar lavage (BAL) and, in another 16 cases, the analysis of a higher number of isolates from independent sputum samples. Analysis of the isolates from BAS/BAL specimens revealed clonal complexity in a very high proportion of cases (5/48); in most of these cases, complexity was not detected when the isolates from sputum samples were analysed. Systematic analysis of isolates from multiple sputum samples also improved the detection of clonal complexity. We found coexisting clonal variants in two of 16 cases that would have gone undetected in the analysis of the isolate from a single sputum specimen. Our results suggest that analysis of isolates from BAS/BAL specimens is highly efficient for recording the true clonal composition of M. tuberculosis in the lungs. When these samples are not available, we recommend increasing the number of isolates from independent sputum specimens, because they might not harbour the same pool of bacteria. Our data suggest that the degree of clonal complexity in tuberculosis has been underestimated because of the deficiencies inherent in a simplified procedure. Copyright © 2014 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Characterization of Fatigue Damage for Bonded Composite Skin/Stringer Configurations

NASA Technical Reports Server (NTRS)

Paris, Isabelle; Cvitkovich, Michael; Krueger, Ronald

2008-01-01

The fatigue damage was characterized in specimens which consisted of a tapered composite flange bonded onto a composite skin. Quasi-static tension tests were performed first to determine the failure load. Subsequently, tension fatigue tests were performed at 40%, 50%, 60% and 70% of the failure load to evaluate the debonding mechanisms. For four specimens, the cycling loading was stopped at intervals. Photographs of the polished specimen edges were taken under a light microscope to document the damage. At two diagonally opposite corners of the flange, a delamination appeared to initiate at the flange tip from a matrix crack in the top 45deg skin ply and propagated at the top 45deg/-45deg skin ply interface. At the other two diagonally opposite corners, a delamination running in the bondline initiated from a matrix crack in the adhesive pocket. In addition, two specimens were cut longitudinally into several sections. Micrographs revealed a more complex pattern inside the specimen where the two delamination patterns observed at the edges are present simultaneously across most of the width of the specimen. The observations suggest that a more sophisticated nondestructive evaluation technique is required to capture the complex damage pattern of matrix cracking and multi-level delaminations.

Evaluation of a commercial ligase chain reaction assay for the diagnosis of pulmonary and extra-pulmonary tuberculosis.

PubMed

Viveiros, M; Pinheiro, S; Moreira, P; Pacheco, T; Brum, L

1999-06-01

Egas Moniz Hospital, Lisbon, Portugal. To evaluate the Ligase Chain Reaction (LCx) Mycobacterium tuberculosis Assay for the direct detection of M. tuberculosis complex in respiratory specimens after smear observation, and its suitability for non-respiratory clinical specimens. Analysis of 156 specimens collected from 123 patients with pulmonary tuberculosis and/or extrapulmonary involvement. Among 93 pulmonary secretions and 63 extra-pulmonary samples and after resolution of discrepancies based on clinical and laboratory findings, two pulmonary samples from a patient with a diagnosis of sarcoidosis, four samples of cerebrospinal and one of seminal fluid were considered as false positives. Two tissue biopsy samples, one pericardial effusion and one pulmonary secretion from patients strongly suspected of having tuberculosis were considered as false negatives for the assay, without inhibition of amplification. All specimens yielding M. avium on culture were LCx negative. The LCx Mycobacterium tuberculosis Assay was found to be useful for the rapid identification of M. tuberculosis complex in all types of specimens. It revealed a high specificity both in pulmonary and extrapulmonary products, and a sensitivity of 97% for the pulmonary secretions and of 75% for the extra-pulmonary specimens, independently of the bacilloscopy results.

Performance of Northeastern United States wood species treated with copper based preservatives: 10 year above-ground decking evaluation

Treesearch

S. T. Lebow; S. A. Halverson

2015-01-01

Research was conducted to evaluate the decking performance of northeastern United States wood species treated with copper based preservatives. Decking specimens were treated with one of four wood preservatives and exposed near Madison, Wisconsin. Specimens were evaluated for biological attack and dimensional stability. After 10 years, none of the preservative treated...

Water without windows: Evaluating the performance of open cell transmission electron microscopy under saturated water vapor conditions, and assessing its potential for microscopy of hydrated biological specimens.

PubMed

Cassidy, Cathal; Yamashita, Masao; Cheung, Martin; Kalale, Chola; Adaniya, Hidehito; Kuwahara, Ryusuke; Shintake, Tsumoru

2017-01-01

We have performed open cell transmission electron microscopy experiments through pure water vapor in the saturation pressure regime (>0.6 kPa), in a modern microscope capable of sub-Å resolution. We have systematically studied achievable pressure levels, stability and gas purity, effective thickness of the water vapor column and associated electron scattering processes, and the effect of gas pressure on electron optical resolution and image contrast. For example, for 1.3 kPa pure water vapor and 300kV electrons, we report pressure stability of ± 20 Pa over tens of minutes, effective thickness of 0.57 inelastic mean free paths, lattice resolution of 0.14 nm on a reference Au specimen, and no significant degradation in contrast or stability of a biological specimen (M13 virus, with 6 nm body diameter). We have also done some brief experiments to confirm feasibility of loading specimens into an in situ water vapor ambient without exposure to intermediate desiccating conditions. Finally, we have also checked if water experiments had any discernible impact on the microscope performance, and report pertinent vacuum and electron optical data, for reference purposes.

Space Station Biological Research Project (SSBRP) Cell Culture Unit (CCU) and incubator for International Space Station (ISS) cell culture experiments

NASA Technical Reports Server (NTRS)

Vandendriesche, Donald; Parrish, Joseph; Kirven-Brooks, Melissa; Fahlen, Thomas; Larenas, Patricia; Havens, Cindy; Nakamura, Gail; Sun, Liping; Krebs, Chris; de Luis, Javier;

Development and validation of an ELISA kit for the detection of ricin toxins from biological specimens and environmental samples.

PubMed

Chen, Hsiao Ying; Tran, Hung; Foo, Ling Yann; Sew, Tracey Wenhui; Loke, Weng Keong

2014-08-01

Ricin is a toxin that can be easily extracted from seeds of Ricinus communis plants. Ricin is considered to be a major bio-threat as it can be freely and easily acquired in large quantities. A deliberate release of such toxin in civilian populations would very likely overwhelm existing public health systems, resulting in public fear and social unrest. There is currently no commercially available or FDA-approved prophylaxis such as vaccines, or therapeutic antitoxins or antidotes, available for ricin intoxication. Patient treatment is typically supportive care based on symptoms, often designed to reinforce the body's natural response. This paper describes the development and validation of a robust ELISA test kit, which can be used to screen for ricin in biological specimens such as whole blood and faeces. Faecal specimens are shown in this study to have better diagnostic sensitivity and a wider diagnostic window compared to whole blood. From these results, it is concluded that faeces is the most suitable clinical specimen for diagnosis of ricin poisoning via the oral route. The ELISA test kit can also detect ricin in environmental samples. An advantage of this ELISA kit over other commercial off-the-shelf (COTS) detection kits currently on the market that are developed to screen environmental samples only is its ability to diagnose ricin poisoning from clinical specimens as well as detect ricin from environmental samples.

Evaluation of Intraosseous Fluid as an Alternative Biological Specimen in Postmortem Toxicology.

PubMed

Rodda, Luke N; Volk, Justin A; Moffat, Ellen; Williams, Chinyere M; Lynch, Kara L; Wu, Alan H B

2018-04-01

The postmortem redistribution phenomenon is an important factor in the interpretation of blood drug concentrations as a cause or factor in death. Intraosseous fluid (IOF) may serve as an alternative matrix for drug testing. Intraosseous fluid was collected from the left and right tibias and humerus of 29 decedents using the Arrow EZ-IO Intraosseous Vascular Access System. Standard autopsy specimens including blood were also collected at the same time during autopsy. Blood and IOF specimens were screened by immunoassay for opioids, fentanyl analogs, oxycodone, methadone, cocaine, methamphetamine, amphetamines, phencyclidine, tricyclic antidepressants, benzodiazepines and cannabinoids, using commercially available enzyme-linked immunosorbent assay (ELISA) kits. Correlation between cardiac/central blood ELISA and IOF ELISA results was mostly 100% for drug targets. Further blood confirmation analysis was performed by gas chromatography mass spectrometry also showed comparable correlation to IOF screen results. There was no significant difference between the IOF sites or sides of the body. This novel study supports the use of IOF as an alternative postmortem specimen for toxicological investigations as a potentially less-compromised tissue in decomposed or traumatized bodies. Preliminary data is provided for the screening of common drugs of abuse in IOF that may show to be subject to alternative rates of postmortem redistribution than to that of other biological specimens in future studies that quantitate IOF drug concentrations.

Harvestmen of the BOS Arthropod Collection of the University of Oviedo (Spain) (Arachnida, Opiliones)

PubMed Central

Merino-Sáinz, Izaskun; Anadón, Araceli; Torralba-Burrial, Antonio

2013-01-01

Abstract There are significant gaps in accessible knowledge about the distribution and phenology of Iberian harvestmen (Arachnida: Opiliones). Harvestmen accessible datasets in Iberian Peninsula are unknown, an only two other datasets available in GBIF are composed exclusively of harvestmen records. Moreover, only a few harvestmen data from Iberian Peninsula are available in GBIF network (or in any network that allows public retrieval or use these data). This paper describes the data associated with the Opiliones kept in the BOS Arthropod Collection of the University of Oviedo, Spain (hosted in the Department of Biología de Organismos y Sistemas), filling some of those gaps. The specimens were mainly collected from the northern third of the Iberian Peninsula. The earliest specimen deposited in the collection, dating back to the early 20th century, belongs to the P. Franganillo Collection. The dataset documents the collection of 16,455 specimens, preserved in 3,772 vials. Approximately 38% of the specimens belong to the family Sclerosomatidae, and 26% to Phalangidae; six other families with fewer specimens are also included. Data quality control was incorporated at several steps of digitisation process to facilitate reuse and improve accuracy. The complete dataset is also provided in Darwin Core Archive format, allowing public retrieval, use and combination with other biological, biodiversity of geographical variables datasets. PMID:24146596

Light sheet-based fluorescence microscopy (LSFM) reduces phototoxic effects and provides new means for the modern life sciences

NASA Astrophysics Data System (ADS)

Pampaloni, Francesco; Ansari, Nari; Girard, Philippe; Stelzer, Ernst H. K.

2011-07-01

Most optical technologies are applied to flat, basically two-dimensional cellular systems. However, physiological meaningful information relies on the morphology, the mechanical properties and the biochemistry of a cell's context. A cell requires the complex three-dimensional relationship to other cells. However, the observation of multi-cellular biological specimens remains a challenge. Specimens scatter and absorb light, thus, the delivery of the probing light and the collection of the signal light become inefficient; many endogenous biochemical compounds also absorb light and suffer degradation of some sort (photo-toxicity), which induces malfunction of a specimen. In conventional and confocal fluorescence microscopy, whenever a single plane, the entire specimen is illuminated. Recording stacks of images along the optical Z-axis thus illuminates the entire specimen once for each plane. Hence, cells are illuminated 10-20 and fish 100-300 times more often than they are observed. This can be avoided by changing the optical arrangement. The basic idea is to use light sheets, which are fed into the specimen from the side and overlap with the focal plane of a wide-field fluorescence microscope. In contrast to an epi-fluorescence arrangement, such an azimuthal fluorescence arrangement uses two independently operated lenses for illumination and detection. Optical sectioning and no photo-toxic damage or photo-bleaching outside a small volume close to the focal plane are intrinsic properties. Light sheet-based fluorescence microscopy (LSFM) takes advantage of modern camera technologies. LSFM can be operated with laser cutters and for fluorescence correlation spectroscopy. During the last few years, LSFM was used to record zebrafish development from the early 32-cell stage until late neurulation with sub-cellular resolution and short sampling periods (60-90 sec/stack). The recording speed was five 4-Megapixel large frames/sec with a dynamic range of 12-14 bit. We followed cell movements during gastrulation, revealed the development during cell migration processes and showed that an LSFM exposes an embryo to 200 times less energy than a conventional and 5,000 times less energy than a confocal fluorescence microscope. Most recently, we implemented incoherent structured illumination in our DSLM. The intensity modulated light sheets can be generated with dynamic frequencies and allow us to estimate the effect of the specimen on the image formation process at various depths in objects of different age.

Preparation of Plant Samples for Phytochemical Research and the Study of Their Biological Activities

USDA-ARS?s Scientific Manuscript database

Prior to investigating plant natural products for biologically active constituents, it is necessary to establish guidelines and procedures for carefully collecting, cataloging, and storing specimens. All field collections should begin with detailed records on location, which should include a list o...

Producing Zirconium Diboride Components with Complex, Near-Net Shape Geometries by Aqueous Room-Temperature Injection Molding

NASA Technical Reports Server (NTRS)

Wiesner, Valerie L.; Youngblood, Jeffrey; Trice, Rodney

2014-01-01

Room-temperature injection molding is proposed as a novel, low-cost and more energy efficient manufacturing process capable of forming complex-shaped zirconium diboride (ZrB2) parts. This innovative processing method utilized aqueous suspensions with high powder loading and a minimal amount (5 vol.) of water-soluble polyvinylpyrrolidone (PVP), which was used as a viscosity modifier. Rheological characterization was performed to evaluate the room-temperature flow properties of ZrB2-PVP suspensions. ZrB2 specimens were fabricated with high green body strength and were machinable prior to binder removal despite their low polymer content. After binder burnout and pressureless sintering, the bulk density and microstructure of specimens were characterized using Archimedes technique and scanning electron microscopy. X-Ray Diffraction was used to determine the phase compositions present in sintered specimens. Ultimate strength of sintered specimens will be determined using ASTM C1323-10 compressive C-ring test.

Paul Langerhans: a prilgrim "traveling" from functional histology to marine biology.

PubMed

Raica, Marius; Cimpean, Anca Maria

2017-06-01

The nineteenth century was the time of a real revolution in science and medicine. A lot of seminal discoveries in medicine and biology were done in this time, and many of them were coincident with the introduction of the compound microscope by Hermann van Deijl and the standard histological technique by Paul Ehrlich. The main tissue types and individual cells were characterized and originally classified more than hundred years ago, although less attention was paid to their basic functions. This was mainly due to the modality of tissue specimen processing that allowed particularly detailed descriptive studies. Even so, we can notice some attempts to correlate the structure with the function. The German scientist Paul Langerhans, well-known for the discovery of Langerhans islets of the pancreas and Langerhans cells from the epidermis, tried to change the conventional fate of morphological studies introducing in his works functional hypothesis based on traditional microscopic observations even from the beginning of his scientific career. Paul Langerhans was a complex personality of the second half of the nineteenth century, not only in medicine, but also in other fields of biology. In the present review, presented is the life and research activity of Paul Langerhans, not only because of the importance of his discoveries, but also for perspectives that were opened by these findings in unexpected fields of medicine and biology.

Synthetical Analysis for Morphology, biological Species, and stable Isotopes (SAMSI) of single-cell planktonic foraminifer

NASA Astrophysics Data System (ADS)

Ujiie, Y.; Kimoto, K.; Ishimura, T.

2017-12-01

Planktonic foraminifers are widely used in the studies of paleontology and paleoceanography, because the morphology of their calcareous shells is enough highly variable to identify the morphospecies and the chemical composition of the shells reflect ambient seawater condition. Although the morphospecies were believed to represent environments associating with latitudinal temperature range of the world ocean, molecular phylogeographic studies have unveiled the presence of multiple biological species in a single morphospecies and their species-specific distributions. This implicates the actual complexity of planktonic foraminiferal ecology. Conversely, these biological species have a high potential for providing novel ecological and environmental information to us. In order to reassess the morphological and geochemical characters of biological species, the DNA extraction method with the guanidium isothiocyanate buffer was developed to preserve the calcareous shells. The present study carefully tested the physical and chemical damages of the DNA extraction process to the shells, by our novel approaches with geochemical analysis of the shells after non-destructive analysis for morphometrics on a same specimen. First, we checked the changes of the shell densities between pre- and post-DNA extraction by using the micro-focus X-ray CT (MXCT) scanning. Based on the simultaneous measurement of a sample and the standard material, we confirmed no significant changes to the shell densities through the DNA extraction process. As a next step, we compared stable oxygen and carbon isotopes among individuals of three sample sets: (1) no chemical and incubation as control, (2) incubation in the DNA extraction buffer at 65-70°C for 40 minutes as standard way, and (3) incubation in the DNA extraction buffer at 65-70°C for 120 minutes, by using the microscale isotopic analytical system (MICAL3c). Consequently, there were no significant differences among the three sample sets. These examinations clearly certified that we define morphological and geochemical features from same specimens after genetic identification. Thus, our novel approach (SAMSI) provides future studies to establish the accurate ecological and environmental proxies both in the modern and past oceans.

Israel Marine Bio-geographic Database (ISRAMAR-BIO)

NASA Astrophysics Data System (ADS)

Greengrass, Eyal; Krivenko, Yevgeniya; Ozer, Tal; Ben Yosef, Dafna; Tom, Moshe; Gertman, Isaac

2015-04-01

The knowledge of the space/time variations of species is the basis for any ecological investigations. While historical observations containing integral concentrations of biological parameters (chlorophyll, abundance, biomass…) are organized partly in ISRAMAR Cast Database, the taxon-specific data collected in Israel has not been sufficiently organized. This has been hindered by the lack of standards, variability of methods and complexity of biological data formalization. The ISRAMAR-BIO DB was developed to store various types of historical and future available information related to marine species observations and related metadata. Currently the DB allows to store biological data acquired by the following sampling devices such as: van veer grab, box corer, sampling bottles, nets (plankton, trawls and fish), quadrates, and cameras. The DB's logical unit is information regarding a specimen (taxa name, barcode, image), related attributes (abundance, size, age, contaminants…), habitat description, sampling device and method, time and space of sampling, responsible organization and scientist, source of information (cruise, project and publication). The following standardization of specimen and attributes naming were implemented: Taxonomy according to World Register of Marine Species (WoRMS: http://www.marinespecies.org). Habitat description according to Coastal and Marine Ecological Classification Standards (CMECS: http://www.cmecscatalog.org) Parameter name; Unit; Device name; Developmental stage; Institution name; Country name; Marine region according to SeaDataNet Vocabularies (http://www.seadatanet.org/Standards-Software/Common-Vocabularies). This system supports two types of data submission procedures, which support the above stated data structure. The first is a downloadable excel file with drop-down fields based on the ISRAMAR-BIO vocabularies. The file is filled and uploaded online by the data contributor. Alternatively, the same dataset can be assembled by filling online forms and then submitted to the DB. Online access to the ISRAMAR-BIO is available through taxon search page, where one can get both biological and geographical data regarding a certain taxon. Further development of the online data access is ongoing. It will include interactive geographical map interface where data may be queried, analyzed and downloaded.

Molecular analysis of Mycobacterium isolates from extrapulmonary specimens obtained from patients in Mexico

PubMed Central

Alvarado-Esquivel, Cosme; García-Corral, Nora; Carrero-Dominguez, David; Enciso-Moreno, José Antonio; Gurrola-Morales, Teodoro; Portillo-Gómez, Leopoldo; Rossau, Rudi; Mijs, Wouter

2009-01-01

Background Little information is available on the molecular epidemiology in Mexico of Mycobacterium species infecting extrapulmonary sites in humans. This study used molecular methods to determine the Mycobacterium species present in tissues and body fluids in specimens obtained from patients in Mexico with extrapulmonary disease. Methods Bacterial or tissue specimens from patients with clinical or histological diagnosis of extrapulmonary tuberculosis were studied. DNA extracts from 30 bacterial cultures grown in Löwenstein Jensen medium and 42 paraffin-embedded tissues were prepared. Bacteria were cultured from urine, cerebrospinal fluid, pericardial fluid, gastric aspirate, or synovial fluid samples. Tissues samples were from lymph nodes, skin, brain, vagina, and peritoneum. The DNA extracts were analyzed by PCR and by line probe assay (INNO-LiPA MYCOBACTERIA v2. Innogenetics NV, Gent, Belgium) in order to identify the Mycobacterium species present. DNA samples positive for M. tuberculosis complex were further analyzed by PCR and line probe assay (INNO-LiPA Rif.TB, Innogenetics NV, Gent, Belgium) to detect mutations in the rpoB gene associated with rifampicin resistance. Results Of the 72 DNA extracts, 26 (36.1%) and 23 (31.9%) tested positive for Mycobacterium species by PCR or line probe assay, respectively. In tissues, M. tuberculosis complex and M. genus were found in lymph nodes, and M. genus was found in brain and vagina specimens. In body fluids, M. tuberculosis complex was found in synovial fluid. M. gordonae, M. smegmatis, M. kansasii, M. genus, M. fortuitum/M. peregrinum complex and M. tuberculosis complex were found in urine. M. chelonae/M. abscessus was found in pericardial fluid and M. kansasii was found in gastric aspirate. Two of M. tuberculosis complex isolates were also PCR and LiPA positive for the rpoB gene. These two isolates were from lymph nodes and were sensitive to rifampicin. Conclusion 1) We describe the Mycobacterium species diversity in specimens derived from extrapulmonary sites in symptomatic patients in Mexico; 2) Nontuberculous mycobacteria were found in a considerable number of patients; 3) Genotypic rifampicin resistance in M. tuberculosis complex infections in lymph nodes was not found. PMID:19272158

Bone morphogenetic protein 7 (BMP-7) influences tendon-bone integration in vitro.

PubMed

Schwarting, Tim; Lechler, Philipp; Struewer, Johannes; Ambrock, Marius; Frangen, Thomas Manfred; Ruchholtz, Steffen; Ziring, Ewgeni; Frink, Michael

2015-01-01

Successful graft ingrowth following reconstruction of the anterior cruciate ligament is governed by complex biological processes at the tendon-bone interface. The aim of this study was to investigate in an in vitro study the effects of bone morphogenetic protein 7 (BMP-7) on tendon-bone integration. To study the biological effects of BMP-7 on the process of tendon-bone-integration, two independent in vitro models were used. The first model involved the mono- and coculture of bovine tendon specimens and primary bovine osteoblasts with and without BMP-7 exposure. The second model comprised the mono- and coculture of primary bovine osteoblasts and fibroblasts. Alkaline phosphatase (ALP), lactate dehydrogenase (LDH), lactate and osteocalcin (OCN) were analyzed by ELISA. Histological analysis and electron microscopy of the tendon specimens were performed. In both models, positive effects of BMP-7 on ALP enzyme activity were observed (p<0.001). Additionally, similar results were noted for LDH activity and lactate concentration. BMP-7 stimulation led to a significant increase in OCN expression. Whereas the effects of BMP-7 on tendon monoculture peaked during an early phase of the experiment (p<0.001), the cocultures showed a maximal increase during the later stages (p<0.001). The histological analysis showed a stimulating effect of BMP-7 on extracellular matrix formation. Organized ossification zones and calcium carbonate-like structures were only observed in the BMP-stimulated cell cultures. This study showed the positive effects of BMP-7 on the biological process of tendon-bone integration in vitro. Histological signs of improved mineralization were paralleled by increased rates of osteoblast-specific protein levels in primary bovine osteoblasts and fibroblasts. Our findings indicated a role for BMP-7 as an adjuvant therapeutic agent in the treatment of ligamentous injuries, and they emphasized the importance of the transdifferentiation process of tendinous fibroblasts at the tendon-bone interface.

Museum samples could help to reconstruct the original distribution of Salmo trutta complex in Italy.

PubMed

Splendiani, A; Fioravanti, T; Giovannotti, M; Olivieri, L; Ruggeri, P; Nisi Cerioni, P; Vanni, S; Enrichetti, F; Caputo Barucchi, V

2017-06-01

Partial D-loop sequences of museum specimens of brown trout and marble trout (Salmo trutta species complex) collected from Mediterranean rivers in the late 19th century were analysed to help to describe the native distribution of these species. All the individuals studied carried native haplotypes, the geographic distribution of which is consistent with published data. These results indicate that museum specimens from the 19th century could represent an opportunity to get a picture of the original genetic diversity distribution of this species complex. © 2017 The Fisheries Society of the British Isles.

X-ray microanalysis in the scanning electron microscope.

PubMed

Roomans, Godfried M; Dragomir, Anca

2014-01-01

X-ray microanalysis conducted using the scanning electron microscope is a technique that allows the determination of chemical elements in bulk or semi-thick specimens. The lowest concentration of an element that can be detected is in the order of a few mmol/kg or a few hundred parts per million, and the smallest amount is in the order of 10(-18) g. The spatial resolution of the analysis depends on the thickness of the specimen. For biological specimen analysis, care must be taken to prevent displacement/loss of the element of interest (usually ions). Protocols are presented for the processing of frozen-hydrated and freeze-dried specimens, as well as for the analysis of small volumes of fluid, cell cultures, and other specimens. Aspects of qualitative and quantitative analysis are covered, including limitations of the technique.

X-ray microanalysis in the scanning electron microscope.

PubMed

Roomans, Godfried M; Dragomir, Anca

2007-01-01

X-ray microanalysis conducted using the scanning electron microscope is a technique that allows the determination of chemical elements in bulk or semithick specimens. The lowest concentration of an element that can be detected is in the order of a few mmol/kg or a few hundred parts per million, and the smallest amount is in the order of 10(-18) g. The spatial resolution of the analysis depends on the thickness of the specimen. For biological specimen analysis, care must be taken to prevent displacement/loss of the element of interest (usually ions). Protocols are presented for the processing of frozen-hydrated and freeze-dried specimens, as well as for the analysis of small volumes of fluid, cell cultures and other specimens. Aspects of qualitative and quantitative analysis are covered, including limitations of the technique.

Senior Laboratory Animal Technician | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Laboratory Animal Sciences Program (LASP) provides exceptional quality animal care and technical support services for animal research performed at the National Cancer Institute at the Frederick National Laboratory for Cancer Research. LASP executes this mission by providing a broad spectrum of state-of-the-art technologies and services that are focused on the design, generation, characterization and application of genetically engineered and biological animal models of human disease, which are aimed at the development of targeted diagnostics and therapies. LASP contributes to advancing human health, developing new treatments, and improving existing treatments for cancer and other diseases while ensuring safe and humane treatment of animals. KEY ROLES/RESPONSIBILITIES The Senior Laboratory Animal Technician will be responsible for: Daily tasks associated with the care, breeding and treatment of research animals for experimental purposes Management of rodent breeding colonies consisting of multiple, genetically complex strains and associated record keeping and database management Colony management procedures including: tail clipping, animal identification, weaning Data entry consistent with complex colony management Collection of routine diagnostic samples Coordinating shipment of live animals and specimens Performing rodent experimental procedures including basic necropsy and blood collection Observation and recording of physical signs of animal health Knowledge of safe working practices using chemical carcinogen and biological hazards Work schedule may include weekend and holiday hours This position is in support of the Center for Cancer Research (CCR).

Towards comprehensive cell lineage reconstructions in complex organisms using light-sheet microscopy.

PubMed

Amat, Fernando; Keller, Philipp J

2013-05-01

Understanding the development of complex multicellular organisms as a function of the underlying cell behavior is one of the most fundamental goals of developmental biology. The ability to quantitatively follow cell dynamics in entire developing embryos is an indispensable step towards such a system-level understanding. In recent years, light-sheet fluorescence microscopy has emerged as a particularly promising strategy for recording the in vivo data required to realize this goal. Using light-sheet fluorescence microscopy, entire complex organisms can be rapidly imaged in three dimensions at sub-cellular resolution, achieving high temporal sampling and excellent signal-to-noise ratio without damaging the living specimen or bleaching fluorescent markers. The resulting datasets allow following individual cells in vertebrate and higher invertebrate embryos over up to several days of development. However, the complexity and size of these multi-terabyte recordings typically preclude comprehensive manual analyses. Thus, new computational approaches are required to automatically segment cell morphologies, accurately track cell identities and systematically analyze cell behavior throughout embryonic development. We review current efforts in light-sheet microscopy and bioimage informatics towards this goal, and argue that comprehensive cell lineage reconstructions are finally within reach for many key model organisms, including fruit fly, zebrafish and mouse. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Structure Optimization of Porous Dental Implant Based on 3D Printing

NASA Astrophysics Data System (ADS)

Ji, Fangqiu; Zhang, Chunyu; Chen, Xianshuai

2018-03-01

In this paper, selective laser melting (SLM) technology is used to process complex structures. In combination with the theory of biomedicine, a porous implant with a porous structure is designed to induce bone cell growth. The mechanical strength advantage of SLM was discussed by observing the metallographic structure of SLM specimen with mechanical microscope and mechanical tensile test. The osseointegration of porous implants was observed and analyzed by biological experiments. By establishing a mechanical model, the mechanical properties of the bone implant combined with the jaw bone were studied by the simple mechanical analysis under static multi loading and the finite element mechanical analysis. According to the experimental observation and mechanical research, the optimization suggestions for the structure design of the implant made by SLM technology were put forward.

Sea-ice induced growth decline in Arctic shrubs.

PubMed

Forchhammer, Mads

2017-08-01

Measures of increased tundra plant productivity have been associated with the accelerating retreat of the Arctic sea-ice. Emerging studies document opposite effects, advocating for a more complex relationship between the shrinking sea-ice and terrestrial plant productivity. I introduce an autoregressive plant growth model integrating effects of biological and climatic conditions for analysing individual ring-width growth time series. Using 128 specimens of Salix arctica , S. glauca and Betula nana sampled across Greenland to Svalbard, an overall negative effect of the retreating June sea-ice extent was found on the annual growth. The negative effect of the retreating June sea-ice was observed for younger individuals with large annual growth allocations and with little or no trade-off between previous and current year's growth. © 2017 The Author(s).

Advancing Translational Space Research Through Biospecimen Sharing: Amplified Impact of Studies Utilizing Analogue Space Platforms

NASA Technical Reports Server (NTRS)

Staten, B.; Moyer, E.; Vizir, V.; Gompf, H.; Hoban-Higgins, T.; Lewis, L.; Ronca, A.; Fuller, C. A.

2016-01-01

Biospecimen Sharing Programs (BSPs) have been organized by NASA Ames Research Center since the 1960s with the goal of maximizing utilization and scientific return from rare, complex and costly spaceflight experiments. BSPs involve acquiring otherwise unused biological specimens from primary space research experiments for distribution to secondary experiments. Here we describe a collaboration leveraging Ames expertise in biospecimen sharing to magnify the scientific impact of research informing astronaut health funded by the NASA Human Research Program (HRP) Human Health Countermeasures (HHC) Element. The concept expands biospecimen sharing to one-off ground-based studies utilizing analogue space platforms (e.g., Hindlimb Unloading (HLU), Artificial Gravity) for rodent experiments, thereby significantly broadening the range of research opportunities with translational relevance for protecting human health in space and on Earth.

Laser Plasma Soft X-ray Microscope with Wolter Mirrors for Observation of Biological Specimens in Air

NASA Astrophysics Data System (ADS)

Hoshino, Masato; Aoki, Sadao

2006-02-01

A laser plasma soft X-ray microscope with Wolter mirrors was developed so that specimens could be set in the atmosphere. Silicon nitride membranes 100 nm thick were used as vacuum-tight windows. Using relatively large windows (0.46× 0.46 mm2), an adequate working distance for samples, which was approximately 1.2 mm, was assured. The endurance of the vacuum-tight window was measured briefly. Dry biological cells could be observed with resolution better than 100 nm. A preliminary observation of wet biological cells was carried out using a wet environmental sample holder which was composed of only two sheets of silicon nitride membrane. An X-ray micrograph of wet red blood cells from a chicken was obtained without apparent effects of radiation damage. The properties of a vacuum-tight window and a wet sample holder are discussed.

Biological field stations: research legacies and sites for serendipity

Treesearch

William K. Michener; Keith L. Bildstein; Arthur McKee; Robert R. Parmenter; William W. Hargrove; Deedra McClearn; Mark Stromberg

2009-01-01

Biological field stations are distributed throughout North America, capturing much of the ecological variability present at the continental scale and encompassing many unique habitats. In addition to their role in supporting research and education, field stations offer legacies of data, specimens, and accumulated knowledge. Such legacies often provide the only...

Biomonitoring: Uses and Considerations for Assessing Non-Occupational Human Exposure to Pesticides

EPA Science Inventory

Biomonitoring is an important tool that can be used to evaluate human exposure to pesticides by measuring the levels of pesticides, pesticide metabolites, or altered biological structures or functions in biological specimens or tissues (Barr et al., 2005b; Needham et al., 2005, 2...

Photographic catalog of Platygastroidea (Hymenoptera) in the Institute of Ecology and Biological Resources (Hanoi, Vietnam)

USDA-ARS?s Scientific Manuscript database

All holotypes of Platygastroidea housed in the Institute of Ecology and Biological Resources were photographed and these images are now publicly available online, as are images of most species represented in this collection by paratypes alone. Following examination of these specimens, the following ...

Gateway BioBox: A Compact, Multi-Purpose Biological Hardware Suite for In Situ Experiments and Analyses in Deep Space

NASA Astrophysics Data System (ADS)

Smith, D. J.; Parra, M.; Lane, M.; Almeida, E. A.; Space Biosciences Research Branch

2018-02-01

A compilation of NASA's smallest biological hardware systems (plus 1-g gravity controls and ancillary sensors) that will allow for a wide range of specimen cultivation and analysis, from molecular measurements to broader cell and tissue assays.

Thinning of Large Biological Cells for Cryo-TEM Characterization by Cryo-FIB Milling

PubMed Central

Strunk, Korrinn M.; Ke, Danxia; Gray, Jennifer L.; Zhang, Peijun

2013-01-01

SUMMARY Focused ion beam milling at cryogenic temperatures (cryo-FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis in a cryo-transmission electron microscope (cryo-TEM) in their frozen-hydrated state. This technique offers the potential benefit of eliminating the mechanical artifacts that are typically found with cryo-ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. In order to address these problems, we have designed a new sample cryo-shuttle that specifically accepts Polara TEM cartridges directly in order to simplify the transfer process between the FIB and TEM. We used the quality of the ice in the sample as an indicator to test various parameters used the process, and demonstrated with successful milling of large mammalian cells. By comparing the results from larger HeLa cells to those from E. coli cells, we discuss some of the artifacts and challenges we have encountered using this technique. PMID:22906009

Evaluating performance in three-dimensional fluorescence microscopy

PubMed Central

MURRAY, JOHN M; APPLETON, PAUL L; SWEDLOW, JASON R; WATERS, JENNIFER C

2007-01-01

In biological fluorescence microscopy, image contrast is often degraded by a high background arising from out of focus regions of the specimen. This background can be greatly reduced or eliminated by several modes of thick specimen microscopy, including techniques such as 3-D deconvolution and confocal. There has been a great deal of interest and some confusion about which of these methods is ‘better’, in principle or in practice. The motivation for the experiments reported here is to establish some rough guidelines for choosing the most appropriate method of microscopy for a given biological specimen. The approach is to compare the efficiency of photon collection, the image contrast and the signal-to-noise ratio achieved by the different methods at equivalent illumination, using a specimen in which the amount of out of focus background is adjustable over the range encountered with biological samples. We compared spot scanning confocal, spinning disk confocal and wide-field/deconvolution (WFD) microscopes and find that the ratio of out of focus background to in-focus signal can be used to predict which method of microscopy will provide the most useful image. We also find that the precision of measurements of net fluorescence yield is very much lower than expected for all modes of microscopy. Our analysis enabled a clear, quantitative delineation of the appropriate use of different imaging modes relative to the ratio of out-of-focus background to in-focus signal, and defines an upper limit to the useful range of the three most common modes of imaging. PMID:18045334

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

Pietrzyk, Robert; McMonigal, K. A.; Sams, C. F.; Johnson, M. A.

2009-01-01

The NASA Biological Specimen Repository (NBSR) has been established to collect, process, annotate, store, and distribute specimens under the authority of the NASA/JSC Committee for the Protection of Human Subjects. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The NBSR is a secure controlled storage facility that is used to maintain biological specimens over extended periods of time, under well-controlled conditions, for future use in approved human spaceflight-related research protocols. The repository supports the Human Research Program, which is charged with identifying and investigating physiological changes that occur during human spaceflight, and developing and implementing effective countermeasures when necessary. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can validate clinical hypotheses, study space-flight related changes, and investigate physiological markers All samples collected require written informed consent from each long duration crewmember. The NBSR collects blood and urine samples from all participating long duration ISS crewmembers. These biological samples are collected pre-flight at approximately 45 days prior to launch, during flight on flight days 15, 30, 60 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days following landing. The number of inflight sessions is dependent on the duration of the mission. Operations began in 2007 and as of October 2009, 23 USOS crewmembers have completed or agreed to participate in this project. As currently planned, these human biological samples will be collected from crewmembers covering multiple ISS missions until the end of U.S. presence on the ISS or 2017. The NBSR will establish guidelines for sample distribution that are consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. A NBSR Advisory Board composed of representatives of all participating agencies will be established to evaluate each request by an investigator for use of the samples to ensure the request reflects the mission of the NBSR.

The Development of a Scanning Soft X-Ray Microscope.

NASA Astrophysics Data System (ADS)

Rarback, Harvey Miles

We have developed a scanning soft X-ray microscope, which can be used to image natural biological specimens at high resolution and with less damage than electron microscopy. The microscope focuses a monochromatic beam of synchrotron radiation to a nearly diffraction limited spot with the aid of a high resolution Fresnel zone plate, specially fabricated for us at the IBM Watson Research Center. The specimen at one atmosphere is mechanically scanned through the spot and the transmitted radiation is efficiently detected with a flow proportional counter. A computer forms a realtime transmission image of the specimen which is displayed on a color monitor. Our first generation optics have produced images of natural wet specimens at a resolution of 300 nm.

Improving signal to noise in labeled biological specimens using energy-filtered TEM of sections with a drift correction strategy and a direct detection device.

PubMed

Ramachandra, Ranjan; Bouwer, James C; Mackey, Mason R; Bushong, Eric; Peltier, Steven T; Xuong, Nguyen-Huu; Ellisman, Mark H

2014-06-01

Energy filtered transmission electron microscopy techniques are regularly used to build elemental maps of spatially distributed nanoparticles in materials and biological specimens. When working with thick biological sections, electron energy loss spectroscopy techniques involving core-loss electrons often require exposures exceeding several minutes to provide sufficient signal to noise. Image quality with these long exposures is often compromised by specimen drift, which results in blurring and reduced resolution. To mitigate drift artifacts, a series of short exposure images can be acquired, aligned, and merged to form a single image. For samples where the target elements have extremely low signal yields, the use of charge coupled device (CCD)-based detectors for this purpose can be problematic. At short acquisition times, the images produced by CCDs can be noisy and may contain fixed pattern artifacts that impact subsequent correlative alignment. Here we report on the use of direct electron detection devices (DDD's) to increase the signal to noise as compared with CCD's. A 3× improvement in signal is reported with a DDD versus a comparably formatted CCD, with equivalent dose on each detector. With the fast rolling-readout design of the DDD, the duty cycle provides a major benefit, as there is no dead time between successive frames.

Plane wave analysis of coherent holographic image reconstruction by phase transfer (CHIRPT).

PubMed

Field, Jeffrey J; Winters, David G; Bartels, Randy A

2015-11-01

Fluorescent imaging plays a critical role in a myriad of scientific endeavors, particularly in the biological sciences. Three-dimensional imaging of fluorescent intensity often requires serial data acquisition, that is, voxel-by-voxel collection of fluorescent light emitted throughout the specimen with a nonimaging single-element detector. While nonimaging fluorescence detection offers some measure of scattering robustness, the rate at which dynamic specimens can be imaged is severely limited. Other fluorescent imaging techniques utilize imaging detection to enhance collection rates. A notable example is light-sheet fluorescence microscopy, also known as selective-plane illumination microscopy, which illuminates a large region within the specimen and collects emitted fluorescent light at an angle either perpendicular or oblique to the illumination light sheet. Unfortunately, scattering of the emitted fluorescent light can cause blurring of the collected images in highly turbid biological media. We recently introduced an imaging technique called coherent holographic image reconstruction by phase transfer (CHIRPT) that combines light-sheet-like illumination with nonimaging fluorescent light detection. By combining the speed of light-sheet illumination with the scattering robustness of nonimaging detection, CHIRPT is poised to have a dramatic impact on biological imaging, particularly for in vivo preparations. Here we present the mathematical formalism for CHIRPT imaging under spatially coherent illumination and present experimental data that verifies the theoretical model.

Quantitative mass spectrometry of unconventional human biological matrices

NASA Astrophysics Data System (ADS)

Dutkiewicz, Ewelina P.; Urban, Pawel L.

2016-10-01

The development of sensitive and versatile mass spectrometric methodology has fuelled interest in the analysis of metabolites and drugs in unconventional biological specimens. Here, we discuss the analysis of eight human matrices-hair, nail, breath, saliva, tears, meibum, nasal mucus and skin excretions (including sweat)-by mass spectrometry (MS). The use of such specimens brings a number of advantages, the most important being non-invasive sampling, the limited risk of adulteration and the ability to obtain information that complements blood and urine tests. The most often studied matrices are hair, breath and saliva. This review primarily focuses on endogenous (e.g. potential biomarkers, hormones) and exogenous (e.g. drugs, environmental contaminants) small molecules. The majority of analytical methods used chromatographic separation prior to MS; however, such a hyphenated methodology greatly limits analytical throughput. On the other hand, the mass spectrometric methods that exclude chromatographic separation are fast but suffer from matrix interferences. To enable development of quantitative assays for unconventional matrices, it is desirable to standardize the protocols for the analysis of each specimen and create appropriate certified reference materials. Overcoming these challenges will make analysis of unconventional human biological matrices more common in a clinical setting. This article is part of the themed issue 'Quantitative mass spectrometry'.

Imaging Analysis of Near-Field Recording Technique for Observation of Biological Specimens

NASA Astrophysics Data System (ADS)

Moriguchi, Chihiro; Ohta, Akihiro; Egami, Chikara; Kawata, Yoshimasa; Terakawa, Susumu; Tsuchimori, Masaaki; Watanabe, Osamu

2006-07-01

We present an analysis of the properties of an imaging based on a near-field recording technique in comparison with simulation results. In the system, the optical field distributions localized near the specimens are recorded as the surface topographic distributions of a photosensitive film. It is possible to observe both soft and moving specimens, because the system does not require a scanning probe to obtain the observed image. The imaging properties are evaluated using fine structures of paramecium, and we demonstrate that it is possible to observe minute differences of refractive indices.

Proposal of a punch biopsy protocol as a pre-requisite for the establishment of a tissue bank from resected esophageal tumors.

PubMed

Bonavina, Luigi; Laface, Letizia; Picozzi, Stefano; Nencioni, Marco; Siboni, Stefano; Bona, Davide; Sironi, Andrea; Sorba, Francesca; Clemente, Claudio

2010-09-01

With the development of tissue banking, a need for homogeneous methods of collection, processing, and storage of tissue has emerged. We describe the implementation of a biological bank in a high-volume, tertiary care University referral center for esophageal cancer surgery. We also propose an original punch biopsy technique of the surgical specimen. The method proved to be simple, reproducible, and not expensive. Unified standards for specimen collection are necessary to improve results of specimen-based diagnostic testing and research in surgical oncology.

Distinguishing geology from biology in the Ediacaran Doushantuo biota relaxes constraints on the timing of the origin of bilaterians.

PubMed

Cunningham, John A; Thomas, Ceri-Wyn; Bengtson, Stefan; Kearns, Stuart L; Xiao, Shuhai; Marone, Federica; Stampanoni, Marco; Donoghue, Philip C J

2012-06-22

The Ediacaran Doushantuo biota has yielded fossils that include the oldest widely accepted record of the animal evolutionary lineage, as well as specimens with alleged bilaterian affinity. However, these systematic interpretations are contingent on the presence of key biological structures that have been reinterpreted by some workers as artefacts of diagenetic mineralization. On the basis of chemistry and crystallographic fabric, we characterize and discriminate phases of mineralization that reflect: (i) replication of original biological structure, and (ii) void-filling diagenetic mineralization. The results indicate that all fossils from the Doushantuo assemblage preserve a complex mélange of mineral phases, even where subcellular anatomy appears to be preserved. The findings allow these phases to be distinguished in more controversial fossils, facilitating a critical re-evaluation of the Doushantuo fossil assemblage and its implications as an archive of Ediacaran animal diversity. We find that putative subcellular structures exhibit fabrics consistent with preservation of original morphology. Cells in later developmental stages are not in original configuration and are therefore uninformative concerning gastrulation. Key structures used to identify Doushantuo bilaterians can be dismissed as late diagenetic artefacts. Therefore, when diagenetic mineralization is considered, there is no convincing evidence for bilaterians in the Doushantuo assemblage.

Exploring Biological and Geological Age-related Changes through Variations in Intra- and Intertooth Proteomes of Ancient Dentine.

PubMed

Procopio, Noemi; Chamberlain, Andrew T; Buckley, Michael

2018-03-02

Proteomic analyses are becoming more widely used in archeology not only due to the greater preservation of proteins in ancient specimens than DNA but also because they can offer different information, particularly relating to compositional preservation and potentially a means to estimate biological and geological age. However, it remains unclear to what extent different burial environments impact these aspects of proteome decay. Teeth have to date been much less studied than bone but are ideal to explore how proteins decay with time due to the negligible turnover that occurs in dentine relative to bone. We investigated the proteome variability and deamidation levels of different sections of molar teeth from archeological bovine mandibles as well as their mandibular bone. We obtained a greater yield of proteins from the crown of the teeth but did not find differences between the different molars analyzed within each mandible. We also obtained the best variety of protein from a well-preserved mandible that was not the youngest one in terms of chronological age, showing the influence of the preservation conditions on the final proteomic outcome. Intriguingly, we also noticed an increase in abundance levels of fetuin-A in biologically younger mandibles as reported previously, but the opposite trend in tooth dentine. Interestingly, we observed higher glutamine deamidation levels in teeth from the geologically oldest mandible despite it being the biologically youngest specimen, showing that the archeological age strongly impacts on the level of deamidations observed, much more so than biological aging. This indicates that the glutamine deamidation ratio of selected peptides may act as a good predictor of the relative geochronological age of archeological specimens.

Defining Hepatocellular Carcinoma Subtypes and Treatment Responses in Patient-Derived Tumorgrafts

DTIC Science & Technology

2017-10-01

models to uncover novel biology and establish a platform to study experimental therapeutics. 1. KEYWORDS: HCC, patient derived xenografts, siRNA...have distinct cell-intrinsic biology in PDX engraftment assays Major Task 1: Expand and characterize PDX models derived from surgical and biopsy HCC...intrinsic biology in PDX engraftment assays Major Task 1: Expand and characterize PDX models derived from surgical and biopsy HCC specimens Pre-task

Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain)

PubMed Central

Torralba-Burrial, Antonio; Ocharan, Francisco J.

2013-01-01

Abstract Odonata are represented from the Iberian Peninsula by 79 species. However, there exists a significant gap in accessible knowledge about these species,especially regarding their distribution. This data paper describes the specimen-based Odonata data of the Arthropod Collection of the Department of Biología de Organismos y Sistemas (BOS), University of Oviedo, Spain. The specimens were mainly collected from the Iberian Peninsula (98.63% of the data records), especially the northern region. The earliest specimen deposited in the collection dates back to 1950, while the 1980’s and 2000’s are the best-represented time periods. Between 1950 and 2009, 16, 604 Odonata specimens were deposited and are documented in the dataset. Approximately 20% of the specimens belong to the families Coenagrionidae and Calopterygidae. Specimens include the holotype and paratypes of the Iberian subspecies Calopteryx haemorrhoidalis asturica Ocharan, 1983 and Sympetrum vulgatum ibericum Ocharan, 1985. The complete dataset is also provided in Darwin Core Archive format. PMID:23794917

Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain).

PubMed

Torralba-Burrial, Antonio; Ocharan, Francisco J

2013-01-01

Odonata are represented from the Iberian Peninsula by 79 species. However, there exists a significant gap in accessible knowledge about these species,especially regarding their distribution. This data paper describes the specimen-based Odonata data of the Arthropod Collection of the Department of Biología de Organismos y Sistemas (BOS), University of Oviedo, Spain. The specimens were mainly collected from the Iberian Peninsula (98.63% of the data records), especially the northern region. The earliest specimen deposited in the collection dates back to 1950, while the 1980's and 2000's are the best-represented time periods. Between 1950 and 2009, 16, 604 Odonata specimens were deposited and are documented in the dataset. Approximately 20% of the specimens belong to the families Coenagrionidae and Calopterygidae. Specimens include the holotype and paratypes of the Iberian subspecies Calopteryx haemorrhoidalis asturica Ocharan, 1983 and Sympetrum vulgatum ibericum Ocharan, 1985. The complete dataset is also provided in Darwin Core Archive format.

Evaluation of the Cobas TaqMan MTB Test for the Detection of Mycobacterium tuberculosis Complex According to Acid-Fast-Bacillus Smear Grades in Respiratory Specimens

PubMed Central

Huh, Hee Jae; Koh, Won-Jung; Song, Dong Joon

2014-01-01

We evaluated the performance of the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), stratified by acid-fast bacilli (AFB) smear grades. The sensitivity of this test in smear-positive specimens was >95% in all grades, while that in trace and negative specimens was 85.3% and 34.4%, respectively. PMID:25428157

Detection of Mycobacterium tuberculosis Complex in Paraffin-Embedded Tissues by the New Automated Abbott RealTime MTB Assay.

PubMed

Fu, Yung-Chieh; Liao, I-Chuang; Chen, Hung-Mo; Yan, Jing-Jou

2016-07-01

The Abbott RealTime MTB assay, launched in June 2014, has been shown to have a competitive performance in the detection of the Mycobacterium tuberculosis (MTB) complex in respiratory specimens. The present study was conducted to investigate the usefulness of the Abbott MTB Realtime assay in the detection of MTB in formalin-fixed paraffin-embedded (FFPE) tissues. A total of 96 FFPE specimens obtained from microbiologically proven MTB cases (N=60) and nontuberculous Mycobacterium cases (N=36) were analyzed. The performance of the Abbott MTB Realtime assay was compared with that of the Roche Cobas TaqMan MTB assay. The overall sensitivity and specificity of the Abbott assay were 63.3% and 97.2%, respectively, compared with 11.7% and 100% for the Cobas assay. The detection rate of the Abbott assay was much higher among 37 acid-fast-positive specimens than among 23 acid-fast-negative specimens (89.3% versus 21.7%, respectively). The detection rate of the assay was higher among 29 resection specimens than among 31 small biopsy specimens (86.2% versus 41.9%, respectively). Our results suggest that the Abbott RealTime MTB assay can be used to differentiate MTB from nontuberculous mycobacterial infections in acid-fast-positive FFPE tissues. © 2016 by the Association of Clinical Scientists, Inc.

Assessment of the stability of DNA in specimens collected under conditions for drug testing-A pilot study.

PubMed

White, Robert M; Mitchell, John M; Hart, E Dale; Evans, Amy; Meaders, Meredith; Norsworthy, Sarah E; Hayes, Eugene D; Flegel, Ron; Maha, George C; Shaffer, Megan D; Hall, Erin M; Rogers, Kelley

2018-02-01

For forensic biological sample collections, the specimen donor is linked solidly to his or her specimen through a chain of custody (CoC) sometimes referenced as a chain of evidence. Rarely, a donor may deny that a urine or oral fluid (OF) specimen is his or her specimen even with a patent CoC. The goal of this pilot study was to determine the potential effects of short-term storage on the quality and quantity of DNA in both types of specimen under conditions that may be encountered with employment-related drug testing specimens. Fresh urine and freshly collected oral fluid all produced complete STR profiles. For the "pad" type OF collectors, acceptable DNA was extractable both from the buffer/preservative and the pad. Although fresh urine and OF produced complete STR profiles, partial profiles were obtained after storage for most samples. An exception was the DNA in the Quantisal OF collector, from which a complete profile was obtained for both freshly collected OF and stored OF. Copyright © 2017 Elsevier B.V. All rights reserved.

Intact Imaging of Human Heart Structure Using X-ray Phase-Contrast Tomography.

PubMed

Kaneko, Yukihiro; Shinohara, Gen; Hoshino, Masato; Morishita, Hiroyuki; Morita, Kiyozo; Oshima, Yoshihiro; Takahashi, Masashi; Yagi, Naoto; Okita, Yutaka; Tsukube, Takuro

2017-02-01

Structural examination of human heart specimens at the microscopic level is a prerequisite for understanding congenital heart diseases. It is desirable not to destroy or alter the properties of such specimens because of their scarcity. However, many of the currently available imaging techniques either destroy the specimen through sectioning or alter the chemical and mechanical properties of the specimen through staining and contrast agent injection. As a result, subsequent studies may not be possible. X-ray phase-contrast tomography is an imaging modality for biological soft tissues that does not destroy or alter the properties of the specimen. The feasibility of X-ray phase-contrast tomography for the structural examination of heart specimens was tested using infantile and fetal heart specimens without congenital diseases. X-ray phase-contrast tomography was carried out at the SPring-8 synchrotron radiation facility using the Talbot grating interferometer at the bending magnet beamline BL20B2 to visualize the structure of five non-pretreated whole heart specimens obtained by autopsy. High-resolution, three-dimensional images were obtained for all specimens. The images clearly showed the myocardial structure, coronary vessels, and conduction bundle. X-ray phase-contrast tomography allows high-resolution, three-dimensional imaging of human heart specimens. Intact imaging using X-ray phase-contrast tomography can contribute to further structural investigation of heart specimens with congenital heart diseases.

ON THE FREEZING AND IDENTIFICATION OF LIPID MONOLAYER 2-D ARRAYS FOR CRYOELECTRON MICROSCOPY

PubMed Central

Taylor, Dianne W.; Kelly, Deborah F.; Cheng, Anchi; Taylor, Kenneth A.

2008-01-01

Lipid monolayers provide a convenient vehicle for the crystallization of biological macromolecules for 3-D electron microscopy. Although numerous examples of 3-D images from 2-D protein arrays have been described from negatively stained specimens, only six structures have been done from frozen hydrated specimens. We describe here a method that makes high quality frozen-hydrated specimens of lipid monolayer arrays for cryoelectron microscopy. The method uses holey carbon films with patterned holes for monolayer recovery, blotting and plunge freezing to produce thin aqueous films which cover >90% of the available grid area. With this method, even specimens with relatively infrequent crystals can be screened using automated data collection techniques. Though developed for microscopic examination of 2-D arrays, the method may have wider application to the preparation of single particle specimens for 3-D image reconstruction. PMID:17561414

A numerical analysis of the Born approximation for image formation modeling of differential interference contrast microscopy for human embryos

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Feigin, Micha; Greenspan, Hayit; Sochen, Nir

2008-03-01

The differential interference contrast (DIC) microscope is commonly used for the visualization of live biological specimens. It enables the view of the transparent specimens while preserving their viability, being a non-invasive modality. Fertility clinics often use the DIC microscope for evaluation of human embryos quality. Towards quantification and reconstruction of the visualized specimens, an image formation model for DIC imaging is sought and the interaction of light waves with biological matter is examined. In many image formation models the light-matter interaction is expressed via the first Born approximation. The validity region of this approximation is defined in a theoretical bound which limits its use to very small specimens with low dielectric contrast. In this work the Born approximation is investigated via the Helmholtz equation, which describes the interaction between the specimen and light. A solution on the lens field is derived using the Gaussian Legendre quadrature formulation. This numerical scheme is considered both accurate and efficient and has shortened significantly the computation time as compared to integration methods that required a great amount of sampling for satisfying the Whittaker - Shannon sampling theorem. By comparing the numerical results with the theoretical values it is shown that the theoretical bound is not directly relevant to microscopic imaging and is far too limiting. The numerical exhaustive experiments show that the Born approximation is inappropriate for modeling the visualization of thick human embryos.

Development of Ultra-Super Sensitive Immunohistochemistry and Its Application to the Etiological Study of Adult T-Cell Leukemia/Lymphoma

PubMed Central

Hasui, Kazuhisa; Wang, Jia; Tanaka, Yuetsu; Izumo, Shuji; Eizuru, Yoshito; Matsuyama, Takami

2012-01-01

Antigen retrieval (AR) and ultra-super sensitive immunohistochemistry (ultra-IHC) have been established for application to archival human pathology specimens. The original ultra-IHC was the ImmunoMax method or the catalyzed signal amplification system (ImmunoMax/CSA method), comprising the streptavidin-biotin complex (sABC) method and catalyzed reporter deposition (CARD) reaction with visualization of its deposition. By introducing procedures to diminish non-specific staining in the original ultra-IHC method, we developed the modified ImmunoMax/CSA method with AR heating sections in an AR solution (heating-AR). The heating-AR and modified ImmunoMax/CSA method visualized expression of the predominantly simple present form of HTLV-1 proviral DNA pX region p40Tax protein (Tax) in adult T-cell leukemia/lymphoma (ATLL) cells in archival pathology specimens in approximately 75% of cases. The simple present form of Tax detected exhibited a close relation with ATLL cell proliferation. We also established a new simplified CSA (nsCSA) system by replacing the sABC method with the secondary antibody- and horse radish peroxidase-labeled polymer reagent method, introducing the pretreatments blocking non-specific binding of secondary antibody reagent, and diminishing the diffusion of deposition in the CARD reaction. Combined with AR treating sections with proteinase K solution (enzymatic-AR), the nsCSA system visualized granular immunostaining of the complex present form of Tax in a small number of ATLL cells in most cases, presenting the possibility of etiological pathological diagnosis of ATLL and suggesting that the complex present form of Tax-positive ATLL cells were young cells derived from ATLL stem cells. The heating-AR and ultra-IHC detected physiological expression of the p53 protein and its probable phosphorylation by Tax in peripheral blood mononuclear cells of peripheral blood tissue specimens from HTLV-1 carriers, as well as physiological and pathological expression of the molecules involved with G1 phase progression and G1–S phase transition (E2F-1, E2F-4, DP-1, and cyclin E) in ATLL and peripheral T-cell lymphoma cells. The ultra-IHC with AR is useful for etiological pathological diagnosis of ATLL since HTLV-1 pathogenicity depends on that of Tax, and can be a useful tool for studies translating advanced molecular biology and pathology to human pathology. PMID:22685351

Biocore experiment. [Apollo 17 mission

NASA Technical Reports Server (NTRS)

Bailey, O. T.; Benton, E. V.; Cruty, M. R.; Harrison, G. A.; Haymaker, W.; Humason, G.; Leon, H. A.; Lindberg, R. L.; Look, B. C.; Lushbaugh, C. C.

1973-01-01

The Apollo 17 biological cosmic ray experiment to determine the effect of heavy cosmic ray particles on the brain and eyes is reported. The pocket mouse was selected as the biological specimen for the experiment. The radiation monitors, animal autopsy and animal processing are described, and the radiation effects on the scalp, retina, and viscera are analyzed.

Non-invasive ancient DNA protocol for fluid-preserved specimens and phylogenetic systematics of the genus Orestias (Teleostei: Cyprinodontidae).

PubMed

Garrigos, Yareli Esquer; Hugueny, Bernard; Koerner, Kellie; Ibañez, Carla; Bonillo, Celine; Pruvost, Patrice; Causse, Romain; Cruaud, Corinne; Gaubert, Philippe

2013-01-01

Specimens stored in museum collections represent a crucial source of morphological and genetic information, notably for taxonomically problematic groups and extinct taxa. Although fluid-preserved specimens of groups such as teleosts may constitute an almost infinite source of DNA, few ancient DNA protocols have been applied to such material. In this study, we describe a non-invasive Guanidine-based (GuSCN) ancient DNA extraction protocol adapted to fluid-preserved specimens that we use to re-assess the systematics of the genus Orestias (Cyprinodontidae: Teleostei). The latter regroups pupfishes endemic to the inter-Andean basin that have been considered as a 'species flock', and for which the morphology-based taxonomic delimitations have been hotly debated. We extracted DNA from the type specimens of Orestias kept at the Muséum National d'Histoire Naturelle of Paris, France, including the extinct species O. cuvieri. We then built the first molecular (control region [CR] and rhodopsin [RH]) phylogeny including historical and recently collected representatives of all the Orestias complexes as recognized by Parenti (1984a): agassizii, cuvieri, gilsoni and mulleri. Our ancient DNA extraction protocol was validated after PCR amplification through an approach based on fragment-by-fragment chimera detection. After optimization, we were able to amplify < 200 bp fragments from both mitochondrial and nuclear DNA (CR and RH, respectively) from probably formalin-fixed type specimens bathed entirely in the extraction fluid. Most of the individuals exhibited few modifications of their external structures after GuSCN bath. Our approach combining type material and 'fresh' specimens allowed us to taxonomically delineate four clades recovered from the well-resolved CR tree into four redefined complexes: agassizii (sensu stricto, i.e. excluding luteus-like species), luteus, cuvieri and gilsoni. The mulleri complex is polyphyletic. Our phylogenetic analyses based on both mitochondrial and nuclear DNA revealed a main, deep dichotomy within the genus Orestias, separating the agassizii complex from a clade grouped under shallow dichotomies as (luteus, (cuvieri, gilsoni)). This 'deep and shallow' diversification pattern could fit within a scenario of ancient divergence between the agassizii complex and the rest of Orestias, followed by a recent diversification or adaptive radiation within each complex during the Pleistocene, in- and outside the Lake Titicaca. We could not recover the reciprocal monophyly of any of the 15 species or morphotypes that were considered in our analyses, possibly due to incomplete lineage sorting and/or hybridization events. As a consequence, our results starkly question the delineation of a series of diagnostic characters listed in the literature for Orestias. Although not included in our phylogenetic analysis, the syntype of O. jussiei could not be assigned to the agassizii complex as newly defined. The CR sequence of the extinct O. cuvieri was recovered within the cuvieri clade (same haplotype as one representative of O. pentlandii), so the mtDNA of the former species might still be represented in the wild.

Water without windows: Evaluating the performance of open cell transmission electron microscopy under saturated water vapor conditions, and assessing its potential for microscopy of hydrated biological specimens

PubMed Central

Yamashita, Masao; Cheung, Martin; Kalale, Chola; Adaniya, Hidehito; Kuwahara, Ryusuke; Shintake, Tsumoru

2017-01-01

We have performed open cell transmission electron microscopy experiments through pure water vapor in the saturation pressure regime (>0.6 kPa), in a modern microscope capable of sub-Å resolution. We have systematically studied achievable pressure levels, stability and gas purity, effective thickness of the water vapor column and associated electron scattering processes, and the effect of gas pressure on electron optical resolution and image contrast. For example, for 1.3 kPa pure water vapor and 300kV electrons, we report pressure stability of ± 20 Pa over tens of minutes, effective thickness of 0.57 inelastic mean free paths, lattice resolution of 0.14 nm on a reference Au specimen, and no significant degradation in contrast or stability of a biological specimen (M13 virus, with 6 nm body diameter). We have also done some brief experiments to confirm feasibility of loading specimens into an in situ water vapor ambient without exposure to intermediate desiccating conditions. Finally, we have also checked if water experiments had any discernible impact on the microscope performance, and report pertinent vacuum and electron optical data, for reference purposes. PMID:29099843

Biological response of Sr-containing coating with various surface treatments on titanium substrate for medical applications

NASA Astrophysics Data System (ADS)

Yang, Shih-Ping; Lee, Tzer-Min; Lui, Truan-Sheng

2015-08-01

An implant requires a suitable surface to trigger osteointegration. The surface characteristics and chemical composition are important factors in this process. Plasma spraying and micro-arc oxidation can be used to fabricate rough and porous structures for medical applications. Strontium (Sr) has been shown to prevent osteoporosis in vitro and in vivo. However, few scientists have evaluated the biological response of Sr-containing coatings on different surface treatments. In this study, a sand-blasted (SB) surface (as the control), plasma-sprayed hydroxyapatite (HA) and Sr-substituted HA coatings (HAPS and SrHAPS, respectively), calcium phosphate and Sr-containing calcium phosphate micro-arc oxidation surface (CPM and SrCPM, respectively) were analyzed in terms of human osteoblastic cell (MG63) response. Sr was confirmed to be incorporated into the surface. SrHAPS and SrCPM specimens had higher cell responses than those of the HAPS and CPM groups, respectively. The cells cultured on SrCPM and SrHAPS specimens exhibited high proliferation and differentiation. However, CPM and SrCPM specimens stimulated more ECM-like structures than other specimens. The results show that Sr-containing coatings have good characteristics that enhance cell response. The SrCPM coating is a suitable implant surface treatment for clinical applications.

Increased epithelial cadherin expression among Japanese intestinal-type gastric cancers compared with specimens from American patients of European descent.

PubMed

Theuer, Charles P; Al-Kuran, Rasha; Akiyama, Yoshiyuki; Okumura, Minoru; Ziogas, Al; Carpenter, Philip M

2006-04-01

The different patterns of gastric cancer in the Far East and West have evolved to the extent that it has been suggested that the disease in Japan is biologically less aggressive than in the West. We studied paraffin-embedded, formalin-fixed tissue blocks from Japanese patients and American patients of European descent who had undergone gastrectomy for gastric cancer not involving the gastroesophageal junction. Specimens were staged (T stage), graded (Lauren classification), and biomarker expression (epithelial cadherin [E-cadherin], c-erbB2, Ki67, and p53) was quantified using immunohistochemistry without knowledge of the country of origin. E-cadherin was expressed in 49 per cent of malignant cells from Japanese specimens compared with 27 per cent of malignant cells from American specimens (P = 0.04). The expression of E-cadherin on diffuse cancers from the two countries was similar (34.4 in Japanese vs 41.5 in American, P = 0.92). E-cadherin expression, however, was significantly higher among intestinal cancers from the two countries: 56.3 per cent of cells from intestinal or mixed cancers from Japan (n = 32) expressed E-cadherin compared with 22.2 per cent of American specimens (n = 12; P = 0.008).-c-erbB2 was expressed on a higher proportion of malignant cells from American specimens (30% vs 22%; P = 0.20). E-cadherin expression, a favorable prognostic factor, is more common in Japanese intestinal-type gastric cancer not involving the gastroesophageal junction. If the biology of gastric cancer in the Far East is less aggressive than that in the United States, it is likely that treatments need to be individualized.

Identification of Logic Relationships between Genes and Subtypes of Non-Small Cell Lung Cancer

PubMed Central

Su, Yansen; Pan, Linqiang

2014-01-01

Non-small cell lung cancer (NSCLC) has two major subtypes: adenocarcinoma (AC) and squamous cell carcinoma (SCC). The diagnosis and treatment of NSCLC are hindered by the limited knowledge about the pathogenesis mechanisms of subtypes of NSCLC. It is necessary to research the molecular mechanisms related with AC and SCC. In this work, we improved the logic analysis algorithm to mine the sufficient and necessary conditions for the presence states (presence or absence) of phenotypes. We applied our method to AC and SCC specimens, and identified lower and higher logic relationships between genes and two subtypes of NSCLC. The discovered relationships were independent of specimens selected, and their significance was validated by statistic test. Compared with the two earlier methods (the non-negative matrix factorization method and the relevance analysis method), the current method outperformed these methods in the recall rate and classification accuracy on NSCLC and normal specimens. We obtained biomarkers. Among biomarkers, genes have been used to distinguish AC from SCC in practice, and other six genes were newly discovered biomarkers for distinguishing subtypes. Furthermore, NKX2-1 has been considered as a molecular target for the targeted therapy of AC, and other genes may be novel molecular targets. By gene ontology analysis, we found that two biological processes (‘epidermis development’ and ‘cell adhesion’) were closely related with the tumorigenesis of subtypes of NSCLC. More generally, the current method could be extended to other complex diseases for distinguishing subtypes and detecting the molecular targets for targeted therapy. PMID:24743794

Accurate single-shot quantitative phase imaging of biological specimens with telecentric digital holographic microscopy.

PubMed

Doblas, Ana; Sánchez-Ortiga, Emilio; Martínez-Corral, Manuel; Saavedra, Genaro; Garcia-Sucerquia, Jorge

2014-04-01

The advantages of using a telecentric imaging system in digital holographic microscopy (DHM) to study biological specimens are highlighted. To this end, the performances of nontelecentric DHM and telecentric DHM are evaluated from the quantitative phase imaging (QPI) point of view. The evaluated stability of the microscope allows single-shot QPI in DHM by using telecentric imaging systems. Quantitative phase maps of a section of the head of the drosophila melanogaster fly and of red blood cells are obtained via single-shot DHM with no numerical postprocessing. With these maps we show that the use of telecentric DHM provides larger field of view for a given magnification and permits more accurate QPI measurements with less number of computational operations.

Adaptive optical microscope for brain imaging in vivo

NASA Astrophysics Data System (ADS)

Wang, Kai

2017-04-01

The optical heterogeneity of biological tissue imposes a major limitation to acquire detailed structural and functional information deep in the biological specimens using conventional microscopes. To restore optimal imaging performance, we developed an adaptive optical microscope based on direct wavefront sensing technique. This microscope can reliably measure and correct biological samples induced aberration. We demonstrated its performance and application in structural and functional brain imaging in various animal models, including fruit fly, zebrafish and mouse.

Search for biological specimens from midwestern parks: pitfalls and solutions

USGS Publications Warehouse

Bennett, J.P.

2001-01-01

This paper describes the results of searches of herbarium and museum collections and databases for records of vertebrate and vascular plant specimens that had been collected in 15 midwestern National Park System units. The records of these specimens were previously unknown to the National Park Service (NPS). In the course of our searches, numerous obstacles were encountered that prevented us from fully completing our task. These ranged from difficulties with the way databases are structured, to poor record-keeping, to incomplete or incorrect information on the actual location of specimens within collections. Despite these problems, we are convinced that the information to be gained from such searches in invaluable, and we believe that our experience, and the recommendations we offer, may well prove instructive to others undertaking this kind of work.

Troublesome Trimes: Potential cryptic speciation of the Trimeresurus (Popeia) popeiorum complex (Serpentes: Crotalidae) around the Isthmus of Kra (Myanmar and Thailand).

PubMed

Mulcahy, Daniel G; Lee, Justin L; Miller, Aryeh H; Zug, George R

2017-11-13

The taxonomic identity of the Trimeresurus (Popeia) popeiorum complex from the Isthmus of Kra and to the north was investigated. Several studies over the last decade have produced several specimens and associated mtDNA sequence data for a variety of individuals of the T. popeiorum and "T. sabahi" complexes. Here, we combine four mitochondrial genes (12S, 16S, ND4, and CytB) from all available specimens in GenBank with the addition of five new specimens collected from the mainland, Tanintharyi Region of Myanmar. Maximum Likelihood and Bayesian analyses identified that T. popeiorum sensu lato is paraphyletic with two geographically distinct clades: a northern clade representing populations from northern Myanmar, Laos and northern Thailand and a southern clade representing samples from the Tanintharyi Region and adjacent west Thailand. While the two clades have considerable genetic distance, they appear to be morphologically identical, leading to the hypothesis that the southern clade represents a cryptic, undescribed species. Because they appear to be cryptic species and the limitation of only five specimens from the southern lineage, this does not permit us to formally describe the new species. In accordance to past molecular studies, we uncovered paraphyly and lack of genetic support for the validity of taxa within the T. sabahi complex. However, we suggest recognizing these populations as subspecies within T. sabahi.

Internet of Things technology-based management methods for environmental specimen banks.

PubMed

Peng, Lihong; Wang, Qian; Yu, Ang

2015-02-01

The establishment and management of environmental specimen banks (ESBs) has long been a problem worldwide. The complexity of specimen environment has made the management of ESB likewise complex. Through an analysis of the development and management of ESBs worldwide and in light of the sophisticated Internet of Things (IOT) technology, this paper presents IOT technology-based ESB management methods. An IOT technology-based ESB management system can significantly facilitate ESB ingress and egress management as well as long-term storage management under quality control. This paper elaborates on the design of IOT technology-based modules, which can be used in ESB management to achieve standardized, smart, information-based ESB management. ESB management has far-reaching implications for environmental management and for research in environmental science.

Biomarker Signatures of Mitochondrial NDUFS3 in Invasive Breast Carcinoma

PubMed Central

Suhane, Sonal; Berel, Dror; Ramanujan, V Krishnan

2011-01-01

We present evidence for potential biomarker utility of a mitochondrial complex I subunit, (NDUFS3) in discriminating normal and highly invasive breast carcinoma specimens obtained from clinical patients. Besides being a robust indicator of breast cancer aggressiveness, NDUFS3 also shows clear signatures of a hypoxia/necrosis marker in invasive ductal carcinoma specimens. Statistically significant positive correlation was observed between nuclear grade and NDUFS3 expression level in the tumor specimens analyzed. We support these findings with a plausible mechanism involving mitochondrial complex I assembly defects and/or redox buffering induced mitochondrial dysfunction during the process of cancer cell transformation. From a clinical standpoint, this novel observation adds value in augmenting the current receptor-based biomarkers for better accuracy in diagnosis and predicting survival rate in patients with breast carcinoma. PMID:21867691

Studying damage accumulation in martensitic corrosion-resistant steel under cold radial reduction

NASA Astrophysics Data System (ADS)

Karamyshev, A. P.; Nekrasov, I. I.; Nesterenko, A. V.; Parshin, V. S.; Smirnov, S. V.; Shveikin, V. P.; Fedulov, A. A.

2017-12-01

Cold radial reduction of specimens made of the Kh17N2 corrosion-resistant martensitic steel is studied on a lever-type radial-forging machine (RFM). The mechanical properties of the deformed specimens, the "damage accumulation - strain" relation in the specimens are obtained with the application of hydrostatic and fractographic methods for fractured specimens. The damage of the Kh17N2 corrosion-resistant steel is evaluated as a result of an experimental study considering the data of simulation by a complex finite element model of cold deformation on a lever-type RFM.

Optimization of the imaging response of scanning microwave microscopy measurements

NASA Astrophysics Data System (ADS)

Sardi, G. M.; Lucibello, A.; Kasper, M.; Gramse, G.; Proietti, E.; Kienberger, F.; Marcelli, R.

2015-07-01

In this work, we present the analytical modeling and preliminary experimental results for the choice of the optimal frequencies when performing amplitude and phase measurements with a scanning microwave microscope. In particular, the analysis is related to the reflection mode operation of the instrument, i.e., the acquisition of the complex reflection coefficient data, usually referred as S11. The studied configuration is composed of an atomic force microscope with a microwave matched nanometric cantilever probe tip, connected by a λ/2 coaxial cable resonator to a vector network analyzer. The set-up is provided by Keysight Technologies. As a peculiar result, the optimal frequencies, where the maximum sensitivity is achieved, are different for the amplitude and for the phase signals. The analysis is focused on measurements of dielectric samples, like semiconductor devices, textile pieces, and biological specimens.

Lattice Light Sheet Microscopy: Imaging Molecules to Embryos at High Spatiotemporal Resolution

PubMed Central

Chen, Bi-Chang; Legant, Wesley R.; Wang, Kai; Shao, Lin; Milkie, Daniel E.; Davidson, Michael W.; Janetopoulos, Chris; Wu, Xufeng S.; Hammer, John A.; Liu, Zhe; English, Brian P.; Mimori-Kiyosue, Yuko; Romero, Daniel P.; Ritter, Alex T.; Lippincott-Schwartz, Jennifer; Fritz-Laylin, Lillian; Mullins, R. Dyche; Mitchell, Diana M.; Bembenek, Joshua N.; Reymann, Anne-Cecile; Böhme, Ralph; Grill, Stephan W.; Wang, Jennifer T.; Seydoux, Geraldine; Tulu, U. Serdar; Kiehart, Daniel P.; Betzig, Eric

2015-01-01

Although fluorescence microscopy provides a crucial window into the physiology of living specimens, many biological processes are too fragile, too small, or occur too rapidly to see clearly with existing tools. We crafted ultra-thin light sheets from two-dimensional optical lattices that allowed us to image three-dimensional (3D) dynamics for hundreds of volumes, often at sub-second intervals, at the diffraction limit and beyond. We applied this to systems spanning four orders of magnitude in space and time, including the diffusion of single transcription factor molecules in stem cell spheroids, the dynamic instability of mitotic microtubules, the immunological synapse, neutrophil motility in a 3D matrix, and embryogenesis in Caenorhabditis elegans and Drosophila melanogaster. The results provide a visceral reminder of the beauty and complexity of living systems. PMID:25342811

Raman spectroscopy in astrobiology.

PubMed

Jorge Villar, Susana E; Edwards, Howell G M

2006-01-01

Raman spectroscopy is proposed as a valuable analytical technique for planetary exploration because it is sensitive to organic and inorganic compounds and able to unambiguously identify key spectral markers in a mixture of biological and geological components; furthermore, sample manipulation is not required and any size of sample can be studied without chemical or mechanical pretreatment. NASA and ESA are considering the adoption of miniaturised Raman spectrometers for inclusion in suites of analytical instrumentation to be placed on robotic landers on Mars in the near future to search for extinct or extant life signals. In this paper we review the advantages and limitations of Raman spectroscopy for the analysis of complex specimens with relevance to the detection of bio- and geomarkers in extremophilic organisms which are considered to be terrestrial analogues of possible extraterrestial life that could have developed on planetary surfaces.

The Beringian coevolution project: Holistic collections of mammals and associated parasites reveal novel perspectives on evolutionary and environmental change in the North

USGS Publications Warehouse

Cook, Joseph A.; Galbreath, Kurt E.; Campbell, Mariel; Carrière, Susanne; Colella, Jocelyn P.; Dawson, Natalie G.; Dunnum, Jonathan L.; Eckerlin, Ralph P.; Greiman, Stephen E.; Fedorov, Vadim B.; Haas, Genevieve M. S.; Haukisalmi, Voitto; Henttonen, Heikki; Hope, Andrew G.; Jackson, Donavan; Jung, Tom; Koehler, Anson V.; Kinsella, John M.; Krejsa, Dianna; Kutz, Susan J.; Liphardt, Schuyler; MacDonald, Stephen O.; Malaney, Jason L.; Makarikov, Arseny; Martin, Jon; McLean, Bryan S.; Mulders, Robert; Nyamsuren, Batsaikhan; Talbot, Sandra L.; Tkach, Vasyl V.; Tsvetkova, Albina; Toman, Heather M.; Waltari, Eric C.; Whitman, Jackson S.; Hoberg, Eric P.

2017-01-01

The Beringian Coevolution Project (BCP), a field program underway in the high northern latitudes since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into how ancient climate and environmental change have shaped faunas, emphasizing processes of assembly, persistence, and diversification across the vast Beringian region. BCP collections also represent baseline records of biotic diversity from across the northern high latitudes at a time of accelerated environmental change. These specimens and associated data form an unmatched resource for identifying hidden diversity, interpreting past responses to climate oscillations, documenting contemporary conditions, and anticipating outcomes for complex biological systems in a regime of ecological perturbation. Because of its dual focus on hosts and parasites, the BCP record also provides a foundation for comparative analyses that can document the effects of dynamic change on the geographic distribution, transmission dynamics, and emergence of pathogens. By using specific examples from carnivores, shrews, lagomorphs, rodents and their associated parasites, we demonstrate how broad, integrated field collections provide permanent infrastructure that informs policy decisions regarding human impact and the effect of climate change on natural populations.

Tropical montane nymphalids in Mexico: DNA barcodes reveal greater diversity.

PubMed

Escalante, Patricia; Ibarra-Vazquez, Adolfo; Rosas-Escobar, Patricia

2010-12-01

DNA sequences obtained for the Barcode of Life library in the All Lepidoptera Campaign project Nymphalidae of Central Mexico were analyzed as a test of species limits and to explore possible phylogenetic groupings in the Preponini tribe. Using specimens in the National Insect Collection of the Instituto de Biología of the Universidad Nacional Autónoma de México, 78 specimens were assayed for cytochrome oxidase c subunit 1. Disregarding the missing data, there were 458 conserved sites, 200 variable sites and 187 parsimony-informative sites. The neighbor-joining and maximum likelihood analyses indicate that none of the three genera of Preponini as currently circumscribed are reciprocally monophyletic. As per species limits, high levels of barcode variation in the Prepona deiphile complex suggest the existence of at least two new endemic species to Mexico. The divergent taxa were escalantiana from the Tuxtlas region in Veracruz, and ibarra from Sierra Madre del Sur in the Pacific states of southern Mexico. The genetic distance in the CO1 fragment between them and the other deiphile populations ranged from 2.7 to 8.0%. We recommend that morphological data need to be re-examined and that additional molecular data for species ought to be gathered before a particular biogeographic model can be proposed for the group in Mesoamerica.

Upregulation of Soluble HLA-G5 and HLA-G6 Isoforms in the Milder Histopathological Stages of Helicobacter pylori Infection: A Role for Subverting Immune Responses?

PubMed

Souza, D M B Oliveira; Genre, J; Silva, T G Alves; Soares, C P; Rocha, K Borges Ferreira; Oliveira, C Nunes; Jatobá, C A Nunes; Andrade, J Marco de Leon; Moreau, P; Medeiros, A da Cunha; Donadi, E A; Crispim, J C de Oliveira

2016-01-01

The subversion mechanisms employed by Helicobacter pylori (H. pylori) to escape from immune surveillance and to establish persistent infection are poorly understood. Growing evidence indicates that expression of HLA-G, a non-classical major histocompatibility complex molecule, negatively regulates immune responses in pathological conditions, including infectious diseases. In this context, we aimed to evaluate HLA-G expression in the gastric microenvironment of individuals harbouring H. pylori and to correlate it with histological variables. Fifty-four gastric specimens from patients harbouring H. pylori infection were evaluated by immunohistochemistry using anti-HLA-G monoclonal antibody. As a result, HLA-G expression was detected in 43 of 54 specimens harbouring H. pylori. The presence of HLA-G was significantly associated with milder colonization by H. pylori (P < 0.02), milder inflammatory activity (P < 0.02) and bacterium histological location in the gastric antrum. This study is the first to explore HLA-G expression in the context of bacterial infection. Whether the biological role of HLA-G during H. pylori infection is beneficial or hazardous for patients remains to be defined. © 2015 The Authors. Scandinavian Journal of Immunology published by John Wiley & Sons Ltd on behalf of The Foundation for the Scandinavian Journal of Immunology.

Recent advances in biochemical and molecular diagnostics for the rapid detection of antibiotic-resistant Enterobacteriaceae: a focus on ß-lactam resistance.

PubMed

Decousser, Jean-Winoc; Poirel, Laurent; Nordmann, Patrice

2017-04-01

The rapid detection of resistance is a challenge for clinical microbiologists who wish to prevent deleterious individual and collective consequences such as (i) delaying efficient antibiotic therapy, which worsens the survival rate of the most severely ill patients, or (ii) delaying the isolation of the carriers of multidrug-resistant bacteria and promoting outbreaks; this last consequence is of special concern, and there are an increasing number of approaches and market-based solutions in response. Areas covered: From simple, cheap biochemical tests to whole-genome sequencing, clinical microbiologists must select the most adequate phenotypic and genotypic tools to promptly detect and confirm β-lactam resistance from cultivated bacteria or from clinical specimens. Here, the authors review the published literature from the last 5 years about the primary technical approaches and commercial laboratory reagents for these purposes, including molecular, biochemical and immune assays. Furthermore, the authors discuss their intrinsic and relative performance, and we challenge their putative clinical impact. Expert commentary: Until the availability of fully automated wet and dry whole genome sequencing solutions, microbiologists should focus on inexpensive biochemical tests for cultured isolates or monomicrobial clinical specimen and on using the expensive molecular PCR-based strategies for the targeted screening of complex biological environments.

21 CFR 864.3600 - Microscopes and accessories.

Code of Federal Regulations, 2010 CFR

2010-04-01

... enlarge images of specimens, preparations, and cultures for medical purposes. Variations of microscopes... light. (3) Inverted stage microscopes, which permit examination of tissue cultures or other biological...

Evaluation of the Abbott RealTime MTB and RealTime MTB INH/RIF Assays for Direct Detection of Mycobacterium tuberculosis Complex and Resistance Markers in Respiratory and Extrapulmonary Specimens.

PubMed

Hofmann-Thiel, Sabine; Molodtsov, Nikolay; Antonenka, Uladzimir; Hoffmann, Harald

2016-12-01

The Abbott RealTime MTB (RT MTB) assay is a new automated nucleic acid amplification test for the detection of Mycobacterium tuberculosis complex (MTBC) in clinical specimens. In combination with the RealTime MTB INH/RIF (RT MTB INH/RIF) resistance assay, which can be applied to RT MTB-positive specimens as an add-on assay, the tests also indicate the genetic markers of resistance to isoniazid (INH) and rifampin (RIF). We aimed to evaluate the diagnostic sensitivity and specificity of RT MTB using different types of respiratory and extrapulmonary specimens and to compare performance characteristics directly with those of the FluoroType MTB assay. The resistance results obtained by RT MTB INH/RIF were compared to those from the GenoType MTBDRplus and from phenotypic drug susceptibility testing. A total of 715 clinical specimens were analyzed. Compared to culture, the overall sensitivity of RT MTB was 92.1%; the sensitivity rates for smear-positive and smear-negative samples were 100% and 76.2%, respectively. The sensitivities of smear-negative specimens were almost identical for respiratory (76.3%) and extrapulmonary (76%) specimens. Specificity rates were 100% and 95.8% for culture-negative specimens and those that grew nontuberculous mycobacteria, respectively. RT MTB INH/RIF was applied to 233 RT MTB-positive samples and identified resistance markers in 7.7% of samples. Agreement with phenotypic and genotypic drug susceptibility testing was 99.5%. In conclusion, RT MTB and RT MTB INH/RIF allow for the rapid and accurate diagnosis of tuberculosis (TB) in different types of specimens and reliably indicate resistance markers. The strengths of this system are the comparably high sensitivity with paucibacillary specimens, its ability to detect INH and RIF resistance, and its high-throughput capacities. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

[Research status and prospects of DNA test on difficult specimens].

PubMed

Dang, Hua-Wei; Mao, Jiong; Wang, Hui; Huang, Jiang-Ping; Bai, Xiao-Gang

2012-02-01

This paper reviews the advances of DNA detection on three types of difficult biological specimens including degraded samples, trace evidences and mixed samples. The source of different samples, processing methods and announcements were analyzed. New methods such as mitochondrial test system, changing the original experimental conditions, low-volume PCR amplification and new technologies such as whole genome amplification techniques, laser capture micro-dissection, and mini-STR technology in recent years are introduced.

Norovirus Real Time RT-PCR Detection Technology Transition to the Joint Biological Identification and Diagnosis System (JBAIDS)

DTIC Science & Technology

2012-09-21

virus and Southampton virus, and II (GII), which includes Bristol virus, Lordsdale virus, Toronto virus, Mexico virus, Hawaii virus and Snow Mountain...Shigella flexneriATCC12022 1 Negative Shigella sonnei ATCC25931 1 Negative Vibrio cholera (NAG) (Culture) 2 Negative Vibrio cholera (Ogawa...Culture) 1 Negative Vibrio cholera (Inaga) (Culture) 1 Negative Sapovivus (Known specimen extract) 2 Negative Rotavirus (Known specimen extract) 2

LifeSat - A new research vehicle

NASA Technical Reports Server (NTRS)

Gilbreath, William P.; Dunning, Robert W.

1990-01-01

LifeSat is a reusable recoverable satellite that will support research in the gravitation and radiation biology fields. It can provide sustained lower gravitational levels than manned vehicles and can access orbits where specimens can be exposed to cosmic radiation. The satellite design encompasses environmental support for vertebrate, invertebrate and plant specimens ranging from cells and tissues up to small mammals. The first launch, in a series of 7 satellite flights, is planned for late 1995.

The Responsible Use of Animals in Biology Classrooms Including Alternatives to Dissection. Monograph IV.

ERIC Educational Resources Information Center

Hairston, Rosalina V., Ed.

This monograph discusses the care and maintenance of animals, suggests some alternative teaching strategies, and affirms the value of teaching biology as the study of living organisms, rather than dead specimens. The lessons in this monograph are intended as guidelines that teachers should adapt for their own particular classroom needs. Chapter 1,…

Amber: Using "Tree Tears Turned to Stone" to Teach Biology, Ecology, and More!

ERIC Educational Resources Information Center

Clary, Renee M.; Wandersee, James H.

2009-01-01

Amber is a fossil by itself, and can also contain plants and animals that lived millions of years ago. Some of these perfectly preserved specimens give scientists a convenient window to past environments, including the biology, ecology, geology, and chemistry of Earth's past. By using an interdisciplinary approach, we can demonstrate to students a…

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--HUMAN BIOLOGICAL MARKERS:BLOOD AND URINE SAMPLE COLLECTION AND ANALYSES (EOHSI-AP-209-040)

EPA Science Inventory

This procedure describes the process for collecting and analyzing blood and urine samples. The presence of chemical contaminants in biological specimens such as blood, urine, and hair represent a measure of the internal dose or body burden for a given individual derived from the ...

Guidelines for Marine Biological Reference Collections. Unesco Reports in Marine Sciences, No. 22.

ERIC Educational Resources Information Center

Hureau, J. C.; Rice, A. L.

This manual provides practical advice on the appropriation, conservation, and documentation of a marine biological reference collection, in response to needs expressed by Mediterranean Arab countries. A reference collection is defined as a working museum containing a series of specimens with which biologists are able to compare their own material.…

Distribution of 10 periodontal bacterial species in children and adolescents over a 7-year period.

PubMed

Nakano, K; Miyamoto, E; Tamura, K; Nemoto, H; Fujita, K; Nomura, R; Ooshima, T

2008-10-01

There is scant information available regarding the distribution of periodontal bacterial species in children and adolescents over an extended period. The purpose of this study was to compare bacterial profiles in the same individuals over a period of 7 years. Twenty-six children and adolescents from whom dental plaque and saliva specimens were obtained during both the first (1999-2000) and second (2006-2007) periods, were analyzed. Bacterial DNA was extracted from each specimen and the presence of 10 periodontal bacterial species was determined using a PCR method, with a focus on the red complex species of Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. Subjects with red complex species in saliva specimens obtained during the second collection possessed a significantly higher number of total bacterial species than those without. The detection rate of the red complex species in the second collection period samples was significantly greater in subjects who had two or more species detected in samples taken during the first collection compared with the other subjects. Subjects possessing red complex species may be at possible risk for infection with a high number of periodontal bacterial species during adolescent and younger adult years.

Physiological response of invasive mussel Limnoperna fortunei (Dunker, 1857) (Bivalvia: Mytilidae) submitted to transport and experimental conditions.

PubMed

Cordeiro, N I S; Andrade, J T M; Montresor, L C; Luz, D M R; Araújo, J M; Martinez, C B; Pinheiro, J; Vidigal, T H D A

2017-03-01

Successful animal rearing under laboratory conditions for commercial processes or laboratory experiments is a complex chain that includes several stressors (e.g., sampling and transport) and incurs, as a consequence, the reduction of natural animal conditions, economic losses and inconsistent and unreliable biological results. Since the invasion of the bivalve Limnoperna fortunei (Dunker, 1857) in South America, several studies have been performed to help control and manage this fouling pest in industrial plants that use raw water. Relatively little attention has been given to the laboratory rearing procedure of L. fortunei, its condition when exposed to a stressor or its acclimation into laboratory conditions. Considering this issue, the aims of this study are to (i) investigate L. fortunei physiological responses when submitted to the depuration process and subsequent air transport (without water/dry condition) at two temperatures, based on glycogen concentrations, and (ii) monitor the glycogen concentrations in different groups when maintained for 28 days under laboratory conditions. Based on the obtained results, depuration did not affect either of the groups when they were submitted to approximately eight hours of transport. The variation in glycogen concentration among the specimens that were obtained from the field under depurated and non-depurated conditions was significant only in the first week of laboratory growth for the non-depurated group and in the second week for the depurated group. In addition, the tested temperature did not affect either of the groups that were submitted to transport. The glycogen concentrations were similar to those of the specimens that were obtained from the field in third week, which suggests that the specimens acclimated to laboratory conditions during this period of time. Thus, the results indicate that the air transport and acclimation time can be successfully incorporated into experimental studies of L. fortunei. Finally, the tolerance of L. fortunei specimens to the stressor tested herein can help us understand the invasive capacity of this mussel during the establishment process.

Evaluation of the Cobas TaqMan MTB test for the detection of Mycobacterium tuberculosis complex according to acid-fast-bacillus smear grades in respiratory specimens.

PubMed

Huh, Hee Jae; Koh, Won-Jung; Song, Dong Joon; Ki, Chang-Seok; Lee, Nam Yong

2015-02-01

We evaluated the performance of the Cobas TaqMan MTB test (Roche Diagnostics, Basel, Switzerland), stratified by acid-fast bacilli (AFB) smear grades. The sensitivity of this test in smear-positive specimens was >95% in all grades, while that in trace and negative specimens was 85.3% and 34.4%, respectively. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The preanalytic phase in veterinary clinical pathology.

PubMed

Braun, Jean-Pierre; Bourgès-Abella, Nathalie; Geffré, Anne; Concordet, Didier; Trumel, Cathy

2015-03-01

This article presents the general causes of preanalytic variability with a few examples showing specialists and practitioners that special and improved care should be given to this too often neglected phase. The preanalytic phase of clinical pathology includes all the steps from specimen collection to analysis. It is the phase where most laboratory errors occur in human, and probably also in veterinary clinical pathology. Numerous causes may affect the validity of the results, including technical factors, such as the choice of anticoagulant, the blood vessel sampled, and the duration and conditions of specimen handling. While the latter factors can be defined, influence of biologic and physiologic factors such as feeding and fasting, stress, and biologic and endocrine rhythms can often not be controlled. Nevertheless, as many factors as possible should at least be documented. The importance of the preanalytic phase is often not given the necessary attention, although the validity of the results and consequent clinical decision making and medical management of animal patients would likely be improved if the quality of specimens submitted to the laboratory was optimized. © 2014 American Society for Veterinary Clinical Pathology.

Magnetic levitation-based Martian and Lunar gravity simulator

NASA Technical Reports Server (NTRS)

Valles, J. M. Jr; Maris, H. J.; Seidel, G. M.; Tang, J.; Yao, W.

2005-01-01

Missions to Mars will subject living specimens to a range of low gravity environments. Deleterious biological effects of prolonged exposure to Martian gravity (0.38 g), Lunar gravity (0.17 g), and microgravity are expected, but the mechanisms involved and potential for remedies are unknown. We are proposing the development of a facility that provides a simulated Martian and Lunar gravity environment for experiments on biological systems in a well controlled laboratory setting. The magnetic adjustable gravity simulator will employ intense, inhomogeneous magnetic fields to exert magnetic body forces on a specimen that oppose the body force of gravity. By adjusting the magnetic field, it is possible to continuously adjust the total body force acting on a specimen. The simulator system considered consists of a superconducting solenoid with a room temperature bore sufficiently large to accommodate small whole organisms, cell cultures, and gravity sensitive bio-molecular solutions. It will have good optical access so that the organisms can be viewed in situ. This facility will be valuable for experimental observations and public demonstrations of systems in simulated reduced gravity. c2005 Published by Elsevier Ltd on behalf of COSPAR.

Magnetic levitation-based Martian and Lunar gravity simulator.

PubMed

Valles, J M; Maris, H J; Seidel, G M; Tang, J; Yao, W

2005-01-01

Missions to Mars will subject living specimens to a range of low gravity environments. Deleterious biological effects of prolonged exposure to Martian gravity (0.38 g), Lunar gravity (0.17 g), and microgravity are expected, but the mechanisms involved and potential for remedies are unknown. We are proposing the development of a facility that provides a simulated Martian and Lunar gravity environment for experiments on biological systems in a well controlled laboratory setting. The magnetic adjustable gravity simulator will employ intense, inhomogeneous magnetic fields to exert magnetic body forces on a specimen that oppose the body force of gravity. By adjusting the magnetic field, it is possible to continuously adjust the total body force acting on a specimen. The simulator system considered consists of a superconducting solenoid with a room temperature bore sufficiently large to accommodate small whole organisms, cell cultures, and gravity sensitive bio-molecular solutions. It will have good optical access so that the organisms can be viewed in situ. This facility will be valuable for experimental observations and public demonstrations of systems in simulated reduced gravity. c2005 Published by Elsevier Ltd on behalf of COSPAR.

Benefit of STR-based chimerism analysis to identify TA-GVHD as a cause of death: Utility of various biological specimens.

PubMed

Raina, Anupuma; Chaudhary, Garima; Dogra, Tirath Das; Khandelwal, Deepchand; Balayan, Ajay; Jain, Vandana; Kanga, Uma; Seth, Tulika

2016-04-01

Transfusion-associated graft-versus-host disease (TA-GVHD) is a rare condition. It can occur after blood transfusion in immune-compromised and occasionally even in immune-competent patients, and is associated with a mortality rate of >90%. The diagnosis of TA-GVHD is often delayed because of its non-specific clinical features. A case of an immune-competent child who developed TA-GVHD is reported here. DNA profiling (short tandem repeat analysis), a technique that has a wide application in forensic medicine, was performed to detect the presence of donor cells in this patient. The findings suggest that more studies are needed with this tool, and the diagnostic potential of using other multiple biological specimens for DNA profiling such as the hair follicle and buccal swab should be evaluated. This is the first case report where the donor's DNA fingerprinting pattern was substantiated from a patient's hair follicle sample. Chimerism was also present in the blood and buccal swab specimens. © The Author(s) 2015.

Examining the reproducibility of stable isotope ratios in the marine bivalve, Astarte borealis, from populations in the White Sea, Russia: implications for biological consequences of climate change

NASA Astrophysics Data System (ADS)

McNabb, Justin; Surge, Donna

2015-04-01

Shells of the marine bivalve, Astarte, are uniquely suited to investigate links between environmental/climate change and biological consequences because of their change in size and biogeographic distribution through time. For example, are there corresponding changes in lifespan and biogeographic distribution depending on warm vs. cold climate states? Does warm vs. cold climate state result in longer or shorter lifespans? Early studies of Astarte have documented a decrease in shell size through geologic time. Modern specimens are much smaller than those from the mid Pliocene at similar latitudes. Astarte had a wide latitudinal and cosmopolitan distribution in the western North Atlantic during the Oligocene to Pliocene. During the early Pleistocene, most of the warm-water species became extinct, and today, their biogeographic distribution is mostly restricted to the northern Pacific, Atlantic, and Arctic Oceans. To answer questions linking biological consequences and climate change, we must first decipher ontogenetic changes in shell growth of modern specimens. Preliminary data using isotope sclerochronology identified slowed shell growth from late summer to winter in modern specimens from the White Sea, Russia, possibly triggered by increasing freshwater input and decreasing temperatures. Here, we present new data examining the reproducibility of isotopic time series and season of slowed growth among modern individuals collected at the same time from the same population.

Bioindicators in the MIDUS National Study: Protocol, Measures, Sample, and Comparative Context

PubMed Central

Love, Gayle Dienberg; Seeman, Teresa E.; Weinstein, Maxine; Ryff, Carol D.

2010-01-01

Objectives MIDUS is a national study of health and aging among individuals aged 25 to 74 at baseline(1995/96). Longitudinal survey assessments (2004/05), were followed by biological assessments on a subsample aged 35–85. To facilitate public use, we describe the protocol, measures, and sample. Methods Respondents traveled to clinics for a two-day data collection protocol that included fasting blood specimens, 12-hour urine specimen, medical history, physical exam, bone densitometry, a laboratory challenge (heart rate variability, blood pressure, respiration, salivary cortisol). Results Response rates for the biological protocol (N = 1,255) were 39.3%, or 43.1% (adjusting for those who could not be located or contacted). Reasons for non-participation were travel, family obligations, and being too busy. Respondents were comparable to the recruitment pool on most demographic characteristics and health assessments. Discussion Strengths of the protocol vis-à-vis other similar studies include opportunities to link biological factors with diverse content from other MIDUS projects. PMID:20876364

A guide to the winged aphids (Homoptera) of Costa Rica.

PubMed

Voegtlin, David; Villalobos, William; Sánchez, Marco Vinicio; Saborio-R, Guido; Rivera, Carmen

2003-05-01

This guide is a compilation of limited morphological and biological information on the winged morphs of 60 species of aphids that have been collected in Costa Rica. It should not be viewed as a definitive taxonomic treatise on the aphids of Costa Rica, rather it is a tool that can be used to assist in research on the biology, host plant relationships, taxonomy, and virus transmission capabilities of aphids. Each species is covered in an identical manner. Morphological and biological information is provided in both Spanish and English as well as photographs of slide mounted specimens. Keys are provided to help the user in identifying the species. Most of the specimens examined were taken in traps associated with epidemiological studies. Limited field collecting has generated host records and these have been added to a list of the aphids of Central America that was compiled by Pamela Anderson and appended in the guide with her permission. The authors hope that this book will be useful to entomologists in Costa Rica and Central America.

Type specimens and basic principles of avian taxonomy

USGS Publications Warehouse

Banks, Richard C.; Goodman, Steven M.; Lanyon, Scott M.; Schulenberg, Thomas S.

1993-01-01

"Ornithology" may be defined as the scientific study of birds. No aspect of avian biology, including management and conservation, can be carried out without reference by name to birds at some taxonomic level. Thus, the names of species of birds, and of groups of species, can fairly be considered to be of primary importance in ornithology. To be useful, these names themselves must be defined and related to biological entities. The definition of a name is accomplished by the designation of a "type." The International Code of Zoological Nomenclature, in paragraph (C) of Article 72 (third edition, 1985), establishes criteria for eligibility of a name-bearing type. The type of a species or sub-species name is the biological specimen defined by the name, and later use of the name implies specific or subspecific identity with the type. It is imperative, therefore, that a type be available for study and comparison so that the identity of other material with it can be established.

Biospecimens | Division of Cancer Prevention

Cancer.gov

The PLCO Biorepository stores approximately 2.9 million biologic specimens collected from PLCO participants. Some of characteristics that make PLCO samples particularly valuable for etiologic and early marker research are: |

Pulsed-voltage atom probe tomography of low conductivity and insulator materials by application of ultrathin metallic coating on nanoscale specimen geometry.

PubMed

Adineh, Vahid R; Marceau, Ross K W; Chen, Yu; Si, Kae J; Velkov, Tony; Cheng, Wenlong; Li, Jian; Fu, Jing

2017-10-01

We present a novel approach for analysis of low-conductivity and insulating materials with conventional pulsed-voltage atom probe tomography (APT), by incorporating an ultrathin metallic coating on focused ion beam prepared needle-shaped specimens. Finite element electrostatic simulations of coated atom probe specimens were performed, which suggest remarkable improvement in uniform voltage distribution and subsequent field evaporation of the insulated samples with a metallic coating of approximately 10nm thickness. Using design of experiment technique, an experimental investigation was performed to study physical vapor deposition coating of needle specimens with end tip radii less than 100nm. The final geometries of the coated APT specimens were characterized with high-resolution scanning electron microscopy and transmission electron microscopy, and an empirical model was proposed to determine the optimal coating thickness for a given specimen size. The optimal coating strategy was applied to APT specimens of resin embedded Au nanospheres. Results demonstrate that the optimal coating strategy allows unique pulsed-voltage atom probe analysis and 3D imaging of biological and insulated samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Automated 100-Position Specimen Loader and Image Acquisition System for Transmission Electron Microscopy

PubMed Central

Lefman, Jonathan; Morrison, Robert; Subramaniam, Sriram

2007-01-01

We report the development of a novel, multi-specimen imaging system for high-throughput transmission electron microscopy. Our cartridge-based loading system, called the “Gatling”, permits the sequential examination of as many as 100 specimens in the microscope for room temperature electron microscopy using mechanisms for rapid and automated specimen exchange. The software for the operation of the Gatling and automated data acquisition has been implemented in an updated version of our in-house program AutoEM. In the current implementation of the system, the time required to deliver 95 specimens into the microscope and collect overview images from each is about 13 hours. Regions of interest are identified from a low magnification atlas generation from each specimen and an unlimited number of higher magnifications images can be subsequently acquired from these regions using fully automated data acquisition procedures that can be controlled from a remote interface. We anticipate that the availability of the Gatling will greatly accelerate the speed of data acquisition for a variety of applications in biology, materials science and nanotechnology that require rapid screening and image analysis of multiple specimens. PMID:17240161

Automated Microbiological Detection/Identification System

PubMed Central

Aldridge, C.; Jones, P. W.; Gibson, S.; Lanham, J.; Meyer, M.; Vannest, R.; Charles, R.

1977-01-01

An automated, computerized system, the AutoMicrobic System, has been developed for the detection, enumeration, and identification of bacteria and yeasts in clinical specimens. The biological basis for the system resides in lyophilized, highly selective and specific media enclosed in wells of a disposable plastic cuvette; introduction of a suitable specimen rehydrates and inoculates the media in the wells. An automated optical system monitors, and the computer interprets, changes in the media, with enumeration and identification results automatically obtained in 13 h. Sixteen different selective media were developed and tested with a variety of seeded (simulated) and clinical specimens. The AutoMicrobic System has been extensively tested with urine specimens, using a urine test kit (Identi-Pak) that contains selective media for Escherichia coli, Proteus species, Pseudomonas aeruginosa, Klebsiella-Enterobacter species, Serratia species, Citrobacter freundii, group D enterococci, Staphylococcus aureus, and yeasts (Candida species and Torulopsis glabrata). The system has been tested with 3,370 seeded urine specimens and 1,486 clinical urines. Agreement with simultaneous conventional (manual) cultures, at levels of 70,000 colony-forming units per ml (or more), was 92% or better for seeded specimens; clinical specimens yielded results of 93% or better for all organisms except P. aeruginosa, where agreement was 86%. System expansion in progress includes antibiotic susceptibility testing and compatibility with most types of clinical specimens. Images PMID:334798

Overview on Techniques to Construct Tissue Arrays with Special Emphasis on Tissue Microarrays

PubMed Central

Vogel, Ulrich

2014-01-01

With the advent of new histopathological staining techniques (histochemistry, immunohistochemistry, in situ hybridization) and the discovery of thousands of new genes, mRNA, and proteins by molecular biology, the need grew for a technique to compare many different cells or tissues on one slide in a cost effective manner and with the possibility to easily track the identity of each specimen: the tissue array (TA). Basically, a TA consists of at least two different specimens per slide. TAs differ in the kind of specimens, the number of specimens installed, the dimension of the specimens, the arrangement of the specimens, the embedding medium, the technique to prepare the specimens to be installed, and the technique to construct the TA itself. A TA can be constructed by arranging the tissue specimens in a mold and subsequently pouring the mold with the embedding medium of choice. In contrast, preformed so-called recipient blocks consisting of the embedding medium of choice have punched, drilled, or poured holes of different diameters and distances in which the cells or tissue biopsies will be deployed manually, semi-automatically, or automatically. The costs of constructing a TA differ from a few to thousands of Euros depending on the technique/equipment used. Remarkably high quality TAs can be also achieved by low cost techniques. PMID:27600339

Compensation method for obtaining accurate, sub-micrometer displacement measurements of immersed specimens using electronic speckle interferometry.

PubMed

Fazio, Massimo A; Bruno, Luigi; Reynaud, Juan F; Poggialini, Andrea; Downs, J Crawford

2012-03-01

We proposed and validated a compensation method that accounts for the optical distortion inherent in measuring displacements on specimens immersed in aqueous solution. A spherically-shaped rubber specimen was mounted and pressurized on a custom apparatus, with the resulting surface displacements recorded using electronic speckle pattern interferometry (ESPI). Point-to-point light direction computation is achieved by a ray-tracing strategy coupled with customized B-spline-based analytical representation of the specimen shape. The compensation method reduced the mean magnitude of the displacement error induced by the optical distortion from 35% to 3%, and ESPI displacement measurement repeatability showed a mean variance of 16 nm at the 95% confidence level for immersed specimens. The ESPI interferometer and numerical data analysis procedure presented herein provide reliable, accurate, and repeatable measurement of sub-micrometer deformations obtained from pressurization tests of spherically-shaped specimens immersed in aqueous salt solution. This method can be used to quantify small deformations in biological tissue samples under load, while maintaining the hydration necessary to ensure accurate material property assessment.

[Incidence and clinicopathological characteristics of incidental prostatic adenocarcinoma in radical cystoprostatectomy specimens].

PubMed

Shen, Qi; Hu, Shuai; Li, Jun; Wang, Jing-hua; He, Qun

2014-08-18

To analyze the incidence and clinicopathological features of incidental prostate cancer (IPCa) in specimens from radical cystoprostatectomy (RCP) for bladder cancer. We retrospectively reviewed the histopathological features of 865 male patients who underwent an RCP between January 2005 and March 2014. No patients had preoperative clinical or biological suspicion of prostate cancer (PCa). Among the 865 specimens, IPCa was diagnosed in 235 patients (27.2%). Most tumors (228/235, 97.0%) were organ-confined (pT2); And 7 cases (3.0 %) of them were diagnosed at T3. Gleason score was < 6 in 84 cases (35.7 %), 6 in 77 cases (32.8%), 7 in 64 cases (27.2 %), and > 7 in 10 cases (4.3 %). The rate of incidentally diagnosed IPCa was 8.5%, and that in RCP and TURP specimens was 19.5% and 4.4% respectively. The majority of these IPCas were organ-confined. Gleason score in most of these specimens was ≤ 7. Moreover, prostate examination in the RCP specimen should be careful and sufficient, whole-amount prostate sections improve diagnostic accuracy.

Joining Inventory by Parataxonomists with DNA Barcoding of a Large Complex Tropical Conserved Wildland in Northwestern Costa Rica

PubMed Central

Janzen, Daniel H.; Hallwachs, Winnie

2011-01-01

Background The many components of conservation through biodiversity development of a large complex tropical wildland, Area de Conservacion Guanacaste (ACG), thrive on knowing what is its biodiversity and natural history. For 32 years a growing team of Costa Rican parataxonomists has conducted biodiversity inventory of ACG caterpillars, their food plants, and their parasitoids. In 2003, DNA barcoding was added to the inventory process. Methodology/Principal Findings We describe some of the salient consequences for the parataxonomists of barcoding becoming part of a field biodiversity inventory process that has centuries of tradition. From the barcoding results, the parataxonomists, as well as other downstream users, gain a more fine-scale and greater understanding of the specimens they find, rear, photograph, database and deliver. The parataxonomists also need to adjust to collecting more specimens of what appear to be the “same species” – cryptic species that cannot be distinguished by eye or even food plant alone – while having to work with the name changes and taxonomic uncertainty that comes with discovering that what looked like one species may be many. Conclusions/Significance These career parataxonomists, despite their lack of formal higher education, have proven very capable of absorbing and working around the additional complexity and requirements for accuracy and detail that are generated by adding barcoding to the field base of the ACG inventory. In the process, they have also gained a greater understanding of the fine details of phylogeny, relatedness, evolution, and species-packing in their own tropical complex ecosytems. There is no reason to view DNA barcoding as incompatible in any way with tropical biodiversity inventory as conducted by parataxonomists. Their year-round on-site inventory effort lends itself well to the sampling patterns and sample sizes needed to build a thorough barcode library. Furthermore, the biological understanding that comes with barcoding increases the scientific penetrance of biodiversity information, DNA understanding, evolution, and ecology into the communities in which the parataxonomists and their families are resident. PMID:21857894

Kits in Motion

ERIC Educational Resources Information Center

Gee, Maureen

1975-01-01

Discusses three kits developed by museums in British Columbia for use in rural classrooms. The science kit on marine biology consists of modules which included specimens, books, audiovisual materials and student activities. (BR)

Laying the groundwork for NEON's continental-scale ecological research

NASA Astrophysics Data System (ADS)

Dethloff, G.; Denslow, M.

2013-12-01

The National Ecological Observatory Network (NEON) is designed to examine a suite of ecological issues. Field-collected data from 96 terrestrial and aquatic sites across the U.S. will be combined with remotely sensed data and existing continental-scale data sets. Field collections will include a range of physical and biological types, including soil, sediment, surface water, groundwater, precipitation, plants, animals, insects, and microbes as well as biological sub-samples such as leaf material, blood and tissue samples, and DNA extracts. Initial data analyses and identifications of approximately 175,000 samples per year will occur at numerous external laboratories when all sites are fully staffed in 2017. Additionally, NEON will archive biotic and abiotic specimens at collections facilities where they will be curated and available for additional analyses by the scientific community. The number of archived specimens is currently estimated to exceed 130,000 per year by 2017. We will detail how NEON is addressing the complexities and challenges around this set of analyses and specimens and how the resulting high-quality data can impact ecological understanding. The raw data returned from external laboratories that is quality checked and served by NEON will be the foundation for many NEON data products. For example, sequence-quality nucleic acids extracted from surface waters, benthic biofilms, and soil samples will be building blocks for data products on microbial diversity. The raw sequence data will also be available for uses such as evolutionary investigations, and the extracts will be archived so others can acquire them for additional research. Currently, NEON is establishing contracts for the analysis and archiving of field-collected samples through 2017. During this period, NEON will gather information on the progress and success of this large-scale effort in order to determine the most effective course to pursue with external facilities. Two areas that NEON already knows to evaluate are the need for geographic expertise in taxonomic identifications and the capacity necessary to handle the volume of samples. NEON is also addressing challenges associated with external entities and the logistics of sample movement, data formatting, data ingestion, and reporting. For example, NEON is considering tools, such as web APIs, which could allow efficient transfer of data from external facilities. Having a standard format in place for that data will be critical to transfer success and quality assessment. NEON is also working on the implementation of quality control measures for diverse analytical and taxonomic processes across laboratories, and is developing an external audit process. Additionally, given NEON's open access approach, the Network is focused on selecting a sample identification protocol that aids in tracking samples with more involved analytical needs and also allows maximum utility for the scientific community. Given the complex nature and breadth of the project, NEON will be developing novel sample management systems as well as metadata schemas. These efforts insure integrity and quality from field to external facility to archive for each sample taken, providing high-quality data now and confidence in future research stemming from raw data generated by NEON and its collection specimens.

Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens.

PubMed

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

2013-11-01

This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10(-2) Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens

NASA Astrophysics Data System (ADS)

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

2013-11-01

This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10-2 Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

Acknowledging tissue donation: Human cadaveric specimens in musculoskeletal research.

PubMed

Winkelmann, Andreas; Heinze, Anne-Kathrin; Hendrix, Sven

2016-01-01

Human cadaveric specimens are an important resource for research, particularly in biomechanical studies, but their use also raises ethical questions and cannot simply be taken for granted. It was asked how much information authors publishing musculoskeletal research actually give about such specimens and about how they were acquired. The aim was to formulate recommendations on how this reporting might be improved. Relevant articles published between 2009 and 2012 in four North American or European journals were scanned for information regarding the characteristics of the human specimens used, their institutional source and the ethical or legal context of their acquisition. While the majority of articles report biological characteristics of specimens (sex, age at death, preservation method), only 40% of articles refer to body donation, only 23% report the institution that provided specimens, and only 17% refer to some kind of formalized approval of their research. There were regional and journal-to-journal differences. No standard for reporting studies involving human specimens could be detected. It is suggested that such a standard be developed by researchers and editors. Information on the source of specimens and on the ethical or legal basis should be regularly reported to acknowledge this unique research resource and to preserve the good relationship between researchers and the communities, that provide the required specimens by body donation and upon which researchers depend. © 2015 Wiley Periodicals, Inc.

[Automated RNA amplification for the rapid identification of Mycobacterium tuberculosis complex in respiratory specimens].

PubMed

Drouillon, V; Houriez, F; Buze, M; Lagrange, P; Herrmann, J-L

2006-01-01

Rapid and sensitive detection of Mycobacterium tuberculosis complex (MTB) directly on clinical respiratory specimens is essential for a correct management of patients suspected of tuberculosis. For this purpose PCR-based kits are available to detect MTB in respiratory specimen but most of them need at least 4 hours to be completed. New methods, based on TRC method (TRC: Transcription Reverse transcription Concerted--TRCRapid M. Tuberculosis--Tosoh Bioscience, Tokyo, Japon) and dedicated monitor have been developed. A new kit (TRC Rapid M. tuberculosis and Real-time monitor TRCRapid-160, Tosoh Corporation, Japan) enabling one step amplification and real-time detection of MTB 16S rRNA by a combination of intercalative dye oxazole yellow-linked DNA probe and isothermal RNA amplification directly on respiratory specimens has been tested in our laboratory. 319 respiratory specimens were tested in this preliminary study and results were compared to smear and culture. Fourteen had a positive culture for MTB. Among theses samples, smear was positive in 11 cases (78.6%) and TRC process was positive in 8 cases (57.1%). Overall sensitivity of TRC compared to smear positive samples is 73%. Theses first results demonstrated that a rapid identification of MTB was possible (less than 2 processing hours for 14 specimens and about 1 hour for 1 specimen) in most cases of smear positive samples using ready to use reagents for real time detection of MTB rRNA in clinical samples. New pretreatment and extraction reagents kits to increase the stability of the sputum RNA and the extraction efficiency are now tested in our laboratory.

Development of procedures for calculating stiffness and damping properties of elastomers in engineering applications. Part 2: Elastomer characteristics at constant temperature

NASA Technical Reports Server (NTRS)

Gupta, P. K.; Tessarzik, J. M.; Cziglenyi, L.

1974-01-01

Dynamic properties of a commerical polybutadiene compound were determined at a constant temperature of 32 C by a forced-vibration resonant mass type of apparatus. The constant thermal state of the elastomer was ensured by keeping the ambient temperature constant and by limiting the power dissipation in the specimen. Experiments were performed with both compression and shear specimens at several preloads (nominal strain varying from 0 to 5 percent), and the results are reported in terms of a complex stiffness as a function of frequency. Very weak frequency dependence is observed and a simple power law type of correlation is shown to represent the data well. Variations in the complex stiffness as a function of preload are also found to be small for both compression and shear specimens.

X-ray microscopy as an approach to increasing accuracy and efficiency of serial block-face imaging for correlated light and electron microscopy of biological specimens.

PubMed

Bushong, Eric A; Johnson, Donald D; Kim, Keun-Young; Terada, Masako; Hatori, Megumi; Peltier, Steven T; Panda, Satchidananda; Merkle, Arno; Ellisman, Mark H

2015-02-01

The recently developed three-dimensional electron microscopic (EM) method of serial block-face scanning electron microscopy (SBEM) has rapidly established itself as a powerful imaging approach. Volume EM imaging with this scanning electron microscopy (SEM) method requires intense staining of biological specimens with heavy metals to allow sufficient back-scatter electron signal and also to render specimens sufficiently conductive to control charging artifacts. These more extreme heavy metal staining protocols render specimens light opaque and make it much more difficult to track and identify regions of interest (ROIs) for the SBEM imaging process than for a typical thin section transmission electron microscopy correlative light and electron microscopy study. We present a strategy employing X-ray microscopy (XRM) both for tracking ROIs and for increasing the efficiency of the workflow used for typical projects undertaken with SBEM. XRM was found to reveal an impressive level of detail in tissue heavily stained for SBEM imaging, allowing for the identification of tissue landmarks that can be subsequently used to guide data collection in the SEM. Furthermore, specific labeling of individual cells using diaminobenzidine is detectable in XRM volumes. We demonstrate that tungsten carbide particles or upconverting nanophosphor particles can be used as fiducial markers to further increase the precision and efficiency of SBEM imaging.

X-ray Microscopy as an Approach to Increasing Accuracy and Efficiency of Serial Block-face Imaging for Correlated Light and Electron Microscopy of Biological Specimens

PubMed Central

Bushong, Eric A.; Johnson, Donald D.; Kim, Keun-Young; Terada, Masako; Hatori, Megumi; Peltier, Steven T.; Panda, Satchidananda; Merkle, Arno; Ellisman, Mark H.

2015-01-01

The recently developed three-dimensional electron microscopic (EM) method of serial block-face scanning electron microscopy (SBEM) has rapidly established itself as a powerful imaging approach. Volume EM imaging with this scanning electron microscopy (SEM) method requires intense staining of biological specimens with heavy metals to allow sufficient back-scatter electron signal and also to render specimens sufficiently conductive to control charging artifacts. These more extreme heavy metal staining protocols render specimens light opaque and make it much more difficult to track and identify regions of interest (ROIs) for the SBEM imaging process than for a typical thin section transmission electron microscopy correlative light and electron microscopy study. We present a strategy employing X-ray microscopy (XRM) both for tracking ROIs and for increasing the efficiency of the workflow used for typical projects undertaken with SBEM. XRM was found to reveal an impressive level of detail in tissue heavily stained for SBEM imaging, allowing for the identification of tissue landmarks that can be subsequently used to guide data collection in the SEM. Furthermore, specific labeling of individual cells using diaminobenzidine is detectable in XRM volumes. We demonstrate that tungsten carbide particles or upconverting nanophosphor particles can be used as fiducial markers to further increase the precision and efficiency of SBEM imaging. PMID:25392009

Smaller than We Normally See: The Fascination of Microscopy Is Not Restricted to Biology

ERIC Educational Resources Information Center

Evennett, Peter

2011-01-01

Microscopes are especially useful for observing fine detail in biological specimens. However, there are many other small items that may be examined with microscopes, and it is important to introduce children to low-magnification images of items they can recognise before moving on to such large magnification that what they observe has no obvious…

Analytical Measurement of Discrete Hydrogen Sulfide Pools in Biological Specimens

PubMed Central

Shen, Xinggui; Peter, Elvis A.; Bir, Shyamal; Wang, Rui; Kevil, Christopher G.

2015-01-01

Hydrogen sulfide (H2S) is a ubiquitous gaseous signaling molecule that plays a vital role in numerous cellular functions and has become the focus of many research endeavors including pharmaco-therapeutic manipulation. Amongst the challenges facing the field is the accurate measurement of biologically active H2S. We have recently reported that the typically used methylene blue method and its associated results are invalid and do not measure bonafide H2S. The complexity of analytical H2S measurement reflects the fact that hydrogen sulfide is a volatile gas and exists in the body in different forms, including a free form, an acid labile pool and as bound sulfane sulfur. Here we describe a new protocol to discretely measure specific H2S pools using the monobromobimane method coupled with RP-HPLC. This new protocol involves selective liberation, trapping and derivatization of H2S. Acid-labile H2S is released by incubating the sample in an acidic solution (pH 2.6) of 100 mM phosphate buffer with 0.1 mM DTPA, in an enclosed system to contain volatilized H2S. Volatilized H2S is then trapped in 100 mM Tris-HCl (pH 9.5, 0.1 mM DTPA) and then reacted with excess monobromobimane. In a separate aliquot, the contribution of bound sulfane sulfur pool was measured by incubating the sample with 1 mM TCEP (Tris(2-carboxyethyl)phosphine hydrochloride), a reducing agent to reduce disulfide bonds, in 100 mM phosphate buffer (pH 2.6, 0.1 mM DTPA), and H2S measurement performed in an analogous manner to the one described above. The acid labile pool was determined by subtracting the free hydrogen sulfide value from the value obtained by the acid liberation protocol. The bound sulfane sulfur pool was determined by subtracting the H2S measurement from the acid liberation protocol alone compared to that of TCEP plus acidic conditions. In summary, our new method protocol allows very sensitive and accurate measurement of the three primary biological pools of H2S including free, acid labile, and bound sulfane sulfur in various biological specimens. PMID:22561703

Unveiling privacy: advances in microtomography of coralline algae.

PubMed

Torrano-Silva, Beatriz N; Ferreira, Simone Gomes; Oliveira, Mariana C

2015-05-01

Marine calcareous algae are widespread in oceans of the world and known for their calcified cell walls and the generation of rhodolith beds that turn sandy bottoms into a complex structured ecosystem with high biodiversity. Rhodoliths are unattached, branching, crustose benthic marine red algae; they provide habitat for a rich variety of marine invertebrates. The resultant excavation is relevant to sediment production, while is common that the fragments or the whole specimens result in vast fossil deposits formed by rich material that can be "mined" for biological and geological data. Accordingly, microtomography (μCT) may enable a detailed investigation of biological and geological signatures preserved within the rhodolith structure in a non-destructive approach that is especially relevant when analyzing herbaria collections or rare samples. Therefore, we prepared coralline algae samples and submitted them to a range of capabilities provided by the SkyScan1176 micro-CT scanner, including reconstruction, virtual slicing, and pinpointing biological and geological signatures. To this end, polychaetes and mollusk shells, or their excavations, coral nucleation, sediment deposits and conceptacles were all observed. Although a similar technique has been applied previously to samples of living rhodoliths in Brazil, we show, for the first time, its successful application to fossil rhodoliths. We also provide a detailed working protocol and discuss the advantages and limitations of the microtomography within the rhodoliths. Copyright © 2015 Elsevier Ltd. All rights reserved.

Direct measurement of catalase activity in living cells and tissue biopsies.

PubMed

Scaglione, Christine N; Xu, Qijin; Ramanujan, V Krishnan

2016-01-29

Spatiotemporal regulation of enzyme-substrate interactions governs the decision-making steps in biological systems. Enzymes, being functional units of every living cell, contribute to the macromolecular stability of cell survival, proliferation and hence are vital windows to unraveling the biological complexity. Experimental measurements capturing this dynamics of enzyme-substrate interactions in real time add value to this understanding. Furthermore these measurements, upon validation in realistic biological specimens such as clinical biopsies - can further improve our capability in disease diagnostics and treatment monitoring. Towards this direction, we describe here a novel, high-sensitive measurement system for measuring diffusion-limited enzyme-substrate kinetics in real time. Using catalase (enzyme) and hydrogen peroxide (substrate) as the example pair, we demonstrate that this system is capable of direct measurement of catalase activity in vitro and the measured kinetics follows the classical Michaelis-Menten reaction kinetics. We further demonstrate the system performance by measuring catalase activity in living cells and in very small amounts of liver biopsies (down to 1 μg total protein). Catalase-specific enzyme activity is demonstrated by genetic and pharmacological tools. Finally we show the clinically-relevant diagnostic capability of our system by comparing the catalase activities in liver biopsies from young and old mouse (liver and serum) samples. We discuss the potential applicability of this system in clinical diagnostics as well as in intraoperative surgical settings. Copyright © 2016 Elsevier Inc. All rights reserved.

Common-path digital holographic microscopy based on a beam displacer unit

NASA Astrophysics Data System (ADS)

Di, Jianglei; Zhang, Jiwei; Song, Yu; Wang, Kaiqiang; Wei, Kun; Zhao, Jianlin

2018-02-01

Digital holographic microscopy (DHM) has become a novel tool with advantages of full field, non-destructive, high-resolution and 3D imaging, which captures the quantitative amplitude and phase information of microscopic specimens. It's a well-established method for digital recording and numerical reconstructing the full complex field of wavefront of the samples with a diffraction-limited lateral resolution down to 0.3 μm depending on the numerical aperture of microscope objective. Meanwhile, its axial resolution through axial direction is less than 10 nm due to the interferometric nature in phase imaging. Compared with the typical optical configurations such as Mach-Zehnder interferometer and Michelson interferometer, the common-path DHM has the advantages of simple and compact configuration, high stability, and so on. Here, a simple, compact, and low-cost common-path DHM based on a beam displacer unit is proposed for quantitative phase imaging of biological cells. The beam displacer unit is completely compatible with commercial microscope and can be easily set up in the output port of the microscope as a compact independent device. This technique can be used to achieve the quantitative phase measurement of biological cells with an excellent temporal stability of 0.51 nm, which makes it having a good prospect in the fields of biological and medical science. Living mouse osteoblastic cells are quantitatively measured with the system to demonstrate its capability and applicability.

Direct Measurement of Catalase Activity in Living Cells and Tissue Biopsies

PubMed Central

Scaglione, Christine N; Xu, Qijin; Ramanujan, V. Krishnan

2016-01-01

Spatiotemporal regulation of enzyme-substrate interactions governs the decision-making steps in biological systems. Enzymes, being functional units of every living cell, contribute to the macromolecular stability of cell survival, proliferation and hence are vital windows to unraveling the biological complexity. Experimental measurements capturing this dynamics of enzyme-substrate interactions in real time add value to this understanding. Furthermore these measurements, upon validation in realistic biological specimens such as clinical biopsies – can further improve our capability in disease diagnostics and treatment monitoring. Towards this direction, we describe here a novel, high-sensitive measurement system for measuring diffusion-limited enzyme-substrate kinetics in real time. Using catalase (enzyme) and hydrogen peroxide (substrate) as the example pair, we demonstrate that this system is capable of direct measurement of catalase activity in vitro and the measured kinetics follows the classical Michaelis-Menten reaction kinetics. We further demonstrate the system performance by measuring catalase activity in living cells and in very small amounts of liver biopsies (down to 1μg total protein). Catalase-specific enzyme activity is demonstrated by genetic and pharamacological tools. Finally we show the clinically-relevant diagnostic capability of our system by comparing the catalase activities in liver biopsies from young and old mouse (liver and serum) samples. We discuss the potential applicability of this system in clinical diagnostics as well as in intraoperative surgical settings. PMID:26772884

Biological Research in Canisters (BRIC) - Light Emitting Diode (LED)

NASA Technical Reports Server (NTRS)

Levine, Howard G.; Caron, Allison

2016-01-01

The Biological Research in Canisters - LED (BRIC-LED) is a biological research system that is being designed to complement the capabilities of the existing BRIC-Petri Dish Fixation Unit (PDFU) for the Space Life and Physical Sciences (SLPS) Program. A diverse range of organisms can be supported, including plant seedlings, callus cultures, Caenorhabditis elegans, microbes, and others. In the event of a launch scrub, the entire assembly can be replaced with an identical back-up unit containing freshly loaded specimens.

Length-weight relationships and condition factor of the eaglebeak pacu Ossubtus xinguense Jégu, 1992 (Characiformes, Serrasalmidae), an endangered species from Rio Xingu rapids, northern Brazil.

PubMed

Andrade, M C; Jesus, A J S; Giarrizzo, T

2015-08-01

This study reports on the length-weight relationships and condition factor for the endangered rheophilic fish Ossubtus xinguense Jégu from Rio Xingu rapids. This species is threatened by construction of the third largest hydroelectric in the world, the Belo Monte dam close to the city of Altamira, northern Brazil. Specimens were collected in the dry season between July 2012 and September 2012. Male specimens have body length larger than females, atypical in serrasalmid fishes, and different length-weight relationships were found between adult and juvenile specimens. This study presents the first biological characteristics for O. xinguense.

The Biology and Clinical Utility of EBV Monitoring in Blood.

PubMed

Kanakry, Jennifer; Ambinder, Richard

2015-01-01

Epstein-Barr virus (EBV) DNA in blood can be quantified in peripheral blood mononuclear cells, in circulating cell-free (CCF) DNA specimens, or in whole blood. CCF viral DNA may be actively released or extruded from viable cells, packaged in virions or passively shed from cells during apoptosis or necrosis. In infectious mononucleosis, viral DNA is detected in each of these kinds of specimens, although it is only transiently detected in CCF specimens. In nasopharyngeal carcinoma, CCF EBV DNA is an established tumor marker. In EBV-associated Hodgkin lymphoma and in EBV-associated extranodal NK-/T-cell lymphoma, there is growing evidence for the utility of CCF DNA as a tumor marker.

Microsatellite typing of ancient maize: insights into the history of agriculture in southern South America

PubMed Central

Lia, Verónica V; Confalonieri, Viviana A; Ratto, Norma; Hernández, Julián A. Cámara; Alzogaray, Ana M. Miante; Poggio, Lidia; Brown, Terence A

2006-01-01

Archaeological maize specimens from Andean sites of southern South America, dating from 400 to 1400 years before present, were tested for the presence of ancient DNA and three microsatellite loci were typed in the specimens that gave positive results. Genotypes were also obtained for 146 individuals corresponding to modern landraces currently cultivated in the same areas and for 21 plants from Argentinian lowland races. Sequence analysis of cloned ancient DNA products revealed a high incidence of substitutions appearing in only one clone, with transitions prevalent. In the archaeological specimens, there was no evidence of polymorphism at any one of the three microsatellite loci: each exhibited a single allelic variant, identical to the most frequent allele found in contemporary populations belonging to races Amarillo Chico, Amarillo Grande, Blanco and Altiplano. Affiliation between ancient specimens and a set of races from the Andean complex was further supported by assignment tests. The striking genetic uniformity displayed by the ancient specimens and their close relationship with the Andean complex suggest that the latter gene pool has predominated in the western regions of southern South America for at least the past 1400 years. The results support hypotheses suggesting that maize cultivation initially spread into South America via a highland route, rather than through the lowlands. PMID:17476775

21 CFR 864.4020 - Analyte specific reagents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... specific binding or chemical reaction with substances in a specimen, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological...

21 CFR 864.4020 - Analyte specific reagents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... specific binding or chemical reaction with substances in a specimen, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological...

21 CFR 864.4020 - Analyte specific reagents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... specific binding or chemical reaction with substances in a specimen, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological...

21 CFR 864.4020 - Analyte specific reagents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... specific binding or chemical reaction with substances in a specimen, are intended for use in a diagnostic application for identification and quantification of an individual chemical substance or ligand in biological...

Blood lipid measurements. Variations and practical utility.

PubMed

Cooper, G R; Myers, G L; Smith, S J; Schlant, R C

1992-03-25

To describe the magnitude and impact of the major biological and analytical sources of variation in serum lipid and lipoprotein levels on risk of coronary heart disease; to present a way to qualitatively estimate the total intraindividual variation; and to demonstrate how to determine the number of specimens required to estimate, with 95% confidence, the "true" underlying total cholesterol value in the serum of a patient. Representative references on each source of variation were selected from more than 300 reviewed publications, most published within the past 5 years, to document current findings and concepts. Most articles reviewed were in English. Studies on biological sources of variation were selected using the following criteria: representative of published findings, clear statement of either significant or insignificant results, and acquisition of clinical and laboratory data under standardized conditions. Representative results for special populations such as women and children are reported when results differ from those of adult men. References were selected based on acceptable experimental design and use of standardized laboratory lipid measurements. The lipid levels considered representative for a selected source of variation arose from quantitative measurements by a suitably standardized laboratory. Statistical analysis of data was examined to assure reliability. The proposed method of estimating the biological coefficient of variation must be considered to give qualitative results, because only two or three serial specimens are collected in most cases for the estimation. Concern has arisen about the magnitude, impact, and interpretation of preanalytical as well as analytical sources of variation on reported results of lipid measurements of an individual. Preanalytical sources of variation from behavioral, clinical, and sampling sources constitute about 60% of the total variation in a reported lipid measurement of an individual. A technique is presented to allow physicians to qualitatively estimate the intraindividual biological variation of a patient from the results of two or more specimens reported from a standardized laboratory and to determine whether additional specimens are needed to meet the National Cholesterol Education Program recommendation that the intraindividual serum total cholesterol coefficient of variation not exceed 5.0. A National Reference Method Network has been established to help solve analytical problems.

Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

NASA Astrophysics Data System (ADS)

Cherkezyan, Lusik; Zhang, Di; Subramanian, Hariharan; Taflove, Allen; Backman, Vadim

2016-02-01

The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density.

HOMER: the Holographic Optical Microscope for Education and Research

NASA Astrophysics Data System (ADS)

Luviano, Anali

Holography was invented in 1948 by Dennis Gabor and has undergone major advancements since the 2000s leading to the development of commercial digital holographic microscopes (DHM). This noninvasive form of microscopy produces a three-dimensional (3-D) digital model of a sample without altering or destroying the sample, thus allowing the same sample to be studied multiple times. HOMER-the Holographic Optical Microscope for Education and Research-produces a 3-D image from a two-dimensional (2-D) interference pattern captured by a camera that is then put through reconstruction software. This 2-D pattern is created when a reference wave interacts with the sample to produce a secondary wave that interferes with the unaltered part of the reference wave. I constructed HOMER to be an efficient, portable in-line DHM using inexpensive material and free reconstruction software. HOMER uses three different-colored LEDs as light sources. I am testing the performance of HOMER with the goal of producing tri-color images of samples. I'm using small basic biological samples to test the effectiveness of HOMER and plan to transition to complex cellular and biological specimens as I pursue my interest in biophysics. Norwich University.

Digestive tumor bank protocol: from surgical specimens to genomic studies of digestive cancers.

PubMed

Popescu, I; Stroescu, C; Dumitrascu, T; Herlea, V; Paslaru, Liliana; Lazar, V; Boissin, H; Taieb, J; Horeanga, Ionela

2006-01-01

Cancer is a complex polygenic and multifactorial disease, resulting from successive dynamic changes in the genome of somatic cells and from the accumulation of molecular alterations in both tumour cells and host cells. For the majority of cancers, including many malignancies of the gastrointestinal tract, our current means of diagnosis and treatment of the tumors are grossly insufficient. In recent years the development of several gene expression profiling methods such as comparative genomic hybridization (CGH), differential display, serial analysis of gene expression (SAGE) and DNA arrays, together with the sequencing of the human genome, has provided an opportunity to monitor and investigate the complete cascade of molecular events leading to tumor development and progression. Given the central role played by surgeons in the current management of patients with solid cancers, it is of paramount importance for them to know the principles characterizing this laboratory tools to critically assess the results originating from this biotechnology. We describe in this article the scientific partnership between Fundeni Clinical Institute Bucharest, Romania and RNtech Company, Paris, France for the development of a center of biological resources (Biobank) as well as the standardized protocol of working with the biological samples, the ongoing projects and the future perspectives.

Molecular changes preceding endometrial and ovarian cancer: a study of consecutive endometrial specimens from Lynch syndrome surveillance.

PubMed

Niskakoski, Anni; Pasanen, Annukka; Lassus, Heini; Renkonen-Sinisalo, Laura; Kaur, Sippy; Mecklin, Jukka-Pekka; Bützow, Ralf; Peltomäki, Päivi

2018-03-27

Molecular alterations preceding endometrial and ovarian cancer and the sequence of events are unknown. Consecutive specimens from lifelong surveillance for Lynch syndrome provides a natural setting to address such questions. To molecularly define the multistep gynecological tumorigenesis, DNA mismatch repair gene mutation carriers with endometrial or ovarian carcinoma or endometrial hyperplasia were identified from a nation-wide registry and endometrial biopsy specimens taken from these individuals during 20 years of screening were collected. A total of 213 endometrial and ovarian specimens from Lynch syndrome individuals and 197 histology-matched (non-serous) samples from sporadic cases were available for this investigation. The specimens were profiled for markers linked to endometrial and ovarian tumorigenesis, including ARID1A protein expression, mismatch repair status, and tumor suppressor gene promoter methylation. In Lynch syndrome-associated endometrial and ovarian carcinomas, ARID1A protein was lost in 61-100% and mismatch repair was deficient in 97-100%, compared to 0-17% and 14-44% in sporadic cases (P = 0.000). ARID1A loss appeared in complex hyperplasia and deficient mismatch repair and tumor suppressor gene promoter methylation in histologically normal endometrium. Despite quantitative differences between Lynch syndrome and sporadic cases, ARID1A expression, mismatch repair, and tumor suppressor gene promoter methylation divided endometrial samples from both patient groups into three categories of increasing abnormality, comprising normal endometrium and simple hyperplasia (I), complex hyperplasia with or without atypia (II), and endometrial cancer (III). Complex hyperplasias without vs. with atypia were molecularly indistinguishable. In conclusion, surveillance specimens from Lynch syndrome identify mismatch repair deficiency, tumor suppressor gene promoter methylation, and ARID1A loss as early changes in tumor development. Our findings are clinically relevant for the classification of endometrial hyperplasias and have potential implications in cancer prevention in Lynch syndrome and beyond.

Imaging mammalian cells with soft x rays: The importance of specimen preparation

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

Brown, J.T.; Meyer-Ilse, W.

1997-04-01

Studies of mammalian cell structure and spatial organization are a very prominent part of modern cell biology. The interest in them as well as their size make them very accommodating subject specimens for imaging with soft x-rays using the XM-1 transmission microscope built and operated by The Center for X-ray Optics on Beam Line 6.1 at the Advanced Light Source. The purpose of these experiments was to determine if the fixative protocols normally used in electron or visible light microscopy were adequate to allow imaging cells, either fibroblasts or neurons, with minimal visible radiation damage due to imaging with softmore » x-rays at 2.4 nm. Two cell types were selected. Fibroblasts are easily cultured but fragile cells which are commonly used as models for the detailed study of cell physiology. Neurons are complex and sensitive cells which are difficult to prepare and to culture for study in isolation from their connections with surrounding cells. These cell types pose problems in their preparation for any microscopy. To improve the contrast and to prevent postmortem alteration of the chemistry and hence the structure of cells extracted from culture or from living organisms, fixation and staining techniques are employed in electron and visible light microscopy. It has been accepted by biologists for years that these treatments create artifacts and false structure. The authors have begun to develop protocols for specimens of each of these two cell types for soft x-ray microscopy which will preserve them in as near normal state as possible using minimal fixation, and make it possible to image them in either a hydrated or dried state free of secondary addition of stains or other labels.« less

Revision of torrent mites (Parasitengona, Torrenticolidae, Torrenticola) of the United States and Canada: 90 descriptions, molecular phylogenetics, and a key to species

PubMed Central

Fisher, J. Ray; Fisher, Danielle M.; Skvarla, Michael J.; Nelson, Whitney A.; Dowling, Ashley P.G.

2017-01-01

Abstract The descriptive biology of torrent mites (Parasitengona: Torrenticolidae: Torrenticola) of North America (north of Mexico) is investigated using integrative methods. Material examined includes approximately 2,300 specimens from nearly 500 localities across the United States and Canada, and a few collections in Mexico and Central America. Species hypotheses are derived from a phylogenetic analysis of the barcoding region of cytochrome c oxidase subunit 1 (COI) for 476 specimens and supported with morphology and biogeography. Relationships between species are examined with a combined analysis of COI and two expansion regions (D2–3) of the large ribosomal subunit (28S rDNA) for 57 specimens. All previously described species from the US and Canada are examined. Our results indicate the need to synonymize four species: T. mercedensis (Marshall, 1943) is a junior synonym of T. sierrensis (Marshall, 1943); T. rectiforma Habeeb, 1974 is a junior synonym of T. ellipsoidalis (Marshall, 1943); T. neoconnexa Habeeb, 1957 is a junior synonym of T. magnexa Habeeb, 1955; and T. esbelta Cramer, 1992 is a junior synonym of T. boettgeri KO Viets, 1977. We describe 66 new species and re-describe all previously described regional species. Our findings indicate that total diversity of Torrenticola in the United States and Canada comprises 90 species, 57 known from the east and 33 from the west. We organize these species into four species complexes that include 13 identification groups. An additional 13 species do not fit within an identification group. The southern Appalachians are suspected to contain the highest concentration of remaining undescribed diversity. A key is provided to all known species in the US and Canada. PMID:29118596

Evaluation of Fast Technology Analysis (FTA) Cards as an improved method for specimen collection and shipment targeting viruses associated with Bovine Respiratory Disease Complex.

PubMed

Liang, Xiao; Chigerwe, Munashe; Hietala, Sharon K; Crossley, Beate M

2014-06-01

In order to improve the analytic quality of respiratory specimens collected from cattle for nucleic acid-based diagnosis, a study was undertaken to verify realtime PCR efficiency of specimens collected and stabilized on FTA Cards™, filter paper which is treated chemically. Nucleic acids collected using FTA Cards without the need for a cold-chain or special liquid media handling provided realtime PCR results consistent (96.8% agreement, kappa 0.923 [95% CI=0.89-0.96]) with the same specimens collected using traditional viral transport media and shipped on ice using the U.S. Department of Transportation mandated liquid handling requirements. Nucleic acid stabilization on FTA Cards was evaluated over a temperature range (-27 °C to +46 °C) for up to 14 days to mimic environmental conditions for diagnostic sample handling between collection and processing in a routine veterinary laboratory. No significant difference (P≥0.05) was observed in realtime PCR cycle threshold values over the temperature range and time storage conditions for Bovine Viral Diarrhea virus, Bovine Respiratory Syncytial virus, Bovine Coronavirus, and Bovine Herpesvirus I. The four viruses evaluated in the study are associated with Bovine Respiratory Disease Complex where improvements in ease and reliability of specimen collection and shipping would enhance the diagnostic quality of specimens collected in the field, and ultimately improve diagnostic efficiency. Copyright © 2014 Elsevier B.V. All rights reserved.

Wetlands Commonwealth

ERIC Educational Resources Information Center

Davis, Millard C.

1970-01-01

Describes the varied animal and plant life of the rocky shore splash pools, salt marshes and tidal mud flats on the eastern coast of North America. Article includes photographs and drawings of biological specimens and plants. (LC)

Research in Biological and Medical Sciences, Including Biochemistry, Communicable Disease and Immunology, Internal Medicine, Nuclear Medicine, Physiology, Psychiatry, Surgery and Veterinary Medicine. Volume 2

DTIC Science & Technology

1975-07-01

hepatitis. In addition, fat vacuoles were observed in one specimen. The specimens from the other two men showed mild hepatocellular unrest and mild fatty...right heart pressures in patients with pulmonary embolism . These clinical observations suggest that urokinase has vaso- motor effects which have not...180: 236-242, 1974. 29. Spence, M. R., and Mason, K. G.: Experimental amniotic fluid embolism in rabbits. Am. J. Obst. Gynec. 119: 1073-1078, 1974

Preparation of the low molecular weight serum proteome for mass spectrometry analysis.

PubMed

Waybright, Timothy J; Chan, King C; Veenstra, Timothy D; Xiao, Zhen

2013-01-01

The discovery of viable biomarkers or indicators of disease states is complicated by the inherent complexity of the chosen biological specimen. Every sample, whether it is serum, plasma, urine, tissue, cells, or a host of others, contains thousands of large and small components, each interacting in multiple ways. The need to concentrate on a group of these components to narrow the focus on a potential biomarker candidate becomes, out of necessity, a priority, especially in the search for immune-related low molecular weight serum biomarkers. One such method in the field of proteomics is to divide the sample proteome into groups based on the size of the protein, analyze each group, and mine the data for statistically significant items. This chapter details a portion of this method, concentrating on a method for fractionating and analyzing the low molecular weight proteome of human serum.

Discrimination of healthy and osteoarthritic articular cartilages by Fourier transform infrared imaging and partial least squares-discriminant analysis

PubMed Central

Zhang, Xue-Xi; Yin, Jian-Hua; Mao, Zhi-Hua; Xia, Yang

2015-01-01

Abstract. Fourier transform infrared imaging (FTIRI) combined with chemometrics algorithm has strong potential to obtain complex chemical information from biology tissues. FTIRI and partial least squares-discriminant analysis (PLS-DA) were used to differentiate healthy and osteoarthritic (OA) cartilages for the first time. A PLS model was built on the calibration matrix of spectra that was randomly selected from the FTIRI spectral datasets of healthy and lesioned cartilage. Leave-one-out cross-validation was performed in the PLS model, and the fitting coefficient between actual and predicted categorical values of the calibration matrix reached 0.95. In the calibration and prediction matrices, the successful identifying percentages of healthy and lesioned cartilage spectra were 100% and 90.24%, respectively. These results demonstrated that FTIRI combined with PLS-DA could provide a promising approach for the categorical identification of healthy and OA cartilage specimens. PMID:26057029

Discrimination of healthy and osteoarthritic articular cartilages by Fourier transform infrared imaging and partial least squares-discriminant analysis.

PubMed

Zhang, Xue-Xi; Yin, Jian-Hua; Mao, Zhi-Hua; Xia, Yang

2015-06-01

Fourier transform infrared imaging (FTIRI) combined with chemometrics algorithm has strong potential to obtain complex chemical information from biology tissues. FTIRI and partial least squares-discriminant analysis (PLS-DA) were used to differentiate healthy and osteoarthritic (OA) cartilages for the first time. A PLS model was built on the calibration matrix of spectra that was randomly selected from the FTIRI spectral datasets of healthy and lesioned cartilage. Leave-one-out cross-validation was performed in the PLS model, and the fitting coefficient between actual and predicted categorical values of the calibration matrix reached 0.95. In the calibration and prediction matrices, the successful identifying percentages of healthy and lesioned cartilage spectra were 100% and 90.24%, respectively. These results demonstrated that FTIRI combined with PLS-DA could provide a promising approach for the categorical identification of healthy and OA cartilage specimens.

X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens

PubMed Central

de Jonge, Martin D.; Ryan, Christopher G.; Jacobsen, Chris J.

2014-01-01

X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer. PMID:25177992

National environmental specimen bank survey. [Location of 657 collections of environmental specimens

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

Van Hook, R.I.; Huber, E.E.

1976-01-01

This report presents the data base developed in the National Environmental Specimen Bank (NESB) Survey. The methodology utilized in developing the mailing lists and in developing and maintaining the data base records also is included. The NESB Survey Data Base is computerized in the Oak Ridge Computerized Hierarchical Information System, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830. The NESB Survey mailing list consisted of 4500 names and addresses. The 657 environmental specimen collections that were located and documented in the NESB Survey Data Base include the following categories: animal, atmospheric, geological, microbiological, plant, and water. However, the majority ofmore » the collections identified are biological in nature. Three indices of the NESB Survey Data Base are included in this report: respondents names and addresses categorized by organizational affiliation; (2) alphabetical listing of respondents; and geographical sampling location for materials in collections.« less

In-line phase contrast micro-CT reconstruction for biomedical specimens.

PubMed

Fu, Jian; Tan, Renbo

2014-01-01

X-ray phase contrast micro computed tomography (micro-CT) can non-destructively provide the internal structure information of soft tissues and low atomic number materials. It has become an invaluable analysis tool for biomedical specimens. Here an in-line phase contrast micro-CT reconstruction technique is reported, which consists of a projection extraction method and the conventional filter back-projection (FBP) reconstruction algorithm. The projection extraction is implemented by applying the Fourier transform to the forward projections of in-line phase contrast micro-CT. This work comprises a numerical study of the method and its experimental verification using a biomedical specimen dataset measured at an X-ray tube source micro-CT setup. The numerical and experimental results demonstrate that the presented technique can improve the imaging contrast of biomedical specimens. It will be of interest for a wide range of in-line phase contrast micro-CT applications in medicine and biology.

The AIDS and Cancer Specimen Resource: Role in HIV/AIDS scientific discovery

PubMed Central

Ayers, Leona W; Silver, Sylvia; McGrath, Michael S; Orenstein, Jan M

2007-01-01

The AIDS Cancer and Specimen Resource (ACSR) supports scientific discovery in the area of HIV/AIDS-associated malignancies. The ACSR was established as a cooperative agreement between the NCI (Office of the Director, Division of Cancer Treatment and Diagnosis) and regional consortia, University of California, San Francisco (West Coast), George Washington University (East Coast) and Ohio State University (Mid-Region) to collect, preserve and disperse HIV-related tissues and biologic fluids and controls along with clinical data to qualified investigators. The available biological samples with clinical data and the application process are described on the ACSR web site. The ACSR tissue bank has more than 100,000 human HIV positive specimens that represent different processing (43), specimen (15), and anatomical site (50) types. The ACSR provides special biospecimen collections and prepares speciality items, e.g., tissue microarrays (TMA), DNA libraries. Requests have been greatest for Kaposi's sarcoma (32%) and non-Hodgkin's lymphoma (26%). Dispersed requests include 83% tissue (frozen and paraffin embedded), 18% plasma/serum and 9% other. ACSR also provides tissue microarrays of, e.g., Kaposi's sarcoma and non-Hodgkin's lymphoma, for biomarker assays and has developed collaborations with other groups that provide access to additional AIDS-related malignancy specimens. ACSR members and associates have completed 63 podium and poster presentations. Investigators have submitted 125 letters of intent requests. Discoveries using ACSR have been reported in 61 scientific publications in notable journals with an average impact factor of 7. The ACSR promotes the scientific exploration of the relationship between HIV/AIDS and malignancy by participation at national and international scientific meetings, contact with investigators who have productive research in this area and identifying, collecting, preserving, enhancing, and dispersing HIV/AIDS-related malignancy specimens to funded, approved researchers at no fee. Scientific discovery has been advanced by this unique biorepository. Investigators are encouraged to browse the ACSR Internet site for materials to enhance their own scientific initiatives. PMID:17335575

New Specimens of the Rare Taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and Comments on the Phylogeny and Functional Morphology of “Archaic” Mammals

PubMed Central

Williamson, Thomas E.; Brusatte, Stephen L.

2013-01-01

Background Taeniodonta is a clade of Late Cretaceous – Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly “generalized” postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous. Methodology/Principal Findings In this paper, we describe three new specimens of the rare taxon Wortmaniaotariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology. Conclusions/Significance The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochiasullivani is a junior synonym of W . otariidens . New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and Onychodectes are basal taeniodonts, Stylinodontidae (including Wortmania) is monophyletic, and a monophyletic Conoryctidae (but not including Onychodectes) is only recovered when certain characters are ordered. PMID:24098738

New specimens of the rare taeniodont Wortmania (Mammalia: Eutheria) from the San Juan Basin of New Mexico and comments on the phylogeny and functional morphology of "archaic" mammals.

PubMed

Williamson, Thomas E; Brusatte, Stephen L

2013-01-01

Taeniodonta is a clade of Late Cretaceous-Paleogene mammals remarkable for their relatively extreme cranial, dental, and postcranial adaptations and notable for being among the first mammals to achieve relatively large size following the Cretaceous-Paleogene mass extinction. Previous workers have hypothesized that taeniodonts can be divided into two clades: Conoryctidae, a group of small-bodied taeniodonts with supposedly "generalized" postcranial skeletons, and Stylinodontidae, a group of large-bodied, robust animals with massive forelimbs and claws adapted for scratch-digging. However, many taeniodont taxa are poorly known and few are represented by postcranial material, leaving many details about their anatomy, biology, and evolution ambiguous. In this paper, we describe three new specimens of the rare taxon Wortmania otariidens from the early Paleocene (Puercan) of New Mexico. Among these specimens is one that includes remarkably complete cranial and dental material, including associated upper and lower teeth, and another that consists of partial forelimbs. These specimens allow for an updated anatomical description of this unusual taxon, supply new data for phylogenetic analyses, and enable a more constrained discussion of taeniodont biology and functional morphology. The new specimen of Wortmania that includes associated upper and lower teeth indicates that previous interpretations of the upper dentition of this taxon were not accurate and the taxon Robertschochia sullivani is a junior synonym of W. otariidens. New specimens that include partial forelimbs indicate that Wortmania is very similar to later, large-bodied taeniodonts, with marked and distinctive adaptations for scratch-digging. Comparisons with other taeniodont taxa that include postcranial material suggest that all taeniodonts may have had scratch-digging adaptations. A phylogenetic analysis shows that Schowalteria and Onychodectes are basal taeniodonts, Stylinodontidae (including Wortmania) is monophyletic, and a monophyletic Conoryctidae (but not including Onychodectes) is only recovered when certain characters are ordered.

The influence of cyclic shear fatigue on the bracket-adhesive-enamel complex: an in vitro study.

PubMed

Daratsianos, Nikolaos; Musabegovic, Ena; Reimann, Susanne; Grüner, Manfred; Jäger, Andreas; Bourauel, Christoph

2013-05-01

To describe the effect of fatigue on the strength of the bracket-adhesive-enamel complex and characterize the fatigue behavior of the materials tested. Upper central incisor brackets (Discovery(®), Dentaurum) were bonded with a light-curing (Transbond XT™, 3M Unitek) and a chemically-curing adhesive (Concise™, 3M Unitek) on bovine teeth embedded in cylindrical resign bases and stored in water at 37(±2)°C for 24 (±2)h. The first 15 specimens were tested with a universal testing machine ZMART.PRO(®) (Zwick GmbH & Co. KG, Ulm, Germany) for ultimate shear bond strength according to the DIN-13990-2-standard. The remaining three groups of 20 specimens underwent fatigue staircase testing of 100, 1000 and 3000 cycles at 1Hz with a self-made testing machine. The survived specimens were subjected to shear strength testing. The fatigued specimens showed decreased shear strength with both adhesives at all cycle levels. The shear strength after fatigue for 100, 1000 and 3000 cycles was in the Concise™-groups 34.8%, 59.0%, 47.3% and in the Transbond™ XT-groups 33.6%, 23.1%, 27.3% relative to the ultimate shear strength. The fatigue life of the Concise™-groups decreased with increasing stress and Transbond™ XT showed lower fatigue ratio with no obvious trend. The specimens bonded with Transbond™ XT showed typically favorable fracture modes in contrary to Concise™. Fatigue of the bracket-adhesive-enamel complex decreased its shear strength. The staircase method can provide a standardized experimental protocol for fatigue studies, however testing at various cycle numbers is recommended. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

A Differential ECG Amplifier with Single-Ended Output

NASA Technical Reports Server (NTRS)

Katchis, L.

1972-01-01

Three-stage amplifier is used for ECG measurements which require conversion of differential input to single-ended output. Circuit may be useful in biological telemetry for amplification of signals from specimen-implanted sensors.

Predictive Analytics to Support Real-Time Management in Pathology Facilities.

PubMed

Lessard, Lysanne; Michalowski, Wojtek; Chen Li, Wei; Amyot, Daniel; Halwani, Fawaz; Banerjee, Diponkar

2016-01-01

Predictive analytics can provide valuable support to the effective management of pathology facilities. The introduction of new tests and technologies in anatomical pathology will increase the volume of specimens to be processed, as well as the complexity of pathology processes. In order for predictive analytics to address managerial challenges associated with the volume and complexity increases, it is important to pinpoint the areas where pathology managers would most benefit from predictive capabilities. We illustrate common issues in managing pathology facilities with an analysis of the surgical specimen process at the Department of Pathology and Laboratory Medicine (DPLM) at The Ottawa Hospital, which processes all surgical specimens for the Eastern Ontario Regional Laboratory Association. We then show how predictive analytics could be used to support management. Our proposed approach can be generalized beyond the DPLM, contributing to a more effective management of pathology facilities and in turn to quicker clinical diagnoses.

Every factor helps: Rapid Ptychographic Reconstruction

NASA Astrophysics Data System (ADS)

Nashed, Youssef

2015-03-01

Recent advances in microscopy, specifically higher spatial resolution and data acquisition rates, require faster and more robust phase retrieval reconstruction methods. Ptychography is a phase retrieval technique for reconstructing the complex transmission function of a specimen from a sequence of diffraction patterns in visible light, X-ray, and electron microscopes. As technical advances allow larger fields to be imaged, computational challenges arise for reconstructing the correspondingly larger data volumes. Waiting to postprocess datasets offline results in missed opportunities. Here we present a parallel method for real-time ptychographic phase retrieval. It uses a hybrid parallel strategy to divide the computation between multiple graphics processing units (GPUs). A final specimen reconstruction is then achieved by different techniques to merge sub-dataset results into a single complex phase and amplitude image. Results are shown on a simulated specimen and real datasets from X-ray experiments conducted at a synchrotron light source.

Predictive Analytics to Support Real-Time Management in Pathology Facilities

PubMed Central

Lessard, Lysanne; Michalowski, Wojtek; Chen Li, Wei; Amyot, Daniel; Halwani, Fawaz; Banerjee, Diponkar

2016-01-01

Predictive analytics can provide valuable support to the effective management of pathology facilities. The introduction of new tests and technologies in anatomical pathology will increase the volume of specimens to be processed, as well as the complexity of pathology processes. In order for predictive analytics to address managerial challenges associated with the volume and complexity increases, it is important to pinpoint the areas where pathology managers would most benefit from predictive capabilities. We illustrate common issues in managing pathology facilities with an analysis of the surgical specimen process at the Department of Pathology and Laboratory Medicine (DPLM) at The Ottawa Hospital, which processes all surgical specimens for the Eastern Ontario Regional Laboratory Association. We then show how predictive analytics could be used to support management. Our proposed approach can be generalized beyond the DPLM, contributing to a more effective management of pathology facilities and in turn to quicker clinical diagnoses. PMID:28269873

Detection of Pathogenic Protozoa in the Diagnostic Laboratory: Result Reproducibility, Specimen Pooling, and Competency Assessment▿

PubMed Central

Libman, M. D.; Gyorkos, T. W.; Kokoskin, E.; MacLean, J. D.

2008-01-01

Stool microscopy as performed in clinical parasitology laboratories is a complex procedure with subjective interpretation. Quality assurance (QA) programs often emphasize proficiency testing as an assessment tool. We describe a result reproducibility assessment tool, which can form part of a broader QA program, and which is based on the blinded resubmission of selected clinical samples, using concordance between the reports of the initial and resubmitted specimen as an indicator. Specimens preserved in sodium acetate-acetic acid-formalin can be stored for several months for use in such a program. The presence of multiple protozoa in one specimen does not affect concordance. Some dilution of specimens occurs in this process, and this may explain poor concordance when specimens with low protozoal concentrations are resubmitted. Evaluation of this tool in a large parasitology laboratory revealed concordance rates for pathogenic protozoa (Entamoeba histolytica/Entamoeba dispar, Giardia lamblia, and Dientamoeba fragilis) of about 80%, which may be considered for use as a benchmark value. We also used this tool to demonstrate that when pairs of specimens from one patient are pooled to create a single specimen, concordance between the results of the individual and pooled specimens is high. PMID:18448690

High-resolution x-ray diffraction microscopy of specifically labeled yeast cells

PubMed Central

Nelson, Johanna; Huang, Xiaojing; Steinbrener, Jan; Shapiro, David; Kirz, Janos; Marchesini, Stefano; Neiman, Aaron M.; Turner, Joshua J.; Jacobsen, Chris

2010-01-01

X-ray diffraction microscopy complements other x-ray microscopy methods by being free of lens-imposed radiation dose and resolution limits, and it allows for high-resolution imaging of biological specimens too thick to be viewed by electron microscopy. We report here the highest resolution (11–13 nm) x-ray diffraction micrograph of biological specimens, and a demonstration of molecular-specific gold labeling at different depths within cells via through-focus propagation of the reconstructed wavefield. The lectin concanavalin A conjugated to colloidal gold particles was used to label the α-mannan sugar in the cell wall of the yeast Saccharomyces cerevisiae. Cells were plunge-frozen in liquid ethane and freeze-dried, after which they were imaged whole using x-ray diffraction microscopy at 750 eV photon energy. PMID:20368463

Computer synthesis of high resolution electron micrographs

NASA Technical Reports Server (NTRS)

Nathan, R.

1976-01-01

Specimen damage, spherical aberration, low contrast and noisy sensors combine to prevent direct atomic viewing in a conventional electron microscope. The paper describes two methods for obtaining ultra-high resolution in biological specimens under the electron microscope. The first method assumes the physical limits of the electron objective lens and uses a series of dark field images of biological crystals to obtain direct information on the phases of the Fourier diffraction maxima; this information is used in an appropriate computer to synthesize a large aperture lens for a 1-A resolution. The second method assumes there is sufficient amplitude scatter from images recorded in focus which can be utilized with a sensitive densitometer and computer contrast stretching to yield fine structure image details. Cancer virus characterization is discussed as an illustrative example. Numerous photographs supplement the text.

Intensity calibration of a laser scanning confocal microscope based on concentrated dyes.

PubMed

Model, Michael A; Blank, James L

2006-10-01

To find water-soluble fluorescent dyes with absorption in various regions of the spectrum and investigate their utility as standards for laser scanning confocal microscopy. Several dyes were found to have characteristics required for fluorescence microscopy standards. The intensity of biological fluorescent specimens was measured against the emission of concentrated dyes. Results using different optics and different microscopes were compared. Slides based on concentrated dyes can be prepared in a highly reproducible manner and are stable under laser scanning. Normalized fluorescence of biological specimens remains consistent with different objective lenses and is tolerant to some mismatch in optical filters or imperfect pinhole alignment. Careful choice of scanning parameters is necessary to ensure linearity of intensity measurements. Concentrated dyes provide a robust and inexpensive intensity standard that can be used in basic research or clinical studies.

Upgrading Reference Set — EDRN Public Portal

Cancer.gov

We are proposing a multi-institutional study to identify molecular biomarkers and clinical measures that will predict presence of Gleason 7 or higher cancer (as evidence in the radical prostatectomy specimen) among patients with a biopsy diagnosis of Gleason score ≤ 6 prostate cancer. This proposal will be conducted in two phases. The first phase will assemble an “Upgrading Reference Set” that will include clinical information as well as biologics on a cohort of 600 men. The first phase will also assess the clinical parameters associated with upgrading, as well as, perform a central pathology review of both biopsies and prostatectomy specimens to confirm tumor grade. The second phase will use the biologics collected in phase 1 to evaluate a series of biomarkers to further refine the prediction of Gleason 7-10 cancer at radical prostatectomy.

High-resolution x-ray diffraction microscopy of specifically labeled yeast cells

DOE PAGES

Nelson, Johanna; Huang, Xiaojing; Steinbrener, Jan; ...

2010-04-20

X-ray diffraction microscopy complements other x-ray microscopy methods by being free of lens-imposed radiation dose and resolution limits, and it allows for high-resolution imaging of biological specimens too thick to be viewed by electron microscopy. We report here the highest resolution (11-13 nm) x-ray diffraction micrograph of biological specimens, and a demonstration of molecular-specific gold labeling at different depths within cells via through-focus propagation of the reconstructed wavefield. The lectin concanavalin A conjugated to colloidal gold particles was used to label the α-mannan sugar in the cell wall of the yeast Saccharomyces cerevisiae. Cells were plunge-frozen in liquid ethane andmore » freeze-dried, after which they were imaged whole using x-ray diffraction microscopy at 750 eV photon energy.« less

Characterization of some biological specimens using TEM and SEM

NASA Astrophysics Data System (ADS)

Ghosh, Nabarun; Smith, Don W.

2009-05-01

The advent of novel techniques using the Transmission and Scanning Electron Microscopes improved observation on various biological specimens to characterize them. We studied some biological specimens using Transmission and Scanning Electron Microscopes. We followed negative staining technique with Phosphotungstic acid using bacterial culture of Bacillus subtilis. Negative staining is very convenient technique to view the structural morphology of different samples including bacteria, phage viruses and filaments in a cell. We could observe the bacterial cell wall and flagellum very well when trapped the negative stained biofilm from bacterial culture on a TEM grid. We cut ultra thin sections from the fixed root tips of Pisum sativum (Garden pea). Root tips were pre fixed with osmium tetroxide and post fixed with uranium acetate and placed in the BEEM capsule for block making. The ultrathin sections on the grid under TEM showed the granular chromatin in the nucleus. The protein bodies and large vacuoles with the storage materials were conspicuous. We followed fixation, critical point drying and sputter coating with gold to view the tissues with SEM after placing on stubs. SEM view of the leaf surface of a dangerous weed Tragia hispida showed the surface trichomes. These trichomes when break on touching releases poisonous content causing skin irritation. The cultured tissue from in vitro culture of Albizia lebbeck, a tree revealed the regenerative structures including leaf buds and stomata on the tissue surface. SEM and TEM allow investigating the minute details characteristic morphological features that can be used for classroom teaching.

BRIC-60: Biological Research in Canisters (BRIC)-60

NASA Technical Reports Server (NTRS)

Richards, Stephanie E. (Compiler); Levine, Howard G.; Romero, Vergel

2016-01-01

The Biological Research in Canisters (BRIC) is an anodized-aluminum cylinder used to provide passive stowage for investigations evaluating the effects of space flight on small organisms. Specimens flown in the BRIC 60 mm petri dish (BRIC-60) hardware include Lycoperscion esculentum (tomato), Arabidopsis thaliana (thale cress), Glycine max (soybean) seedlings, Physarum polycephalum (slime mold) cells, Pothetria dispar (gypsy moth) eggs and Ceratodon purpureus (moss).

The effect on biological and moisture resistance of epichlorohydrin chemically modified wood

Treesearch

Rebecca E. Ibach; Beom-Goo Lee

2002-01-01

Southern pine solid wood and fiber were chemically modified with epichlorohydrin to help in understanding the role of moisture in the mechanism of biological effectiveness of chemically modified wood. The solid wood had weight gains from 11% to 34%, while the fiber had weight gains from 9% to 75%. After modification, part of the specimens were water leached for 2 weeks...

BIOLOGICAL IRRADIATION FACILITY

DOEpatents

McCorkle, W.H.; Cern, H.S.

1962-04-24

A facility for irradiating biological specimens with neutrons is described. It includes a reactor wherein the core is off center in a reflector. A high-exposure room is located outside the reactor on the side nearest the core while a low-exposure room is located on the opposite side. Means for converting thermal neutrons to fast neutrons are movably disposed between the reactor core and the high and low-exposure rooms. (AEC)

Collection of biological samples in forensic toxicology.

PubMed

Dinis-Oliveira, R J; Carvalho, F; Duarte, J A; Remião, F; Marques, A; Santos, A; Magalhães, T

2010-09-01

Forensic toxicology is the study and practice of the application of toxicology to the purposes of the law. The relevance of any finding is determined, in the first instance, by the nature and integrity of the specimen(s) submitted for analysis. This means that there are several specific challenges to select and collect specimens for ante-mortem and post-mortem toxicology investigation. Post-mortem specimens may be numerous and can endow some special difficulties compared to clinical specimens, namely those resulting from autolytic and putrefactive changes. Storage stability is also an important issue to be considered during the pre-analytic phase, since its consideration should facilitate the assessment of sample quality and the analytical result obtained from that sample. The knowledge on degradation mechanisms and methods to increase storage stability may enable the forensic toxicologist to circumvent possible difficulties. Therefore, advantages and limitations of specimen preservation procedures are thoroughfully discussed in this review. Presently, harmonized protocols for sampling in suspected intoxications would have obvious utility. In the present article an overview is given on sampling procedures for routinely collected specimens as well as on alternative specimens that may provide additional information on the route and timing of exposure to a specific xenobiotic. Last, but not least, a discussion on possible bias that can influence the interpretation of toxicological results is provided. This comprehensive review article is intented as a significant help for forensic toxicologists to accomplish their frequently overwhelming mission.

Optimization of routine KRAS mutation PCR-based testing procedure for rational individualized first-line-targeted therapy selection in metastatic colorectal cancer.

PubMed

Chretien, Anne-Sophie; Harlé, Alexandre; Meyer-Lefebvre, Magali; Rouyer, Marie; Husson, Marie; Ramacci, Carole; Harter, Valentin; Genin, Pascal; Leroux, Agnès; Merlin, Jean-Louis

2013-02-01

KRAS mutation detection represents a crucial issue in metastatic colorectal cancer (mCRC). The optimization of KRAS mutation detection delay enabling rational prescription of first-line treatment in mCRC including anti-EGFR-targeted therapy requires robust and rapid molecular biology techniques. Routine analysis of mutations in codons 12 and 13 on 674 paraffin-embedded tissue specimens of mCRC has been performed for KRAS mutations detection using three molecular biology techniques, that is, high-resolution melting (HRM), polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP), and allelic discrimination PCR (TaqMan PCR). Discordant cases were assessed with COBAS 4800 KRAS CE-IVD assay. Among the 674 tumor specimens, 1.5% (10/674) had excessive DNA degradation and could not be analyzed. KRAS mutations were detected in 38.0% (256/674) of the analysable specimens (82.4% in codon 12 and 17.6% in codon 13). Among 613 specimens in whom all three techniques were used, 12 (2.0%) cases of discordance between the three techniques were observed. 83.3% (10/12) of the discordances were due to PCR-RFLP as confirmed by COBAS 4800 retrospective analysis. The three techniques were statistically comparable (κ > 0.9; P < 0.001). From these results, optimization of the routine procedure consisted of proceeding to systematic KRAS detection using HRM and TaqMan and PCR-RFLP in case of discordance and allowed significant decrease in delays. The results showed an excellent correlation between the three techniques. Using HRM and TaqMan warrants high-quality and rapid-routine KRAS mutation detection in paraffin-embedded tumor specimens. The new procedure allowed a significant decrease in delays for reporting results, enabling rational prescription of first-line-targeted therapy in mCRC.

Increasing the efficiency of digitization workflows for herbarium specimens.

PubMed

Tulig, Melissa; Tarnowsky, Nicole; Bevans, Michael; Anthony Kirchgessner; Thiers, Barbara M

2012-01-01

The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate.Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR) of specimen images. With the launch of the National Science Foundation's new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time.

Increasing the efficiency of digitization workflows for herbarium specimens

PubMed Central

Tulig, Melissa; Tarnowsky, Nicole; Bevans, Michael; Anthony Kirchgessner; Thiers,  Barbara M.

2012-01-01

Abstract The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate. Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR) of specimen images. With the launch of the National Science Foundation’s new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time. PMID:22859882

Evaluation of a menstrual cup to collect shed endometrium for in vitro studies.

PubMed

Koks, C A; Dunselman, G A; de Goeij, A F; Arends, J W; Evers, J L

1997-09-01

To evaluate whether a menstrual cup is a suitable instrument to collect antegradely shed endometrium for in vitro studies. A prospective, descriptive, cell biological and immunohistochemical study. Tertiary care university medical center. Nine female volunteers with regular cycles. Menstrual effluent was collected with a menstrual cup. Experience with the menstrual cup was described. Cytospin specimens, frozen sections, and cultures were prepared from the obtained menstrual tissue. The acceptability of the menstrual cup. The presence and viability of endometrial tissue was evaluated using immunohistochemical staining and culture outcome. All women except one described the menstrual cup as acceptable. Menstrual effluent contained single cells, clumps of cells, and glandlike structures. After 5 days of culture, the endometrial tissue appeared to be viable. Immunohistochemistry showed positive staining for vimentin in most cytospin specimens, in all cryostat specimens, and in 10 of 17 cultures. Cytokeratin 18 stained most cytospin specimens, all cryostat specimens, and 10 of 17 cultures. Positive staining for BW495/36 was observed in most cytospin specimens, all cryostat specimens, and 11 of 17 cultures. A menstrual cup in an acceptable instrument to collect antegradely shed menstrual tissue. Menstruum contains viable endometrial tissue that can be used for in vitro studies of endometrium and endometriosis.

Spatial Resolution in Scanning Electron Microscopy and Scanning Transmission Electron Microscopy Without a Specimen Vacuum Chamber.

PubMed

Nguyen, Kayla X; Holtz, Megan E; Richmond-Decker, Justin; Muller, David A

2016-08-01

A long-standing goal of electron microscopy has been the high-resolution characterization of specimens in their native environment. However, electron optics require high vacuum to maintain an unscattered and focused probe, a challenge for specimens requiring atmospheric or liquid environments. Here, we use an electron-transparent window at the base of a scanning electron microscope's objective lens to separate column vacuum from the specimen, enabling imaging under ambient conditions, without a specimen vacuum chamber. We demonstrate in-air imaging of specimens at nanoscale resolution using backscattered scanning electron microscopy (airSEM) and scanning transmission electron microscopy. We explore resolution and contrast using Monte Carlo simulations and analytical models. We find that nanometer-scale resolution can be obtained at gas path lengths up to 400 μm, although contrast drops with increasing gas path length. As the electron-transparent window scatters considerably more than gas at our operating conditions, we observe that the densities and thicknesses of the electron-transparent window are the dominant limiting factors for image contrast at lower operating voltages. By enabling a variety of detector configurations, the airSEM is applicable to a wide range of environmental experiments including the imaging of hydrated biological specimens and in situ chemical and electrochemical processes.

Spatial Resolution in Scanning Electron Microscopy and Scanning Transmission Electron Microscopy Without a Specimen Vacuum Chamber

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

Nguyen, Kayla X.; Holtz, Megan E.; Richmond-Decker, Justin

2016-07-25

Abstract A long-standing goal of electron microscopy has been the high-resolution characterization of specimens in their native environment. However, electron optics require high vacuum to maintain an unscattered and focused probe, a challenge for specimens requiring atmospheric or liquid environments. Here, we use an electron-transparent window at the base of a scanning electron microscope’s objective lens to separate column vacuum from the specimen, enabling imaging under ambient conditions, without a specimen vacuum chamber. We demonstrate in-air imaging of specimens at nanoscale resolution using backscattered scanning electron microscopy (airSEM) and scanning transmission electron microscopy. We explore resolution and contrast using Montemore » Carlo simulations and analytical models. We find that nanometer-scale resolution can be obtained at gas path lengths up to 400μm, although contrast drops with increasing gas path length. As the electron-transparent window scatters considerably more than gas at our operating conditions, we observe that the densities and thicknesses of the electron-transparent window are the dominant limiting factors for image contrast at lower operating voltages. By enabling a variety of detector configurations, the airSEM is applicable to a wide range of environmental experiments including the imaging of hydrated biological specimens andin situchemical and electrochemical processes.« less

Performance of the new automated Abbott RealTime MTB assay for rapid detection of Mycobacterium tuberculosis complex in respiratory specimens.

PubMed

Chen, J H K; She, K K K; Kwong, T-C; Wong, O-Y; Siu, G K H; Leung, C-C; Chang, K-C; Tam, C-M; Ho, P-L; Cheng, V C C; Yuen, K-Y; Yam, W-C

2015-09-01

The automated high-throughput Abbott RealTime MTB real-time PCR assay has been recently launched for Mycobacterium tuberculosis complex (MTBC) clinical diagnosis. This study would like to evaluate its performance. We first compared its diagnostic performance with the Roche Cobas TaqMan MTB assay on 214 clinical respiratory specimens. Prospective analysis of a total 520 specimens was then performed to further evaluate the Abbott assay. The Abbott assay showed a lower limit of detection at 22.5 AFB/ml, which was more sensitive than the Cobas assay (167.5 AFB/ml). The two assays demonstrated a significant difference in diagnostic performance (McNemar's test; P = 0.0034), in which the Abbott assay presented significantly higher area under curve (AUC) than the Cobas assay (1.000 vs 0.880; P = 0.0002). The Abbott assay demonstrated extremely low PCR inhibition on clinical respiratory specimens. The automated Abbott assay required only very short manual handling time (0.5 h), which could help to improve the laboratory management. In the prospective analysis, the overall estimates for sensitivity and specificity of the Abbott assay were both 100 % among smear-positive specimens, whereas the smear-negative specimens were 96.7 and 96.1 %, respectively. No cross-reactivity with non-tuberculosis mycobacterial species was observed. The superiority in sensitivity of the Abbott assay for detecting MTBC in smear-negative specimens could further minimize the risk in MTBC false-negative detection. The new Abbott RealTime MTB assay has good diagnostic performance which can be a useful diagnostic tool for rapid MTBC detection in clinical laboratories.

Broadening diversity in the Arostilepis species complex: Arostrilepis kontrimavichusi in the western red-backed vole Myodes californicus from temperate latitudes of the Pacific Northwest, North America

USDA-ARS?s Scientific Manuscript database

Specimens originally identified provisionally as Hymenolepis horrida (= Arostrilepis horrida) in Myodes californicus from near the Pacific coastal zone of southern Oregon are revised. Specimens in western red-backed voles represent an undescribed species of Arostrilepis, contributing to recognition ...

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

PubMed

Dahdul, Wasila M; Balhoff, James P; Engeman, Jeffrey; Grande, Terry; Hilton, Eric J; Kothari, Cartik; Lapp, Hilmar; Lundberg, John G; Midford, Peter E; Vision, Todd J; Westerfield, Monte; Mabee, Paula M

2010-05-20

The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.

Orthopoxvirus detection in environmental specimens during suspected bioterror attacks: inhibitory influences of common household products.

PubMed

Kurth, Andreas; Achenbach, John; Miller, Liljia; Mackay, Ian M; Pauli, Georg; Nitsche, Andreas

2008-01-01

After terrorists attacked the United States in 2001, the appearance of letters and other objects containing powdery substances with unknown potentials for biological threat focused attention on the speed, sensitivity, and reliability of diagnostic methods. This study summarizes the abilities and limitations of real-time PCR, electron microscopy (EM), and virus isolation when used to detect potential bioweapons. In particular, we investigated the inhibitory influences of different common household products present in environmental specimens on PCR yield, EM detection, and virus isolation. We used vaccinia virus as a model for orthopoxviruses by spiking it into specimens. In the second part of the study, we describe modifications of diagnostic methods to overcome inhibitory effects. A variety of PCR amplification enhancers, DNA extraction protocols, and applications of internal controls were evaluated to improve diagnostic simplicity, speed, and reliability. As a result, we strongly recommend using at least two different frontline techniques in parallel, e.g., EM and PCR. A positive result obtained by any one of these techniques should be followed by a biological method to confirm the putative diagnosis. Confirmatory methods include virus isolation followed by an agent-specific immunofluorescence assay to confirm the presence of replication-competent particles.

Crystallographic orientation of the c-axis of biological apatite as a new index of the quality of subchondral bone in knee joint osteoarthritis.

PubMed

Lee, Jee-Wook; Kobayashi, Akio; Nakano, Takayoshi

2017-05-01

The aim of the present study was to investigate the preferred orientation of biological apatite (BAp) as a new index of the quality of subchondral bone (SB) in knee joint osteoarthritis (OA). Ten OA and five normal knee joints were obtained. Thickness, quantity and bone mineral density (BMD) of SB were analyzed at the medial condyle of the femur in dry conditions by peripheral quantitative computed tomography. In addition, the preferred crystallographic orientation of the c-axis of BAp was evaluated as bone quality parameter using a microbeam X-ray diffractometer technique. BMD and thickness of SB were significantly increased in OA specimens compared to normal knee specimens (P < 0.01), and the preferred orientation of the c-axis of BAp along the normal direction of SB surface was significantly higher in OA specimens (P < 0.01), reflecting the change in stress of concentration in the pathological portion without cartilage. SB sclerosis in OA results in both proliferation of bone tissues and enhanced degree of preferential alignment of the c-axis of BAp. Our findings could have major implications for the diagnosis of clinical studies, including pathologic elucidation in OA.

Evaluation of cryoanalysis as a tool for analyzing elemental distribution in "live" tardigrades using micro-PIXE

NASA Astrophysics Data System (ADS)

Nilsson, E. J. C.; Pallon, J.; Przybylowicz, W. J.; Wang, Y. D.; Jönsson, K. I.

2014-08-01

Although heavy on labor and equipment, thus not often applied, cryoanalysis of frozen hydrated biological specimens can provide information that better reflects the living state of the organism, compared with analysis in the freeze-dried state. In this paper we report a study where the cryoanalysis facility with cryosectioning capabilities at Materials Research Department, iThemba LABS, South Africa was employed to evaluate the usefulness of combining three ion beam analytical methods (μPIXE, RBS and STIM) to analyze a biological target where a better elemental compositional description is needed - the tardigrade. Imaging as well as quantification results are of interest. In a previous study, the element composition and redistribution of elements in the desiccated and active states of two tardigrade species was investigated. This study included analysis of both whole and sectioned tardigrades, and the aim was to analyze each specimen twice; first frozen hydrated and later freeze-dried. The combination of the three analytical techniques proved useful: elements from C to Rb in the tardigrades could be determined and certain differences in distribution of elements between the frozen hydrated and the freeze-dried states were observed. RBS on frozen hydrated specimens provided knowledge of matrix elements.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

NASA Astrophysics Data System (ADS)

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing; He, You; Zhou, Guangzhao; Sun, Zhibin; Zhang, Jianhua; Huang, Qingjie; Xiao, Tiqiao; Jiang, Huaidong

2016-03-01

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique over conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ˜1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.

Equally sloped X-ray microtomography of living insects with low radiation dose and improved resolution capability

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

Yao, Shengkun; Fan, Jiadong; Zong, Yunbing

Three-dimensional X-ray imaging of living specimens is challenging due to the limited resolution of conventional absorption contrast X-ray imaging and potential irradiation damage of biological specimens. In this letter, we present microtomography of a living specimen combining phase-contrast imaging and a Fourier-based iterative algorithm termed equally sloped tomography. Non-destructive 3D imaging of an anesthetized living yellow mealworm Tenebrio molitor was demonstrated with a relatively low dose using synchrotron generated X-rays. Based on the high-quality 3D images, branching tracheoles and different tissues of the insect in a natural state were identified and analyzed, demonstrating a significant advantage of the technique overmore » conventional X-ray radiography or histotomy. Additionally, the insect survived without problem after a 1.92-s X-ray exposure and subsequent absorbed radiation dose of ∼1.2 Gy. No notable physiological effects were observed after reviving the insect from anesthesia. The improved static tomographic method demonstrated in this letter shows advantage in the non-destructive structural investigation of living insects in three dimensions due to the low radiation dose and high resolution capability, and offers many potential applications in biological science.« less

Orthopoxvirus Detection in Environmental Specimens during Suspected Bioterror Attacks: Inhibitory Influences of Common Household Products▿

PubMed Central

Kurth, Andreas; Achenbach, John; Miller, Liljia; Mackay, Ian M.; Pauli, Georg; Nitsche, Andreas

2008-01-01

After terrorists attacked the United States in 2001, the appearance of letters and other objects containing powdery substances with unknown potentials for biological threat focused attention on the speed, sensitivity, and reliability of diagnostic methods. This study summarizes the abilities and limitations of real-time PCR, electron microscopy (EM), and virus isolation when used to detect potential bioweapons. In particular, we investigated the inhibitory influences of different common household products present in environmental specimens on PCR yield, EM detection, and virus isolation. We used vaccinia virus as a model for orthopoxviruses by spiking it into specimens. In the second part of the study, we describe modifications of diagnostic methods to overcome inhibitory effects. A variety of PCR amplification enhancers, DNA extraction protocols, and applications of internal controls were evaluated to improve diagnostic simplicity, speed, and reliability. As a result, we strongly recommend using at least two different frontline techniques in parallel, e.g., EM and PCR. A positive result obtained by any one of these techniques should be followed by a biological method to confirm the putative diagnosis. Confirmatory methods include virus isolation followed by an agent-specific immunofluorescence assay to confirm the presence of replication-competent particles. PMID:17965204

2012 best practices for repositories collection, storage, retrieval, and distribution of biological materials for research international society for biological and environmental repositories.

PubMed

2012-04-01

Third Edition [Formula: see text] [Box: see text] Printed with permission from the International Society for Biological and Environmental Repositories (ISBER) © 2011 ISBER All Rights Reserved Editor-in-Chief Lori D. Campbell, PhD Associate Editors Fay Betsou, PhD Debra Leiolani Garcia, MPA Judith G. Giri, PhD Karen E. Pitt, PhD Rebecca S. Pugh, MS Katherine C. Sexton, MBA Amy P.N. Skubitz, PhD Stella B. Somiari, PhD Individual Contributors to the Third Edition Jonas Astrin, Susan Baker, Thomas J. Barr, Erica Benson, Mark Cada, Lori Campbell, Antonio Hugo Jose Froes Marques Campos, David Carpentieri, Omoshile Clement, Domenico Coppola, Yvonne De Souza, Paul Fearn, Kelly Feil, Debra Garcia, Judith Giri, William E. Grizzle, Kathleen Groover, Keith Harding, Edward Kaercher, Joseph Kessler, Sarah Loud, Hannah Maynor, Kevin McCluskey, Kevin Meagher, Cheryl Michels, Lisa Miranda, Judy Muller-Cohn, Rolf Muller, James O'Sullivan, Karen Pitt, Rebecca Pugh, Rivka Ravid, Katherine Sexton, Ricardo Luis A. Silva, Frank Simione, Amy Skubitz, Stella Somiari, Frans van der Horst, Gavin Welch, Andy Zaayenga 2012 Best Practices for Repositories: Collection, Storage, Retrieval and Distribution of Biological Materials for Research INTERNATIONAL SOCIETY FOR BIOLOGICAL AND ENVIRONMENTAL REPOSITORIES (ISBER) INTRODUCTION T he availability of high quality biological and environmental specimens for research purposes requires the development of standardized methods for collection, long-term storage, retrieval and distribution of specimens that will enable their future use. Sharing successful strategies for accomplishing this goal is one of the driving forces for the International Society for Biological and Environmental Repositories (ISBER). For more information about ISBER see www.isber.org . ISBER's Best Practices for Repositories (Best Practices) reflect the collective experience of its members and has received broad input from other repository professionals. Throughout this document effective practices are presented for the management of specimen collections and repositories. The term "Best Practice" is used in cases where a level of operation is indicated that is above the basic recommended practice or more specifically designates the most effective practice. It is understood that repositories in certain locations or with particular financial constraints may not be able to adhere to each of the items designated as "Best Practices". Repositories fitting into either of these categories will need to decide how they might best adhere to these recommendations within their particular circumstances. While adherence to ISBER Best Practices is strictly on a voluntary basis, it is important to note that some aspects of specimen management are governed by national/federal, regional and local regulations. The reader should refer directly to regulations for their national/federal, regional and local requirements, as appropriate. ISBER has strived to include terminology appropriate to the various specimen types covered under these practices, but here too, the reader should take steps to ensure the appropriateness of the recommendations to their particular repository type prior to the implementation of any new approaches. Important terms within the document are italicized when first used in a section and defined in the glossary. The ISBER Best Practices are periodically reviewed and revised to reflect advances in research and technology. The third edition of the Best Practices builds on the foundation established in the first and second editions which were published in 2005 and 2008, respectively.

Morphological anomalies in two Lutzomyia (Psathyromyia) shannoni (Diptera: Psychodidae: Phlebotominae) specimens collected from Fort Rucker, Alabama, and Fort Campbell, Kentucky.

PubMed

Florin, David A; Lawyer, Phillip; Rowton, Edgar; Schultz, George; Wilkerson, Richard; Davies, Stephen J; Lipnick, Robert; Keep, Lisa

2010-09-01

This report describes two male specimens of the sand fly species Lutzomyia shannoni (Dyar) (Diptera: Psychodidae: Phlebotominae) collected at Fort Rucker, AL, and Fort Campbell, KY, in dry ice-baited light traps during September 2005. The specimens were observed to have anomalies to the number of spines on the gonostyli. The taxonomic keys of Young and Perkins (Mosq. News 44: 263-285; 1984) use the number of spines on the gonostylus in the first couplet to differentiate two major groupings of North American sand flies. The two anomalous specimens were identified as L. shannoni based on the following criteria: (1) both specimens possess antennal ascoids with long, distinct proximal spurs (a near diagnostic character of L. shannoni in North America), (2) the sequences of the partial cytochrome c oxidase subunit 1 gene from both specimens indicated L. shannoni, and (3) the sequences of the internal transcribed spacer 2 molecular marker from both specimens indicated L. shannoni. The anomalous features are fundamentally different from each other as the Fort Rucker specimen possesses a fifth spine (basally located) on just one gonostylus, whereas the Fort Campbell specimen possesses five spines (extra spines subterminally located) on both gonostyli. Because the gonostyli are part of the external male genitalia, anomalies in the number of spines on the gonostyli may have serious biological consequences, such as reduced reproductive success, for the possessors. These anomalies are of taxonomic interest as the specimens could easily have been misidentified using available morphological keys.

Initiatives, prospects, and challenges in tropical marine biosciences in Jagna Bay, Bohol Island, Philippines

NASA Astrophysics Data System (ADS)

Bernido, Christopher C.; Halasan, Lorenzo C.; Carpio-Bernido, M. Victoria; Saguil, Noel A.; Sadudaquil, Jerome A.; Salas, Rochelle I.; Nayga, Prince Niño I.; Baja, Paz Kenneth S.; Jumawan, Ethel Jade V.

2017-08-01

Marine specimens exhibit diversity in structure as an offshoot of their survival and ecological role in marine communities. The shell structure of gastropods, for example, is so diverse that taxonomic classification could hardly catch up with the myriad specimens many of which remain unidentified, nameless, or worse, unrecorded as large numbers become extinct. As a step towards alleviating the lack of comprehensive marine life assessment, we discuss initial studies conducted in Jagna Bay in the northern part of Bohol Sea to determine the level of biodiversity in this locale. The methods of collecting specimens and their identification are discussed as exemplified by a specimen belonging to the genus Cycloscala. Data collected for specimens whose sizes range from around 1 mm to 250 mm helps establish baseline indicators that could determine ecological balance in this area for monitoring longitudinal effects of climate and human intervention. Given the remarkable marine biodiversity, the perennial challenge is to uncover and learn from the biological structure and functions of many marine specimens for possible applications in different emerging technologies. We illustrate this by citing recent examples where our understanding of marine life inspires innovations for tomorrow's technology.

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging.

PubMed

Nakasako, Masayoshi; Takayama, Yuki; Oroguchi, Tomotaka; Sekiguchi, Yuki; Kobayashi, Amane; Shirahama, Keiya; Yamamoto, Masaki; Hikima, Takaaki; Yonekura, Koji; Maki-Yonekura, Saori; Kohmura, Yoshiki; Inubushi, Yuichi; Takahashi, Yukio; Suzuki, Akihiro; Matsunaga, Sachihiro; Inui, Yayoi; Tono, Kensuke; Kameshima, Takashi; Joti, Yasumasa; Hoshi, Takahiko

2013-09-01

We have developed an experimental apparatus named KOTOBUKI-1 for use in coherent X-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. For cryogenic specimen stage with small positional fluctuation for a long exposure time of more than several minutes, we here use a cryogenic pot cooled by the evaporation cooling effect for liquid nitrogen. In addition, a loading device is developed to bring specimens stored in liquid nitrogen to the specimen stage in vacuum. The apparatus allows diffraction data collection for frozen-hydrated specimens at 66 K with a positional fluctuation of less than 0.4 μm and provides an experimental environment to easily exchange specimens from liquid nitrogen storage to the specimen stage. The apparatus was developed and utilized in diffraction data collection of non-crystalline particles with dimensions of μm from material and biological sciences, such as metal colloid particles and chloroplast, at BL29XU of SPring-8. Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA.

Physical interpretation and development of ultrasonic nondestructive evaluation techniques applied to the quantitative characterization of textile composite materials

NASA Technical Reports Server (NTRS)

Miller, James G.

1994-01-01

In this Progress Report, we describe our continuing research activities concerning the development and implementation of advanced ultrasonic nondestructive evaluation methods applied to the inspection and characterization of complex composite structures. We explore the feasibility of implementing medical linear array imaging technology as a viable ultrasonic-based nondestructive evaluation method to inspect and characterize complex materials. As an initial step toward the application of linear array imaging technology to the interrogation of a wide range of complex composite structures, we present images obtained using an unmodified medical ultrasonic imaging system of two epoxy-bonded aluminum plate specimens, each with intentionally disbonded regions. These images are compared with corresponding conventional ultrasonic contact transducer measurements in order to assess whether these images can detect disbonded regions and provide information regarding the nature of the disbonded region. We present a description of a standoff/delay fixture which has been designed, constructed, and implemented on a Hewlett-Packard SONOS 1500 medical imaging system. This standoff/delay fixture, when attached to a 7.5 MHz linear array probe, greatly enhances our ability to interrogate flat plate specimens. The final section of this Progress Report describes a woven composite plate specimen that has been specially machined to include intentional flaws. This woven composite specimen will allow us to assess the feasibility of applying linear array imaging technology to the inspection and characterization of complex textile composite materials. We anticipate the results of this on-going investigation may provide a step toward the development of a rapid, real-time, and portable method of ultrasonic inspection and characterization based on linear array technology.

Test of superplastically formed corrugated aluminum compression specimens with beaded webs

NASA Technical Reports Server (NTRS)

Davis, Randall C.; Royster, Dick M.; Bales, Thomas T.; James, William F.; Shinn, Joseph M., Jr.

1991-01-01

Corrugated wall sections provide a highly efficient structure for carrying compressive loads in aircraft and spacecraft fuselages. The superplastic forming (SPF) process offers a means to produce complex shells and panels with corrugated wall shapes. A study was made to investigate the feasibility of superplastically forming 7475-T6 aluminum sheet into a corrugated wall configuration and to demonstrate the structural integrity of the construction by testing. The corrugated configuration selected has beaded web segments separating curved-cap segments. Eight test specimens were fabricated. Two specimens were simply a single sheet of aluminum superplastically formed to a beaded-web, curved-cap corrugation configuration. Six specimens were single-sheet corrugations modified by adhesive bonding additional sheet material to selectively reinforce the curved-cap portion of the corrugation. The specimens were tested to failure by crippling in end compression at room temperature.

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.

New data on the taxonomy, ecology, and conservation of the rediscovered Louisea edeaensis (Bott, 1969) (Brachyura: Potamoidea: Potamonautidae), an endangered freshwater crab from Cameroon.

PubMed

Ndongo, Pierre A Mvogo; Rintelen, Thomas VON; Schubart, Christoph D; Albrecht, Christian; Tamesse, Joseph L; Cumberlidge, Neil

2017-02-09

The rare and endangered Cameroonian potamonautid freshwater crab Louisea edeaensis (Bott, 1969) was recently rediscovered during a biological inventory of the freshwater decapods of southern Cameroon. The previous record dated back more than 100 years. The new specimens allow an updated diagnosis of the species based on comparisons of important taxonomic characters. Photographs of the carapace, gonopods, third maxillipeds, and chelipeds of the largest adult male specimen from Lake Ossa, Cameroon are provided, as are the first photographs of living specimens. The conservation implications of the new data on habitat, population structure, distribution, and threats for this rare and endangered species are discussed.

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Improved specimen reconstruction by Hilbert phase contrast tomography.

PubMed

Barton, Bastian; Joos, Friederike; Schröder, Rasmus R

2008-11-01

The low signal-to-noise ratio (SNR) in images of unstained specimens recorded with conventional defocus phase contrast makes it difficult to interpret 3D volumes obtained by electron tomography (ET). The high defocus applied for conventional tilt series generates some phase contrast but leads to an incomplete transfer of object information. For tomography of biological weak-phase objects, optimal image contrast and subsequently an optimized SNR are essential for the reconstruction of details such as macromolecular assemblies at molecular resolution. The problem of low contrast can be partially solved by applying a Hilbert phase plate positioned in the back focal plane (BFP) of the objective lens while recording images in Gaussian focus. Images recorded with the Hilbert phase plate provide optimized positive phase contrast at low spatial frequencies, and the contrast transfer in principle extends to the information limit of the microscope. The antisymmetric Hilbert phase contrast (HPC) can be numerically converted into isotropic contrast, which is equivalent to the contrast obtained by a Zernike phase plate. Thus, in-focus HPC provides optimal structure factor information without limiting effects of the transfer function. In this article, we present the first electron tomograms of biological specimens reconstructed from Hilbert phase plate image series. We outline the technical implementation of the phase plate and demonstrate that the technique is routinely applicable for tomography. A comparison between conventional defocus tomograms and in-focus HPC volumes shows an enhanced SNR and an improved specimen visibility for in-focus Hilbert tomography.

Peri-implant stress correlates with bone and cement morphology: Micro-FE modeling of implanted cadaveric glenoids.

PubMed

Wee, Hwabok; Armstrong, April D; Flint, Wesley W; Kunselman, Allen R; Lewis, Gregory S

2015-11-01

Aseptic loosening of cemented joint replacements is a complex biological and mechanical process, and remains a clinical concern especially in patients with poor bone quality. Utilizing high resolution finite element analysis of a series of implanted cadaver glenoids, the objective of this study was to quantify relationships between construct morphology and resulting mechanical stresses in cement and trabeculae. Eight glenoid cadavers were implanted with a cemented central peg implant. Specimens were imaged by micro-CT, and subject-specific finite element models were developed. Bone volume fraction, glenoid width, implant-cortex distance, cement volume, cement-cortex contact, and cement-bone interface area were measured. Axial loading was applied to the implant of each model and stress distributions were characterized. Correlation analysis was completed across all specimens for pairs of morphological and mechanical variables. The amount of trabecular bone with high stress was strongly negatively correlated with both cement volume and contact between the cement and cortex (r = -0.85 and -0.84, p < 0.05). Bone with high stress was also correlated with both glenoid width and implant-cortex distance. Contact between the cement and underlying cortex may dramatically reduce trabecular bone stresses surrounding the cement, and this contact depends on bone shape, cement amount, and implant positioning. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

A morphological database for 606 colombian bird species.

PubMed

Montoya, Paola; Gonzalez, Mailyn A; Tenorio, Elkin A; López-Ordóñez, Juan Pablo; Pinto Gómez, Alejandro; Cueva, Diego; Acevedo Rincón, Aldemar A; Angarita Yanes, Camilo; Arango Martínez, Héctor Manuel; Armesto, Orlando; Betancur, Jefry S; Caguazango Castro, Angela; Calderon Leyton, Jhon Jairo; Calpa-Anaguano, Edna Viviana; Cárdenas-Posada, Ghislaine; Castaño Díaz, Michael; Chaparro-Herrera, Sergio; Diago-Muñoz, Nicolás; Franco Espinosa, Laura; Gómez Bernal, Luis Germán; Gonzalez-Zapata, Fanny L; Gutiérrez Zamora, Eduardo Aquiles; Gutiérrez-Zuluaga, Ana M; Lizcano Jiménez, Robinson Stivel; Lopera-Salazar, Andrea; Martínez Alvarado, Dariel; Maya Girón, Ana María; Medina, Wilderson; Montealegre-Talero, Carolina; Parra, Juan L; Pérez-Peña, Sebastián; Ramírez Ramírez, Francis; Reyes, Julián; Rivera-Gutiérrez, Héctor Fabio; Rosero Mora, Yuri; Trujillo-Torres, Carlos M; Vidal-Maldonado, Cristian Camilo; Salgado-Negret, Beatriz

2018-04-27

Colombia is the country with the highest bird diversity in the world. Despite active research in ornithology, compelling morphological information of most bird species is still sparse. However, morphological information is the baseline to understand how species respond to environmental variation and how ecosystems respond to species loss. As part of a national initiative, the Instituto Alexander von Humboldt in collaboration with twelve Colombian institutions and seven biological collections, measured up to 15 morphological traits of 9892 individuals corresponding to 606 species: 3492 from individuals captured in field and 6400 from museum specimens. Species measured are mainly distributed in high Andean forest, páramo, and wetland ecosystems. Overall, seven ornithological collections in Colombia and 18 páramo complexes throughout Colombia were visited from 2013 to 2015. The morphological traits involved measurements from bill (total and exposed culmen, bill width and depth), wing (length, area, wingspan and the distance between longest primary and longest secondary), tail (length and shape), tarsus (length), hallux (length and claw hallux) and weight. The number of measured specimens per species was variable, ranging from 1 to 321 individuals with a median of 4 individuals per species. Overall, this database gathered morphological information for more than 30% of Colombian bird diversity. No copyright, proprietary, or cost restrictions apply; the data should be cited appropriately when used. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

PyXRD v0.6.7: a free and open-source program to quantify disordered phyllosilicates using multi-specimen X-ray diffraction profile fitting

NASA Astrophysics Data System (ADS)

Dumon, M.; Van Ranst, E.

2016-01-01

This paper presents a free and open-source program called PyXRD (short for Python X-ray diffraction) to improve the quantification of complex, poly-phasic mixed-layer phyllosilicate assemblages. The validity of the program was checked by comparing its output with Sybilla v2.2.2, which shares the same mathematical formalism. The novelty of this program is the ab initio incorporation of the multi-specimen method, making it possible to share phases and (a selection of) their parameters across multiple specimens. PyXRD thus allows for modelling multiple specimens side by side, and this approach speeds up the manual refinement process significantly. To check the hypothesis that this multi-specimen set-up - as it effectively reduces the number of parameters and increases the number of observations - can also improve automatic parameter refinements, we calculated X-ray diffraction patterns for four theoretical mineral assemblages. These patterns were then used as input for one refinement employing the multi-specimen set-up and one employing the single-pattern set-ups. For all of the assemblages, PyXRD was able to reproduce or approximate the input parameters with the multi-specimen approach. Diverging solutions only occurred in single-pattern set-ups, which do not contain enough information to discern all minerals present (e.g. patterns of heated samples). Assuming a correct qualitative interpretation was made and a single pattern exists in which all phases are sufficiently discernible, the obtained results indicate a good quantification can often be obtained with just that pattern. However, these results from theoretical experiments cannot automatically be extrapolated to all real-life experiments. In any case, PyXRD has proven to be useful when X-ray diffraction patterns are modelled for complex mineral assemblages containing mixed-layer phyllosilicates with a multi-specimen approach.

Experimental Investigation on Deformation Failure Characteristics of Crystalline Marble Under Triaxial Cyclic Loading

NASA Astrophysics Data System (ADS)

Yang, Sheng-Qi; Tian, Wen-Ling; Ranjith, P. G.

2017-11-01

The deformation failure characteristics of marble subjected to triaxial cyclic loading are significant when evaluating the stability and safety of deep excavation damage zones. To date, however, there have been notably few triaxial experimental studies on marble under triaxial cyclic loading. Therefore, in this research, a series of triaxial cyclic tests was conducted to analyze the mechanical damage characteristics of a marble. The post-peak deformation of the marble changed gradually from strain softening to strain hardening as the confining pressure increased from 0 to 10 MPa. Under uniaxial compression, marble specimens showed brittle failure characteristics with a number axial splitting tensile cracks; in the range of σ 3 = 2.5-7.5 MPa, the marble specimens assumed single shear fracture characteristics with larger fracture angles of about 65°. However, at σ 3 = 10 MPa, the marble specimens showed no obvious shear fracture surfaces. The triaxial cyclic experimental results indicate that in the range of the tested confining pressures, the triaxial strengths of the marble specimens under cyclic loading were approximately equal to those under monotonic loading. With the increase in cycle number, the elastic strains of the marble specimens all increased at first and later decreased, achieving maximum values, but the plastic strains of the marble specimens increased nonlinearly. To evaluate quantitatively the damage extent of the marble under triaxial cyclic loading, a damage variable is defined according to the irreversible deformation for each cycle. The evolutions of the elastic modulus for the marble were characterized by four stages: material strengthening, material degradation, material failure and structure slippage. Based on the experimental results of the marble specimens under complex cyclic loading, the cohesion of the marble decreased linearly, but the internal friction angles did not depend on the damage extent. To describe the peak strength characteristics of the marble specimens under complex cyclic loadings with various deformation positions, a revised strength criterion for damaged rocks is offered.

Novel molecular approach to define pest species status and tritrophic interactions from historical Bemisia specimens.

PubMed

Tay, W T; Elfekih, S; Polaszek, A; Court, L N; Evans, G A; Gordon, K H J; De Barro, P J

2017-03-27

Museum specimens represent valuable genomic resources for understanding host-endosymbiont/parasitoid evolutionary relationships, resolving species complexes and nomenclatural problems. However, museum collections suffer DNA degradation, making them challenging for molecular-based studies. Here, the mitogenomes of a single 1912 Sri Lankan Bemisia emiliae cotype puparium, and of a 1942 Japanese Bemisia puparium are characterised using a Next-Generation Sequencing approach. Whiteflies are small sap-sucking insects including B. tabaci pest species complex. Bemisia emiliae's draft mitogenome showed a high degree of homology with published B. tabaci mitogenomes, and exhibited 98-100% partial mitochondrial DNA Cytochrome Oxidase I (mtCOI) gene identity with the B. tabaci species known as Asia II-7. The partial mtCOI gene of the Japanese specimen shared 99% sequence identity with the Bemisia 'JpL' genetic group. Metagenomic analysis identified bacterial sequences in both Bemisia specimens, while hymenopteran sequences were also identified in the Japanese Bemisia puparium, including complete mtCOI and rRNA genes, and various partial mtDNA genes. At 88-90% mtCOI sequence identity to Aphelinidae wasps, we concluded that the 1942 Bemisia nymph was parasitized by an Eretmocerus parasitoid wasp. Our approach enables the characterisation of genomes and associated metagenomic communities of museum specimens using 1.5 ng gDNA, and to infer historical tritrophic relationships in Bemisia whiteflies.

Polyphenism in social insects: insights from a transcriptome-wide analysis of gene expression in the life stages of the key pollinator, Bombus terrestris

PubMed Central

2011-01-01

Background Understanding polyphenism, the ability of a single genome to express multiple morphologically and behaviourally distinct phenotypes, is an important goal for evolutionary and developmental biology. Polyphenism has been key to the evolution of the Hymenoptera, and particularly the social Hymenoptera where the genome of a single species regulates distinct larval stages, sexual dimorphism and physical castes within the female sex. Transcriptomic analyses of social Hymenoptera will therefore provide unique insights into how changes in gene expression underlie such complexity. Here we describe gene expression in individual specimens of the pre-adult stages, sexes and castes of the key pollinator, the buff-tailed bumblebee Bombus terrestris. Results cDNA was prepared from mRNA from five life cycle stages (one larva, one pupa, one male, one gyne and two workers) and a total of 1,610,742 expressed sequence tags (ESTs) were generated using Roche 454 technology, substantially increasing the sequence data available for this important species. Overlapping ESTs were assembled into 36,354 B. terrestris putative transcripts, and functionally annotated. A preliminary assessment of differences in gene expression across non-replicated specimens from the pre-adult stages, castes and sexes was performed using R-STAT analysis. Individual samples from the life cycle stages of the bumblebee differed in the expression of a wide array of genes, including genes involved in amino acid storage, metabolism, immunity and olfaction. Conclusions Detailed analyses of immune and olfaction gene expression across phenotypes demonstrated how transcriptomic analyses can inform our understanding of processes central to the biology of B. terrestris and the social Hymenoptera in general. For example, examination of immunity-related genes identified high conservation of important immunity pathway components across individual specimens from the life cycle stages while olfactory-related genes exhibited differential expression with a wider repertoire of gene expression within adults, especially sexuals, in comparison to immature stages. As there is an absence of replication across the samples, the results of this study are preliminary but provide a number of candidate genes which may be related to distinct phenotypic stage expression. This comprehensive transcriptome catalogue will provide an important gene discovery resource for directed programmes in ecology, evolution and conservation of a key pollinator. PMID:22185240

Adaptive optical fluorescence microscopy.

PubMed

Ji, Na

2017-03-31

The past quarter century has witnessed rapid developments of fluorescence microscopy techniques that enable structural and functional imaging of biological specimens at unprecedented depth and resolution. The performance of these methods in multicellular organisms, however, is degraded by sample-induced optical aberrations. Here I review recent work on incorporating adaptive optics, a technology originally applied in astronomical telescopes to combat atmospheric aberrations, to improve image quality of fluorescence microscopy for biological imaging.

A high throughput array microscope for the mechanical characterization of biomaterials

NASA Astrophysics Data System (ADS)

Cribb, Jeremy; Osborne, Lukas D.; Hsiao, Joe Ping-Lin; Vicci, Leandra; Meshram, Alok; O'Brien, E. Tim; Spero, Richard Chasen; Taylor, Russell; Superfine, Richard

2015-02-01

In the last decade, the emergence of high throughput screening has enabled the development of novel drug therapies and elucidated many complex cellular processes. Concurrently, the mechanobiology community has developed tools and methods to show that the dysregulation of biophysical properties and the biochemical mechanisms controlling those properties contribute significantly to many human diseases. Despite these advances, a complete understanding of the connection between biomechanics and disease will require advances in instrumentation that enable parallelized, high throughput assays capable of probing complex signaling pathways, studying biology in physiologically relevant conditions, and capturing specimen and mechanical heterogeneity. Traditional biophysical instruments are unable to meet this need. To address the challenge of large-scale, parallelized biophysical measurements, we have developed an automated array high-throughput microscope system that utilizes passive microbead diffusion to characterize mechanical properties of biomaterials. The instrument is capable of acquiring data on twelve-channels simultaneously, where each channel in the system can independently drive two-channel fluorescence imaging at up to 50 frames per second. We employ this system to measure the concentration-dependent apparent viscosity of hyaluronan, an essential polymer found in connective tissue and whose expression has been implicated in cancer progression.

CALIBRATION AND VALIDATION OF CONFOCAL SPECTRAL IMAGING SYSTEMS

EPA Science Inventory

Confocal spectral imaging (CSI) microscope systems now on the market can perform spectral characterization of biological specimens containing fluorescent proteins, labels or dyes. Some CSI have been found to present inconsistent spectral characterizations within a particular syst...

X-ray phase contrast imaging of biological specimens with femtosecond pulses of betatron radiation from a compact laser plasma wakefield accelerator

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

Kneip, S.; Center for Ultrafast Optical Science, University of Michigan, Ann Arbor 48109; McGuffey, C.

2011-08-29

We show that x-rays from a recently demonstrated table top source of bright, ultrafast, coherent synchrotron radiation [Kneip et al., Nat. Phys. 6, 980 (2010)] can be applied to phase contrast imaging of biological specimens. Our scheme is based on focusing a high power short pulse laser in a tenuous gas jet, setting up a plasma wakefield accelerator that accelerates and wiggles electrons analogously to a conventional synchrotron, but on the centimeter rather than tens of meter scale. We use the scheme to record absorption and phase contrast images of a tetra fish, damselfly and yellow jacket, in particular highlightingmore » the contrast enhancement achievable with the simple propagation technique of phase contrast imaging. Coherence and ultrafast pulse duration will allow for the study of various aspects of biomechanics.« less

A hybrid scanning force and light microscope for surface imaging and three-dimensional optical sectioning in differential interference contrast.

PubMed

Stemmer, A

1995-04-01

The design of a scanned-cantilever-type force microscope is presented which is fully integrated into an inverted high-resolution video-enhanced light microscope. This set-up allows us to acquire thin optical sections in differential interference contrast (DIC) or polarization while the force microscope is in place. Such a hybrid microscope provides a unique platform to study how cell surface properties determine, or are affected by, the three-dimensional dynamic organization inside the living cell. The hybrid microscope presented in this paper has proven reliable and versatile for biological applications. It is the only instrument that can image a specimen by force microscopy and high-power DIC without having either to translate the specimen or to remove the force microscope. Adaptation of the design features could greatly enhance the suitability of other force microscopes for biological work.

Snapshot Hyperspectral Volumetric Microscopy

NASA Astrophysics Data System (ADS)

Wu, Jiamin; Xiong, Bo; Lin, Xing; He, Jijun; Suo, Jinli; Dai, Qionghai

2016-04-01

The comprehensive analysis of biological specimens brings about the demand for capturing the spatial, temporal and spectral dimensions of visual information together. However, such high-dimensional video acquisition faces major challenges in developing large data throughput and effective multiplexing techniques. Here, we report the snapshot hyperspectral volumetric microscopy that computationally reconstructs hyperspectral profiles for high-resolution volumes of ~1000 μm × 1000 μm × 500 μm at video rate by a novel four-dimensional (4D) deconvolution algorithm. We validated the proposed approach with both numerical simulations for quantitative evaluation and various real experimental results on the prototype system. Different applications such as biological component analysis in bright field and spectral unmixing of multiple fluorescence are demonstrated. The experiments on moving fluorescent beads and GFP labelled drosophila larvae indicate the great potential of our method for observing multiple fluorescent markers in dynamic specimens.

Multispectral digital lensless holographic microscopy: from femtosecond laser to white light LED

NASA Astrophysics Data System (ADS)

Garcia-Sucerquia, J.

2015-04-01

The use of femtosecond laser radiation and super bright white LED in digital lensless holographic microscopy is presented. For the ultrafast laser radiation two different configurations of operation of the microscope are presented and the dissimilar performance of each one analyzed. The microscope operating with a super bright white light LED in combination with optical filters shows very competitive performance as it is compared with more expensive optical sources. The broadband emission of both radiation sources allows the multispectral imaging of biological samples to obtain spectral responses and/or full color images of the microscopic specimens; sections of the head of a Drosophila melanogaster fly are imaged in this contribution. The simple, solid, compact, lightweight, and reliable architecture of digital lensless holographic microscopy operating with broadband light sources to image biological specimens exhibiting micrometer-sized details is evaluated in the present contribution.

Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules

DOE PAGES

Han, Bong-Gyoon; Watson, Zoe; Kang, Hannah; ...

2016-06-15

We describe a rapid and convenient method of growing streptavidin (SA) monolayer crystals directly on holey-carbon EM grids. As expected, these SA monolayer crystals retain their biotin-binding function and crystalline order through a cycle of embedding in trehalose and, later, its removal. This fact allows one to prepare, and store for later use, EM grids on which SA monolayer crystals serve as an affinity substrate for preparing specimens of biological macromolecules. In addition, we report that coating the lipid-tail side of trehalose-embedded monolayer crystals with evaporated carbon appears to improve the consistency with which well-ordered, single crystals are observed tomore » span over entire, 2 μm holes of the support films. Randomly biotinylated 70S ribosomes are used as a test specimen to show that these support films can be used to obtain a high-resolution cryo-EM structure« less

Centrifuge Facility Conceptual System Study. Volume 1: Facility overview and habitats

NASA Technical Reports Server (NTRS)

Synnestvedt, Robert (Editor)

1990-01-01

The results are presented for a NASA Phase 1 study conducted from mid 1987 through mid 1989 at Ames Research Center. The Centrifuge Facility is the major element of the biological research facility for the implementation of NASA's Life Science Research Program on Space Station Freedom using non-human specimens (such as small primates, rodents, plants, insects, cell tissues). Five systems are described which comprise the Facility: habitats, holding units, centrifuge, glovebox, and service unit. Volume 1 presents a facility overview and describes the habitats - modular units which house living specimens.

Biological parameters used in setting captive-breeding quotas for Indonesia's breeding facilities.

PubMed

Janssen, Jordi; Chng, Serene C L

2018-02-01

The commercial captive breeding of wildlife is often seen as a potential conservation tool to relieve pressure on wild populations, but laundering of wild-sourced specimens as captive bred can seriously undermine conservation efforts and provide a false sense of sustainability. Indonesia is at the center of such controversy; therefore, we examined Indonesia's captive-breeding production plan (CBPP) for 2016. We compared the biological parameters used in the CBPP with parameters in the literature and with parameters suggested by experts on each species and identified shortcomings of the CBPP. Production quotas for 99 out of 129 species were based on inaccurate or unrealistic biological parameters and production quotas deviated more than 10% from what parameters in the literature allow for. For 38 species, the quota exceeded the number of animals that can be bred based on the biological parameters (range 100-540%) calculated with equations in the CBPP. We calculated a lower reproductive output for 88 species based on published biological parameters compared with the parameters used in the CBPP. The equations used in the production plan did not appear to account for other factors (e.g., different survival rate for juveniles compared to adult animals) involved in breeding the proposed large numbers of specimens. We recommend the CBPP be adjusted so that realistic published biological parameters are applied and captive-breeding quotas are not allocated to species if their captive breeding is unlikely to be successful or no breeding stock is available. The shortcomings in the current CBPP create loopholes that mean mammals, reptiles, and amphibians from Indonesia declared captive bred may have been sourced from the wild. © 2017 Society for Conservation Biology.

A transmission line method for the measurement of microwave permittivity and permeability

NASA Astrophysics Data System (ADS)

Lederer, P. G.

1990-12-01

A method for determining complex permittivity and permeability at microwave frequencies from two port S parameter measurements of lossy solids in coaxial or waveguide transmission lines is described. The use of the TRL (Through Reflect Line) calibration scheme allows the measuring system to be calibrated right up to the specimen faces thereby eliminating most of the sample cell from the measurement and allowing suitable materials to be molded directly into the specimen cell in order to eliminate air gaps between specimen and transmission line walls. Some illustrative measurements for dielectric and magnetic materials are presented.

Using wood creep data to discuss the contribution of cell-wall reinforcing material.

PubMed

Gril, Joseph; Hunt, David; Thibaut, Bernard

2004-01-01

Longitudinal four-point creep bending tests were performed on small clear-wood spruce specimens having various microfibrillar angles. Cell-wall compliance was deduced from macroscopic data by accounting for porosity. Time-dependent compliance was converted into complex compliance and rigidity using the value and the slope of the compliance versus logarithm of time. Complex rigidity plots of all specimens, for the time range 10(3)-10(6) s, could be superimposed by a horizontal shift depending on the microfibrillar angle. The shape of complex trajectories allowed a decomposition of the cell-wall relaxation modulus as the sum of an elastic contribution function of the microfibrillar angle and a time-dependent term unrelated to it, and suggested a discussion on the contribution of the various cell-wall layers to the observed relaxation process.

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...

Microgravity

NASA Image and Video Library

2000-04-20

Cindy Barnes of University Space Research Association (USRA) at NASA's Marshall Space Flight Center pipettes a protein solution in preparation to grow crystals as part of NASA's structural biology program. Research on Earth helps scientists define conditions and specimens they will use in space experiments.

Miniature grinder for solid specimens

NASA Technical Reports Server (NTRS)

Houser, C. P.; Pesch, W. A.

1971-01-01

Machine grinds fines to appropriate micron sizes with the least biological trauma and greatest degree of reproducibility. Device controls destruction of material so that recovery of microorganisms is as great as possible and protects operation and grinding products from exogenous contamination.

WAVELENGTH AND ALIGNMENT TESTS FOR CONFOCAL SPECTRAL IMAGING SYSTEMS

EPA Science Inventory

Confocal spectral imaging (CSI) microscope systems now on the market delineate multiple fluorescent proteins, labels, or dyes within biological specimens by performing spectral characterizations. However, we find that some CSI present inconsistent spectral profiles of reference s...

Dynamics of supersonic microparticle impact on elastomers revealed by real–time multi–frame imaging

PubMed Central

Veysset, David; Hsieh, Alex J.; Kooi, Steven; Maznev, Alexei A.; Masser, Kevin A.; Nelson, Keith A.

2016-01-01

Understanding high–velocity microparticle impact is essential for many fields, from space exploration to medicine and biology. Investigations of microscale impact have hitherto been limited to post–mortem analysis of impacted specimens, which does not provide direct information on the impact dynamics. Here we report real–time multi–frame imaging studies of the impact of 7 μm diameter glass spheres traveling at 700–900 m/s on elastomer polymers. With a poly(urethane urea) (PUU) sample, we observe a hyperelastic impact phenomenon not seen on the macroscale: a microsphere undergoes a full conformal penetration into the specimen followed by a rebound which leaves the specimen unscathed. The results challenge the established interpretation of the behaviour of elastomers under high–velocity impact. PMID:27156501

New insights to ecology, ontogeny and teratology of Larger Benthic Foraminifera by biometrics based on microCT.

NASA Astrophysics Data System (ADS)

Briguglio, A.; Fabienke, W.; Wolfgring, E.; Ferrández Cañadell, C.; Hohenegger, J.

2012-04-01

The main function of tests in Larger Benthic Foraminifera (LBF) is to provide their endosymbiotic algae with enough light to obtain net photosynthetic rates and to create sufficient accommodation space. To study the relation between these two factors and to understand how the cell reacts to growth and to the environment, the newly developed technique of X-ray micro-Computer-Tomography (microCT) allows measurement of all characters of complex tests without destruction. Growth studies on 48 specimens of living and fossil species have been performed. The volumes of the lumina have been calculated as well as further 2-dimensional parameters related to volumes as chamber height, chamber width and septal distance. The volumes of chamber lumina represent cell growth in their sequence, thus demonstrating interruptions, increase/decrease or oscillations in growth rates caused by external factors affecting growth during life time (e.g. seasons). Correlations between volumes and the one-dimensional parameters have been calculated to check the form of relationship. According to our results, some parameters seem to oscillate exactly as the volume (therefore accommodating it), while others seem to oscillate constantly around a given growth function. Concerning the palaeobiology, beside the study of specimens with 'normal' growth, thus not drastically affected by external factors, some interesting morphologies have been investigated. Pluriembryonal apparati as well as secondary equatorial layers have been segmented, extracted and quantified in almost 15 specimens of Cycloclypeus carpenteri, 8 twin specimens of nummulitids tests have been also investigated to show where and how the fusion starts and volumetric quantifications of each single spiral in multispiral grown test of some large Eocene Nummulitids has also been calculated to show in which way and when (ontogenetically) a new spiral starts. The combination of all measurements allows interpretation of different biological and environmental dependencies of LBF. Varying growth rates determines environmental abiotic (e.g. seasons, instantaneous events) and biotic influence (e.g. predation), leading to life time estimation for the fossil forms by comparison with their living relatives.

Contributions to the mammalogy of Chile

USGS Publications Warehouse

Pine, Ronald H.; Miller, Sterling D.; Schamberger, Mel L.

1979-01-01

Collections of mammals were made during more than three years of biological investigations in Chile sponsored by the Corporación Nacional Forestal under the aegis of the Peace Corps (Smithsonian Environmental Program). Genera and species hitherto unreported for that country were taken and many useful data concerning distributional patterns of other (mostly little-known) species were gathered. These collections have also proved valuable in better understanding Chilean mammals from a taxonomic point of view and contribute knowledge of the species' natural history. Specimens are to be deposited in the (United States) National Museum of Natural History (USNM) or are to be retained by the Corporación Nacional Forestal, Avda, Bulnes 285, Depto. 401, Santiago. Numbers provided below are field numbers. A final division of specimens between the two institutions has not yet been made. A number of specimens reported here were not taken by Peace Corps personnel but have been obtained by the National Museum of Natural History from other sources. Specimens in the Field Museum of Natural History (FMNH) were used in making comparisons. Some of Fulk's (GWF) specimens are at Texas Tech University. Other are at the Servicio Agricola y Ganadero in Santiago (as are specimens of some introduced species taken by Schamberger). Reise's (DF) are at the Universidad de Chile-Concepción and in his personal collection.

A simple cryo-holder facilitates specimen observation under a conventional scanning electron microscope.

PubMed

Tang, Chih-Yuan; Huang, Rong-Nan; Kuo-Huang, Ling-Long; Kuo, Tai-Chih; Yang, Ya-Yun; Lin, Ching-Yeh; Jane, Wann-Neng; Chen, Shiang-Jiuun

2012-02-01

A pre-cryogenic holder (cryo-holder) facilitating cryo-specimen observation under a conventional scanning electron microscope (SEM) is described. This cryo-holder includes a specimen-holding unit (the stub) and a cryogenic energy-storing unit (a composite of three cylinders assembled with a screw). After cooling, the cryo-holder can continue supplying cryogenic energy to extend the observation time for the specimen in a conventional SEM. Moreover, the cryogenic energy-storing unit could retain appropriate liquid nitrogen that can evaporate to prevent frost deposition on the surface of the specimen. This device is proved feasible for various tissues and cells, and can be applied to the fields of both biology and material science. We have employed this novel cryo-holder for observation of yeast cells, trichome, and epidermal cells in the leaf of Arabidopsis thaliana, compound eyes of insects, red blood cells, filiform papillae on the surface of rat tongue, agar medium, water molecules, penicillium, etc. All results suggested that the newly designed cryo-holder is applicable for cryo-specimen observation under a conventional SEM without cooling system. Most importantly, the design of this cryo-holder is simple and easy to operate and could adapt a conventional SEM to a plain type cryo-SEM affordable for most laboratories. Copyright © 2011 Wiley Periodicals, Inc.

Optical workstation with concurrent, independent multiphoton imaging and experimental laser microbeam capabilities

PubMed Central

Wokosin, David L.; Squirrell, Jayne M.; Eliceiri, Kevin W.; White, John G.

2008-01-01

Experimental laser microbeam techniques have become established tools for studying living specimens. A steerable, focused laser beam may be used for a variety of experimental manipulations such as laser microsurgery, optical trapping, localized photolysis of caged bioactive probes, and patterned photobleaching. Typically, purpose-designed experimental systems have been constructed for each of these applications. In order to assess the consequences of such experimental optical interventions, long-term, microscopic observation of the specimen is often required. Multiphoton excitation, because of its ability to obtain high-contrast images from deep within a specimen with minimal phototoxic effects, is a preferred technique for in vivo imaging. An optical workstation is described that combines the functionality of an experimental optical microbeam apparatus with a sensitive multiphoton imaging system designed for use with living specimens. Design considerations are discussed and examples of ongoing biological applications are presented. The integrated optical workstation concept offers advantages in terms of flexibility and versatility relative to systems implemented with separate imaging and experimental components. PMID:18607511

Optical workstation with concurrent, independent multiphoton imaging and experimental laser microbeam capabilities

NASA Astrophysics Data System (ADS)

Wokosin, David L.; Squirrell, Jayne M.; Eliceiri, Kevin W.; White, John G.

2003-01-01

Experimental laser microbeam techniques have become established tools for studying living specimens. A steerable, focused laser beam may be used for a variety of experimental manipulations such as laser microsurgery, optical trapping, localized photolysis of caged bioactive probes, and patterned photobleaching. Typically, purpose-designed experimental systems have been constructed for each of these applications. In order to assess the consequences of such experimental optical interventions, long-term, microscopic observation of the specimen is often required. Multiphoton excitation, because of its ability to obtain high-contrast images from deep within a specimen with minimal phototoxic effects, is a preferred technique for in vivo imaging. An optical workstation is described that combines the functionality of an experimental optical microbeam apparatus with a sensitive multiphoton imaging system designed for use with living specimens. Design considerations are discussed and examples of ongoing biological applications are presented. The integrated optical workstation concept offers advantages in terms of flexibility and versatility relative to systems implemented with separate imaging and experimental components.

Novel spectral imaging system combining spectroscopy with imaging applications for biology

NASA Astrophysics Data System (ADS)

Malik, Zvi; Cabib, Dario; Buckwald, Robert A.; Garini, Yuval; Soenksen, Dirk G.

1995-02-01

A novel analytical spectral-imaging system and its results in the examination of biological specimens are presented. The SpectraCube 1000 system measures the transmission, absorbance, or fluorescence spectra of images studied by light microscopy. The system is based on an interferometer combined with a CCD camera, enabling measurement of the interferogram for each pixel constructing the image. Fourier transformation of the interferograms derives pixel by pixel spectra for 170 X 170 pixels of the image. A special `similarity mapping' program has been developed, enabling comparisons of spectral algorithms of all the spatial and spectral information measured by the system in the image. By comparing the spectrum of each pixel in the specimen with a selected reference spectrum (similarity mapping), there is a depiction of the spatial distribution of macromolecules possessing the characteristics of the reference spectrum. The system has been applied to analyses of bone marrow blood cells as well as fluorescent specimens, and has revealed information which could not be unveiled by other techniques. Similarity mapping has enabled visualization of fine details of chromatin packing in the nucleus of cells and other cytoplasmic compartments. Fluorescence analysis by the system has enabled the determination of porphyrin concentrations and distribution in cytoplasmic organelles of living cells.

Use of newborn screening program blood spots for exposure assessment: declining levels of perluorinated compounds in New York State infants.

PubMed

Spliethoff, Henry M; Tao, Lin; Shaver, Shannon M; Aldous, Kenneth M; Pass, Kenneth A; Kannan, Kurunthachalam; Eadon, George A

2008-07-15

Temporal biomonitoring studies can assess changes in population exposures to contaminants, but collection of biological specimens with adequate representation and sufficient temporal resolution can be resource-intensive. Newborn Screening Programs (NSPs) collect blood as dried spots on filter paper from nearly all infants born in the United States (U.S.). In this study, we investigated the use of NSP blood spots for temporal biomonitoring by analyzing perfluorooctane sulfonate (PFOS), perfluorooctane sulfonamide (PFOSA), perfluorohexane sulfonate (PFHxS), perfluorooctanoic acid (PFOA), and perfluorononanoic acid (PFNA) in 110 New York State (NYS) NSP blood spot composite specimens collected between 1997 and 2007, representing a total of 2640 infants. All analytes were detected in > or =90% of the specimens. Concentrations of PFOS, PFOSA, PFHxS, and PFOA exhibited significant exponential declines after the year 2000, coinciding with the phase-out in PFOS production in the U.S. Calculated disappearance half-lives for PFOS, PFHxS, and PFOA (4.4, 8.2, and 4.1 years, respectively) were similar to biological half-lives reported for retired fluorochemical workers. Our results suggest sharp decreases in perinatal exposure of NYS infants to PFOS, PFOSA, PFHxS, and PFOA and demonstrate, for the first time, the utility of NSP blood spots for assessment of temporal trends in exposure.

Controlled microaspiration for high-pressure freezing: a new method for ultrastructural preservation of fragile and sparse tissues for TEM and electron tomography

PubMed Central

Triffo, W. J.; Palsdottir, H.; McDonald, K. L.; Lee, J. K.; Inman, J. L.; Bissell, M. J.; Raphael, R. M.; Auer, M.

2009-01-01

Summary High-pressure freezing is the preferred method to prepare thick biological specimens for ultrastructural studies. However, the advantages obtained by this method often prove unattainable for samples that are difficult to handle during the freezing and substitution protocols. Delicate and sparse samples are difficult to manipulate and maintain intact throughout the sequence of freezing, infiltration, embedding and final orientation for sectioning and subsequent transmission electron microscopy. An established approach to surmount these difficulties is the use of cellulose microdialysis tubing to transport the sample. With an inner diameter of 200 µm, the tubing protects small and fragile samples within the thickness constraints of high-pressure freezing, and the tube ends can be sealed to avoid loss of sample. Importantly, the transparency of the tubing allows optical study of the specimen at different steps in the process. Here, we describe the use of a micromanipulator and microinjection apparatus to handle and position delicate specimens within the tubing. We report two biologically significant examples that benefit from this approach, 3D cultures of mammary epithelial cells and cochlear outer hair cells. We illustrate the potential for correlative light and electron microscopy as well as electron tomography. PMID:18445158

Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

NASA Astrophysics Data System (ADS)

Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

2016-10-01

The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms

PubMed Central

Mirkovic, Djordje; Stepanian, Phillip M.; Kelly, Jeffrey F.; Chilson, Phillip B.

2016-01-01

The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification. PMID:27762292

Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

PubMed Central

Flores-Villela, Oscar; Fujita, Matthew K.

2015-01-01

Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the “climatic niche”); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus. PMID:26107178

Limitations of climatic data for inferring species boundaries: insights from speckled rattlesnakes.

PubMed

Meik, Jesse M; Streicher, Jeffrey W; Lawing, A Michelle; Flores-Villela, Oscar; Fujita, Matthew K

2015-01-01

Phenotypes, DNA, and measures of ecological differences are widely used in species delimitation. Although rarely defined in such studies, ecological divergence is almost always approximated using multivariate climatic data associated with sets of specimens (i.e., the "climatic niche"); the justification for this approach is that species-specific climatic envelopes act as surrogates for physiological tolerances. Using identical statistical procedures, we evaluated the usefulness and validity of the climate-as-proxy assumption by comparing performance of genetic (nDNA SNPs and mitochondrial DNA), phenotypic, and climatic data for objective species delimitation in the speckled rattlesnake (Crotalus mitchellii) complex. Ordination and clustering patterns were largely congruent among intrinsic (heritable) traits (nDNA, mtDNA, phenotype), and discordance is explained by biological processes (e.g., ontogeny, hybridization). In contrast, climatic data did not produce biologically meaningful clusters that were congruent with any intrinsic dataset, but rather corresponded to regional differences in atmospheric circulation and climate, indicating an absence of inherent taxonomic signal in these data. Surrogating climate for physiological tolerances adds artificial weight to evidence of species boundaries, as these data are irrelevant for that purpose. Based on the evidence from congruent clustering of intrinsic datasets, we recommend that three subspecies of C. mitchellii be recognized as species: C. angelensis, C. mitchellii, and C. Pyrrhus.

The Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort study: assessment of environmental exposures.

PubMed

Takaro, Tim K; Scott, James A; Allen, Ryan W; Anand, Sonia S; Becker, Allan B; Befus, A Dean; Brauer, Michael; Duncan, Joanne; Lefebvre, Diana L; Lou, Wendy; Mandhane, Piush J; McLean, Kathleen E; Miller, Gregory; Sbihi, Hind; Shu, Huan; Subbarao, Padmaja; Turvey, Stuart E; Wheeler, Amanda J; Zeng, Leilei; Sears, Malcolm R; Brook, Jeffrey R

2015-01-01

The Canadian Healthy Infant Longitudinal Development birth cohort was designed to elucidate interactions between environment and genetics underlying development of asthma and allergy. Over 3600 pregnant mothers were recruited from the general population in four provinces with diverse environments. The child is followed to age 5 years, with prospective characterization of diverse exposures during this critical period. Key exposure domains include indoor and outdoor air pollutants, inhalation, ingestion and dermal uptake of chemicals, mold, dampness, biological allergens, pets and pests, housing structure, and living behavior, together with infections, nutrition, psychosocial environment, and medications. Assessments of early life exposures are focused on those linked to inflammatory responses driven by the acquired and innate immune systems. Mothers complete extensive environmental questionnaires including time-activity behavior at recruitment and when the child is 3, 6, 12, 24, 30, 36, 48, and 60 months old. House dust collected during a thorough home assessment at 3-4 months, and biological specimens obtained for multiple exposure-related measurements, are archived for analyses. Geo-locations of homes and daycares and land-use regression for estimating traffic-related air pollution complement time-activity-behavior data to provide comprehensive individual exposure profiles. Several analytical frameworks are proposed to address the many interacting exposure variables and potential issues of co-linearity in this complex data set.

Electromagnetic Model Reliably Predicts Radar Scattering Characteristics of Airborne Organisms.

PubMed

Mirkovic, Djordje; Stepanian, Phillip M; Kelly, Jeffrey F; Chilson, Phillip B

2016-10-20

The radar scattering characteristics of aerial animals are typically obtained from controlled laboratory measurements of a freshly harvested specimen. These measurements are tedious to perform, difficult to replicate, and typically yield only a small subset of the full azimuthal, elevational, and polarimetric radio scattering data. As an alternative, biological applications of radar often assume that the radar cross sections of flying animals are isotropic, since sophisticated computer models are required to estimate the 3D scattering properties of objects having complex shapes. Using the method of moments implemented in the WIPL-D software package, we show for the first time that such electromagnetic modeling techniques (typically applied to man-made objects) can accurately predict organismal radio scattering characteristics from an anatomical model: here the Brazilian free-tailed bat (Tadarida brasiliensis). The simulated scattering properties of the bat agree with controlled measurements and radar observations made during a field study of bats in flight. This numerical technique can produce the full angular set of quantitative polarimetric scattering characteristics, while eliminating many practical difficulties associated with physical measurements. Such a modeling framework can be applied for bird, bat, and insect species, and will help drive a shift in radar biology from a largely qualitative and phenomenological science toward quantitative estimation of animal densities and taxonomic identification.

Use of fluorescence and scanning electron microscopy as tools in teaching biology

NASA Astrophysics Data System (ADS)

Ghosh, Nabarun; Silva, Jessica; Vazquez, Aracely; Das, A. B.; Smith, Don W.

2011-06-01

Recent nationwide surveys reveal significant decline in students' interest in Math and Sciences. The objective of this project was to inspire young minds in using various techniques involved in Sciences including Scanning Electron Microscopy. We used Scanning Electron Microscope in demonstrating various types of Biological samples. An SEM Tabletop model in the past decade has revolutionized the use of Scanning Electron Microscopes. Using SEM Tabletop model TM 1000 we studied biological specimens of fungal spores, pollen grains, diatoms, plant fibers, dust mites, insect parts and leaf surfaces. We also used fluorescence microscopy to view, to record and analyze various specimens with an Olympus BX40 microscope equipped with FITC and TRITC fluorescent filters, a mercury lamp source, DP-70 digital camera with Image Pro 6.0 software. Micrographs were captured using bright field microscopy, the fluoresceinisothiocyanate (FITC) filter, and the tetramethylrhodamine (TRITC) filter settings at 40X. A high pressure mercury lamp or UV source was used to excite the storage molecules or proteins which exhibited autofluorescence. We used fluorescent microscopy to confirm the localization of sugar beet viruses in plant organs by viewing the vascular bundles in the thin sections of the leaves and other tissues. We worked with the REU summer students on sample preparation and observation on various samples utilizing the SEM. Critical Point Drying (CPD) and metal coating with the sputter coater was followed before observing some cultured specimen and the samples that were soft in textures with high water content. SEM Top allowed investigating the detailed morphological features that can be used for classroom teaching. Undergraduate and graduate researchers studied biological samples of Arthropods, pollen grains and teeth collected from four species of snakes using SEM. This project inspired the research students to pursue their career in higher studies in science and 45% of the undergraduates participated in this project entered Graduate school.

The investigation of vertebral injury sustained during aircrew ejection

NASA Technical Reports Server (NTRS)

Benedict, J. V.

1972-01-01

A series of tests were performed on excised human vertebral segments to determine the static and dynamic response of the thoraco-lumbar spine when loaded in flexion. A total of fifteen tests were performed on eleven specimens. Specimens were obtained from male donors ranging in age from 34 to 60 years. Demographic data pertinent to each specimen and the elapsed time between death of the donor and testing of each corresponding specimen are presented. Only spinal segments comprised of lower thoracic and upper lumbar vertebrae were tested because in aircraft ejection injuries clinical complications in this anatomical region predominate. A complex continuum mathematical model describing the dynamic response of the human spine was formulated, solved, and verified experimentally. Detailed results are presented in figures, tables, and equations.

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study.

PubMed

Kridel, Robert; Chan, Fong Chun; Mottok, Anja; Boyle, Merrill; Farinha, Pedro; Tan, King; Meissner, Barbara; Bashashati, Ali; McPherson, Andrew; Roth, Andrew; Shumansky, Karey; Yap, Damian; Ben-Neriah, Susana; Rosner, Jamie; Smith, Maia A; Nielsen, Cydney; Giné, Eva; Telenius, Adele; Ennishi, Daisuke; Mungall, Andrew; Moore, Richard; Morin, Ryan D; Johnson, Nathalie A; Sehn, Laurie H; Tousseyn, Thomas; Dogan, Ahmet; Connors, Joseph M; Scott, David W; Steidl, Christian; Marra, Marco A; Gascoyne, Randy D; Shah, Sohrab P

2016-12-01

Follicular lymphoma (FL) is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points: histological transformation and early progression after immunochemotherapy. The nature of tumor clonal dynamics leading to these clinical end points is poorly understood, and previously determined genetic alterations do not explain the majority of transformed cases or accurately predict early progressive disease. We contend that detailed knowledge of the expansion patterns of specific cell populations plus their associated mutations would provide insight into therapeutic strategies and disease biology over the time course of FL clinical histories. Using a combination of whole genome sequencing, targeted deep sequencing, and digital droplet PCR on matched diagnostic and relapse specimens, we deciphered the constituent clonal populations in 15 transformation cases and 6 progression cases, and measured the change in clonal population abundance over time. We observed widely divergent patterns of clonal dynamics in transformed cases relative to progressed cases. Transformation specimens were generally composed of clones that were rare or absent in diagnostic specimens, consistent with dramatic clonal expansions that came to dominate the transformation specimens. This pattern was independent of time to transformation and treatment modality. By contrast, early progression specimens were composed of clones that were already present in the diagnostic specimens and exhibited only moderate clonal dynamics, even in the presence of immunochemotherapy. Analysis of somatic mutations impacting 94 genes was undertaken in an extension cohort consisting of 395 samples from 277 patients in order to decipher disrupted biology in the two clinical end points. We found 12 genes that were more commonly mutated in transformed samples than in the preceding FL tumors, including TP53, B2M, CCND3, GNA13, S1PR2, and P2RY8. Moreover, ten genes were more commonly mutated in diagnostic specimens of patients with early progression, including TP53, BTG1, MKI67, and XBP1. Our results illuminate contrasting modes of evolution shaping the clinical histories of transformation and progression. They have implications for interpretation of evolutionary dynamics in the context of treatment-induced selective pressures, and indicate that transformation and progression will require different clinical management strategies.

Histological Transformation and Progression in Follicular Lymphoma: A Clonal Evolution Study

PubMed Central

Mottok, Anja; Boyle, Merrill; Tan, King; Meissner, Barbara; Bashashati, Ali; Roth, Andrew; Shumansky, Karey; Nielsen, Cydney; Giné, Eva; Moore, Richard; Morin, Ryan D.; Sehn, Laurie H.; Tousseyn, Thomas; Dogan, Ahmet; Scott, David W.; Steidl, Christian; Gascoyne, Randy D.; Shah, Sohrab P.

2016-01-01

Background Follicular lymphoma (FL) is an indolent, yet incurable B cell malignancy. A subset of patients experience an increased mortality rate driven by two distinct clinical end points: histological transformation and early progression after immunochemotherapy. The nature of tumor clonal dynamics leading to these clinical end points is poorly understood, and previously determined genetic alterations do not explain the majority of transformed cases or accurately predict early progressive disease. We contend that detailed knowledge of the expansion patterns of specific cell populations plus their associated mutations would provide insight into therapeutic strategies and disease biology over the time course of FL clinical histories. Methods and Findings Using a combination of whole genome sequencing, targeted deep sequencing, and digital droplet PCR on matched diagnostic and relapse specimens, we deciphered the constituent clonal populations in 15 transformation cases and 6 progression cases, and measured the change in clonal population abundance over time. We observed widely divergent patterns of clonal dynamics in transformed cases relative to progressed cases. Transformation specimens were generally composed of clones that were rare or absent in diagnostic specimens, consistent with dramatic clonal expansions that came to dominate the transformation specimens. This pattern was independent of time to transformation and treatment modality. By contrast, early progression specimens were composed of clones that were already present in the diagnostic specimens and exhibited only moderate clonal dynamics, even in the presence of immunochemotherapy. Analysis of somatic mutations impacting 94 genes was undertaken in an extension cohort consisting of 395 samples from 277 patients in order to decipher disrupted biology in the two clinical end points. We found 12 genes that were more commonly mutated in transformed samples than in the preceding FL tumors, including TP53, B2M, CCND3, GNA13, S1PR2, and P2RY8. Moreover, ten genes were more commonly mutated in diagnostic specimens of patients with early progression, including TP53, BTG1, MKI67, and XBP1. Conclusions Our results illuminate contrasting modes of evolution shaping the clinical histories of transformation and progression. They have implications for interpretation of evolutionary dynamics in the context of treatment-induced selective pressures, and indicate that transformation and progression will require different clinical management strategies. PMID:27959929

Sequence-based classification and identification of fungi

USDA-ARS?s Scientific Manuscript database

Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomi...

The taphonomy of unmineralised Palaeozoic fossils preserved as siliciclastic moulds and casts, and their utility in assessing the interaction between environmental change and the fossil record

NASA Astrophysics Data System (ADS)

MacGabhann, Breandán; Schiffbauer, James; Hagadorn, James; Van Roy, Peter; Lynch, Edward; Morrsion, Liam; Murray, John

2015-04-01

The enhanced preservation potential of biomineralised tissues in fossil organisms is a key factor in their utility in the investigation of palaeoenvironmental change on fossil ecosystems. By contrast, the considerably lower preservation potential of entirely unmineralised organisms severely reduces the utility of their temporal and spatial distribution in such analyses. However, understanding the taphonomic processes which lead to the preservation of such soft-bodied fossils may be an under-appreciated source of information, particularly in the case of specimens preserved as moulds and casts in coarser siliciclastic sediments. This information potential is well demonstrated by fossil eldonids, a Cambrian to Devonian clade of unmineralised asymmetrical discoidal basal or stem deuterostomes, with an apparently conservative biology and no clear palaeoenvironmental or biogeographical controls on their distribution. We investigated the taphonomic processes involved in the preservation of fossil eldonids as moulds and casts on bedding surfaces and within event beds from sandstones of the Ordovician Tafilalt lagerstätte in south-eastern Morocco, and from siltstones of the Devonian West Falls Group of New York, USA. Laser Raman microspectroscopy, SEM BSE imaging and EDS elemental mapping of fossil specimens reveals that moulded biological surfaces are coated by a fossil surface veneer primarily consisting of mixed iron oxides and oxyhydroxides (including pseudomorphs after pyrite), and aluminosilicate clay minerals. Moreover, comparison to fossil eldonids preserved as carbonaceous compressions in the Burgess Shale reveals that the biological structures preserved in the Tafilalt and New York specimens - the dorsal surface and a coiled sac containing the digestive tract - represent only specific portions of the anatomy of the complete animal. We suggest that the preserved remains were the only parts of these eldonid organisms composed primarily of complex organic biopolymers, and that these tissues were preferentially fossilised by the formation of an early diagenic mould directly on the organic surfaces. Excess divalent iron ions, produced during decay of more labile tissues by means of bacterial iron reduction, would have adsorbed to anionic functional groups in the biopolymeric tissues. This would have provided a ready substrate for the formation and growth of such an early diagenic mineralised mould, including aluminosilicate minerals produced via reaction with seawater silica and metal ions, and iron sulphide minerals produced via reaction with hydrogen sulphide and free sulphur produced from seawater sulphate through bacterial sulphate reduction associated with further decay. Subsequent weathering would have oxidised such iron sulphides to oxides and oxyhydroxides. This taphonomic model supports the lack of utility of the eldonid palaeobiological record in analysing environmental influence on biological communities, due to the lack of preservation of key anatomical components. However, it also suggests that the very occurrence of fossils preserved in this style is dependent on extrinsic palaeoenvironmental factors - including pH, Eh, and the concentration of other ions in the contemporaneous seawater. Analyses of the distribution of fossils preserved in this style may therefore provide information on ambient conditions which may have affected the distribution of contemporaneous mineralised fossils, potentially allowing a more complete analysis of the effects of palaeoenvironmental change on fossil ecosystems.

Use of shuttle for life sciences

NASA Technical Reports Server (NTRS)

Mcgaughy, R. E.

1972-01-01

The use of the space shuttle in carrying out biological and medical research programs, with emphasis on the sortie module, is examined. Detailed descriptions are given of the goals of space life science disciplines, how the sortie can meet these goals, and what shuttle design features are necessary for a viable biological and medical experiment program. Conclusions show that the space shuttle sortie module is capable of accommodating all biological experiments contemplated at this time except for those involving large specimens or large populations of small animals; however, these experiments can be done with a specially designed module. It was also found that at least two weeks is required to do a meaningful survey of biological effects.

Unveiling an ancient biological invasion: molecular analysis of an old European alien, the crested porcupine (Hystrix cristata).

PubMed

Trucchi, Emiliano; Sbordoni, Valerio

2009-05-18

Biological invasions can be considered one of the main threats to biodiversity, and the recognition of common ecological and evolutionary features among invaders can help developing a predictive framework to control further invasions. In particular, the analysis of successful invasive species and of their autochthonous source populations by means of genetic, phylogeographic and demographic tools can provide novel insights into the study of biological invasion patterns. Today, long-term dynamics of biological invasions are still poorly understood and need further investigations. Moreover, distribution and molecular data on native populations could contribute to the recognition of common evolutionary features of successful aliens. We analyzed 2,195 mitochondrial base pairs, including Cytochrome b, Control Region and rRNA 12S, in 161 Italian and 27 African specimens and assessed the ancient invasive origin of Italian crested porcupine (Hystrix cristata) populations from Tunisia. Molecular coalescent-based Bayesian analyses proposed the Roman Age as a putative timeframe of introduction and suggested a retention of genetic diversity during the early phases of colonization. The characterization of the native African genetic background revealed the existence of two differentiated clades: a Mediterranean group and a Sub-Saharan one. Both standard population genetic and advanced molecular demography tools (Bayesian Skyline Plot) did not evidence a clear genetic signature of the expected increase in population size after introduction. Along with the genetic diversity retention during the bottlenecked steps of introduction, this finding could be better described by hypothesizing a multi-invasion event. Evidences of the ancient anthropogenic invasive origin of the Italian Hystrix cristata populations were clearly shown and the native African genetic background was preliminary described. A more complex pattern than a simple demographic exponential growth from a single propagule seems to have characterized this long-term invasion.

Preservation of pathological tissue specimens by freeze-drying for immunohistochemical staining and various molecular biological analyses.

PubMed

Matsuo, S; Sugiyama, T; Okuyama, T; Yoshikawa, K; Honda, K; Takahashi, R; Maeda, S

1999-05-01

Conditions of preserving DNA, RNA and protein in pathological specimens are of great importance as degradation of such macromolecules would critically affect results of molecular biological analysis. The feasibility of freeze-drying as a means of preserving pathological tissue samples for molecular analysis has previously been shown. In the present study, further tests on long-term storage conditions and analyses of freeze-dried samples by polymerase chain reaction (PCR), reverse transcriptase (RT)-PCR, western blotting and immunohistochemistry are reported. Rat chromosomal DNA of freeze-dried samples stored for 4 years showed slight degradation while RNA degradation was more prominently seen at an earlier stage of storage. However, these 4 year DNA and RNA samples were still able to serve as a template for some PCR and RT-PCR analyses, respectively. Overexpression of c-erbB-2 and p53 protein was demonstrated by western blotting and immunohistochemical staining using freeze-dried human breast cancer tissues. Although macromolecules in freeze-dried samples degrade to some extent during the preservation period, they should still be of value for certain molecular biological analyses and morphological examination; hence, providing more convenient and inexpensive ways of pathological tissue storage.

PREFACE: Ultrafast biophotonics Ultrafast biophotonics

NASA Astrophysics Data System (ADS)

Gu, Min; Reid, Derryck; Ben-Yakar, Adela

2010-08-01

The use of light to explore biology can be traced to the first observations of tissue made with early microscopes in the mid-seventeenth century, and has today evolved into the discipline which we now know as biophotonics. This field encompasses a diverse range of activities, each of which shares the common theme of exploiting the interaction of light with biological material. With the rapid advancement of ultrafast optical technologies over the last few decades, ultrafast lasers have increasingly found applications in biophotonics, to the extent that the distinctive new field of ultrafast biophotonics has now emerged, where robust turnkey ultrafast laser systems are facilitating cutting-edge studies in the life sciences to take place in everyday laboratories. The broad spectral bandwidths, precision timing resolution, low coherence and high peak powers of ultrafast optical pulses provide unique opportunities for imaging and manipulating biological systems. Time-resolved studies of bio-molecular dynamics exploit the short pulse durations from such lasers, while other applications such as optical coherence tomography benefit from the broad optical bandwidths possible by using super-continuum generation and additionally allowing for high speed imaging with speeds as high as 47 000 scans per second. Continuing progress in laser-system technology is accelerating the adoption of ultrafast techniques across the life sciences, both in research laboratories and in clinical applications, such as laser-assisted in situ keratomileusis (LASIK) eye surgery. Revolutionizing the field of optical microscopy, two-photon excitation fluorescence (TPEF) microscopy has enabled higher spatial resolution with improved depth penetration into biological specimens. Advantages of this nonlinear optical process include: reduced photo-interactions, allowing for extensive imaging time periods; simultaneously exciting multiple fluorescent molecules with only one excitation wavelength; and reduced chromatic aberration effects. These extensive advantages have led to further exploration of nonlinear processes including second-harmonic generation (SHG) microscopy and third-harmonic generation (THG) microscopy. Second-harmonic generation has provided biologists with an extremely powerful tool for generating contrast in biological imaging, with the additional benefit of non-invasive three-dimensional imaging. The recent popularity of THG microscopy is largely due to the fact that three-dimensional imaging is achievable without the need for any labels, but rather relying on the intrinsic properties of the biological specimen itself. This optical nonlinear technique has attracted much attention recently from the biological community due to its non-invasive capabilities. Users of ultrafast lasers in the biological and medical fields are becoming a fast-growing community, employing pulse-shaping microscopy, resolution-enhancing microscopy techniques, linear and nonlinear micro-spectroscopy, functional deep-tissue imaging, optical coherence tomography, nonlinear fluorescence microscopy, molecular imaging and control, harmonic microscopy and femtosecond lifetime imaging, for cutting-edge research concerning the interaction of light with biological dynamics. The adaptability of ultrafast lasers to interact with a large array of materials through nonlinear excitation has enabled precise control of laser fluence allowing for highly localized material interactions, permitting micro-structured fabricated surfaces. The resultant multi-dimensional fabricated micro-structures are capable of replicating and/or manipulating microenvironments for controlled cell biology. In this special issue of Journal of Optics readers have a chance to view a collection of new contributions to the growing research field of ultrafast biophotonics. They are presented with recent advances in ultrafast technology applied to biological and medical investigations, where topics include advances in the visualization and identification of photo-reaction dynamics of biological functions under relevant physiological conditions, theoretically proposed imaging designs for obtaining super-resolved optical sectioned images in single exposures and fabricated micro-structured surfaces for biological micro-environments. We hope the collection will stimulate innovative new research in this growing field by showcasing new techniques for the visualization and manipulation of complex biological systems using linear and and nonlinear optical processes. Professor Min Gu would like to acknowledge Dr Betty Kouskousis for her contribution and support towards this editorial.

Evaluation of the Cepheid Xpert MTB/RIF assay for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.

PubMed

Marlowe, Elizabeth M; Novak-Weekley, Susan M; Cumpio, Joven; Sharp, Susan E; Momeny, Michelle A; Babst, Anna; Carlson, Jonathan S; Kawamura, Masae; Pandori, Mark

2011-04-01

A total of 217 specimens submitted for routine smear and culture from three different sites within the western United States were used to evaluate the GeneXpert MTB/RIF assay (for research use only) (Cepheid, Sunnyvale, CA). Overall agreement compared to culture was 89% (98% for smear positives and 72% for smear negatives) for detection of Mycobacterium tuberculosis.

Atom probe trajectory mapping using experimental tip shape measurements.

PubMed

Haley, D; Petersen, T; Ringer, S P; Smith, G D W

2011-11-01

Atom probe tomography is an accurate analytical and imaging technique which can reconstruct the complex structure and composition of a specimen in three dimensions. Despite providing locally high spatial resolution, atom probe tomography suffers from global distortions due to a complex projection function between the specimen and detector which is different for each experiment and can change during a single run. To aid characterization of this projection function, this work demonstrates a method for the reverse projection of ions from an arbitrary projection surface in 3D space back to an atom probe tomography specimen surface. Experimental data from transmission electron microscopy tilt tomography are combined with point cloud surface reconstruction algorithms and finite element modelling to generate a mapping back to the original tip surface in a physically and experimentally motivated manner. As a case study, aluminium tips are imaged using transmission electron microscopy before and after atom probe tomography, and the specimen profiles used as input in surface reconstruction methods. This reconstruction method is a general procedure that can be used to generate mappings between a selected surface and a known tip shape using numerical solutions to the electrostatic equation, with quantitative solutions to the projection problem readily achievable in tens of minutes on a contemporary workstation. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Diagnostics of plasma-biological surface interactions in low pressure and atmospheric pressure plasmas

NASA Astrophysics Data System (ADS)

Ishikawa, Kenji; Hori, Masaru

2014-08-01

Mechanisms of plasma-surface interaction are required to understand in order to control the reactions precisely. Recent progress in atmospheric pressure plasma provides to apply as a tool of sterilization of contaminated foodstuffs. To use the plasma with safety and optimization, the real time in situ detection of free radicals - in particular dangling bonds by using the electron-spin-resonance (ESR) technique has been developed because the free radical plays important roles for dominantly biological reactions. First, the kinetic analysis of free radicals on biological specimens such as fungal spores of Penicillium digitatum interacted with atomic oxygen generated plasma electric discharge. We have obtained information that the in situ real time ESR signal from the spores was observed and assignable to semiquinone radical with a g-value of around 2.004 and a line width of approximately 5G. The decay of the signal was correlated with a link to the inactivation of the fungal spore. Second, we have studied to detect chemical modification of edible meat after the irradiation. Using matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy (MALDI-TOF-MS) and ESR, signals give qualification results for chemical changes on edible liver meat. The in situ real-time measurements have proven to be a useful method to elucidate plasma-induced surface reactions on biological specimens.

Modern dosimetric tools for 60Co irradiation at high containment laboratories

PubMed Central

Twardoski, Barri; Feldmann, Heinz; Bloom, Marshall E.; Ward, Joe

2011-01-01

Purpose To evaluate an innovative photo-fluorescent film as a routine dosimetric tool during 60Co irradiations at a high containment biological research laboratory, and to investigate whether manufacturer-provided chamber exposure rates can be used to accurately administer a prescribed dose to biological specimens. Materials and methods Photo-fluorescent, lithium fluoride film dosimeters and National Institutes of Standards and Technology (NIST) transfer dosimeters were co-located in a self-shielded 60Co irradiator and exposed to γ-radiation with doses ranging from 5–85 kGy. Film dose-response relationships were developed for varying temperatures simulating conditions present when irradiating infectious biological specimens. Dose measurement results from NIST transfer dosimeters were compared to doses predicted using manufacturer-provided irradiator chamber exposure rates. Results The film dosimeter exhibited a photo-fluorescent response signal that was consistent and nearly linear in relationship to γ-radiation exposure over a wide dose range. The dosimeter response also showed negligible effects from dose fractionization and humidity. Significant disparities existed between manufacturer-provided chamber exposure rates and actual doses administered. Conclusion This study demonstrates the merit of utilizing dosimetric tools to validate the process of exposing dangerous and exotic biological agents to γ-radiation at high containment laboratories. The film dosimeter used in this study can be utilized to eliminate potential for improperly administering γ-radiation doses. PMID:21961968

Comprehensive analysis of the lipophilic reactive carbonyls present in biological specimens by LC/ESI-MS/MS.

PubMed

Tomono, Susumu; Miyoshi, Noriyuki; Ohshima, Hiroshi

2015-04-15

A new analytical method has been developed for profiling lipophilic reactive carbonyls (RCs) such as aldehydes and ketones in biological samples using liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) with selected reaction monitoring (SRM). The method consists of several phases, including (1) extraction of lipophilic RCs with a chloroform/methanol mixture; (2) derivatization of the extracted RCs with dansyl hydrazine (DH); and (3) SRM detection of the characteristic product ion of the 5-dimethylaminonaphthalene-1-sulfonyl moiety (m/z 236.1). The analytical results were expressed as RC maps, which allowed for the occurrence and levels of different lipophilic RCs to be visualized. We also developed a highly reproducible and accurate method to extract, purify and derivatize RCs in small volumes of biological specimens. This method was applied to the detection of free RCs in mice plasma samples, and resulted in the detection of more than 400 RCs in samples obtained from C57BL/6J mice. Thirty-four of these RCs were identified by comparison with authentic RCs. This method could be used to investigate the levels of RCs in biological and environmental samples, as well as studying the role of lipid peroxidation in oxidative stress related-disorders and discovering new biomarkers for the early diagnosis of these diseases. Copyright © 2015 Elsevier B.V. All rights reserved.

Electrical properties and dielectric spectroscopy of Ar{sup +} implanted polycarbonate

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

Chawla, Mahak, E-mail: mahak.chawla@gmail.com; Shekhawat, Nidhi; Aggarwal, Sanjeev

2015-05-15

The aim of the present paper is to study the effect of argon ion implantation on electrical and dielectric properties of polycarbonate. Specimens were implanted with 130 keV Ar{sup +} ions in the fluence ranging from 1×10{sup 14} to 1×10{sup 16} ions cm{sup −2}. The beam current used was ∼0.40 µA cm{sup −2}. The electrical conduction behaviour of virgin and Ar{sup +} implanted polycarbonate specimens have been studied through current-voltage (I-V characteristic) measurements. It has been observed that after implantation conductivity increases with increasing ion fluence. The dielectric spectroscopy of these specimens has been done in the frequency range of 100 kHz-100 MHz.more » Relaxation processes were studied by Cole-Cole plot of complex permittivity (real part of complex permittivity, ε′ vs. imaginary part of complex permittivity, ε″). The Cole-Cole plots have also been used to determine static dielectric constant (ε{sub s}), optical dielectric constant (ε{sub ∞}), spreading factor (α), average relaxation time (τ{sub 0}) and molecular relaxation time (τ). The dielectric behaviour has been found to be significantly affected due to Ar{sup +} implantation. The possible correlation between this behaviour and the changes induced by the implantation has been discussed.« less

Wing morphometrics as a possible tool for the diagnosis of the Ceratitis fasciventris, C. anonae, C. rosa complex (Diptera, Tephritidae).

PubMed

Van Cann, Joannes; Virgilio, Massimiliano; Jordaens, Kurt; De Meyer, Marc

2015-01-01

Previous attempts to resolve the Ceratitis FAR complex (Ceratitis fasciventris, Ceratitis anonae, Ceratitis rosa, Diptera, Tephritidae) showed contrasting results and revealed the occurrence of five microsatellite genotypic clusters (A, F1, F2, R1, R2). In this paper we explore the potential of wing morphometrics for the diagnosis of FAR morphospecies and genotypic clusters. We considered a set of 227 specimens previously morphologically identified and genotyped at 16 microsatellite loci. Seventeen wing landmarks and 6 wing band areas were used for morphometric analyses. Permutational multivariate analysis of variance detected significant differences both across morphospecies and genotypic clusters (for both males and females). Unconstrained and constrained ordinations did not properly resolve groups corresponding to morphospecies or genotypic clusters. However, posterior group membership probabilities (PGMPs) of the Discriminant Analysis of Principal Components (DAPC) allowed the consistent identification of a relevant proportion of specimens (but with performances differing across morphospecies and genotypic clusters). This study suggests that wing morphometrics and PGMPs might represent a possible tool for the diagnosis of species within the FAR complex. Here, we propose a tentative diagnostic method and provide a first reference library of morphometric measures that might be used for the identification of additional and unidentified FAR specimens.

Rapid and Portable Methods for Identification of Bacterially Influenced Calcite: Application of Laser-Induced Breakdown Spectroscopy and AOTF Reflectance Spectroscopy, Fort Stanton Cave, New Mexico

NASA Astrophysics Data System (ADS)

McMillan, N. J.; Chavez, A.; Chanover, N.; Voelz, D.; Uckert, K.; Tawalbeh, R.; Gariano, J.; Dragulin, I.; Xiao, X.; Hull, R.

2014-12-01

Rapid, in-situ methods for identification of biologic and non-biologic mineral precipitation sites permit mapping of biological hot spots. Two portable spectrometers, Laser-Induced Breakdown Spectroscopy (LIBS) and Acoustic-Optic Tunable Filter Reflectance Spectroscopy (AOTFRS) were used to differentiate between bacterially influenced and inorganically precipitated calcite specimens from Fort Stanton Cave, NM, USA. LIBS collects light emitted from the decay of excited electrons in a laser ablation plasma; the spectrum is a chemical fingerprint of the analyte. AOTFRS collects light reflected from the surface of a specimen and provides structural information about the material (i.e., the presence of O-H bonds). These orthogonal data sets provide a rigorous method to determine the origin of calcite in cave deposits. This study used a set of 48 calcite samples collected from Fort Stanton cave. Samples were examined in SEM for the presence of biologic markers; these data were used to separate the samples into biologic and non-biologic groups. Spectra were modeled using the multivariate technique Partial Least Squares Regression (PLSR). Half of the spectra were used to train a PLSR model, in which biologic samples were assigned to the independent variable "0" and non-biologic samples were assigned the variable "1". Values of the independent variable were calculated for each of the training samples, which were close to 0 for the biologic samples (-0.09 - 0.23) and close to 1 for the non-biologic samples (0.57 - 1.14). A Value of Apparent Distinction (VAD) of 0.55 was used to numerically distinguish between the two groups; any sample with an independent variable value < 0.55 was classified as having a biologic origin; a sample with a value > 0.55 was determined to be non-biologic in origin. After the model was trained, independent variable values for the remaining half of the samples were calculated. Biologic or non-biologic origin was assigned by comparison to the VAD. Using LIBS data alone, the model has a 92% success rate, correctly identifying 23 of 25 samples. Modeling of AOTFRS spectra and the combined LIBS-AOTFRS data set have similar success rates. This study demonstrates that rapid, portable LIBS and AOTFRS instruments can be used to map the spatial distribution of biologic precipitation in caves.

Fractography of induction-hardened steel fractured in fatigue and overload

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

Santos, C.G.; Laird, C.

1997-07-01

The fracture surfaces of induction-hardened steel specimens obtained from an auto axle were characterized, macroscopically and microscopically, after being fractured in fatigue and monotonic overload. Specimens were tested in cyclic three-point bending under load control, and the S-N curve was established for specimens that had been notched by spark machining to facilitate fractography. Scanning electron microscopy of the fractured surfaces obtained for lives spanning the range 17,000 to 418,000 cycles revealed diverse fracture morphologies, including intergranular fracture and transgranular fatigue fracture. The results are being offered to assist in the analysis of complex field failures in strongly hardened steel.

Accretion of biopsy specimens of vaginal adenosis from patients exposed in utero to diethylstilbestrol, when transplanted to athymic nude mice.

PubMed

Pienkowski, M M; Mann, L C; Rosloniec, E F; Welsch, C W

1979-03-01

Vaginal adenosis biopsy specimens from 10 patients exposed in utero to diethylstilbestrol were transplanted for 30 days into athymic (nude) mice. Almost all grafts were recovered, and they had morphologic features closely resembling those of the original biopsy specimens, i.e., cystic, complex, and simple occult glands covered mainly with an endocervical type of epithelium showing extensive squamous metaplasia. Autoradiographic analysis of these grafts after pulse administration of [3H]thymidine into the mice revealed extensive labeling of epithelial cells. These results imply that female athymic (nude) mice are compatible hosts for accretion of the human adenosis.

A comparative study of the microstructures observed in statically cast and continuously cast Bi-In-Sn ternary eutectic alloy

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

Sengupta, S.; Soda, H.; McLean, A.

2000-01-01

A ternary eutectic alloy with a composition of 57.2 pct Bi, 24.8 pct In, and 18 pct Sn was continuously cast into wire of 2 mm diameter with casting speeds of 14 and 79 mm/min using the Ohno Continuous Casting (OCC) process. The microstructures obtained were compared with those of statically cast specimens. Extensive segregation of massive Bi blocks, Bi complex structures, and tin-rich dendrites was found in specimens that were statically cast. Decomposition of {radical}Sn by a eutectoid reaction was confirmed based on microstructural evidence. Ternary eutectic alloy with a cooling rate of approximately 1 C/min formed a doublemore » binary eutectic. The double binary eutectic consisted of regions of BiIn and decomposed {radical}Sn in the form of a dendrite cell structure and regions of Bi and decomposed {radical}Sn in the form of a complex-regular cell. The Bi complex-regular cells, which are a ternary eutectic constituent, existed either along the boundaries of the BiIn-decomposed {radical}Sn dendrite cells or at the front of elongated dendrite cell structures. In the continuously cast wires, primary Sn dendrites coupled with a small Bi phase were uniformly distributed within the Bi-In alloy matrix. Neither massive Bi phase, Bi complex-regular cells, no BiIn eutectic dendrite cells were observed, resulting in a more uniform microstructure in contrast to the heavily segregated structures of the statically cast specimens.« less

Composition of the cellular infiltrate in patients with simple and complex appendicitis.

PubMed

Gorter, Ramon R; Wassenaar, Emma C E; de Boer, Onno J; Bakx, Roel; Roelofs, Joris J T H; Bunders, Madeleine J; van Heurn, L W Ernst; Heij, Hugo A

2017-06-15

It is now well established that there are two types of appendicitis: simple (nonperforating) and complex (perforating). This study evaluates differences in the composition of the immune cellular infiltrate in children with simple and complex appendicitis. A total of 47 consecutive children undergoing appendectomy for acute appendicitis between January 2011 and December 2012 were included. Intraoperative criteria were used to identify patients with either simple or complex appendicitis and were confirmed histopathologically. Immune histochemical techniques were used to identify immune cell markers in the appendiceal specimens. Digital imaging analysis was performed using Image J. In the specimens of patients with complex appendicitis, significantly more myeloperoxidase positive cells (neutrophils) (8.7% versus 1.2%, P < 0.001) were detected compared to patients with a simple appendicitis. In contrast, fewer CD8+ T cells (0.4% versus 1.3%, P = 0.016), CD20 + cells (2.9% versus 9.0%, P = 0.027), and CD21 + cells (0.2% versus 0.6%, P = 0.028) were present in tissue from patients with complex compared to simple appendicitis. The increase in proinflammatory innate cells and decrease of adaptive cells in patients with complex appendicitis suggest potential aggravating processes in complex appendicitis. Further research into the underlying mechanisms may identify novel biomarkers to be able to differentiate simple and complex appendicitis. Copyright © 2017 Elsevier Inc. All rights reserved.

Idea Bank.

ERIC Educational Resources Information Center

Talesnick, Irwin, Ed.

1984-01-01

Provides innovative ideas in biology, chemistry, and physics on the following topics: enzyme decomposition; chemical waste; time measurement; acid-base color magic; ball bouncing properties; heat; cell theory; and specimen boxes. Materials and procedures are listed when appropriate along with hints for expanding these ideas and investigations. (JM)

HOME-BASED COLLECTION OF BIOLOGICAL MEASUREMENTS AND SPECIMENS FROM MEN

EPA Science Inventory

Environmental epidemiology studies of relations between exposures and male reproductive health face the same challenges as studies of female reproductive health in geographically dispersed individuals or groups (as discussed in the previous talk). Semen quality can be used as an...

Using Spot Biomarker Data to Inform Chronic Exposure and Health Risk

EPA Science Inventory

The U.S. NHANES and other health surveys frequently collect and analyze spot biological specimens to inform chemical exposures. These spot measurements can be compared to biomarker-based reference levels, such as “Biomonitoring Equivalents” (BEs), to evaluate health r...

Optical path difference microscopy with a Shack-Hartmann wavefront sensor.

PubMed

Gong, Hai; Agbana, Temitope E; Pozzi, Paolo; Soloviev, Oleg; Verhaegen, Michel; Vdovin, Gleb

2017-06-01

In this Letter, we show that a Shack-Hartmann wavefront sensor can be used for the quantitative measurement of the specimen optical path difference (OPD) in an ordinary incoherent optical microscope, if the spatial coherence of the illumination light in the plane of the specimen is larger than the microscope resolution. To satisfy this condition, the illumination numerical aperture should be smaller than the numerical aperture of the imaging lens. This principle has been successfully applied to build a high-resolution reference-free instrument for the characterization of the OPD of micro-optical components and microscopic biological samples.

A New Camera for Powder Diffraction of Macromolecular Crystallography at SPring-8

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

Miura, Keiko; Inoue, Katsuaki; Goto, Shunji

2004-05-12

A powder diffractometer of Guinier geometry was developed and tested on a beamline, BL40B2, at SPring-8. The long specimen-to-detector distance, 1,000 mm, is advantageous in recording diffraction from Bragg spacing of 20 nm or larger. The angular resolution, 0.012 degrees, was realized together with the focusing optics, the long specimen-to-detector distance and the small pixel size of Blue-type Imaging Plate detector. Such a high resolution makes the peak separation possible in the powder diffraction from microcrystals with large unit cell and low symmetry of biological macromolecules.

High-resolution low-dose scanning transmission electron microscopy.

PubMed

Buban, James P; Ramasse, Quentin; Gipson, Bryant; Browning, Nigel D; Stahlberg, Henning

2010-01-01

During the past two decades instrumentation in scanning transmission electron microscopy (STEM) has pushed toward higher intensity electron probes to increase the signal-to-noise ratio of recorded images. While this is suitable for robust specimens, biological specimens require a much reduced electron dose for high-resolution imaging. We describe here protocols for low-dose STEM image recording with a conventional field-emission gun STEM, while maintaining the high-resolution capability of the instrument. Our findings show that a combination of reduced pixel dwell time and reduced gun current can achieve radiation doses comparable to low-dose TEM.

Centrifuge facility conceptual system study. Volume 2: Facility systems and study summary

NASA Technical Reports Server (NTRS)

Synnestvedt, Robert (Editor); Blair, Patricia; Cartledge, Alan; Garces-Porcile, Jorge; Garin, Vladimir; Guerrero, Mike; Haddeland, Peter; Horkachuck, Mike; Kuebler, Ulrich; Nguyen, Frank

1991-01-01

The Centrifuge Facility is a major element of the biological research facility for the implementation of NASA's Life Science Research Program on Space Station Freedom using nonhuman species (small primates, rodents, plants, insects, cell tissues, etc.). The Centrifuge Facility consists of a variable gravity Centrifuge to provide artificial gravity up to 2 earth G's' a Holding System to maintain specimens at microgravity levels, a Glovebox, and a Service Unit for servicing specimen chambers. The following subject areas are covered: (1) Holding System; (2) Centrifuge System; (3) Glovebox System; (4) Service System; and (5) system study summary.

Epoxy Resins in Electron Microscopy

PubMed Central

Finck, Henry

1960-01-01

A method of embedding biological specimens in araldite 502 (Ciba) has been developed for materials available in the United States. Araldite-embedded tissues are suitable for electron microscopy, but the cutting qualities of the resin necessitates more than routine attention during microtomy. The rather high viscosity of araldite 502 also seems to be an unnecessary handicap. The less viscous epoxy epon 812 (Shell) produces specimens with improved cutting qualities, and has several features—low shrinkage and absence of specimen damage during cure, minimal compression of sections, relative absence of electron beam-induced section damage, etc.—which recommends it as a routine embedding material. The hardness of the cured resin can be easily adjusted by several methods to suit the materials embedded in it. Several problems and advantages of working with sections of epoxy resins are also discussed. PMID:13822825

The role of the pathologist in translational and personalized medicine.

PubMed

Perl, Daniel P

2007-04-01

Over the years, pathologists have served to make morphologic diagnoses for clinicians when provided with a biopsy or surgically resected tissue specimen. Traditionally, pathologists have used a series of morphologic techniques and relied on the microscopic appearance of resected tissues to determine a pathologic diagnosis and, with respect to neoplastic lesions, provide predictions of the potential growth pattern that might be anticipated. With the introduction of the techniques of molecular biology in medicine, the role of the pathologist has changed as have the tools available for characterizing pathologic specimens. With the pathologist's unique perspective on disease processes and access to tissue specimens from the operating room, he has become a key player in the area of translational and personalized medicine and the development of new approaches to diagnosis and translational research. Copyright (c) 2007 Mount Sinai School of Medicine.

Using Web-Based Key Character and Classification Instruction for Teaching Undergraduate Students Insect Identification

NASA Astrophysics Data System (ADS)

Golick, Douglas A.; Heng-Moss, Tiffany M.; Steckelberg, Allen L.; Brooks, David. W.; Higley, Leon G.; Fowler, David

2013-08-01

The purpose of the study was to determine whether undergraduate students receiving web-based instruction based on traditional, key character, or classification instruction differed in their performance of insect identification tasks. All groups showed a significant improvement in insect identifications on pre- and post-two-dimensional picture specimen quizzes. The study also determined student performance on insect identification tasks was not as good as for family-level identification as compared to broader insect orders and arthropod classification identification tasks. Finally, students erred significantly more by misidentification than misspelling specimen names on prepared specimen quizzes. Results of this study support that short web-based insect identification exercises can improve insect identification performance. Also included is a discussion of how these results can be used in teaching and future research on biological identification.

Biomedical Experiments Scientific Satellite /BESS/

NASA Technical Reports Server (NTRS)

Berry, W. E.; Tremor, J. W.; Aepli, T. C.

1976-01-01

The Biomedical Experiments Scientific Satellite (BESS) program is proposed to provide a long-duration, earth-orbiting facility to expose selected specimens in a series of biomedical experiments through the 1980's. Launched and retrieved by the Space Transportation System, the fully reusable, free-flying BESS will contain all systems necessary to conduct a six-month to one-year spaceflight mission. The spacecraft system will consist of a large pressurized experiment module and a standard NASA service module currently conceived as the Goddard Multi-Mission Spacecraft (MMS). The experiment module will contain the life-support systems, waste management system, specimen-holding facilities, and monitoring, evaluating, and data-handling equipment. Although a variety of specimens will be flown in basic biological and medical studies, the primate was taken as the principal design driver since it has a maximal life-support demand.

[Tissue repositories for research at Sheba Medical Center(SMC].

PubMed

Cohen, Yehudit; Barshack, Iris; Onn, Amir

2013-06-01

Cancer is the number one cause of death in both genders. Breakthroughs in the understanding of cancer biology, the identification of prognostic factors, and the development of new treatments are increasingly dependent on access to human cancer tissues with linked clinicopathological data. Access to human tumor samples and a large investment in translational research are needed to advance this research. The SMC tissue repositories provide researchers with biological materials, which are essential tools for cancer research. SMC tissue repositories for research aim to collect, document and preserve human biospecimens from patients with cancerous diseases. This is in order to provide the highest quality and well annotated biological biospecimens, used as essential tools to achieve the growing demands of scientific research needs. Such repositories are partners in acceLerating biomedical research and medical product development through clinical resources, in order to apply best options to the patients. Following Institutional Review Board approval and signing an Informed Consent Form, the tumor and tumor-free specimens are coLLected by a designated pathologist at the operating room only when there is a sufficient amount of the tumor, in excess of the routine needs. Blood samples are collected prior to the procedure. Other types of specimens collected include ascites fluid, pleural effusion, tissues for Optimal Cutting Temperature [OCT] and primary culture etc. Demographic, clinical, pathologicaL, and follow-up data are collected in a designated database. SMC has already established several organ or disease-specific tissue repositories within different departments. The foundation of tissue repositories requires the concentrated effort of a multidisciplinary team composed of paramedical, medical and scientific professionals. Research projects using these specimens facilitate the development of 'targeted therapy', accelerate basic research aimed at clarifying molecular mechanisms involved in cancer, and support the development of novel diagnostic tools.

Real imaging and size values of Saccharomyces cerevisiae cells with comparable contrast tuning to two environmental scanning electron microscopy modes.

PubMed

Misirli, Zulal; Oner, Ebru Toksoy; Kirdar, Betul

2007-01-01

The combined application of electron microscopy (EM) is frequently used for the microstructural investigation of biological specimens and plays two important roles in the quantification and in gaining an improved understanding of biological phenomena by making use of the highest resolution capability provided by EM. The possibility of imaging wet specimens in their "native" states in the environmental scanning electron microscope (ESEM) at high resolution and large depth of focus in real time is discussed in this paper. It is demonstrated here that new features can be discovered by the elimination of even the least hazardous approaches in some preparation techniques, that destroy the samples. Since the analysis conditions may influence the morphology and the extreme surface sensitivity of living biological systems, the results obtained from the same cultured cell with two different ESEM modes (Lvac mode and wet mode) were compared. This offers new opportunities compared with ESEM-wet/Lvac-mode imaging, since wet-mode imaging involves a real contrast and gives an indication of the changes in cell morphology and structure required for cell viability. In this study, wet-mode imaging was optimized using the unique ability of cell quantities for microcharacterization in situ giving very fine features of topological effects. Accordingly, the progress is reported by comparing the results of these two modes, which demonstrate interesting application details. In general, the functional comparisons have revealed that the fresh unprocessed Saccharomyces cerevisiae cells (ESEM-wet mode) were essentially unaltered with improved and minimal specimen preparation timescales, and the optimal cell viability degree was visualized and also measured quantitatively while the cell size remained unchanged with continuous images.

Advantages of intermediate X-ray energies in Zernike phase contrast X-ray microscopy.

PubMed

Wang, Zhili; Gao, Kun; Chen, Jian; Hong, Youli; Ge, Xin; Wang, Dajiang; Pan, Zhiyun; Zhu, Peiping; Yun, Wenbing; Jacobsen, Chris; Wu, Ziyu

2013-01-01

Understanding the hierarchical organizations of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. Light microscopy is a powerful tool for observations of the dynamics of live cells, its resolution attainable is limited and insufficient. While electron microscopy can produce images with astonishing resolution and clarity of ultra-thin (<1 μm thick) sections of biological specimens, many questions involve the three-dimensional organization of a cell or the interconnectivity of cells. X-ray microscopy offers superior imaging resolution compared to light microscopy, and unique capability of nondestructive three-dimensional imaging of hydrated unstained biological cells, complementary to existing light and electron microscopy. Until now, X-ray microscopes operating in the "water window" energy range between carbon and oxygen k-shell absorption edges have produced outstanding 3D images of cryo-preserved cells. The relatively low X-ray energy (<540 eV) of the water window imposes two important limitations: limited penetration (<10 μm) not suitable for imaging larger cells or tissues, and small depth of focus (DoF) for high resolution 3D imaging (e.g., ~1 μm DoF for 20 nm resolution). An X-ray microscope operating at intermediate energy around 2.5 keV using Zernike phase contrast can overcome the above limitations and reduces radiation dose to the specimen. Using a hydrated model cell with an average chemical composition reported in literature, we calculated the image contrast and the radiation dose for absorption and Zernike phase contrast, respectively. The results show that an X-ray microscope operating at ~2.5 keV using Zernike phase contrast offers substantial advantages in terms of specimen size, radiation dose and depth-of-focus. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia.

PubMed

Alikhani, Mehdi; Mirzaei, Mehdi; Sabbaghian, Marjan; Parsamatin, Pouria; Karamzadeh, Razieh; Adib, Samane; Sodeifi, Niloofar; Gilani, Mohammad Ali Sadighi; Zabet-Moghaddam, Masoud; Parker, Lindsay; Wu, Yunqi; Gupta, Vivek; Haynes, Paul A; Gourabi, Hamid; Baharvand, Hossein; Salekdeh, Ghasem Hosseini

2017-06-06

Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS). The abundance of 520 proteins was significantly changed across three groups of samples. We were able to identify several functional biological pathways enriched in azoospermia samples and confirm selected differentially abundant proteins, using multiple histological methods. The results revealed that cell cycle and proteolysis, and RNA splicing were the most significant biological processes impaired by the substantial suppression of proteins related to the aforementioned categories in SCOS tissues. In the MA patient testes, generation of precursor metabolites and energy as well as oxidation-reduction were the most significantly altered processes. Novel candidate proteins identified in this study include key transcription factors, many of which have not previously been shown to be associated with azoospermia. Our findings can provide substantial insights into the molecular regulation of spermatogenesis and human reproduction. The obtained data showed a drastic suppression of proteins involved in spliceosome, cell cycle and proteasome proteins, as well as energy and metabolic production in Sertoli cell only syndrome testis tissue, and to a lesser extent in maturation arrest samples. Moreover, we identified new transcription factors that are highly down-regulated in SCOS and MA patients, thus helping to understand the molecular complexity of spermatogenesis in male infertility. Our findings provide novel candidate protein targets associated with SCOS or MA azoospermia. Copyright © 2017 Elsevier B.V. All rights reserved.

Modern Focused-Ion-Beam-Based Site-Specific Specimen Preparation for Atom Probe Tomography.

PubMed

Prosa, Ty J; Larson, David J

2017-04-01

Approximately 30 years after the first use of focused ion beam (FIB) instruments to prepare atom probe tomography specimens, this technique has grown to be used by hundreds of researchers around the world. This past decade has seen tremendous advances in atom probe applications, enabled by the continued development of FIB-based specimen preparation methodologies. In this work, we provide a short review of the origin of the FIB method and the standard methods used today for lift-out and sharpening, using the annular milling method as applied to atom probe tomography specimens. Key steps for enabling correlative analysis with transmission electron-beam backscatter diffraction, transmission electron microscopy, and atom probe tomography are presented, and strategies for preparing specimens for modern microelectronic device structures are reviewed and discussed in detail. Examples are used for discussion of the steps for each of these methods. We conclude with examples of the challenges presented by complex topologies such as nanowires, nanoparticles, and organic materials.

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.

Mars Analytical Microimager

NASA Astrophysics Data System (ADS)

Batory, Krzysztof J.; Govindjee; Andersen, Dale; Presley, John; Lucas, John M.; Sears, S. Kelly; Vali, Hojatollah

Unambiguous detection of extraterrestrial nitrogenous hydrocarbon microbiology requires an instrument both to recognize potential biogenic specimens and to successfully discriminate them from geochemical settings. Such detection should ideally be in-situ and not jeopardize other experiments by altering samples. Taken individually most biomarkers are inconclusive. For example, since amino acids can be synthesized abiotically they are not always considered reliable biomarkers. An enantiomeric imbalance, which is characteristic of all terrestrial life, may be questioned because chirality can also be altered abiotically. However, current scientific understanding holds that aggregates of identical proteins or proteinaceous complexes, with their well-defined amino acid residue sequences, are indisputable biomarkers. Our paper describes the Mars Analytical Microimager, an instrument for the simultaneous imaging of generic autofluorescent biomarkers and overall morphology. Autofluorescence from ultraviolet to near-infrared is emitted by all known terrestrial biology, and often as consistent complex bands uncharacteristic of abiotic mineral luminescence. The MAM acquires morphology, and even sub-micron morphogenesis, at a 3-centimeter working distance with resolution approaching a laser scanning microscope. Luminescence is simultaneously collected via a 2.5-micron aperture, thereby permitting accurate correlation of multi-dimensional optical behavior with specimen morphology. A variable wavelength excitation source and photospectrometer serve to obtain steady-state and excitation spectra of biotic and luminescent abiotic sources. We believe this is the first time instrumentation for detecting hydrated or desiccated microbiology non-destructively in-situ has been demonstrated. We have obtained excellent preliminary detection of biota and inorganic matrix discrimination from terrestrial polar analogues, and perimetric morphology of individual magnetotactic bacteria. Proposed analytical components for enhanced detection are: fluorescence anisotropy which analyzes chromophore-based proteins, anisotropy depletion to detect the presence of a fluid environment, anisotropy excitation spectrum for augmented characterization, and fluorescence-detected circular dichroism. Because all its analytical components are independent of chirality and amino acid types, life detection ability of the MAM is not limited to the terrestrial core biomolecular subsets.

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.

Characterization of Cytokinetic Mutants Using Small Fluorescent Probes.

PubMed

Smertenko, Andrei; Moschou, Panagiotis; Zhang, Laining; Fahy, Deirdre; Bozhkov, Peter

2016-01-01

Cytokinesis is a powerful paradigm for addressing fundamental questions of plant biology including molecular mechanisms of development, cell division, cell signaling, membrane trafficking, cell wall synthesis, and cytoskeletal dynamics. Genetics was instrumental in identification of proteins regulating cytokinesis. Characterization of mutant lines generated using forward or reverse genetics includes microscopic analysis for defects in cell division. Typically, failure of cytokinesis results in appearance of multinucleate cells, formation of cell wall stubs, and isotropic cell expansion in the root elongation zone. Small fluorescent probes served as a very effective tool for the detection of cytokinetic defects. Such probes stain living or formaldehyde-fixed specimens avoiding complex preparatory steps. Although resolution of the fluorescence probes is inferior to electron microscopy, the procedure is fast, easy, and does not require expensive materials or equipment. This chapter describes techniques for staining DNA with the probes DAPI and SYTO82, for staining membranes with FM4-64, and for staining cell wall with propidium iodide.

The Use of the Developmental Rate of the Aquatic Midge Chironomus riparius (Diptera, Chironomidae) in the Assessment of the Postsubmersion Interval.

PubMed

González Medina, Alejandro; Soriano Hernando, Óscar; Jiménez Ríos, Gilberto

2015-05-01

Nonbiting midges (Diptera, Chironomidae) are the most abundant members of the fauna associated with submerged carcasses, but their use in the medicolegal context is very restricted because of their complex ontogeny. In this case, the corpse of a woman was recovered in late spring from a river in Granada (Iberian Peninsula). It showed obvious signs of long permanence in the aquatic environment and, along with pulmonary and microscopical analyses, led to the conclusion that the cause of death was drowning. Several larvae-like specimens were sampled from the scalp and later identified by morphological external features as IV instar larvae of Chironomus riparius Meigen, 1804 (Diptera, Chironomidae). Sequencing of cytochrome oxidase subunit I was performed to confirm the identification. The knowledge of the biology of C. riparius at low temperatures was critical to assess a postsubmersion interval of 16-17 days. © 2015 American Academy of Forensic Sciences.

Quantitatively characterizing the microstructural features of breast ductal carcinoma tissues in different progression stages by Mueller matrix microscope.

PubMed

Dong, Yang; Qi, Ji; He, Honghui; He, Chao; Liu, Shaoxiong; Wu, Jian; Elson, Daniel S; Ma, Hui

2017-08-01

Polarization imaging has been recognized as a potentially powerful technique for probing the microstructural information and optical properties of complex biological specimens. Recently, we have reported a Mueller matrix microscope by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission-light microscope, and applied it to differentiate human liver and cervical cancerous tissues with fibrosis. In this paper, we apply the Mueller matrix microscope for quantitative detection of human breast ductal carcinoma samples at different stages. The Mueller matrix polar decomposition and transformation parameters of the breast ductal tissues in different regions and at different stages are calculated and analyzed. For more quantitative comparisons, several widely-used image texture feature parameters are also calculated to characterize the difference in the polarimetric images. The experimental results indicate that the Mueller matrix microscope and the polarization parameters can facilitate the quantitative detection of breast ductal carcinoma tissues at different stages.

ScanImage: flexible software for operating laser scanning microscopes.

PubMed

Pologruto, Thomas A; Sabatini, Bernardo L; Svoboda, Karel

2003-05-17

Laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. Although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. A major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope. We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality. We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.

Nanoscale assembly processes revealed in the nacroprismatic transition zone of Pinna nobilis mollusc shells

PubMed Central

Hovden, Robert; Wolf, Stephan E.; Holtz, Megan E.; Marin, Frédéric; Muller, David A.; Estroff, Lara A.

2015-01-01

Intricate biomineralization processes in molluscs engineer hierarchical structures with meso-, nano- and atomic architectures that give the final composite material exceptional mechanical strength and optical iridescence on the macroscale. This multiscale biological assembly inspires new synthetic routes to complex materials. Our investigation of the prism–nacre interface reveals nanoscale details governing the onset of nacre formation using high-resolution scanning transmission electron microscopy. A wedge-polishing technique provides unprecedented, large-area specimens required to span the entire interface. Within this region, we find a transition from nanofibrillar aggregation to irregular early-nacre layers, to well-ordered mature nacre suggesting the assembly process is driven by aggregation of nanoparticles (∼50–80 nm) within an organic matrix that arrange in fibre-like polycrystalline configurations. The particle number increases successively and, when critical packing is reached, they merge into early-nacre platelets. These results give new insights into nacre formation and particle-accretion mechanisms that may be common to many calcareous biominerals. PMID:26631940

Proteomic analysis of the gamma human papillomavirus type 197 E6 and E7 associated cellular proteins

PubMed Central

Grace, Miranda; Munger, Karl

2016-01-01

Gamma HPV197 was the most frequently identified HPV when human skin cancer specimens were analyzed by deep sequencing. To gain insight into the biological activities of HPV197, we investigated the cellular interactomes of HPV197 E6 and E7. HPV197 E6 protein interacts with a broad spectrum of cellular LXXLL domain proteins, including UBE3A and MAML1. HPV197 E6 also binds and inhibits the TP53 tumor suppressor and interacts with the CCR4-NOT ubiquitin ligase and deadenylation complex. Despite lacking a canonical retinoblastoma (RB1) tumor suppressor binding site, HPV197 E7 binds RB1 and activates E2F transcription. Hence, HPV197 E6 and E7 proteins interact with a similar set of cellular proteins as E6 and E7 proteins encoded by HPVs that have been linked to human carcinogenesis and/or have transforming activities in vitro. PMID:27771561

Effects of long-term preservation on amphibian body conditions: implications for historical morphological research

PubMed Central

Shu, Guocheng; Gong, Yuzhou; Xie, Feng; Wu, Nicholas C.

2017-01-01

Measurements of historical specimens are widely applied in studies of taxonomy, systematics, and ecology, but biologists often assume that the effects of preservative chemicals on the morphology of amphibian specimens are minimal in their analyses. We compared the body length and body mass of 182 samples of 13 live and preserved (up to 10 years) anuran species and found that the body length and body mass of preserved specimens significantly decreased by 6.1% and 24.8%, respectively, compared to those measurements of their live counterparts. The changes in body length and mass also exhibited highly significant variations between species. Similarly, there were significant differences in shrinkage of body length and body mass between sexes, where males showed greater shrinkage in body length and body mass compared to females. Preservation distorted the magnitude of the interspecific differences in body length observed in the fresh specimens. Overall, the reduction in body length or mass was greater in longer or heavier individuals. Due to the effects of preservation on amphibian morphology, we propose two parsimonious conversion equations to back-calculate the original body length and body mass of studied anurans for researchers working with historical data, since morphological data from preserved specimens may lead to incorrect biological interpretations when comparing to fresh specimens. Therefore, researchers should correct for errors due to preservation effects that may lead to the misinterpretation of results. PMID:28929024

The Seasonality and Ecology of the Anopheles gambiae complex (Dipetra: Culicidae) in Liberia Using Molecular Identification.

PubMed

Fahmy, N T; Villinski, J T; Bolay, F; Stoops, C A; Tageldin, R A; Fakoli, L; Okasha, O; Obenauer, P J; Diclaro, J W

2015-05-01

Members of the Anopheles gambiae sensu lato (Giles) complex define a group of seven morphologically indistinguishable species, including the principal malaria vectors in Sub-Saharan Africa. Members of this complex differ in behavior and ability to transmit malaria; hence, precise identification of member species is critical to monitoring and evaluating malaria threat levels. We collected mosquitoes from five counties in Liberia every other month from May 2011 until May 2012, using various trapping techniques. A. gambiae complex members were identified using molecular techniques based on differences in the ribosomal DNA (rDNA) region between species and the molecular forms (S and M) of A. gambiae sensu stricto (s.s) specimens. In total, 1,696 A. gambiae mosquitoes were collected and identified. DNA was extracted from legs of each specimen with species identification determined by multiplex polymerase chain reaction using specific primers. The molecular forms (M or S) of A. gambiae s.s were determined by restriction fragment length polymorphism. Bivariate and multivariate logistic regression models identified environmental variables associated with genomic differentiation. Our results indicate widespread occurrence of A. gambiae s.s., the principal malaria vector in the complex, although two Anopheles melas Theobald/A. merus Donitz mosquitoes were detected. We found 72.6, 25.5, and 1.9% of A. gambiae s.s specimens were S, M, and hybrid forms, respectively. Statistical analysis indicates that the S form was more likely to be found in rural areas during rainy seasons and indoor catchments. This information will enhance vector control efforts in Liberia. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by US Government employees and is in the public domain in the US.

Exploiting the Lichen Liaison.

ERIC Educational Resources Information Center

Raham, R. Gary

1978-01-01

For teachers in search of an easily obtainable, readily dissectable, and unique living specimen to arouse the interest of their students and illustrate important biological principles, lichens are the perfect selection. Background information and experiments on lichen anatomy, physiology, and chemistry are given. An appendix gives culture media.…

Harnessing the Power of Digital Data for Science and Society

DTIC Science & Technology

2009-01-01

development and that the research process is responsive to the real-world needs of the implementation sector. Relationship to the Scientific Collections IWG...The Scientific Collections Interagency Working Group focuses on collections of physical objects relevant to science (e.g., biological specimens

77 FR 38774 - Marine Mammals; File No. 16193

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-29

... whole blood taken from dead or captive individuals to study reproductive physiology, including endocrinology, gamete biology, and cryophysiology. Specimens from dead animals, located solely within the... harvesting; killed incidentally to fishing or other operations; found dead at sea or beached; or that died of...

Safety in the Chemical Laboratory: Atmospheric Formaldehyde Levels in an Academic Laboratory.

ERIC Educational Resources Information Center

Clausz, John C.; And Others

1984-01-01

Determined whether improved ventilation and use of "formaldehyde-free" biological specimens could reduce the levels of formaldehyde in air to which students and faculty would be exposed. Both methods were found to be effective in reducing formaldehyde levels in air. (JN)

An economical alternative for the secondary container used for transporting infectious disease substances.

DOT National Transportation Integrated Search

1995-12-01

The safe containment of biological specimens during air transport is of growing concern as the number of shipments and hazards associated with such material increases. The purpose of this study was to examine the durability of adhesive-closure polyet...

Water Habitat Study: Prediction Makes It More Meaningful.

ERIC Educational Resources Information Center

Glasgow, Dennis R.

1982-01-01

Suggests a teaching strategy for water habitat studies to help students make a meaningful connection between physiochemical data (dissolved oxygen content, pH, and water temperature) and biological specimens they collect. Involves constructing a poster and using it to make predictions. Provides sample poster. (DC)

Herpetofauna of the Beni Biological Station Biosphere Reserve, Amazonian Bolivia: Additional information, and current knowledge in context

USGS Publications Warehouse

Middendorf, G.; Reynolds, R.; Herrera-MacBryde, Olga; Dallmeier, Francisco; MacBryde, Bruce; Cominskey, James A.; Miranda, Carmen

2000-01-01

Previous collections in the Departamento del Beni in tropical Bolivia only hinted at high levels of herpetological biodiversity (Fugler 1986, 1988; de la Riva 1990a; Fugler and de la Riva 1990). Fieldwork (totaling 48 days) in July-August 1988 and September 1987 (dry seasons) and November-December 1990 (wet season) has resulted in collection and identification of 401 amphibian and reptilian specimens from the general area of the Beni Biological Station's (EBB) headquarters at El Porvenir. These collections represent 33 amphibian and 17 reptilian species in 29 genera (14 amphibian, 15 reptilian). The inventory of herpetofauna scientifically documented to occur in the Departamento del Beni is considered to have been increased by 6 amphibian and 10 reptilian species. Specimens that could not be definitively identified (reflecting taxonomic uncertainty and/or probably species new to science) include 3 amphibian species (anurans) and 2 reptilian species (snakes). The EBB harbors the richest savanna for anuran species known in South America.

Surface smoothing, decimation, and their effects on 3D biological specimens.

PubMed

Veneziano, Alessio; Landi, Federica; Profico, Antonio

2018-06-01

Smoothing and decimation filters are commonly used to restore the realistic appearance of virtual biological specimens, but they can cause a loss of topological information of unknown extent. In this study, we analyzed the effect of smoothing and decimation on a 3D mesh to highlight the consequences of an inappropriate use of these filters. Topological noise was simulated on four anatomical regions of the virtual reconstruction of an orangutan cranium. Sequential levels of smoothing and decimation were applied, and their effects were analyzed on the overall topology of the 3D mesh and on linear and volumetric measurements. Different smoothing algorithms affected mesh topology and measurements differently, although the influence on the latter was generally low. Decimation always produced detrimental effects on both topology and measurements. The application of smoothing and decimation, both separate and combined, is capable of recovering topological information. Based on the results, objective guidelines are provided to minimize information loss when using smoothing and decimation on 3D meshes. © 2018 Wiley Periodicals, Inc.

High-contrast multilayer imaging of biological organisms through dark-field digital refocusing.

PubMed

Faridian, Ahmad; Pedrini, Giancarlo; Osten, Wolfgang

2013-08-01

We have developed an imaging system to extract high contrast images from different layers of biological organisms. Utilizing a digital holographic approach, the system works without scanning through layers of the specimen. In dark-field illumination, scattered light has the main contribution in image formation, but in the case of coherent illumination, this creates a strong speckle noise that reduces the image quality. To remove this restriction, the specimen has been illuminated with various speckle-fields and a hologram has been recorded for each speckle-field. Each hologram has been analyzed separately and the corresponding intensity image has been reconstructed. The final image has been derived by averaging over the reconstructed images. A correlation approach has been utilized to determine the number of speckle-fields required to achieve a desired contrast and image quality. The reconstructed intensity images in different object layers are shown for different sea urchin larvae. Two multimedia files are attached to illustrate the process of digital focusing.

A View of the Therapy for Bell's Palsy Based on Molecular Biological Analyses of Facial Muscles.

PubMed

Moriyama, Hiroshi; Mitsukawa, Nobuyuki; Itoh, Masahiro; Otsuka, Naruhito

2017-12-01

Details regarding the molecular biological features of Bell's palsy have not been widely reported in textbooks. We genetically analyzed facial muscles and clarified these points. We performed genetic analysis of facial muscle specimens from Japanese patients with severe (House-Brackmann facial nerve grading system V) and moderate (House-Brackmann facial nerve grading system III) dysfunction due to Bell's palsy. Microarray analysis of gene expression was performed using specimens from the healthy and affected sides, and gene expression was compared. Changes in gene expression were defined as an affected side/healthy side ratio of >1.5 or <0.5. We observed that the gene expression in Bell's palsy changes with the degree of facial nerve palsy. Especially, muscle, neuron, and energy category genes tended to fluctuate with the degree of facial nerve palsy. It is expected that this study will aid in the development of new treatments and diagnostic/prognostic markers based on the severity of facial nerve palsy.

Preparation of the planarian Schmidtea mediterranea for high-resolution histology and transmission electron microscopy

PubMed Central

Brubacher, John L.; Vieira, Ana P.; Newmark, Phillip A.

2014-01-01

The flatworm Schmidtea mediterranea is an emerging model species in such fields as stem-cell biology, regeneration, and evolutionary biology. Excellent molecular tools have been developed for S. mediterranea, but ultrastructural techniques have received far less attention. Processing specimens for histology and transmission electron microscopy is notoriously idiosyncratic for particular species or specimen types. Unfortunately however, most methods for S. mediterranea described in the literature lack numerous essential details, and those few that do provide them rely on specialized equipment that may not be readily available. Here we present an optimized protocol for ultrastructural preparation of S. mediterranea. The protocol can be completed in six days, much of which is “hands-off” time. To aid with troubleshooting, we also illustrate the significant effects of seemingly minor variations in fixative, buffer concentration, and dehydration steps. This procedure will be useful for all planarian researchers, particularly those with relatively little experience in tissue processing. PMID:24556788

Plasmonics and metamaterials based super-resolution imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Liu, Zhaowei

2017-05-01

In recent years, surface imaging of various biological dynamics and biomechanical phenomena has seen a surge of interest. Imaging of processes such as exocytosis and kinesin motion are most effective when depth is limited to a very thin region of interest at the edge of the cell or specimen. However, many objects and processes of interest are of size scales below the diffraction limit for safe, visible wavelength illumination. Super-resolution imaging methods such as structured illumination microscopy and others have offered various compromises between resolution, imaging speed, and bio-compatibility. In this talk, I will present our most recent progress in plasmonic structured illumination microscopy (PSIM) and localized plasmonic structured illumination microscopy (LPSIM), and their applications in bio-imaging. We have achieved wide-field surface imaging with resolution down to 75 nm while maintaining reasonable speed and compatibility with biological specimens. These plasmonic enhanced super resolution techniques offer unique solutions to obtain 50nm spatial resolution and 50 frames per second wide imaging speed at the same time.

Digital holographic microscopy long-term and real-time monitoring of cell division and changes under simulated zero gravity.

PubMed

Pan, Feng; Liu, Shuo; Wang, Zhe; Shang, Peng; Xiao, Wen

2012-05-07

The long-term and real-time monitoring the cell division and changes of osteoblasts under simulated zero gravity condition were succeed by combing a digital holographic microscopy (DHM) with a superconducting magnet (SM). The SM could generate different magnetic force fields in a cylindrical cavity, where the gravitational force of biological samples could be canceled at a special gravity position by a high magnetic force. Therefore the specimens were levitated and in a simulated zero gravity environment. The DHM was modified to fit with SM by using single mode optical fibers and a vertically-configured jig designed to hold specimens and integrate optical device in the magnet's bore. The results presented the first-phase images of living cells undergoing dynamic divisions and changes under simulated zero gravity environment for a period of 10 hours. The experiments demonstrated that the SM-compatible DHM setup could provide a highly efficient and versatile method for research on the effects of microgravity on biological samples.

Quirks of dye nomenclature. 5. Rhodamines.

PubMed

Cooksey, C J

2016-01-01

Rhodamines were first produced in the late 19(th) century, when they constituted a new class of synthetic dyes. These compounds since have been used to color many things including cosmetics, inks, textiles, and in some countries, food products. Certain rhodamine dyes also have been used to stain biological specimens and currently are widely used as fluorescent probes for mitochondria in living cells. The early history and current biological applications are sketched briefly and an account of the ambiguities, complications and confusions concerning dye identification and nomenclature are discussed.

Variable bright-darkfield-contrast, a new illumination technique for improved visualizations of complex structured transparent specimens.

PubMed

Piper, Timm; Piper, Jörg

2012-04-01

Variable bright-darkfield contrast (VBDC) is a new technique in light microscopy which promises significant improvements in imaging of transparent colorless specimens especially when characterized by a high regional thickness and a complex three-dimensional architecture. By a particular light pathway, two brightfield- and darkfield-like partial images are simultaneously superimposed so that the brightfield-like absorption image based on the principal zeroth order maximum interferes with the darkfield-like reflection image which is based on the secondary maxima. The background brightness and character of the resulting image can be continuously modulated from a brightfield-dominated to a darkfield-dominated appearance. When the weighting of the dark- and brightfield components is balanced, medium background brightness will result showing the specimen in a phase- or interference contrast-like manner. Specimens can either be illuminated axially/concentrically or obliquely/eccentrically. In oblique illumination, the angle of incidence and grade of eccentricity can be continuously changed. The condenser aperture diaphragm can be used for improvements of the image quality in the same manner as usual in standard brightfield illumination. By this means, the illumination can be optimally adjusted to the specific properties of the specimen. In VBDC, the image contrast is higher than in normal brightfield illumination, blooming and scattering are lower than in standard darkfield examinations, and any haloing is significantly reduced or absent. Although axial resolution and depth of field are higher than in concurrent standard techniques, the lateral resolution is not visibly reduced. Three dimensional structures, reliefs and fine textures can be perceived in superior clarity. Copyright © 2011 Wiley-Liss, Inc.

A review of the taxonomy of chondrichthyan fishes: a modern perspective.

PubMed

White, W T; Last, P R

2012-04-01

Taxonomic clarity is a fundamental requirement as it forms the foundation of all other life sciences. In the last decade, chondrichthyan taxonomy has undergone a scientific renaissance with >180 new species formally described. This effort encompasses c. 15% of the global chondrichthyan fauna, which consists of 1185 currently recognized species. The important role of chondrichthyan taxonomy for conservation management has been highlighted in recent years with new species descriptions or taxonomic resolution of a number of threatened species. These include Australian gulper (genus Centrophorus) and speartooth sharks (genus Glyphis) in coastal waters of Australia and Borneo. Closer examination of other wide-ranging species, for which the taxonomy was thought to be stable, has shown that they consist of species complexes, e.g. manta rays (Manta spp.) and spotted eagle rays (the Aetobatus narinari complex), and highlights the need for critical re-examination of other wide-ranging species. Molecular methods have provided another useful tool to taxonomists and they have proven to assist greatly with identifying cryptic species and species complexes. The limitations of particular molecular methods being used need, however, to be carefully considered and there are some concerns about how these are being integrated with classical taxonomy. The fundamental importance of taxonomic nomenclature to life sciences is often poorly understood but striving for nomenclatural stability is a critical component of taxonomy. Similarly, biological collections are an extremely vital asset to both taxonomists and the broader scientific community. These collections are becoming increasingly important due in part to molecular species identification initiatives such as the Barcode of Life which has resulted in a large number of voucher specimens linked to tissue samples being deposited. Biological collections are also proving to be imperative in biodiversity studies as they contain a 'gold mine' of historical collection information important for assessing changes in faunal assemblages. Resources are typically limited for taxonomic research and the ageing taxonomic community is another issue of concern for the future of taxonomy on this important group. Succession planning and better resource allocation will be essential to ensure that this fundamental discipline is maintained into the future. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Multicenter evaluation of the performance characteristics of the bayer VERSANT HCV RNA 3.0 assay (bDNA).

PubMed

Elbeik, Tarek; Surtihadi, Johan; Destree, Mark; Gorlin, Jed; Holodniy, Mark; Jortani, Saeed A; Kuramoto, Ken; Ng, Valerie; Valdes, Roland; Valsamakis, Alexandra; Terrault, Norah A

2004-02-01

In this multicenter evaluation, the VERSANT HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Tarrytown, N.Y.) was shown to have excellent reproducibility, linearity, and analytical sensitivity across specimen collection matrices (serum, EDTA, ACD-A), and hepatitis C virus (HCV) genotypes 1 to 6. The VERSANT HCV bDNA Assay has a reportable range of 615 to 7690000 (7.69 x 10(6)) IU/ml. The total coefficient of variation (CV) ranged from 32.4% at 615 IU/ml to 17% at 6.8 x 10(6) IU/ml. The assay was linear across the reportable range. Analytical specificity of 98.8% was determined by testing 999 specimens from volunteer blood donors. Evaluation of HCV genotypes using RNA transcripts of representative clones of 1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a, and 6a and patient specimens showed that the largest difference between genotype 1, upon which the assay is standardized, and non-1 genotypes was within 1.5-fold. Testing of potentially interfering endogenous substances and exogenous substances and conditions found no interference in HCV-positive or HCV-negative specimens except for unconjugated bilirubin at concentrations of >or=20 mg/dl and protein at concentrations of >or=9 g/dl. Biological variability was estimated from 29 clinically stable individuals not on HCV therapy who were tested weekly over an 8-week period. The combined estimate of total (biologic plus assay) variability was 0.15 log(10) standard deviation (CV, 36.1%), a fold change of 2.6. Thus, the observed fold change between any two consecutive HCV RNA measures is expected to be less than 2.6-fold (equivalent to 0.41 log(10) IU/ml) 95% of the time in clinically stable individuals.

Monte Carlo Simulation to Determine Geometry Effects on Quantitative X-ray Microanalysis in Plant Cell Walls Using Gelatin Standards

NASA Astrophysics Data System (ADS)

Tylko, Grzegorz; Dubchak, Sergyi; Banach, Zuzanna; Turnau, Katarzyna

2010-04-01

Monte Carlo simulations of gelatin matrices with known elemental concentrations confirmed the suitability of protein standards to quantify elements of cellulose material in x-ray microanalysis. However, gelatin standards and cellulose plant cell walls differ in structure, what influences x-ray generation and emission in both specimens. The goal of the project was to establish the influence of gelatin structure on x-ray generation and its usefulness to calculate elemental concentrations in plant cell walls of different width. Roots of Medicago truncatula as well as gelatin standards with known elemental composition were prepared according to freeze-drying protocols. The thermanox polymer was chosen to establish background formation for flat and compact organic materials. All analyses were performed with the scanning electron microscope operated at 10 keV and probe current of 350 pA. The Monte Carlo code Casino was applied to calculate the intensities of the generated and the emitted x-rays from biological matrix of different width. No topography effects of gelatin structure were visible when the raster mode of electron impact was applied to the specimen. Monte Carlo simulations of gelatin of different width revealed that a significant decrease of the generated x-ray intensity appears at the width of the specimen around 3.5 μm. However, an increase of emission of low energy x-ray intensities (Na, Mg) was noted at 3.5 μm size with constant emission of higher energy x-rays (Cl, K) down to 2.5 μm width. It determines the minimal size of plant specimen useful for comparison to bulk gelatin standard when quantitative analysis is performed for biologically important elements.

Morphology versus DNA barcoding: two sides of the same coin. A case study of Ceutorhynchus erysimi and C. contractus identification.

PubMed

Stepanović, Svetlana; Kosovac, Andrea; Krstić, Oliver; Jović, Jelena; Toševski, Ivo

2016-08-01

Genotyping of 2 well-known weevil species from the genus Ceutorhynchus (Coleoptera: Curculionidae) distributed in west Palearctic, C. erysimi and C. contractus, revealed phenotype versus genotype inconsistencies in a set of 56 specimens (25 C. erysimi and 31 C. contractus) collected from 25 locations in Serbia and Montenegro. An analysis of the mitochondrial cytochrome oxidase subunit I gene (COI), widely used as a barcoding region, and a nuclear gene, elongation factor-1α (EF-1α), revealed stable genetic divergence among these species. The average uncorrected pairwise distances for the COI and EF-1α genes were 3.8%, and 1.3%, respectively, indicating 2 genetically well-segregated species. However, the genetic data were not congruent with the phenotypic characteristics of the studied specimens. In the first place, C. erysimi genotypes were attached to specimens with phenotypic characteristics of C. contractus. Species-specific PCR-RFLP assays for the barcoding gene COI were applied for the molecular identification of 101 additional specimens of both morphospecies (33 C. erysimi and 68 C. contractus) and were found to confirm this incongruity. The discrepancy between the genetic and morphological data raises the question of the accuracy of using a barcoding approach, as it may result in misleading conclusions about the taxonomic position of the studied organism. Additionally, the typological species concept shows considerable weakness when genetic data are not supported with phenotypic characteristics as in case of asymmetric introgression, which may cause certain problems, especially in applied studies such as biological control programs in which the biological properties of the studied organisms are the main focus. © 2015 Institute of Zoology, Chinese Academy of Sciences.

Applying the institutional review board data repository approach to manage ethical considerations in evaluating and studying medical education

PubMed Central

Thayer, Erin K.; Rathkey, Daniel; Miller, Marissa Fuqua; Palmer, Ryan; Mejicano, George C.; Pusic, Martin; Kalet, Adina; Gillespie, Colleen; Carney, Patricia A.

2016-01-01

Issue Medical educators and educational researchers continue to improve their processes for managing medical student and program evaluation data using sound ethical principles. This is becoming even more important as curricular innovations are occurring across undergraduate and graduate medical education. Dissemination of findings from this work is critical, and peer-reviewed journals often require an institutional review board (IRB) determination. Approach IRB data repositories, originally designed for the longitudinal study of biological specimens, can be applied to medical education research. The benefits of such an approach include obtaining expedited review for multiple related studies within a single IRB application and allowing for more flexibility when conducting complex longitudinal studies involving large datasets from multiple data sources and/or institutions. In this paper, we inform educators and educational researchers on our analysis of the use of the IRB data repository approach to manage ethical considerations as part of best practices for amassing, pooling, and sharing data for educational research, evaluation, and improvement purposes. Implications Fostering multi-institutional studies while following sound ethical principles in the study of medical education is needed, and the IRB data repository approach has many benefits, especially for longitudinal assessment of complex multi-site data. PMID:27443407

Quantitative analysis of biomedical samples using synchrotron radiation microbeams

NASA Astrophysics Data System (ADS)

Ektessabi, Ali; Shikine, Shunsuke; Yoshida, Sohei

2001-07-01

X-ray fluorescence (XRF) using a synchrotron radiation (SR) microbeam was applied to investigate distributions and concentrations of elements in single neurons of patients with neurodegenerative diseases. In this paper we introduce a computer code that has been developed to quantify the trace elements and matrix elements at the single cell level. This computer code has been used in studies of several important neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD) and parkinsonism-dementia complex (PDC), as well as in basic biological experiments to determine the elemental changes in cells due to incorporation of foreign metal elements. The substantial nigra (SN) tissue obtained from the autopsy specimens of patients with Guamanian parkinsonism-dementia complex (PDC) and control cases were examined. Quantitative XRF analysis showed that neuromelanin granules of Parkinsonian SN contained higher levels of Fe than those of the control. The concentrations were in the ranges of 2300-3100 ppm and 2000-2400 ppm respectively. On the contrary, Zn and Ni in neuromelanin granules of SN tissue from the PDC case were lower than those of the control. Especially Zn was less than 40 ppm in SN tissue from the PDC case while it was 560-810 ppm in the control. These changes are considered to be closely related to the neuro-degeneration and cell death.

[Preparation and applications of a supported liquid-liquid extraction column with a composite diatomite material].

PubMed

Bao, Jianmin; Ma, Zhishuang; Sun, Ying; Wang, Yongzun; Li, Youxin

2012-08-01

A rapid and special supported liquid-liquid extraction (SLE) column was developed with a composite diatomite material. The SLE column was evaluated by high performance liquid chromatography (HPLC) with acidic, neutral and alkaline compounds dissolved in water. Furthermore, some real complex samples were also analyzed by HPLC with the SLE method. The recoveries of benzoic acid (acidic), p-nitroaniline (alkaline) and 4-hydroxy-benzoic methyl ester (neutral) treated by the SLE column were 90.6%, 98.1% and 97.7%. However, the recoveries of the three compounds treated by traditional liquid-liquid extraction (LLE) method were 71.9%, 81.9% and 83.9%. The results showed that the SLE technique had higher recoveries than the traditional LLE method. The spiked recoveries of the complex samples, such as benzoic acid in Sprite and dexamethasone acetate, chlorphenamine maleate, indomethacin in bovine serum, were between 80% and 110% and the relative standard deviations (RSDs) were less than 15%. For biological specimen, the results could be accepted. Meantime, many disadvantages associated with traditional LLE method, such as emulsion formation, didn't occur using SLE column. The SLE column technique is a good sample preparation method with many advantages, such as rapid, simple, robust, easily automated, high recovery and high-throughput, which would be widely used in the future.

The unexpected detection of varicella-zoster virus in genital specimens using the Lyra™ Direct HSV 1+2/VZV Assay.

PubMed

Granato, Paul A; DeGilio, Marcia A; Wilson, Elsie M

2016-11-01

The Lyra™ Direct HSV 1+2/VZV Assay is a moderately complex, multiplex PCR assay that qualitatively detects the presence of HSV 1, HSV 2, and VZV DNA in cutaneous and mucocutaneous specimens with a time-to-result of less than 60min. To report a one-year laboratory experience using Lyra assay for testing cutaneous and mucocutaneous specimens for HSV and VZV that resulted in the unexpected detection of VZV in 14 male and female genital specimens. Over a one-year period, 2113 cutaneous and mucocutaneous specimens from male and female patients were submitted for testing using the Lyra assay. An unexpected 14 genital specimens were positive for the presence VZV DNA. Eleven of the 14 specimens were available for confirmatory testing using two alternative molecular methods and Sanger sequencing. Fourteen male and female genital specimens were positive for the presence of VZV DNA. All of the 11 specimens (9 female and 2 male) that were available for confirmatory testing by the alternative molecular method and Sanger sequencing were confirmed as containing VZV DNA. Using of the Lyra assay over a one-year time period, VZV DNA was detected in 126 specimens of which 14 (11.1%) were from male and female genital sites. This rare and unexpected finding suggests that the appearance of zoster lesions in the genital area may not be as uncommon as previously thought and that this finding would have considerable impact on patient counseling and public health considerations. Copyright © 2016 Elsevier B.V. All rights reserved.

Development and validation of a multiplex PCR for detection of Scedosporium spp. in respiratory tract specimens from patients with cystic fibrosis.

PubMed

Harun, Azian; Blyth, Christopher C; Gilgado, Felix; Middleton, Peter; Chen, Sharon C-A; Meyer, Wieland

2011-04-01

The emergence of Scedosporium infections in diverse groups of individuals, which are often treatment refractory, warrants timely and accurate laboratory diagnosis. Species- or group-specific primers based on internal transcribed spacer (ITS) sequence polymorphisms were designed for Scedosporium aurantiacum, Scedosporium dehoogii, Scedosporium prolificans, Pseudallescheria boydii species complex (former clade 5)/Pseudallescheria apiosperma (formerly classified as S. apiospermum sensu lato) and Pseudallescheria minutispora. Primers for S. aurantiacum, S. prolificans, and P. boydii species complex/P. apiosperma were incorporated into a multiplex PCR assay for the detection and identification of the three major clinically important Scedosporium species and validated using sputum specimens collected from patients seen at a major Australian cystic fibrosis clinic. The multiplex PCR assay showed 100% specificity in identifying the three major clinically relevant Scedosporium species from pure culture. When evaluated using DNA extracts from sputa, sensitivity and specificity of the multiplex PCR assay were 62.1% and 97.2%, respectively. This highly species-specific multiplex PCR assay offers a rapid and simple method of detection of the most clinically important Scedosporium species in respiratory tract specimens.

Effectiveness of saliva and fingerprints as alternative specimens to urine and blood in forensic drug testing.

PubMed

Kuwayama, Kenji; Miyaguchi, Hajime; Yamamuro, Tadashi; Tsujikawa, Kenji; Kanamori, Tatsuyuki; Iwata, Yuko T; Inoue, Hiroyuki

2016-07-01

In forensic drug testing, it is important to immediately take biological specimens from suspects and victims to prove their drug intake. We evaluated the effectiveness of saliva and fingerprints as alternative specimens to urine and blood in terms of ease of sampling, drug detection sensitivity, and drug detection periods for each specimen type. After four commercially available pharmaceutical products were administered to healthy subjects, each in a single dose, their urine, blood, saliva, and fingerprints were taken at predetermined sampling times over approximately four weeks. Fourteen analytes (the administered drugs and their main metabolites) were extracted from each specimen using simple pretreatments, such as dilution and deproteinization, and were analyzed using liquid chromatography/mass spectrometry (LC/MS). Most of the analytes were detected in saliva and fingerprints, as well as in urine and blood. The time-courses of drug concentrations were similar between urine and fingerprints, and between blood and saliva. Compared to the other compounds, the acidic compounds, for example ibuprofen, acetylsalicylic acid, were more difficult to detect in all specimens. Acetaminophen, dihydrocodeine, and methylephedrine were detected in fingerprints at later sampling times than in urine. However, a relationship between the drug structures and their detection periods in each specimen was not found. Saliva and fingerprints could be easily sampled on site without using special techniques or facilities. In addition, fingerprints could be immediately analyzed after simple and rapid treatment. In cases where it would be difficult to immediately obtain urine and blood, saliva and fingerprints could be effective alternative specimens for drug testing. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

Rapid embedding methods into epoxy and LR White resins for morphological and immunological analysis of cryofixed biological specimens.

PubMed

McDonald, Kent L

2014-02-01

A variety of specimens including bacteria, ciliates, choanoflagellates (Salpingoeca rosetta), zebrafish (Danio rerio) embryos, nematode worms (Caenorhabditis elegans), and leaves of white clover (Trifolium repens) plants were high pressure frozen, freeze-substituted, infiltrated with either Epon, Epon-Araldite, or LR White resins, and polymerized. Total processing time from freezing to blocks ready to section was about 6 h. For epoxy embedding the specimens were freeze-substituted in 1% osmium tetroxide plus 0.1% uranyl acetate in acetone. For embedding in LR White the freeze-substitution medium was 0.2% uranyl acetate in acetone. Rapid infiltration was achieved by centrifugation through increasing concentrations of resin followed by polymerization at 100°C for 1.5-2 h. The preservation of ultrastructure was comparable to standard freeze substitution and resin embedding methods that take days to complete. On-section immunolabeling results for actin and tubulin molecules were positive with very low background labeling. The LR White methods offer a safer, quicker, and less-expensive alternative to Lowicryl embedding of specimens processed for on-section immunolabeling without traditional aldehyde fixatives.

High-speed polarized light microscopy for in situ, dynamic measurement of birefringence properties

NASA Astrophysics Data System (ADS)

Wu, Xianyu; Pankow, Mark; Shadow Huang, Hsiao-Ying; Peters, Kara

2018-01-01

A high-speed, quantitative polarized light microscopy (QPLM) instrument has been developed to monitor the optical slow axis spatial realignment during controlled medium to high strain rate experiments at acquisition rates up to 10 kHz. This high-speed QPLM instrument is implemented within a modified drop tower and demonstrated using polycarbonate specimens. By utilizing a rotating quarter wave plate and a high-speed camera, the minimum acquisition time to generate an alignment map of a birefringent specimen is 6.1 ms. A sequential analysis method allows the QPLM instrument to generate QPLM data at the high-speed camera imaging frequency 10 kHz. The obtained QPLM data is processed using a vector correlation technique to detect anomalous optical axis realignment and retardation changes throughout the loading event. The detected anomalous optical axis realignment is shown to be associated with crack initiation, propagation, and specimen failure in a dynamically loaded polycarbonate specimen. The work provides a foundation for detecting damage in biological tissues through local collagen fiber realignment and fracture during dynamic loading.

Virtual dissection and lifestyle of a 165 -million-year-old female polychelidan lobster.

PubMed

Jauvion, Clément; Audo, Denis; Charbonnier, Sylvain; Vannier, Jean

2016-03-01

Polychelidan lobsters are fascinating crustaceans that were known as fossils before being discovered in the deep-sea. They differ from other crustaceans by having four to five pairs of claws. Although recent palaeontological studies have clarified the systematics and phylogeny of the group, the biology of extant polychelidans and--first of all--their anatomy are poorly documented. Numerous aspects of the evolutionary history of the group remain obscure, in particular, how and when polychelidans colonized the deep-sea and became restricted to it. Surprisingly, the biology of extant polychelidans and the anatomy of all species, fossil and recent, are poorly documented. Here, X-ray microtomography (XTM), applied to an exceptionally well-preserved specimen from the La Voulte Lagerstätte, reveals for the first time vital aspects of the external and internal morphology of Voulteryon parvulus (Eryonidae), a 165-million-year-old polychelidan: 1) its mouthparts (maxillae and maxillipeds), 2) its digestive tract and 3) its reproductive organs. Comparisons with dissected specimens clearly identify this specimen as a female with mature ovaries. This set of new information offers new insights into the feeding and reproductive habits of Mesozoic polychelidans. Contrasting with other Jurassic polychelidans that lived in shallow-water environments, V. parvulus spawned in, and probably inhabited, relatively deep-water environments, as do the survivors of the group. Copyright © 2015 Elsevier Ltd. All rights reserved.

High-resolution elemental mapping of human placental chorionic villi using synchrotron X-ray fluorescence spectroscopy

DOE PAGES

Punshon, Tracy; Chen, Si; Finney, Lydia; ...

2015-07-03

The placenta is the organ that mediates transport of nutrients and waste materials between mother and fetus. Synchrotron X-ray fluorescence (SXRF) microanalysis is a tool for imaging the distribution and quantity of elements in biological tissue, which can be used to study metal transport across biological membranes. Our aims were to pilot placental biopsy specimen preparation techniques that could be integrated into an ongoing epidemiology birth cohort study without harming rates of sample acquisition. We studied the effects of fixative (formalin or glutaraldehyde) and storage duration (30 days or immediate processing) on metal distribution and abundance and investigated a thaw-fixationmore » protocol for archived specimens stored at -80° C. We measured fixative elemental composition with and without a placental biopsy via inductively coupled plasma mass spectrometry (ICP-MS) to quantify fixative-induced elemental changes. Formalin-fixed specimens showed hemolysis of erythrocytes. The glutaraldehyde-paraformaldehyde solution in HEPES buffer (GTA-HEPES) had superior anatomical preservation, avoided hemolysis, and minimized elemental loss, although some cross-linking of exogenous Zn was evident. Elemental loss from tissue stored in fixative for 1 month showed variable losses (≈ 40 % with GTA-HEPES), suggesting storage duration be controlled for. Lastly, thawing of tissue held at -80 °C in a GTA-HEPES solution provided high-quality visual images and elemental images« less

Discovering Physical Samples Through Identifiers, Metadata, and Brokering

NASA Astrophysics Data System (ADS)

Arctur, D. K.; Hills, D. J.; Jenkyns, R.

2015-12-01

Physical samples, particularly in the geosciences, are key to understanding the Earth system, its history, and its evolution. Our record of the Earth as captured by physical samples is difficult to explain and mine for understanding, due to incomplete, disconnected, and evolving metadata content. This is further complicated by differing ways of classifying, cataloguing, publishing, and searching the metadata, especially when specimens do not fit neatly into a single domain—for example, fossils cross disciplinary boundaries (mineral and biological). Sometimes even the fundamental classification systems evolve, such as the geological time scale, triggering daunting processes to update existing specimen databases. Increasingly, we need to consider ways of leveraging permanent, unique identifiers, as well as advancements in metadata publishing that link digital records with physical samples in a robust, adaptive way. An NSF EarthCube Research Coordination Network (RCN) called the Internet of Samples (iSamples) is now working to bridge the metadata schemas for biological and geological domains. We are leveraging the International Geo Sample Number (IGSN) that provides a versatile system of registering physical samples, and working to harmonize this with the DataCite schema for Digital Object Identifiers (DOI). A brokering approach for linking disparate catalogues and classification systems could help scale discovery and access to the many large collections now being managed (sometimes millions of specimens per collection). This presentation is about our community building efforts, research directions, and insights to date.

ICON-MIC: Implementing a CPU/MIC Collaboration Parallel Framework for ICON on Tianhe-2 Supercomputer.

PubMed

Wang, Zihao; Chen, Yu; Zhang, Jingrong; Li, Lun; Wan, Xiaohua; Liu, Zhiyong; Sun, Fei; Zhang, Fa

2018-03-01

Electron tomography (ET) is an important technique for studying the three-dimensional structures of the biological ultrastructure. Recently, ET has reached sub-nanometer resolution for investigating the native and conformational dynamics of macromolecular complexes by combining with the sub-tomogram averaging approach. Due to the limited sampling angles, ET reconstruction typically suffers from the "missing wedge" problem. Using a validation procedure, iterative compressed-sensing optimized nonuniform fast Fourier transform (NUFFT) reconstruction (ICON) demonstrates its power in restoring validated missing information for a low-signal-to-noise ratio biological ET dataset. However, the huge computational demand has become a bottleneck for the application of ICON. In this work, we implemented a parallel acceleration technology ICON-many integrated core (MIC) on Xeon Phi cards to address the huge computational demand of ICON. During this step, we parallelize the element-wise matrix operations and use the efficient summation of a matrix to reduce the cost of matrix computation. We also developed parallel versions of NUFFT on MIC to achieve a high acceleration of ICON by using more efficient fast Fourier transform (FFT) calculation. We then proposed a hybrid task allocation strategy (two-level load balancing) to improve the overall performance of ICON-MIC by making full use of the idle resources on Tianhe-2 supercomputer. Experimental results using two different datasets show that ICON-MIC has high accuracy in biological specimens under different noise levels and a significant acceleration, up to 13.3 × , compared with the CPU version. Further, ICON-MIC has good scalability efficiency and overall performance on Tianhe-2 supercomputer.

[Periampullary gangliocytic paraganglioma].

PubMed

Sankot, J; Svarcová, I

2008-01-01

We present the case of very rare periampullary gangliocytic paraganglioma in which we preferred proximal duodenopancreatectomy to local resection of the ampula of Vater because of not clear preoperative pathohistology and biologic behavior of the tumor. Although the definitive examination of the specimen proved its benign character we consider our procedure reasonable.

75 FR 65505 - Endangered Species; Receipt of Applications for Permit

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-25

... Applications A. Endangered Species Applicant: International Elephant Foundation, Fort Worth, TX; PRT- 15923A The applicant requests a permit to import biological specimens of Asian elephant (Elephus maximus) and African elephant (Loxodonta africana) from wild animals in all range countries and captive-held animals in...

Phytochemical, antimicrobial and antiplasmodial investigations of Terminalia brownii

USDA-ARS?s Scientific Manuscript database

The stem bark of Terminalia brownii was collected from Machakos county, Kenya, in November 2011, and identified at the University Herbarium, School of Biological Sciences, University of Nairobi, where a voucher specimen (JM2011/502) was deposited. The stem bark was air dried in shade and pulverized....

Measurement of the complex refractive index and complex dielectric permittivity of T.P.S. Space Shuttle tile materials at millimeter wavelengths

NASA Technical Reports Server (NTRS)

Afsar, Mohammed Nurul; Chi, Hua; Li, Xiaohui

1990-01-01

Complex refractive index and dielectric permittivity studies of presently used Space Shuttle tile materials at millimeter wavelengths reveal these tiles to exhibit similar absorption characteristics to those of fused silica materials. This absorption is mainly related to the water content in the specimen. A strong birefringence is observed at least in one of these fibrous refractory composite materials.

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.

42 CFR 493.1495 - Standard; Testing personnel responsibilities.

Code of Federal Regulations, 2013 CFR

2013-10-01

... experience, and technical abilities. (b) Each individual performing high complexity testing must— (1) Follow the laboratory's procedures for specimen handling and processing, test analyses, reporting and...

Vertical distribution of living ostracods in deep-sea sediments, North Atlantic Ocean

NASA Astrophysics Data System (ADS)

Jöst, Anna B.; Yasuhara, Moriaki; Okahashi, Hisayo; Ostmann, Alexandra; Arbizu, Pedro Martínez; Brix, Saskia

2017-04-01

The depth distribution of living specimens of deep-sea benthic ostracods (small crustaceans with calcareous shells that are preserved as microfossils) in sediments is poorly understood, despite the importance of this aspect of basic ostracod biology for paleoecologic and paleoceanographic interpretations. Here, we investigated living benthic ostracod specimens from deep-sea multiple core samples, to reveal their depths distributions within sediment cores. The results showed shallow distribution and low population density of living deep-sea benthic ostracods (which are mostly composed of Podocopa). The living specimens are concentrated in the top 1 cm of the sediment, hence deep-sea benthic ostracods are either epifauna or shallow infauna. This observation is consistent with the information from shallow-water species. We also confirmed shallow infaunal (0.5-2 cm) and very shallow infaunal (0-1 cm) habitats of the deep-sea ostracod genera Krithe and Argilloecia, respectively.

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.

A reevaluation of the specimens of Mesocoelium (Trematoda: Mesocoeliidae) in the Colección Nacional de Helmintos, Mexico.

PubMed

López-García, Ashley Samara; García-Prieto, Luis

2017-06-02

Species of Mesocoelium Odhner, 1901 (Digenea) are generally similar and are often difficult to distinguish. Currently there are 42 specimens of this genus held in the Colección Nacional de Helmintos (CNHE) of the Instituto de Biología, Universidad Nacional Autónoma de Mexico, which previously have been assigned to three species: M. monas Rudolphi, 1819, M. travassosi Pereira & Cuocolo, 1940 and M. leiperi Bhalerao, 1936. Upon reevaluation of these specimens it was determined that 27, could not be assigned to species level and 15 could only be assigned to body type (carli and leiperi) because of the poor conditions of preservation of the material. The remaining 15 specimens were of sufficient quality to be identified to species and were found to represent M. americanum Harwood, 1932, M. danforthi Hoffman, 1935, M. meggitti Bhalerao, 1927, M. cf. americanum Harwood, 1932, and M. cf. danforthi Hoffman, 1935. Neither M. monas nor M. travassosi could be confirmed among these specimens; however, Mesocoelium meggitti (syn. M. travassosi) was confirmed. Mesocoelium danforthi is recorded for the first time in the Mexican collection. The presence of M. cf. gonocephali Singh, 1967 and M. cf. microon Nicoll, 1914 also among the 15 specimens of sufficient quality to be identified to species, needs to be confirmed through collects of new material. Finally, in future studies, we propose to improve the quality of specimens by fixing them considering the modifications to this process proposed herein, and compliment these morphological studies with molecular studies.