Application of a Nanostructured Enzymatic Biosensor Based on Fullerene and Gold Nanoparticles to Polyphenol Detection.

PubMed

Tortolini, Cristina; Sanzò, Gabriella; Antiochia, Riccarda; Mazzei, Franco; Favero, Gabriele

2017-01-01

Electrochemical biosensors provide an attractive means of analyzing the content of a biological sample due to the direct conversion of a biological event to an electronic signal. The signal transduction and the general performance of electrochemical biosensors are often determined by the surface architectures that connect the sensing element to the biological sample at the nanometer scale. The most common surface modification techniques, the various electrochemical transduction mechanisms, and the choice of the recognition receptor molecules all influence the ultimate sensitivity of the sensor. We show herein a novel electrochemical biosensing platform based on the coupling of two different nanostructured materials (gold nanoparticles and fullerenols) displaying interesting electrochemical features. The use of these nanomaterials improved the electrochemical performance of the proposed biosensor.An application of the nanostructured enzyme-based biosensor has been developed for evaluating the detection of polyphenols either in buffer solution or in real wine samples.

Terahertz time-domain spectroscopy for non-invasive assessment of water content in biological samples.

PubMed

Borovkova, Mariia; Khodzitsky, Mikhail; Demchenko, Petr; Cherkasova, Olga; Popov, Alexey; Meglinski, Igor

2018-05-01

We apply terahertz time-domain spectroscopy for the quantitative non-invasive assessment of the water content in biological samples, such as Carpinus caroliniana tree leaves and pork muscles. The developed experimental terahertz time-domain spectroscopy system operates both in transmission and reflection modes. The Landau-Looyenga-Lifshitz-based model is used for the calculation of the water concentration within the samples. The results of the water concentration measurements are compared with the results of the gravimetric measurements. The obtained results show that the water content in biological samples can be measured non-invasively, with a high accuracy, utilizing terahertz waves in transmission and reflection modes.

Identification of nanoparticles and nanosystems in biological matrices with scanning probe microscopy.

PubMed

Angeloni, Livia; Reggente, Melania; Passeri, Daniele; Natali, Marco; Rossi, Marco

2018-04-17

Identification of nanoparticles and nanosystems into cells and biological matrices is a hot research topic in nanobiotechnologies. Because of their capability to map physical properties (mechanical, electric, magnetic, chemical, or optical), several scanning probe microscopy based techniques have been proposed for the subsurface detection of nanomaterials in biological systems. In particular, atomic force microscopy (AFM) can be used to reveal stiff nanoparticles in cells and other soft biomaterials by probing the sample mechanical properties through the acquisition of local indentation curves or through the combination of ultrasound-based methods, like contact resonance AFM (CR-AFM) or scanning near field ultrasound holography. Magnetic force microscopy can detect magnetic nanoparticles and other magnetic (bio)materials in nonmagnetic biological samples, while electric force microscopy, conductive AFM, and Kelvin probe force microscopy can reveal buried nanomaterials on the basis of the differences between their electric properties and those of the surrounding matrices. Finally, scanning near field optical microscopy and tip-enhanced Raman spectroscopy can visualize buried nanostructures on the basis of their optical and chemical properties. Despite at a still early stage, these methods are promising for detection of nanomaterials in biological systems as they could be truly noninvasive, would not require destructive and time-consuming specific sample preparation, could be performed in vitro, on alive samples and in water or physiological environment, and by continuously imaging the same sample could be used to dynamically monitor the diffusion paths and interaction mechanisms of nanomaterials into cells and biological systems. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology. © 2018 Wiley Periodicals, Inc.

Capacity for DNA-barcode based taxonomy in support of Great Lakes biological monitoring

EPA Science Inventory

Enumerating organisms collected via nets and sediment grabs is a mainstay of aquatic ecology. Since morphological taxonomy can require considerable resources and expertise, DNA barcode-based identification of mixed-organism samples offers a valuable tool in support of biological...

Biopolymers for sample collection, protection, and preservation.

PubMed

Sorokulova, Iryna; Olsen, Eric; Vodyanoy, Vitaly

2015-07-01

One of the principal challenges in the collection of biological samples from air, water, and soil matrices is that the target agents are not stable enough to be transferred from the collection point to the laboratory of choice without experiencing significant degradation and loss of viability. At present, there is no method to transport biological samples over considerable distances safely, efficiently, and cost-effectively without the use of ice or refrigeration. Current techniques of protection and preservation of biological materials have serious drawbacks. Many known techniques of preservation cause structural damages, so that biological materials lose their structural integrity and viability. We review applications of a novel bacterial preservation process, which is nontoxic and water soluble and allows for the storage of samples without refrigeration. The method is capable of protecting the biological sample from the effects of environment for extended periods of time and then allows for the easy release of these collected biological materials from the protective medium without structural or DNA damage. Strategies for sample collection, preservation, and shipment of bacterial, viral samples are described. The water-soluble polymer is used to immobilize the biological material by replacing the water molecules within the sample with molecules of the biopolymer. The cured polymer results in a solid protective film that is stable to many organic solvents, but quickly removed by the application of the water-based solution. The process of immobilization does not require the use of any additives, accelerators, or plastifiers and does not involve high temperature or radiation to promote polymerization.

Detecting Biological Warfare Agents

PubMed Central

Song, Linan; Ahn, Soohyoun

2005-01-01

We developed a fiber-optic, microsphere-based, high-density array composed of 18 species-specific probe microsensors to identify biological warfare agents. We simultaneously identified multiple biological warfare agents in environmental samples by looking at specific probe responses after hybridization and response patterns of the multiplexed array. PMID:16318712

Evaluating Biology Achievement Scores in an ICT Integrated PBL Environment

ERIC Educational Resources Information Center

Osman, Kamisah; Kaur, Simranjeet Judge

2014-01-01

Students' achievement in Biology is often looked up as a benchmark to evaluate the mode of teaching and learning in higher education. Problem-based learning (PBL) is an approach that focuses on students' solving a problem through collaborative groups. There were eighty samples involved in this study. The samples were divided into three groups: ICT…

Employment Opportunities in Applied Biological and Agricultural Occupations in the Metropolitan Area of Chicago.

ERIC Educational Resources Information Center

Thomas, Hollie B.; Neavill, Arthur

Based on questionnaire data collected from a sample of employers, this phase of a larger research project ascertained employment opportunities in the area of applied biological and agricultural occupations in the metropolitan area of Chicago. Specific fields of business surveyed by stratified random sample were animal care, animal health care,…

Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris

DOEpatents

Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Grace, Karen M [Los Alamos, NM; Grace, Wynne K [Los Alamos, NM; Shreve, Andrew P [Santa Fe, NM

2009-06-02

An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

Applying a low energy HPGe detector gamma ray spectrometric technique for the evaluation of Pu/Am ratio in biological samples.

PubMed

Singh, I S; Mishra, Lokpati; Yadav, J R; Nadar, M Y; Rao, D D; Pradeepkumar, K S

2015-10-01

The estimation of Pu/(241)Am ratio in the biological samples is an important input for the assessment of internal dose received by the workers. The radiochemical separation of Pu isotopes and (241)Am in a sample followed by alpha spectrometry is a widely used technique for the determination of Pu/(241)Am ratio. However, this method is time consuming and many times quick estimation is required. In this work, Pu/(241)Am ratio in the biological sample was estimated with HPGe detector based measurements using gamma/X-rays emitted by these radionuclides. These results were compared with those obtained from alpha spectroscopy of sample after radiochemical analysis and found to be in good agreement. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fully Integrated Microfluidic Device for Direct Sample-to-Answer Genetic Analysis

NASA Astrophysics Data System (ADS)

Liu, Robin H.; Grodzinski, Piotr

Integration of microfluidics technology with DNA microarrays enables building complete sample-to-answer systems that are useful in many applications such as clinic diagnostics. In this chapter, a fully integrated microfluidic device [1] that consists of microfluidic mixers, valves, pumps, channels, chambers, heaters, and a DNA microarray sensor to perform DNA analysis of complex biological sample solutions is present. This device can perform on-chip sample preparation (including magnetic bead-based cell capture, cell preconcentration and purification, and cell lysis) of complex biological sample solutions (such as whole blood), polymerase chain reaction, DNA hybridization, and electrochemical detection. A few novel microfluidic techniques were developed and employed. A micromix-ing technique based on a cavitation microstreaming principle was implemented to enhance target cell capture from whole blood samples using immunomagnetic beads. This technique was also employed to accelerate DNA hybridization reaction. Thermally actuated paraffin-based microvalves were developed to regulate flows. Electrochemical pumps and thermopneumatic pumps were integrated on the chip to provide pumping of liquid solutions. The device is completely self-contained: no external pressure sources, fluid storage, mechanical pumps, or valves are necessary for fluid manipulation, thus eliminating possible sample contamination and simplifying device operation. Pathogenic bacteria detection from ~mL whole blood samples and single-nucleotide polymorphism analysis directly from diluted blood were demonstrated. The device provides a cost-effective solution to direct sample-to-answer genetic analysis, and thus has a potential impact in the fields of point-of-care genetic analysis, environmental testing, and biological warfare agent detection.

Profiling of polar metabolites in biological extracts using diamond hydride-based aqueous normal phase chromatography.

PubMed

Callahan, Damien L; De Souza, David; Bacic, Antony; Roessner, Ute

2009-07-01

Highly polar metabolites, such as sugars and most amino acids are not retained by conventional RP LC columns. Without sufficient retention low concentration compounds are not detected due ion suppression and structural isomers are not resolved. In contrast, hydrophilic interaction chromatography (HILIC) and aqueous normal phase chromatography (ANP) retain compounds based on their hydrophilicity and therefore provides a means of separating highly polar compounds. Here, an ANP method based on the diamond hydride stationary phase is presented for profiling biological small molecules by LC. A rapid separation system based upon a fast gradient that delivers reproducible chromatography is presented. Approximately 1000 compounds were reproducibly detected in human urine samples and clear differences between these samples were identified. This chromatography was also applied to xylem fluid from soyabean (Glycine max) plants to which 400 compounds were detected. This method greatly increases the metabolite coverage over RP-only metabolite profiling in biological samples. We show that both forms of chromatography are necessary for untargeted comprehensive metabolite profiling and that the diamond hydride stationary phase provides a good option for polar metabolite analysis.

Moving beyond the van Krevelen Diagram: A New Stoichiometric Approach for Compound Classification in Organisms

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

Rivas-Ubach, Albert; Liu, Yina; Bianchi, Thomas S.

van Krevelen diagrams (O:C vs H:C ratios of elemental formulas) have been widely used in studies to obtain an estimation of the main compound categories present in environmental samples. However, the limits defining a specific compound category based solely on O:C and H:C ratios of elemental formulas have never been accurately listed or proposed to classify metabolites in biological samples. Furthermore, while O:C vs. H:C ratios of elemental formulas can provide an overview of the compound categories, such classification is inefficient because of the large overlap among different compound categories along both axes. We propose a more accurate compound classificationmore » for biological samples analyzed by high-resolution mass spectrometry-based on an assessment of the C:H:O:N:P stoichiometric ratios of over 130,000 elemental formulas of compounds classified in 6 main categories: lipids, peptides, amino-sugars, carbohydrates, nucleotides and phytochemical compounds (oxy-aromatic compounds). Our multidimensional stoichiometric compound classification (MSCC) constraints showed a highly accurate categorization of elemental formulas to the main compound categories in biological samples with over 98% of accuracy representing a substantial improvement over any classification based on the classic van Krevelen diagram. This method represents a significant step forward in environmental research, especially ecological stoichiometry and eco-metabolomics studies, by providing a novel and robust tool to further our understanding the ecosystem structure and function through the chemical characterization of different biological samples.« less

14C sample preparation for AMS microdosing studies at Lund University using online combustion and septa-sealed vials

NASA Astrophysics Data System (ADS)

Sydoff, Marie; Stenström, Kristina

2010-04-01

The Department of Physics at Lund University is participating in a European Union project called EUMAPP (European Union Microdose AMS Partnership Programme), in which sample preparation and accelerator mass spectrometry (AMS) measurements of biological samples from microdosing studies have been made. This paper describes a simplified method of converting biological samples to solid graphite for 14C analysis with AMS. The method is based on online combustion of the samples, and reduction of CO 2 in septa-sealed vials. The septa-sealed vials and disposable materials are used to eliminate sample cross-contamination. Measurements of ANU and Ox I standards show deviations of 2% and 3%, respectively, relative to reference values. This level of accuracy is sufficient for biological samples from microdosing studies. Since the method has very few handling steps from sample to graphite, the risk of failure during the sample preparation process is minimized, making the method easy to use in routine preparation of samples.

Advances in imaging secondary ion mass spectrometry for biological samples

DOE PAGES

Boxer, Steven G.; Kraft, Mary L.; Weber, Peter K.

2008-12-16

Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this hasmore » been a major barrier for applications to biological systems. Furthermore, recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.« less

Effect-based assessment of persistent organic pollutant and pesticide dumpsite using mammalian CALUX reporter cell lines.

PubMed

Pieterse, B; Rijk, I J C; Simon, E; van Vugt-Lussenburg, B M A; Fokke, B F H; van der Wijk, M; Besselink, H; Weber, R; van der Burg, B

2015-10-01

A combined chemical and biological analysis of samples from a major obsolete pesticide and persistent organic pollutant (POP) dumpsite in Northern Tajikistan was carried out. The chemical analytical screening focused on a range of prioritized compounds and compounds known to be present locally. Since chemical analytics does not allow measurements of hazards in complex mixtures, we tested the use of a novel effect-based approach using a panel of quantitative high-throughput CALUX reporter assays measuring distinct biological effects relevant in hazard assessment. Assays were included for assessing effects related to estrogen, androgen, and progestin signaling, aryl hydrocarbon receptor-mediated signaling, AP1 signaling, genotoxicity, oxidative stress, chemical hypoxia, and ER stress. With this panel of assays, we first quantified the biological activities of the individual chemicals measured in chemical analytics. Next, we calculated the expected sum activity by these chemicals in the samples of the pesticide dump site and compared the results with the measured CALUX bioactivity of the total extracts of these samples. The results showed that particularly endocrine disruption-related effects were common among the samples. This was consistent with the toxicological profiles of the individual chemicals that dominated these samples. However, large discrepancies between chemical and biological analysis were found in a sample from a burn place present in this site, with biological activities that could not be explained by chemical analysis. This is likely to be caused by toxic combustion products or by spills of compounds that were not targeted in the chemical analysis.

The Generation R Study: Biobank update 2015.

PubMed

Kruithof, Claudia J; Kooijman, Marjolein N; van Duijn, Cornelia M; Franco, Oscar H; de Jongste, Johan C; Klaver, Caroline C W; Mackenbach, Johan P; Moll, Henriëtte A; Raat, Hein; Rings, Edmond H H M; Rivadeneira, Fernando; Steegers, Eric A P; Tiemeier, Henning; Uitterlinden, Andre G; Verhulst, Frank C; Wolvius, Eppo B; Hofman, Albert; Jaddoe, Vincent W V

2014-12-01

The Generation R Study is a population-based prospective cohort study from fetal life until adulthood. The study is designed to identify early environmental and genetic causes and causal pathways leading to normal and abnormal growth, development and health from fetal life, childhood and young adulthood. In total, 9,778 mothers were enrolled in the study. Data collection in children and their parents include questionnaires, interviews, detailed physical and ultrasound examinations, behavioural observations, Magnetic Resonance Imaging and biological samples. Efforts have been conducted for collecting biological samples including blood, hair, faeces, nasal swabs, saliva and urine samples and generating genomics data on DNA, RNA and microbiome. In this paper, we give an update of the collection, processing and storage of these biological samples and available measures. Together with detailed phenotype measurements, these biological samples provide a unique resource for epidemiological studies focused on environmental exposures, genetic and genomic determinants and their interactions in relation to growth, health and development from fetal life onwards.

[Assessment of biological sampling's quality in a medical laboratory: case of Côte d' Ivoire Institute Pasteur].

PubMed

Kouassi-M'Bengue, Alphonsine; Koffi, Stephane; Manizan, Pascale; Ouattara, Abdoulaye; N'Douba, Adele Kacou; Dosso, Mireille

2008-01-01

Assurance quality is important in medical laboratory, but in Africa, few laboratories are involved in this process. The aim of this study was to assess biological sampling's quality in a bacteriological laboratory. A cross sectional study was undertaken in medical bacteriological laboratory of Côte d' Ivoire Institute Pasteur during 6 months. All urines, saddles, and bronchial expectorations collected from ambulatory patients during this period were included in the study. The quality of urine's, saddles and bronchial expectorations' sampling for a bacteriological analysis was evaluated. An interview based on Guidelines of good laboratories practices and referential ISO 15189 was used. A total of 300 samples were indexed. On a total of 300 recorded biological samples, 224 (74.7%) were not in conformity. In 87.5% of the cases of nonconformities, an antibiotic's treatment were preliminary instituted before the sampling. Corrective actions were carried in the laboratory on 30 samples with 56.6% for the urines, 26.7% for the saddles and 16.7% for the bronchial expectorations. At the end of this study, it arises that the quality of the biological sampling received at the medical bacteriology laboratory need to be improved.

Scanning transmission ion microscopy mass measurements for quantitative trace element analysis within biological samples and validation using atomic force microscopy thickness measurements

NASA Astrophysics Data System (ADS)

Devès, Guillaume; Cohen-Bouhacina, Touria; Ortega, Richard

2004-10-01

We used the nuclear microprobe techniques, micro-PIXE (particle-induced X-ray emission), micro-RBS (Rutherford backscattering spectrometry) and scanning transmission ion microscopy (STIM) in order to perform the characterization of trace element content and spatial distribution within biological samples (dehydrated cultured cells, tissues). The normalization of PIXE results was usually expressed in terms of sample dry mass as determined by micro-RBS recorded simultaneously to micro-PIXE. However, the main limit of RBS mass measurement is the sample mass loss occurring during irradiation and which could be up to 30% of the initial sample mass. We present here a new methodology for PIXE normalization and quantitative analysis of trace element within biological samples based on dry mass measurement performed by mean of STIM. The validation of STIM cell mass measurements was obtained in comparison with AFM sample thickness measurements. Results indicated the reliability of STIM mass measurement performed on biological samples and suggested that STIM should be performed for PIXE normalization. Further information deriving from direct confrontation of AFM and STIM analysis could as well be obtained, like in situ measurements of cell specific gravity within cells compartment (nucleolus and cytoplasm).

Biotechnical use of polymerase chain reaction for microbiological analysis of biological samples.

PubMed

Lantz, P G; Abu al-Soud, W; Knutsson, R; Hahn-Hägerdal, B; Rådström, P

2000-01-01

Since its introduction in the mid-80s, polymerase chain reaction (PCR) technology has been recognised as a rapid, sensitive and specific molecular diagnostic tool for the analysis of micro-organisms in clinical, environmental and food samples. Although this technique can be extremely effective with pure solutions of nucleic acids, it's sensitivity may be reduced dramatically when applied directly to biological samples. This review describes PCR technology as a microbial detection method, PCR inhibitors in biological samples and various sample preparation techniques that can be used to facilitate PCR detection, by either separating the micro-organisms from PCR inhibitors and/or by concentrating the micro-organisms to detectable concentrations. Parts of this review are updated and based on a doctoral thesis by Lantz [1] and on a review discussing methods to overcome PCR inhibition in foods [2].

Optimization of microwave digestion for mercury determination in marine biological samples by cold vapour atomic absorption spectrometry.

PubMed

Cardellicchio, Nicola; Di Leo, Antonella; Giandomenico, Santina; Santoro, Stefania

2006-01-01

Optimization of acid digestion method for mercury determination in marine biological samples (dolphin liver, fish and mussel tissues) using a closed vessel microwave sample preparation is presented. Five digestion procedures with different acid mixtures were investigated: the best results were obtained when the microwave-assisted digestion was based on sample dissolution with HNO3-H2SO4-K2Cr2O7 mixture. A comparison between microwave digestion and conventional reflux digestion shows there are considerable losses of mercury in the open digestion system. The microwave digestion method has been tested satisfactorily using two certified reference materials. Analytical results show a good agreement with certified values. The microwave digestion proved to be a reliable and rapid method for decomposition of biological samples in mercury determination.

Macro to microfluidics system for biological environmental monitoring.

PubMed

Delattre, Cyril; Allier, Cédric P; Fouillet, Yves; Jary, Dorothée; Bottausci, Frederic; Bouvier, Denis; Delapierre, Guillaume; Quinaud, Manuelle; Rival, Arnaud; Davoust, Laurent; Peponnet, Christine

2012-01-01

Biological environmental monitoring (BEM) is a growing field of research which challenges both microfluidics and system automation. The aim is to develop a transportable system with analysis throughput which satisfies the requirements: (i) fully autonomous, (ii) complete protocol integration from sample collection to final analysis, (iii) detection of diluted molecules or biological species in a large real life environmental sample volume, (iv) robustness and (v) flexibility and versatility. This paper discusses all these specifications in order to define an original fluidic architecture based on three connected modules, a sampling module, a sample preparation module and a detection module. The sample preparation module highly concentrates on the pathogens present in a few mL samples of complex and unknown solutions and purifies the pathogens' nucleic acids into a few μL of a controlled buffer. To do so, a two-step concentration protocol based on magnetic beads is automated in a reusable macro-to-micro fluidic system. The detection module is a PCR based miniaturized platform using digital microfluidics, where reactions are performed in 64 nL droplets handled by electrowetting on dielectric (EWOD) actuation. The design and manufacture of the two modules are reported as well as their respective performances. To demonstrate the integration of the complete protocol in the same system, first results of pathogen detection are shown. Copyright © 2012 Elsevier B.V. All rights reserved.

Technology-Supported Learning in Secondary and Undergraduate Biological Education: Observations from Literature Review

ERIC Educational Resources Information Center

Lee, Silvia Wen-Yu; Tsai, Chin-Chung

2013-01-01

We conducted a literature review of using educational technology in biology learning from 2001 to 2010. A total of 36 empirical articles were included for review. Based upon the content analyses of these studies, such as technologies utilized, student sample, biological topics involved, the research purpose, and methodology, the following…

Repeatability and reproducibility of intracellular molar concentration assessed by synchrotron-based x-ray fluorescence microscopy

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

Merolle, L., E-mail: lucia.merolle@elettra.eu; Gianoncelli, A.; Malucelli, E., E-mail: emil.malucelli@unibo.it

2016-01-28

Elemental analysis of biological sample can give information about content and distribution of elements essential for human life or trace elements whose absence is the cause of abnormal biological function or development. However, biological systems contain an ensemble of cells with heterogeneous chemistry and elemental content; therefore, accurate characterization of samples with high cellular heterogeneity may only be achieved by analyzing single cells. Powerful methods in molecular biology are abundant, among them X-Ray microscopy based on synchrotron light source has gaining increasing attention thanks to its extremely sensitivity. However, reproducibility and repeatability of these measurements is one of the majormore » obstacles in achieving a statistical significance in single cells population analysis. In this study, we compared the elemental content of human colon adenocarcinoma cells obtained by three distinct accesses to synchrotron radiation light.« less

Measuring Biological Age via Metabonomics: The Metabolic Age Score.

PubMed

Hertel, Johannes; Friedrich, Nele; Wittfeld, Katharina; Pietzner, Maik; Budde, Kathrin; Van der Auwera, Sandra; Lohmann, Tobias; Teumer, Alexander; Völzke, Henry; Nauck, Matthias; Grabe, Hans Jörgen

2016-02-05

Chronological age is one of the most important risk factors for adverse clinical outcome. Still, two individuals at the same chronological age could have different biological aging states, leading to different individual risk profiles. Capturing this individual variance could constitute an even more powerful predictor enhancing prediction in age-related morbidity. Applying a nonlinear regression technique, we constructed a metabonomic measurement for biological age, the metabolic age score, based on urine data measured via (1)H NMR spectroscopy. We validated the score in two large independent population-based samples by revealing its significant associations with chronological age and age-related clinical phenotypes as well as its independent predictive value for survival over approximately 13 years of follow-up. Furthermore, the metabolic age score was prognostic for weight loss in a sample of individuals who underwent bariatric surgery. We conclude that the metabolic age score is an informative measurement of biological age with possible applications in personalized medicine.

Tissue-based standoff biosensors for detecting chemical warfare agents

DOEpatents

Greenbaum, Elias; Sanders, Charlene A.

2003-11-18

A tissue-based, deployable, standoff air quality sensor for detecting the presence of at least one chemical or biological warfare agent, includes: a cell containing entrapped photosynthetic tissue, the cell adapted for analyzing photosynthetic activity of the entrapped photosynthetic tissue; means for introducing an air sample into the cell and contacting the air sample with the entrapped photosynthetic tissue; a fluorometer in operable relationship with the cell for measuring photosynthetic activity of the entrapped photosynthetic tissue; and transmitting means for transmitting analytical data generated by the fluorometer relating to the presence of at least one chemical or biological warfare agent in the air sample, the sensor adapted for deployment into a selected area.

A simple microviscometric approach based on Brownian motion tracking.

PubMed

Hnyluchová, Zuzana; Bjalončíková, Petra; Karas, Pavel; Mravec, Filip; Halasová, Tereza; Pekař, Miloslav; Kubala, Lukáš; Víteček, Jan

2015-02-01

Viscosity-an integral property of a liquid-is traditionally determined by mechanical instruments. The most pronounced disadvantage of such an approach is the requirement of a large sample volume, which poses a serious obstacle, particularly in biology and biophysics when working with limited samples. Scaling down the required volume by means of microviscometry based on tracking the Brownian motion of particles can provide a reasonable alternative. In this paper, we report a simple microviscometric approach which can be conducted with common laboratory equipment. The core of this approach consists in a freely available standalone script to process particle trajectory data based on a Newtonian model. In our study, this setup allowed the sample to be scaled down to 10 μl. The utility of the approach was demonstrated using model solutions of glycerine, hyaluronate, and mouse blood plasma. Therefore, this microviscometric approach based on a newly developed freely available script can be suggested for determination of the viscosity of small biological samples (e.g., body fluids).

Inferring Biological Structures from Super-Resolution Single Molecule Images Using Generative Models

PubMed Central

Maji, Suvrajit; Bruchez, Marcel P.

2012-01-01

Localization-based super resolution imaging is presently limited by sampling requirements for dynamic measurements of biological structures. Generating an image requires serial acquisition of individual molecular positions at sufficient density to define a biological structure, increasing the acquisition time. Efficient analysis of biological structures from sparse localization data could substantially improve the dynamic imaging capabilities of these methods. Using a feature extraction technique called the Hough Transform simple biological structures are identified from both simulated and real localization data. We demonstrate that these generative models can efficiently infer biological structures in the data from far fewer localizations than are required for complete spatial sampling. Analysis at partial data densities revealed efficient recovery of clathrin vesicle size distributions and microtubule orientation angles with as little as 10% of the localization data. This approach significantly increases the temporal resolution for dynamic imaging and provides quantitatively useful biological information. PMID:22629348

Context Matters: Volunteer Bias, Small Sample Size, and the Value of Comparison Groups in the Assessment of Research-Based Undergraduate Introductory Biology Lab Courses

PubMed Central

Brownell, Sara E.; Kloser, Matthew J.; Fukami, Tadashi; Shavelson, Richard J.

2013-01-01

The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course. PMID:24358380

Context matters: volunteer bias, small sample size, and the value of comparison groups in the assessment of research-based undergraduate introductory biology lab courses.

PubMed

Brownell, Sara E; Kloser, Matthew J; Fukami, Tadashi; Shavelson, Richard J

2013-01-01

The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.

Novel microbial diversity retrieved by autonomous robotic exploration of the world's deepest vertical phreatic sinkhole.

PubMed

Sahl, Jason W; Fairfield, Nathaniel; Harris, J Kirk; Wettergreen, David; Stone, William C; Spear, John R

2010-03-01

The deep phreatic thermal explorer (DEPTHX) is an autonomous underwater vehicle designed to navigate an unexplored environment, generate high-resolution three-dimensional (3-D) maps, collect biological samples based on an autonomous sampling decision, and return to its origin. In the spring of 2007, DEPTHX was deployed in Zacatón, a deep (approximately 318 m), limestone, phreatic sinkhole (cenote) in northeastern Mexico. As DEPTHX descended, it generated a 3-D map based on the processing of range data from 54 onboard sonars. The vehicle collected water column samples and wall biomat samples throughout the depth profile of the cenote. Post-expedition sample analysis via comparative analysis of 16S rRNA gene sequences revealed a wealth of microbial diversity. Traditional Sanger gene sequencing combined with a barcoded-amplicon pyrosequencing approach revealed novel, phylum-level lineages from the domains Bacteria and Archaea; in addition, several novel subphylum lineages were also identified. Overall, DEPTHX successfully navigated and mapped Zacatón, and collected biological samples based on an autonomous decision, which revealed novel microbial diversity in a previously unexplored environment.

Small-scale laser based electron accelerators for biology and medicine: a comparative study of the biological effectiveness

NASA Astrophysics Data System (ADS)

Labate, Luca; Andreassi, Maria Grazia; Baffigi, Federica; Basta, Giuseppina; Bizzarri, Ranieri; Borghini, Andrea; Candiano, Giuliana C.; Casarino, Carlo; Cresci, Monica; Di Martino, Fabio; Fulgentini, Lorenzo; Ghetti, Francesco; Gilardi, Maria Carla; Giulietti, Antonio; Köster, Petra; Lenci, Francesco; Levato, Tadzio; Oishi, Yuji; Russo, Giorgio; Sgarbossa, Antonella; Traino, Claudio; Gizzi, Leonida A.

2013-05-01

Laser-driven electron accelerators based on the Laser Wakefield Acceleration process has entered a mature phase to be considered as alternative devices to conventional radiofrequency linear accelerators used in medical applications. Before entering the medical practice, however, deep studies of the radiobiological effects of such short bunches as the ones produced by laser-driven accelerators have to be performed. Here we report on the setup, characterization and first test of a small-scale laser accelerator for radiobiology experiments. A brief description of the experimental setup will be given at first, followed by an overview of the electron bunch characterization, in particular in terms of dose delivered to the samples. Finally, the first results from the irradiation of biological samples will be briefly discussed.

Spectrochemical analysis of powdered biological samples using transversely excited atmospheric carbon dioxide laser plasma excitation

NASA Astrophysics Data System (ADS)

Zivkovic, Sanja; Momcilovic, Milos; Staicu, Angela; Mutic, Jelena; Trtica, Milan; Savovic, Jelena

2017-02-01

The aim of this study was to develop a simple laser induced breakdown spectroscopy (LIBS) method for quantitative elemental analysis of powdered biological materials based on laboratory prepared calibration samples. The analysis was done using ungated single pulse LIBS in ambient air at atmospheric pressure. Transversely-Excited Atmospheric pressure (TEA) CO2 laser was used as an energy source for plasma generation on samples. The material used for the analysis was a blue-green alga Spirulina, widely used in food and pharmaceutical industries and also in a few biotechnological applications. To demonstrate the analytical potential of this particular LIBS system the obtained spectra were compared to the spectra obtained using a commercial LIBS system based on pulsed Nd:YAG laser. A single sample of known concentration was used to estimate detection limits for Ba, Ca, Fe, Mg, Mn, Si and Sr and compare detection power of these two LIBS systems. TEA CO2 laser based LIBS was also applied for quantitative analysis of the elements in powder Spirulina samples. Analytical curves for Ba, Fe, Mg, Mn and Sr were constructed using laboratory produced matrix-matched calibration samples. Inductively coupled plasma optical emission spectroscopy (ICP-OES) was used as the reference technique for elemental quantification, and reasonably well agreement between ICP and LIBS data was obtained. Results confirm that, in respect to its sensitivity and precision, TEA CO2 laser based LIBS can be successfully applied for quantitative analysis of macro and micro-elements in algal samples. The fact that nearly all classes of materials can be prepared as powders implies that the proposed method could be easily extended to a quantitative analysis of different kinds of materials, organic, biological or inorganic.

The Recent Developments in Sample Preparation for Mass Spectrometry-Based Metabolomics.

PubMed

Gong, Zhi-Gang; Hu, Jing; Wu, Xi; Xu, Yong-Jiang

2017-07-04

Metabolomics is a critical member in systems biology. Although great progress has been achieved in metabolomics, there are still some problems in sample preparation, data processing and data interpretation. In this review, we intend to explore the roles, challenges and trends in sample preparation for mass spectrometry- (MS-) based metabolomics. The newly emerged sample preparation methods were also critically examined, including laser microdissection, in vivo sampling, dried blood spot, microwave, ultrasound and enzyme-assisted extraction, as well as microextraction techniques. Finally, we provide some conclusions and perspectives for sample preparation in MS-based metabolomics.

[Valorization of biological resources in tumour libraries].

PubMed

Keelaghan, Thérèse

2006-01-01

The transfer and commercialization of biological materials, whether in the form of tumour samples, tissue samples or chemicals, and of the data base pertaining to such material have become a subject of considerable importance for both the private and public sectors involved in medical research. In order to fully appreciate and apprehend the process for the protection and the valuation of the transferred material, intellectual property law must be taken into account. As a result, a distinction is made between the tangible and intangible elements of the biological material and of the attached data base, thus providing the transferring entity the possibility to claim property rights to future intellectual property arising from the research regarding the transferred material. The transfer of biological material and attached data base without such contractual provisions can lead to the loss of this potential value as well as of physical and legal control over the material transferred by the providing entity. The intentions and the assumptions of the parties must be negotiated and written into terms of contract, at the risk of losing future value due to unexpressed assumptions concerning intangible property rights.

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

NASA Astrophysics Data System (ADS)

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

2017-06-01

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

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge.

PubMed

Lee, Ju Seok; Chen, Junghuei; Deaton, Russell; Kim, Jin-Woo

2014-01-01

Genetic material extracted from in situ microbial communities has high promise as an indicator of biological system status. However, the challenge is to access genomic information from all organisms at the population or community scale to monitor the biosystem's state. Hence, there is a need for a better diagnostic tool that provides a holistic view of a biosystem's genomic status. Here, we introduce an in vitro methodology for genomic pattern classification of biological samples that taps large amounts of genetic information from all genes present and uses that information to detect changes in genomic patterns and classify them. We developed a biosensing protocol, termed Biological Memory, that has in vitro computational capabilities to "learn" and "store" genomic sequence information directly from genomic samples without knowledge of their explicit sequences, and that discovers differences in vitro between previously unknown inputs and learned memory molecules. The Memory protocol was designed and optimized based upon (1) common in vitro recombinant DNA operations using 20-base random probes, including polymerization, nuclease digestion, and magnetic bead separation, to capture a snapshot of the genomic state of a biological sample as a DNA memory and (2) the thermal stability of DNA duplexes between new input and the memory to detect similarities and differences. For efficient read out, a microarray was used as an output method. When the microarray-based Memory protocol was implemented to test its capability and sensitivity using genomic DNA from two model bacterial strains, i.e., Escherichia coli K12 and Bacillus subtilis, results indicate that the Memory protocol can "learn" input DNA, "recall" similar DNA, differentiate between dissimilar DNA, and detect relatively small concentration differences in samples. This study demonstrated not only the in vitro information processing capabilities of DNA, but also its promise as a genomic pattern classifier that could access information from all organisms in a biological system without explicit genomic information. The Memory protocol has high potential for many applications, including in situ biomonitoring of ecosystems, screening for diseases, biosensing of pathological features in water and food supplies, and non-biological information processing of memory devices, among many.

The Effects of 3D Computer Simulation on Biology Students' Achievement and Memory Retention

ERIC Educational Resources Information Center

Elangovan, Tavasuria; Ismail, Zurida

2014-01-01

A quasi experimental study was conducted for six weeks to determine the effectiveness of two different 3D computer simulation based teaching methods, that is, realistic simulation and non-realistic simulation on Form Four Biology students' achievement and memory retention in Perak, Malaysia. A sample of 136 Form Four Biology students in Perak,…

Imaging systems and algorithms to analyze biological samples in real-time using mobile phone microscopy.

PubMed

Shanmugam, Akshaya; Usmani, Mohammad; Mayberry, Addison; Perkins, David L; Holcomb, Daniel E

2018-01-01

Miniaturized imaging devices have pushed the boundaries of point-of-care imaging, but existing mobile-phone-based imaging systems do not exploit the full potential of smart phones. This work demonstrates the use of simple imaging configurations to deliver superior image quality and the ability to handle a wide range of biological samples. Results presented in this work are from analysis of fluorescent beads under fluorescence imaging, as well as helminth eggs and freshwater mussel larvae under white light imaging. To demonstrate versatility of the systems, real time analysis and post-processing results of the sample count and sample size are presented in both still images and videos of flowing samples.

Estimating the biological value of soft-bottom sediments with sediment profile imaging and grab sampling

NASA Astrophysics Data System (ADS)

Van Hoey, Gert; Birchenough, Silvana N. R.; Hostens, Kris

2014-02-01

Biological value estimation is based on a set of assessment questions and several thresholds to delineate areas of ecological importance (e.g. biodiversity). An existing framework, that was specifically designed to assess the ecosystem biodiversity, was expanded by adding new questions on the productivity, functionality and biogeochemical status of benthic habitats. The additional ecological and sedimentological information was collected by using sediment profile imagery (SPI) and grab sampling. Additionally, information on the performance and comparability of both techniques is provided in this study. The research idea was tested at a site near the harbor of Zeebrugge, an area under consideration as a new disposal site for dredged material from the harbor entrance. The sedimentology of the area can be adequately described based on the information from both SPI and Van Veen grab samples, but only the SPI revealed structural information on the physical habitat (layering, a-RPD). The latter information represented the current status of the benthic habitat, which was confirmed by the Van Veen grab samples. All information was summarized through the biological valuation framework, and provided clear evidence of the differences in biological value for the different sediment types within the area. We concluded that the installation of a new dredged material disposal site in this area was not in conflict with the benthic ecology. This area has a low biological value and the benthic system is adapted to changing conditions, which was signaled by the dominance of mobile, short living and opportunistic species. This study showed that suitable sedimentological and ecological information can be gathered by these traditional and complementary techniques, to estimate the biological value of an area in the light of marine spatial planning and environmental impact assessments.

Sample handling for mass spectrometric proteomic investigations of human sera.

PubMed

West-Nielsen, Mikkel; Høgdall, Estrid V; Marchiori, Elena; Høgdall, Claus K; Schou, Christian; Heegaard, Niels H H

2005-08-15

Proteomic investigations of sera are potentially of value for diagnosis, prognosis, choice of therapy, and disease activity assessment by virtue of discovering new biomarkers and biomarker patterns. Much debate focuses on the biological relevance and the need for identification of such biomarkers while less effort has been invested in devising standard procedures for sample preparation and storage in relation to model building based on complex sets of mass spectrometric (MS) data. Thus, development of standardized methods for collection and storage of patient samples together with standards for transportation and handling of samples are needed. This requires knowledge about how sample processing affects MS-based proteome analyses and thereby how nonbiological biased classification errors are avoided. In this study, we characterize the effects of sample handling, including clotting conditions, storage temperature, storage time, and freeze/thaw cycles, on MS-based proteomics of human serum by using principal components analysis, support vector machine learning, and clustering methods based on genetic algorithms as class modeling and prediction methods. Using spiking to artificially create differentiable sample groups, this integrated approach yields data that--even when working with sample groups that differ more than may be expected in biological studies--clearly demonstrate the need for comparable sampling conditions for samples used for modeling and for the samples that are going into the test set group. Also, the study emphasizes the difference between class prediction and class comparison studies as well as the advantages and disadvantages of different modeling methods.

Actinide bioimaging in tissues: Comparison of emulsion and solid track autoradiography techniques with the iQID camera

PubMed Central

Miller, Brian W.; Van der Meeren, Anne; Tazrart, Anissa; Angulo, Jaime F.; Griffiths, Nina M.

2017-01-01

This work presents a comparison of three autoradiography techniques for imaging biological samples contaminated with actinides: emulsion-based, plastic-based autoradiography and a quantitative digital technique, the iQID camera, based on the numerical analysis of light from a scintillator screen. In radiation toxicology it has been important to develop means of imaging actinide distribution in tissues as these radionuclides may be heterogeneously distributed within and between tissues after internal contamination. Actinide distribution determines which cells are exposed to alpha radiation and is thus potentially critical for assessing absorbed dose. The comparison was carried out by generating autoradiographs of the same biological samples contaminated with actinides with the three autoradiography techniques. These samples were cell preparations or tissue sections collected from animals contaminated with different physico-chemical forms of actinides. The autoradiograph characteristics and the performances of the techniques were evaluated and discussed mainly in terms of acquisition process, activity distribution patterns, spatial resolution and feasibility of activity quantification. The obtained autoradiographs presented similar actinide distribution at low magnification. Out of the three techniques, emulsion autoradiography is the only one to provide a highly-resolved image of the actinide distribution inherently superimposed on the biological sample. Emulsion autoradiography is hence best interpreted at higher magnifications. However, this technique is destructive for the biological sample. Both emulsion- and plastic-based autoradiography record alpha tracks and thus enabled the differentiation between ionized forms of actinides and oxide particles. This feature can help in the evaluation of decorporation therapy efficacy. The most recent technique, the iQID camera, presents several additional features: real-time imaging, separate imaging of alpha particles and gamma rays, and alpha activity quantification. The comparison of these three autoradiography techniques showed that they are complementary and the choice of the technique depends on the purpose of the imaging experiment. PMID:29023595

Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples

PubMed Central

Feist, Peter; Hummon, Amanda B.

2015-01-01

Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed. PMID:25664860

Impacts of Sampling and Handling Procedures on DNA- and RNA-based Microbial Characterization and Quantification of Groundwater and Saturated Soil

DTIC Science & Technology

2012-07-01

use of molecular biological techniques (MBTs) has allowed microbial ecologists and environmental engineers to determine microbial community...metabolic genes). The most common approaches used in bioremediation research are those based on the polymerase chain reaction (PCR) amplification of... bioremediation . Because of its sensitivity compared to direct hybridization/probing, PCR is increasingly used to analyze groundwater samples and soil samples

Towards a future molecular diagnosis of autism: Recent advances in biomarkers research from saliva samples.

PubMed

Galiana-Simal, Adrian; Muñoz-Martinez, Victoria; Calero-Bueno, Paloma; Vela-Romero, Maria; Beato-Fernandez, Luis

2018-06-01

Autism spectrum disorder diagnosis is currently based on clinical observations and behavioral evaluations exclusively, without any biological determination. Molecular biomarkers are usually obtained from biological fluids, such as blood or urine, generally through invasive and uncomfortable procedures. Patients with autism are characterized by sensory reactivity and behavioral difficulties which make sample collection problematic. Saliva has emerged as a feasible alternative to obtain relevant biological information and is especially indicated in the case of children with autism due to its painless and noninvasive sampling characteristics. Furthermore, saliva represents a valuable resource to study candidate biomarkers of autism. This has resulted in a number of interesting studies reported during the last 5 years that we have gathered and briefly discussed. Copyright © 2018. Published by Elsevier Ltd.

Evaluation of the Biological Sampling Kit (BiSKit) for Large-Area Surface Sampling

PubMed Central

Buttner, Mark P.; Cruz, Patricia; Stetzenbach, Linda D.; Klima-Comba, Amy K.; Stevens, Vanessa L.; Emanuel, Peter A.

2004-01-01

Current surface sampling methods for microbial contaminants are designed to sample small areas and utilize culture analysis. The total number of microbes recovered is low because a small area is sampled, making detection of a potential pathogen more difficult. Furthermore, sampling of small areas requires a greater number of samples to be collected, which delays the reporting of results, taxes laboratory resources and staffing, and increases analysis costs. A new biological surface sampling method, the Biological Sampling Kit (BiSKit), designed to sample large areas and to be compatible with testing with a variety of technologies, including PCR and immunoassay, was evaluated and compared to other surface sampling strategies. In experimental room trials, wood laminate and metal surfaces were contaminated by aerosolization of Bacillus atrophaeus spores, a simulant for Bacillus anthracis, into the room, followed by settling of the spores onto the test surfaces. The surfaces were sampled with the BiSKit, a cotton-based swab, and a foam-based swab. Samples were analyzed by culturing, quantitative PCR, and immunological assays. The results showed that the large surface area (1 m2) sampled with the BiSKit resulted in concentrations of B. atrophaeus in samples that were up to 10-fold higher than the concentrations obtained with the other methods tested. A comparison of wet and dry sampling with the BiSKit indicated that dry sampling was more efficient (efficiency, 18.4%) than wet sampling (efficiency, 11.3%). The sensitivities of detection of B. atrophaeus on metal surfaces were 42 ± 5.8 CFU/m2 for wet sampling and 100.5 ± 10.2 CFU/m2 for dry sampling. These results demonstrate that the use of a sampling device capable of sampling larger areas results in higher sensitivity than that obtained with currently available methods and has the advantage of sampling larger areas, thus requiring collection of fewer samples per site. PMID:15574898

A generic standard additions based method to determine endogenous analyte concentrations by immunoassays to overcome complex biological matrix interference.

PubMed

Pang, Susan; Cowen, Simon

2017-12-13

We describe a novel generic method to derive the unknown endogenous concentrations of analyte within complex biological matrices (e.g. serum or plasma) based upon the relationship between the immunoassay signal response of a biological test sample spiked with known analyte concentrations and the log transformed estimated total concentration. If the estimated total analyte concentration is correct, a portion of the sigmoid on a log-log plot is very close to linear, allowing the unknown endogenous concentration to be estimated using a numerical method. This approach obviates conventional relative quantification using an internal standard curve and need for calibrant diluent, and takes into account the individual matrix interference on the immunoassay by spiking the test sample itself. This technique is based on standard additions for chemical analytes. Unknown endogenous analyte concentrations within even 2-fold diluted human plasma may be determined reliably using as few as four reaction wells.

Quantification of 2D elemental distribution maps of intermediate-thick biological sections by low energy synchrotron μ-X-ray fluorescence spectrometry

NASA Astrophysics Data System (ADS)

Kump, P.; Vogel-Mikuš, K.

2018-05-01

Two fundamental-parameter (FP) based models for quantification of 2D elemental distribution maps of intermediate-thick biological samples by synchrotron low energy μ-X-ray fluorescence spectrometry (SR-μ-XRF) are presented and applied to the elemental analysis in experiments with monochromatic focused photon beam excitation at two low energy X-ray fluorescence beamlines—TwinMic, Elettra Sincrotrone Trieste, Italy, and ID21, ESRF, Grenoble, France. The models assume intermediate-thick biological samples composed of measured elements, the sources of the measurable spectral lines, and by the residual matrix, which affects the measured intensities through absorption. In the first model a fixed residual matrix of the sample is assumed, while in the second model the residual matrix is obtained by the iteration refinement of elemental concentrations and an adjusted residual matrix. The absorption of the incident focused beam in the biological sample at each scanned pixel position, determined from the output of a photodiode or a CCD camera, is applied as a control in the iteration procedure of quantification.

Imaging systems and algorithms to analyze biological samples in real-time using mobile phone microscopy

PubMed Central

Mayberry, Addison; Perkins, David L.; Holcomb, Daniel E.

2018-01-01

Miniaturized imaging devices have pushed the boundaries of point-of-care imaging, but existing mobile-phone-based imaging systems do not exploit the full potential of smart phones. This work demonstrates the use of simple imaging configurations to deliver superior image quality and the ability to handle a wide range of biological samples. Results presented in this work are from analysis of fluorescent beads under fluorescence imaging, as well as helminth eggs and freshwater mussel larvae under white light imaging. To demonstrate versatility of the systems, real time analysis and post-processing results of the sample count and sample size are presented in both still images and videos of flowing samples. PMID:29509786

Impact of calcium and TOC on biological acidification assessment in Norwegian rivers.

PubMed

Schneider, Susanne C

2011-02-15

Acidification continues to be a major impact in freshwaters of northern Europe, and the biotic response to chemical recovery from acidification is often not a straightforward process. The focus on biological recovery is relevant within the context of the EU Water Framework Directive, where a biological monitoring system is needed that detects differences in fauna and flora compared to undisturbed reference conditions. In order to verify true reference sites for biological analyses, expected river pH is modeled based on Ca and TOC, and 94% of variability in pH at reference sites is explained by Ca alone, while 98% is explained by a combination of Ca and TOC. Based on 59 samples from 28 reference sites, compared to 547 samples from 285 non-reference sites, the impact of calcium and total organic carbon (TOC) on benthic algae species composition, expressed as acidification index periphyton (AIP), is analyzed. Rivers with a high Ca concentration have a naturally higher AIP, and TOC affects reference AIP only at low Ca concentrations. Four biological river types are needed for assessment of river acidification in Norway based on benthic algae: very calcium-poor, humic rivers (Ca<1 mg/l and TOC>2 mg/l); very calcium-poor, clear rivers (Ca<1 mg/l and TOC<2 mg/l); calcium-poor rivers (Ca between 1 and 4 mg/l); moderately calcium rich rivers (Ca>4 mg/l). A biological assessment system for river acidification in Norway based on benthic algae is presented, following the demands of the Water Framework Directive. Copyright © 2010 Elsevier B.V. All rights reserved.

Meta-Analysis of Inquiry-Based Instruction Research

NASA Astrophysics Data System (ADS)

Hasanah, N.; Prasetyo, A. P. B.; Rudyatmi, E.

2017-04-01

Inquiry-based instruction in biology has been the focus of educational research conducted by Unnes biology department students in collaboration with their university supervisors. This study aimed to describe the methodological aspects, inquiry teaching methods critically, and to analyse the results claims, of the selected four student research reports, grounded in inquiry, based on the database of Unnes biology department 2014. Four experimental quantitative research of 16 were selected as research objects by purposive sampling technique. Data collected through documentation study was qualitatively analysed regarding methods used, quality of inquiry syntax, and finding claims. Findings showed that the student research was still the lack of relevant aspects of research methodology, namely in appropriate sampling procedures, limited validity tests of all research instruments, and the limited parametric statistic (t-test) not supported previously by data normality tests. Their consistent inquiry syntax supported the four mini-thesis claims that inquiry-based teaching influenced their dependent variables significantly. In other words, the findings indicated that positive claims of the research results were not fully supported by good research methods, and well-defined inquiry procedures implementation.

How Parents Influence School Grades: Hints from a Sample of Adoptive and Biological Families

ERIC Educational Resources Information Center

Johnson, Wendy; McGue, Matt; Iacono, William G.

2007-01-01

Using the biological and adoptive families in the Minnesota-based Sibling Interaction and Behavior Study, we investigated the associations among genetic and environmental influences on IQ, parenting, parental expectations for offspring educational attainment, engagement in school, and school grades. All variables showed substantial genetic…

Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens

PubMed Central

Kilian, Norbert; Henning, Tilo; Plitzner, Patrick; Müller, Andreas; Güntsch, Anton; Stöver, Ben C.; Müller, Kai F.; Berendsohn, Walter G.; Borsch, Thomas

2015-01-01

We present the model and implementation of a workflow that blazes a trail in systematic biology for the re-usability of character data (data on any kind of characters of pheno- and genotypes of organisms) and their additivity from specimen to taxon level. We take into account that any taxon characterization is based on a limited set of sampled individuals and characters, and that consequently any new individual and any new character may affect the recognition of biological entities and/or the subsequent delimitation and characterization of a taxon. Taxon concepts thus frequently change during the knowledge generation process in systematic biology. Structured character data are therefore not only needed for the knowledge generation process but also for easily adapting characterizations of taxa. We aim to facilitate the construction and reproducibility of taxon characterizations from structured character data of changing sample sets by establishing a stable and unambiguous association between each sampled individual and the data processed from it. Our workflow implementation uses the European Distributed Institute of Taxonomy Platform, a comprehensive taxonomic data management and publication environment to: (i) establish a reproducible connection between sampled individuals and all samples derived from them; (ii) stably link sample-based character data with the metadata of the respective samples; (iii) record and store structured specimen-based character data in formats allowing data exchange; (iv) reversibly assign sample metadata and character datasets to taxa in an editable classification and display them and (v) organize data exchange via standard exchange formats and enable the link between the character datasets and samples in research collections, ensuring high visibility and instant re-usability of the data. The workflow implemented will contribute to organizing the interface between phylogenetic analysis and revisionary taxonomic or monographic work. Database URL: http://campanula.e-taxonomy.net/ PMID:26424081

Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

NASA Astrophysics Data System (ADS)

HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

2016-04-01

Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

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

PubMed Central

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

2017-01-01

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

Non-invasive optoacoustic probing of the density and stiffness of single biological cells

NASA Astrophysics Data System (ADS)

Dehoux, T.; Audoin, B.

2012-12-01

Recently, the coherent generation of GHz acoustic waves using ultrashort laser pulses has demonstrated the ability to probe the sound velocity in vegetal cells and in cell-mimicking soft micro-objects with micrometer resolution, opening tremendous potentialities for single-cell biology. However, manipulating biological media in physiological conditions is often a technical challenge when using a laser-based setup. In this article, we present a new opto-acoustic bio-transducer composed of a thin metal film sputtered on a transparent heat sink that allows reducing importantly the laser-induced cellular stresses, and offers a wide variety of optical configurations. In particular, by exploiting the acoustic reflection coefficient at the sample-transducer interface and the photoacoustic interaction inside the transparent sample, the density and compressibility of the sample can be probed simultaneously. Using an ad hoc signal analysis based on Hilbert and wavelet transforms, these quantities are measured accurately for a reference fluid. Similar analysis performed in a single vegetal cell also suggests high sensitivity to the state of the transducer-cell interface, and notably to the presence of the plasma membrane that encloses the cell vacuole.

Clinically referred children and adolescents: fathers, family constellations, and other demographic factors.

PubMed

Phares, V; Lum, J J

1997-06-01

Investigated the likelihood that clinically referred youth have contact with their biological father. Family demographics such as family constellation, race/ethnicity, and socioeconomic status were also explored. Based on 356 consecutive therapy and assessment referrals to an outpatient clinic, slightly less than half (42.4%) of the children and adolescents referred due to psychological problems and more than half (67.8%) of the youth referred due to learning difficulties lived with both their biological mother and biological father. For those who did not live with both of their biological parents, 40.0% and 56.0%, respectively, had regular face-to-face contact with both biological parents. These figures suggest that, although the percentages of intact families are somewhat lower in treatment samples than in the general population or in a sample referred for learning difficulties, close to half of clinically referred youth continue to live with both of their biological parents. Future directions for the inclusion of fathers in clinical research are discussed.

In vivo microsampling to capture the elusive exposome

NASA Astrophysics Data System (ADS)

Bessonneau, Vincent; Ings, Jennifer; McMaster, Mark; Smith, Richard; Bragg, Leslie; Servos, Mark; Pawliszyn, Janusz

2017-03-01

Loss and/or degradation of small molecules during sampling, sample transportation and storage can adversely impact biological interpretation of metabolomics data. In this study, we performed in vivo sampling using solid-phase microextraction (SPME) in combination with non-targeted liquid chromatography and high-resolution tandem mass spectrometry (LC-MS/MS) to capture the fish tissue exposome using molecular networking analysis, and the results were contrasted with molecular differences obtained with ex vivo SPME sampling. Based on 494 MS/MS spectra comparisons, we demonstrated that in vivo SPME sampling provided better extraction and stabilization of highly reactive molecules, such as 1-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoleoyl-glycero-3-phosphocholine, from fish tissue samples. This sampling approach, that minimizes sample handling and preparation, offers the opportunity to perform longitudinal monitoring of the exposome in biological systems and improve the reliability of exposure-measurement in exposome-wide association studies.

In vivo microsampling to capture the elusive exposome

PubMed Central

Bessonneau, Vincent; Ings, Jennifer; McMaster, Mark; Smith, Richard; Bragg, Leslie; Servos, Mark; Pawliszyn, Janusz

2017-01-01

Loss and/or degradation of small molecules during sampling, sample transportation and storage can adversely impact biological interpretation of metabolomics data. In this study, we performed in vivo sampling using solid-phase microextraction (SPME) in combination with non-targeted liquid chromatography and high-resolution tandem mass spectrometry (LC-MS/MS) to capture the fish tissue exposome using molecular networking analysis, and the results were contrasted with molecular differences obtained with ex vivo SPME sampling. Based on 494 MS/MS spectra comparisons, we demonstrated that in vivo SPME sampling provided better extraction and stabilization of highly reactive molecules, such as 1-oleoyl-sn-glycero-3-phosphocholine and 1-palmitoleoyl-glycero-3-phosphocholine, from fish tissue samples. This sampling approach, that minimizes sample handling and preparation, offers the opportunity to perform longitudinal monitoring of the exposome in biological systems and improve the reliability of exposure-measurement in exposome-wide association studies. PMID:28266605

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

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

Nicora, Carrie D.; Burnum-Johnson, Kristin E.; Nakayasu, Ernesto S.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created bymore » adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.« less

Standoff laser-induced fluorescence of suspensions from different bacterial strains

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

Polymer monolithic capillary microextraction combined on-line with inductively coupled plasma MS for the determination of trace rare earth elements in biological samples.

PubMed

Zhang, Lin; Chen, Beibei; He, Man; Hu, Bin

2013-07-01

A rapid and sensitive method based on polymer monolithic capillary microextraction combined on-line with microconcentric nebulization inductively coupled plasma MS has been developed for the determination of trace/ultratrace rare earth elements in biological samples. For this purpose, the iminodiacetic acid modified poly(glycidyl methacrylate-trimethylolpropane trimethacrylate) monolithic capillary was prepared and characterized by SEM and FTIR spectroscopy. Factors affecting the extraction efficiency, such as sample pH, sample flow rate, sample/eluent volume, and coexisting ions were investigated in detail. Under the optimal conditions, the LODs for rare earth elements were in the range of 0.08 (Er) to 0.97 ng/L (Nd) with a sampling frequency of 8.5 h(-1), and the RSDs were between 1.5% (Sm) and 7.4% (Nd) (c = 20 ng/L, n = 7). The proposed method was successfully applied to the analysis of trace/ultratrace rare earth elements in human urine and serum samples, and the recoveries for the spiked samples were in the range of 82-105%. The developed method was simple, rapid, sensitive, and favorable for the analysis of trace/ultratrace rare earth elements in biological samples with limited sample volume. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SOLID2: An Antibody Array-Based Life-Detector Instrument in a Mars Drilling Simulation Experiment (MARTE)

NASA Astrophysics Data System (ADS)

Parro, Víctor; Fernández-Calvo, Patricia; Rodríguez Manfredi, José A.; Moreno-Paz, Mercedes; Rivas, Luis A.; García-Villadangos, Miriam; Bonaccorsi, Rosalba; González-Pastor, José Eduardo; Prieto-Ballesteros, Olga; Schuerger, Andrew C.; Davidson, Mark; Gómez-Elvira, Javier; Stoker, Carol R.

2008-10-01

A field prototype of an antibody array-based life-detector instrument, Signs Of LIfe Detector (SOLID2), has been tested in a Mars drilling mission simulation called MARTE (Mars Astrobiology Research and Technology Experiment). As one of the analytical instruments on the MARTE robotic drilling rig, SOLID2 performed automatic sample processing and analysis of ground core samples (0.5 g) with protein microarrays that contained 157 different antibodies. Core samples from different depths (down to 5.5 m) were analyzed, and positive reactions were obtained in antibodies raised against the Gram-negative bacterium Leptospirillum ferrooxidans, a species of the genus Acidithiobacillus (both common microorganisms in the Río Tinto area), and extracts from biofilms and other natural samples from the Río Tinto area. These positive reactions were absent when the samples were previously subjected to a high-temperature treatment, which indicates the biological origin and structural dependency of the antibody-antigen reactions. We conclude that an antibody array-based life-detector instrument like SOLID2 can detect complex biological material, and it should be considered as a potential analytical instrument for future planetary missions that search for life.

4D (x-y-z-t) imaging of thick biological samples by means of Two-Photon inverted Selective Plane Illumination Microscopy (2PE-iSPIM)

PubMed Central

Lavagnino, Zeno; Sancataldo, Giuseppe; d’Amora, Marta; Follert, Philipp; De Pietri Tonelli, Davide; Diaspro, Alberto; Cella Zanacchi, Francesca

2016-01-01

In the last decade light sheet fluorescence microscopy techniques, such as selective plane illumination microscopy (SPIM), has become a well established method for developmental biology. However, conventional SPIM architectures hardly permit imaging of certain tissues since the common sample mounting procedure, based on gel embedding, could interfere with the sample morphology. In this work we propose an inverted selective plane microscopy system (iSPIM), based on non-linear excitation, suitable for 3D tissue imaging. First, the iSPIM architecture provides flexibility on the sample mounting, getting rid of the gel-based mounting typical of conventional SPIM, permitting 3D imaging of hippocampal slices from mouse brain. Moreover, all the advantages brought by two photon excitation (2PE) in terms of reduction of scattering effects and contrast improvement are exploited, demonstrating an improved image quality and contrast compared to single photon excitation. The system proposed represents an optimal platform for tissue imaging and it smooths the way to the applicability of light sheet microscopy to a wider range of samples including those that have to be mounted on non-transparent surfaces. PMID:27033347

SOLID2: an antibody array-based life-detector instrument in a Mars Drilling Simulation Experiment (MARTE).

PubMed

Parro, Víctor; Fernández-Calvo, Patricia; Rodríguez Manfredi, José A; Moreno-Paz, Mercedes; Rivas, Luis A; García-Villadangos, Miriam; Bonaccorsi, Rosalba; González-Pastor, José Eduardo; Prieto-Ballesteros, Olga; Schuerger, Andrew C; Davidson, Mark; Gómez-Elvira, Javier; Stoker, Carol R

2008-10-01

A field prototype of an antibody array-based life-detector instrument, Signs Of LIfe Detector (SOLID2), has been tested in a Mars drilling mission simulation called MARTE (Mars Astrobiology Research and Technology Experiment). As one of the analytical instruments on the MARTE robotic drilling rig, SOLID2 performed automatic sample processing and analysis of ground core samples (0.5 g) with protein microarrays that contained 157 different antibodies. Core samples from different depths (down to 5.5 m) were analyzed, and positive reactions were obtained in antibodies raised against the Gram-negative bacterium Leptospirillum ferrooxidans, a species of the genus Acidithiobacillus (both common microorganisms in the Río Tinto area), and extracts from biofilms and other natural samples from the Río Tinto area. These positive reactions were absent when the samples were previously subjected to a high-temperature treatment, which indicates the biological origin and structural dependency of the antibody-antigen reactions. We conclude that an antibody array-based life-detector instrument like SOLID2 can detect complex biological material, and it should be considered as a potential analytical instrument for future planetary missions that search for life.

Real-time Measurements of Biological Particles at Several Continental Sites using the WIBS-4A

NASA Astrophysics Data System (ADS)

McMeeking, G. R.; Kok, G. L.; Petters, M. D.; Wright, T.; Hader, J.; Mccubbin, I. B.; Hallar, A. G.; Twohy, C. H.; Toohey, D. W.; DeMott, P. J.; McCluskey, C.; Baumgardner, D.

2013-12-01

Biological particles (bacteria, fungi/fungal spores, viruses, algae and fragments of biological material) may play a significant role in modifying cloud properties by acting as ice nuclei and thus have an indirect effect on climate forcing. Little is known, however, regarding the abundance and distribution of biological particles and their importance to cloud microphysics in different environments. On-line, continuous measurement systems offer the potential to measure biological systems at high time resolution and sensitivity, providing greater insight into their distribution in the atmosphere, dispersal mechanisms and potential soures. The WIBS-4A (Wideband Integrated Bioaerosol Sensor) detects fluorescent biological material in real-time associated with individual particles. It measures five properties: a) optical size via light scattering, b) fluorescent emissions in the wavelength range 310-400 following excitation by 280 nm light, c) fluorescent emissions in the wavelength range 420-650 following excitation by 280 nm light, d) fluorescent emissions in the wavelength range 420-650 following excitation by 370 nm light, and e) particle asymmetry factor based on intensities of forward scattered light onto a 4-element detector. Together, these properties aid the classification of sampled particles that contain biofluorophores such as tryptophan or NAD(P)H, which can be found in biological particles. Here we present results from a series of laboratory, ground- and aircraft-based measurements of biological particles using the WIBS-4A. The studies include airborne measurements over the United States, ground-based measurements at a coastal site, an urban site in the southeast US and a high alpine site, and laboratory measurements of a variety of biological and non-biological particles. Our analysis focused on both the characterization of the instrument response as well as an evaluation of its suitability for performing ambient measurements and potential artifacts. We also present recommendations for field operation of the instrument, sample system design considerations, and data analysis approaches.

Geographic, seasonal, and precipitation chemistry influence on the abundance and activity of biological ice nucleators in rain and snow

PubMed Central

Christner, Brent C.; Cai, Rongman; Morris, Cindy E.; McCarter, Kevin S.; Foreman, Christine M.; Skidmore, Mark L.; Montross, Scott N.; Sands, David C.

2008-01-01

Biological ice nucleators (IN) function as catalysts for freezing at relatively warm temperatures (warmer than −10 °C). We examined the concentration (per volume of liquid) and nature of IN in precipitation collected from Montana and Louisiana, the Alps and Pyrenees (France), Ross Island (Antarctica), and Yukon (Canada). The temperature of detectable ice-nucleating activity for more than half of the samples was ≥ −5 °C based on immersion freezing testing. Digestion of the samples with lysozyme (i.e., to hydrolyze bacterial cell walls) led to reductions in the frequency of freezing (0–100%); heat treatment greatly reduced (95% average) or completely eliminated ice nucleation at the measured conditions in every sample. These behaviors were consistent with the activity being bacterial and/or proteinaceous in origin. Statistical analysis revealed seasonal similarities between warm-temperature ice-nucleating activities in snow samples collected over 7 months in Montana. Multiple regression was used to construct models with biogeochemical data [major ions, total organic carbon (TOC), particle, and cell concentration] that were accurate in predicting the concentration of microbial cells and biological IN in precipitation based on the concentration of TOC, Ca2+, and NH4+, or TOC, cells, Ca2+, NH4+, K+, PO43−, SO42−, Cl−, and HCO3−. Our results indicate that biological IN are ubiquitous in precipitation and that for some geographic locations the activity and concentration of these particles is related to the season and precipitation chemistry. Thus, our research suggests that biological IN are widespread in the atmosphere and may affect meteorological processes that lead to precipitation. PMID:19028877

High resolution computational on-chip imaging of biological samples using sparsity constraint (Conference Presentation)

NASA Astrophysics Data System (ADS)

Rivenson, Yair; Wu, Chris; Wang, Hongda; Zhang, Yibo; Ozcan, Aydogan

2017-03-01

Microscopic imaging of biological samples such as pathology slides is one of the standard diagnostic methods for screening various diseases, including cancer. These biological samples are usually imaged using traditional optical microscopy tools; however, the high cost, bulkiness and limited imaging throughput of traditional microscopes partially restrict their deployment in resource-limited settings. In order to mitigate this, we previously demonstrated a cost-effective and compact lens-less on-chip microscopy platform with a wide field-of-view of >20-30 mm^2. The lens-less microscopy platform has shown its effectiveness for imaging of highly connected biological samples, such as pathology slides of various tissue samples and smears, among others. This computational holographic microscope requires a set of super-resolved holograms acquired at multiple sample-to-sensor distances, which are used as input to an iterative phase recovery algorithm and holographic reconstruction process, yielding high-resolution images of the samples in phase and amplitude channels. Here we demonstrate that in order to reconstruct clinically relevant images with high resolution and image contrast, we require less than 50% of the previously reported nominal number of holograms acquired at different sample-to-sensor distances. This is achieved by incorporating a loose sparsity constraint as part of the iterative holographic object reconstruction. We demonstrate the success of this sparsity-based computational lens-less microscopy platform by imaging pathology slides of breast cancer tissue and Papanicolaou (Pap) smears.

Conduct, Biological Factors and Adult Delinquency in a Longitudinal Perspective.

ERIC Educational Resources Information Center

Magnusson, David

In the course of a longitudinal research program conducted in Sweden, data were being collected on biological and psychological aspects of individual functioning and on environmental factors for a fairly large representative sample (approximately 1,000) of Swedish males and females between 10 and 27 years of age. Based on data from the…

Equivalency of general biology (for majors) across a state-system

NASA Astrophysics Data System (ADS)

Regier, Kimberly Fayette

General biology courses (for majors) are often transferred from one institution to another. These courses must prepare students for upper division courses in biology. A survey of U.S. college biology faculty was conducted and revealed that more 4-year faculty do not believe that all general biology courses are equivalent. An evaluation of course grades in two upper division biology courses at University of Colorado Denver (N = 2129) based upon course grades in general biology and the type of institution where general biology was taken (2-year school, 4-year, in-residence at UCD, AP credit, CLEP credit, or IB credit) was conducted. Students who transferred general biology credit received lower grades in upper division biology courses and withdrew from upper division biology courses more frequently. Syllabi from a small sample (N = 9) of general biology courses offered at Colorado 2- and 4-year schools show variation in course design. Only 30% of the courses had detailed learning objectives. Sample exams reveal a range in variation between 3-69% of questions requiring higher-order thinking according to Bloom's Taxonomy. Increasing communication between high school, 2-year and 4-year biology faculty is necessary if consistency is to be gained. Professional development for faculty to increase awareness about exam development, curriculum alignment, and curriculum mapping may reduce the disparities between the preparation of students in biology. Transfer student grade outcomes should be further investigated across the state.

Statistical inference from multiple iTRAQ experiments without using common reference standards.

PubMed

Herbrich, Shelley M; Cole, Robert N; West, Keith P; Schulze, Kerry; Yager, James D; Groopman, John D; Christian, Parul; Wu, Lee; O'Meally, Robert N; May, Damon H; McIntosh, Martin W; Ruczinski, Ingo

2013-02-01

Isobaric tags for relative and absolute quantitation (iTRAQ) is a prominent mass spectrometry technology for protein identification and quantification that is capable of analyzing multiple samples in a single experiment. Frequently, iTRAQ experiments are carried out using an aliquot from a pool of all samples, or "masterpool", in one of the channels as a reference sample standard to estimate protein relative abundances in the biological samples and to combine abundance estimates from multiple experiments. In this manuscript, we show that using a masterpool is counterproductive. We obtain more precise estimates of protein relative abundance by using the available biological data instead of the masterpool and do not need to occupy a channel that could otherwise be used for another biological sample. In addition, we introduce a simple statistical method to associate proteomic data from multiple iTRAQ experiments with a numeric response and show that this approach is more powerful than the conventionally employed masterpool-based approach. We illustrate our methods using data from four replicate iTRAQ experiments on aliquots of the same pool of plasma samples and from a 406-sample project designed to identify plasma proteins that covary with nutrient concentrations in chronically undernourished children from South Asia.

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.

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

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

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.

2016-05-03

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of thismore » protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical). IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.« less

[Quality of DNA from archival pathological samples of gallbladder cancer].

PubMed

Roa, Iván; de Toro, Gonzalo; Sánchez, Tamara; Slater, Jeannie; Ziegler, Anne Marie; Game, Anakaren; Arellano, Leonardo; Schalper, Kurt; de Aretxabala, Xabier

2013-12-01

The quality of the archival samples stored at pathology services could be a limiting factor for molecular biology studies. To determine the quality of DNA extracted from gallbladder cancer samples at different institutions. One hundred ninety four samples coming from five medical centers in Chile, were analyzed. DNA extraction was quantified determining genomic DNA concentration. The integrity of DNA was determined by polymerase chain reaction amplification of different length fragments of a constitutive gene (β-globin products of 110, 268 and 501 base pairs). The mean DNA concentration obtained in 194 gallbladder cancer samples was 48 ± 43.1 ng/µl. In 22% of samples, no amplification was achieved despite obtaining a mean DNA concentration of 58.3 ng/ul. In 81, 67 and 22% of samples, a DNA amplification of at least 110, 268 or 501 base pairs was obtained, respectively. No differences in DNA concentration according to the source of the samples were demonstrated. However, there were marked differences in DNA integrity among participating centers. Samples from public hospitals were of lower quality than those from private clinics. Despite some limitations, in 80% of cases, the integrity of DNA in archival samples from pathology services in our country would allow the use of molecular biology techniques.

Using the mixed media according to internet-based on the instructional multimedia for developing students' learning achievements in biology course on foundational cell issue of secondary students at the 10th grade level in Rangsit University demonstration school

NASA Astrophysics Data System (ADS)

Kangloan, Pichet; Chayaburakul, Kanokporn; Santiboon, Toansakul

2018-01-01

The aims of this research study were 1) to develop students' learning achievements in biology course on foundational cell issue, 2) to examine students' satisfactions of their learning activities through the mixed media according to internet-based multi-instruction in biology on foundational cell issue at the 10th grade level were used in the first semester in the academic year 2014, which a sample size of 17 students in Rangsit University Demonstration School with cluster random sampling was selected. Students' learning administrations were instructed with the 3-instructional lesson plans according to the 5-Step Ladder Learning Management Plan (LLMP) namely; the maintaining lesson plan on the equilibrium of cell issue, a lesson plan for learning how to communicate between cell and cell division. Students' learning achievements were assessed with the 30-item Assessment of Learning Biology Test (ALBT), students' perceptions of their satisfactions were satisfied with the 20-item Questionnaire on Students Satisfaction (QSS), and students' learning activities were assessed with the Mixed Media Internet-Based Instruction (MMIBI) on foundational cell issue was designed. The results of this research study have found that: statistically significant of students' post-learning achievements were higher than their pre-learning outcomes and indicated that the differences were significant at the .05 level. Students' performances of their satisfaction to their perceptions toward biology class with the mixed media according to internet-based multi instruction in biology on foundational cell issue were the highest level and evidence of average mean score as 4.59.

Biological classification with RNA-Seq data: Can alternatively spliced transcript expression enhance machine learning classifier?

PubMed

Johnson, Nathan T; Dhroso, Andi; Hughes, Katelyn J; Korkin, Dmitry

2018-06-25

The extent to which the genes are expressed in the cell can be simplistically defined as a function of one or more factors of the environment, lifestyle, and genetics. RNA sequencing (RNA-Seq) is becoming a prevalent approach to quantify gene expression, and is expected to gain better insights to a number of biological and biomedical questions, compared to the DNA microarrays. Most importantly, RNA-Seq allows to quantify expression at the gene and alternative splicing isoform levels. However, leveraging the RNA-Seq data requires development of new data mining and analytics methods. Supervised machine learning methods are commonly used approaches for biological data analysis, and have recently gained attention for their applications to the RNA-Seq data. In this work, we assess the utility of supervised learning methods trained on RNA-Seq data for a diverse range of biological classification tasks. We hypothesize that the isoform-level expression data is more informative for biological classification tasks than the gene-level expression data. Our large-scale assessment is done through utilizing multiple datasets, organisms, lab groups, and RNA-Seq analysis pipelines. Overall, we performed and assessed 61 biological classification problems that leverage three independent RNA-Seq datasets and include over 2,000 samples that come from multiple organisms, lab groups, and RNA-Seq analyses. These 61 problems include predictions of the tissue type, sex, or age of the sample, healthy or cancerous phenotypes and, the pathological tumor stage for the samples from the cancerous tissue. For each classification problem, the performance of three normalization techniques and six machine learning classifiers was explored. We find that for every single classification problem, the isoform-based classifiers outperform or are comparable with gene expression based methods. The top-performing supervised learning techniques reached a near perfect classification accuracy, demonstrating the utility of supervised learning for RNA-Seq based data analysis. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

3D nanoscale imaging of biological samples with laboratory-based soft X-ray sources

NASA Astrophysics Data System (ADS)

Dehlinger, Aurélie; Blechschmidt, Anne; Grötzsch, Daniel; Jung, Robert; Kanngießer, Birgit; Seim, Christian; Stiel, Holger

2015-09-01

In microscopy, where the theoretical resolution limit depends on the wavelength of the probing light, radiation in the soft X-ray regime can be used to analyze samples that cannot be resolved with visible light microscopes. In the case of soft X-ray microscopy in the water-window, the energy range of the radiation lies between the absorption edges of carbon (at 284 eV, 4.36 nm) and oxygen (543 eV, 2.34 nm). As a result, carbon-based structures, such as biological samples, posses a strong absorption, whereas e.g. water is more transparent to this radiation. Microscopy in the water-window, therefore, allows the structural investigation of aqueous samples with resolutions of a few tens of nanometers and a penetration depth of up to 10μm. The development of highly brilliant laser-produced plasma-sources has enabled the transfer of Xray microscopy, that was formerly bound to synchrotron sources, to the laboratory, which opens the access of this method to a broader scientific community. The Laboratory Transmission X-ray Microscope at the Berlin Laboratory for innovative X-ray technologies (BLiX) runs with a laser produced nitrogen plasma that emits radiation in the soft X-ray regime. The mentioned high penetration depth can be exploited to analyze biological samples in their natural state and with several projection angles. The obtained tomogram is the key to a more precise and global analysis of samples originating from various fields of life science.

Preservation of Liquid Biological Samples

NASA Technical Reports Server (NTRS)

Putcha, Lakshmi (Inventor); Nimmagudda, Ramalingeshwara (Inventor)

2004-01-01

The present invention related to the preservation of a liquid biological sample. The biological sample is exposed to a preservative containing at least about 0.15 g of sodium benzoate and at least about 0.025 g of citric acid per 100 ml of sample. The biological sample may be collected in a vessel or an absorbent mass. The biological sample may also be exposed to a substrate and/or a vehicle.

Overview of chemical imaging methods to address biological questions.

PubMed

da Cunha, Marcel Menezes Lyra; Trepout, Sylvain; Messaoudi, Cédric; Wu, Ting-Di; Ortega, Richard; Guerquin-Kern, Jean-Luc; Marco, Sergio

2016-05-01

Chemical imaging offers extensive possibilities for better understanding of biological systems by allowing the identification of chemical components at the tissue, cellular, and subcellular levels. In this review, we introduce modern methods for chemical imaging that can be applied to biological samples. This work is mainly addressed to the biological sciences community and includes the bases of different technologies, some examples of its application, as well as an introduction to approaches on combining multimodal data. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Enzyme Biosensors for Biomedical Applications: Strategies for Safeguarding Analytical Performances in Biological Fluids

PubMed Central

Rocchitta, Gaia; Spanu, Angela; Babudieri, Sergio; Latte, Gavinella; Madeddu, Giordano; Galleri, Grazia; Nuvoli, Susanna; Bagella, Paola; Demartis, Maria Ilaria; Fiore, Vito; Manetti, Roberto; Serra, Pier Andrea

2016-01-01

Enzyme-based chemical biosensors are based on biological recognition. In order to operate, the enzymes must be available to catalyze a specific biochemical reaction and be stable under the normal operating conditions of the biosensor. Design of biosensors is based on knowledge about the target analyte, as well as the complexity of the matrix in which the analyte has to be quantified. This article reviews the problems resulting from the interaction of enzyme-based amperometric biosensors with complex biological matrices containing the target analyte(s). One of the most challenging disadvantages of amperometric enzyme-based biosensor detection is signal reduction from fouling agents and interference from chemicals present in the sample matrix. This article, therefore, investigates the principles of functioning of enzymatic biosensors, their analytical performance over time and the strategies used to optimize their performance. Moreover, the composition of biological fluids as a function of their interaction with biosensing will be presented. PMID:27249001

Field-based Metabolomics for Assessing Contaminated Surface Waters

EPA Science Inventory

Metabolomics is becoming well-established for studying chemical contaminant-induced alterations to normal biological function. For example, the literature contains a wealth of laboratory-based studies involving analysis of samples from organisms exposed to individual chemical tox...

Identifying misclassification in youth self-reported smoking status: testing different consent processes of biological sample collection to capture misclassification.

PubMed

Dietz, Noella A; Arheart, Kristopher L; Lee, David J; Sly, David F; McClure, Laura A

2015-04-01

In Florida, since 1998, identical survey items have been used to measure youth smoking status for the CDC sponsored state school-based survey and the tobacco control program evaluation telephone survey. The two surveys should parallel one another to track tobacco use. Tobacco items collected in the two surveys closely paralleled one another until recently. Since 2008, data show dramatically divergent youth smoking estimates (e.g., relative differences as high as 50%), which cannot be explained by differences in survey and sampling design. As a first step in detecting misclassification of smoking status, we examined the feasibility of asking youth to self-report their smoking behavior and collect a biological sample, with the expectation that some youth will misreport their smoking status. Using a cross-sectional population level telephone survey, youth were randomly assigned to one of three groups to test mode effects of collecting biological data with self-reported survey data (n = 303). It showed two groups of youth (those who are not asked for a biological and those asked for a biological with an indirect explanation of its use) had similar response rates and self-reported smoking status, while the third group (biological request with a direct explanation of its use) had a substantially lower response rate and self-reported smoking status. The data show youth who are given an indirect explanation of how biological data are to be used were as likely to self-report their smoking status as youth who were not asked to provide a biological sample. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments.

PubMed

Dona, Anthony C; Kyriakides, Michael; Scott, Flora; Shephard, Elizabeth A; Varshavi, Dorsa; Veselkov, Kirill; Everett, Jeremy R

2016-01-01

Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), the latter typically with hyphenation to a chromatography system such as liquid chromatography (LC), in a configuration known as LC-MS. With both NMR and MS-based detection technologies, the identification of the metabolites in the biological sample remains a significant obstacle and bottleneck. This article provides guidance on methods for metabolite identification in biological fluids using NMR spectroscopy, and is illustrated with examples from recent studies on mice.

Advantages of tandem LC-MS for the rapid assessment of tissue-specific metabolic complexity using a pentafluorophenylpropyl stationary phase

PubMed Central

Lv, Haitao; Palacios, Gustavo; Hartil, Kirsten; Kurland, Irwin J.

2014-01-01

In this study a UPLC-tandem (Waters Xevo TQ) MRM based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The developed method was successfully applied to analyze various biological samples from C57BL/6 mice; including urine, duodenum, liver, plasma, kidney, heart, and skeletal muscle. As result, a total 112 of hydrophilic metabolites were detected within 8 min of running time to obtain a metabolite profile of the biological samples. The analysis of this number of hydrophilic metabolites is significantly faster than previous studies. Classification separation for metabolites from different tissues was globally analyzed by PCA, PLS-DA and HCA biostatistical methods. Overall, most of the hydrophilic metabolites were found to have a “fingerprint” characteristic of tissue dependency. In general, a higher level of most metabolites was found in urine, duodenum and kidney. Altogether, these results suggest that this method has potential application for targeted metabolomic analyzes of hydrophilic metabolites in a wide ranges of biological samples. PMID:21322650

Advantages of tandem LC-MS for the rapid assessment of tissue-specific metabolic complexity using a pentafluorophenylpropyl stationary phase.

PubMed

Lv, Haitao; Palacios, Gustavo; Hartil, Kirsten; Kurland, Irwin J

2011-04-01

In this study, a tandem LC-MS (Waters Xevo TQ) MRM-based MS method was developed for rapid, broad profiling of hydrophilic metabolites from biological samples, in either positive or negative ion modes without the need for an ion pairing reagent, using a reversed-phase pentafluorophenylpropyl (PFPP) column. The developed method was successfully applied to analyze various biological samples from C57BL/6 mice, including urine, duodenum, liver, plasma, kidney, heart, and skeletal muscle. As result, a total 112 of hydrophilic metabolites were detected within 8 min of running time to obtain a metabolite profile of the biological samples. The analysis of this number of hydrophilic metabolites is significantly faster than previous studies. Classification separation for metabolites from different tissues was globally analyzed by PCA, PLS-DA and HCA biostatistical methods. Overall, most of the hydrophilic metabolites were found to have a "fingerprint" characteristic of tissue dependency. In general, a higher level of most metabolites was found in urine, duodenum, and kidney. Altogether, these results suggest that this method has potential application for targeted metabolomic analyzes of hydrophilic metabolites in a wide ranges of biological samples.

Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation.

PubMed

Ashtiani, Dariush; Venugopal, Hari; Belousoff, Matthew; Spicer, Bradley; Mak, Johnson; Neild, Adrian; de Marco, Alex

2018-04-06

Cryo-Electron Microscopy (cryo-EM) has become an invaluable tool for structural biology. Over the past decade, the advent of direct electron detectors and automated data acquisition has established cryo-EM as a central method in structural biology. However, challenges remain in the reliable and efficient preparation of samples in a manner which is compatible with high time resolution. The delivery of sample onto the grid is recognized as a critical step in the workflow as it is a source of variability and loss of material due to the blotting which is usually required. Here, we present a method for sample delivery and plunge freezing based on the use of Surface Acoustic Waves to deploy 6-8 µm droplets to the EM grid. This method minimises the sample dead volume and ensures vitrification within 52.6 ms from the moment the sample leaves the microfluidics chip. We demonstrate a working protocol to minimize the atomised volume and apply it to plunge freeze three different samples and provide proof that no damage occurs due to the interaction between the sample and the acoustic waves. Copyright © 2018 Elsevier Inc. All rights reserved.

Controlled power delivery for super-resolution imaging of biological samples using digital micromirror device

NASA Astrophysics Data System (ADS)

Valiya Peedikakkal, Liyana; Cadby, Ashley

2017-02-01

Localization based super resolution images of a biological sample is generally achieved by using high power laser illumination with long exposure time which unfortunately increases photo-toxicity of a sample, making super resolution microscopy, in general, incompatible with live cell imaging. Furthermore, the limitation of photobleaching reduces the ability to acquire time lapse images of live biological cells using fluorescence microscopy. Digital Light Processing (DLP) technology can deliver light at grey scale levels by flickering digital micromirrors at around 290 Hz enabling highly controlled power delivery to samples. In this work, Digital Micromirror Device (DMD) is implemented in an inverse Schiefspiegler telescope setup to control the power and pattern of illumination for super resolution microscopy. We can achieve spatial and temporal patterning of illumination by controlling the DMD pixel by pixel. The DMD allows us to control the power and spatial extent of the laser illumination. We have used this to show that we can reduce the power delivered to the sample to allow for longer time imaging in one area while achieving sub-diffraction STORM imaging in another using higher power densities.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

PubMed

Reinhold, William C

2015-12-10

There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

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.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

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

PubMed

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

2015-07-01

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

Electrochemical Biosensors - Sensor Principles and Architectures

PubMed Central

Grieshaber, Dorothee; MacKenzie, Robert; Vörös, Janos; Reimhult, Erik

2008-01-01

Quantification of biological or biochemical processes are of utmost importance for medical, biological and biotechnological applications. However, converting the biological information to an easily processed electronic signal is challenging due to the complexity of connecting an electronic device directly to a biological environment. Electrochemical biosensors provide an attractive means to analyze the content of a biological sample due to the direct conversion of a biological event to an electronic signal. Over the past decades several sensing concepts and related devices have been developed. In this review, the most common traditional techniques, such as cyclic voltammetry, chronoamperometry, chronopotentiometry, impedance spectroscopy, and various field-effect transistor based methods are presented along with selected promising novel approaches, such as nanowire or magnetic nanoparticle-based biosensing. Additional measurement techniques, which have been shown useful in combination with electrochemical detection, are also summarized, such as the electrochemical versions of surface plasmon resonance, optical waveguide lightmode spectroscopy, ellipsometry, quartz crystal microbalance, and scanning probe microscopy. The signal transduction and the general performance of electrochemical sensors are often determined by the surface architectures that connect the sensing element to the biological sample at the nanometer scale. The most common surface modification techniques, the various electrochemical transduction mechanisms, and the choice of the recognition receptor molecules all influence the ultimate sensitivity of the sensor. New nanotechnology-based approaches, such as the use of engineered ion-channels in lipid bilayers, the encapsulation of enzymes into vesicles, polymersomes, or polyelectrolyte capsules provide additional possibilities for signal amplification. In particular, this review highlights the importance of the precise control over the delicate interplay between surface nano-architectures, surface functionalization and the chosen sensor transducer principle, as well as the usefulness of complementary characterization tools to interpret and to optimize the sensor response. PMID:27879772

LASER METHODS IN BIOLOGY: Optical anisotropy of fibrous biological tissues: analysis of the influence of structural properties

NASA Astrophysics Data System (ADS)

Zimnyakov, D. A.; Sinichkin, Yu P.; Ushakova, O. V.

2007-08-01

The results of theoretical analysis of the optical anisotropy of multiply scattering fibrillar biological tissues based on the model of an effective anisotropic medium are compared with the experimental in vivo birefringence data for the rat derma obtained earlier in spectral polarisation measurements of rat skin samples in the visible region. The disordered system of parallel dielectric cylinders embedded into an isotropic dielectric medium was considered as a model medium. Simulations were performed taking into account the influence of a partial mutual disordering of the bundles of collagen and elastin fibres in derma on birefringence in samples. The theoretical optical anisotropy averaged over the spectral interval 550-650 nm for the model medium with parameters corresponding to the structural parameters of derma is in good agreement with the results of spectral polarisation measurements of skin samples in the corresponding wavelength range.

Occurrence of Cryptosporidium and Giardia in recycled waters used for irrigation and first description of Cryptosporidium parvum and C. muris in Greece.

PubMed

Spanakos, Gregory; Biba, Anastasia; Mavridou, Athena; Karanis, Panagiotis

2015-05-01

Here, we present the first time findings regarding the occurrence of Cryptosporidium and Giardia in sewage waters and the first molecular characterization of Cryptosporidium species in Greece. Biological treatment plants from three regions in Greece have been investigated. The detection of Cryptosporidium oocysts was by modified Ziehl-Neelsen acid fast (MZN-AF) and by immunofluorescence microscopy (IFT) for Cryptosporidium and Giardia (oo)cysts, whereas nested PCR based on the SSU rDNA assay was used for molecular detection of Cryptosporidium followed by sequencing for the genetic characterization of the species. In total, 73 samples (37 raw sewage samples and 38 of treated water samples) were collected and analyzed. Of the 73 water samples, 4 samples were Cryptosporidium-positive by IFT and staining, 12 samples were Cryptosporidium-positive by nested PCR; 9 samples were Giardia-positive by IFT. We showed that Cryptosporidium cysts are found both in the input and the discharge of the biological treatment plants. Molecular characterization of Cryptosporidium based on the small subunit ribosomal DNA gene resulted in the determination of Cryptosporidium parvum and Cryptosporidium muris Greek isolates. This is the first report of Cryptosporidium and Giardia occurrence in wastewaters and the first molecular identification of Cryptosporidium species in Greek environments. As the treated water is used for irrigation, or it is discharged into the sea, our findings indicate that biological treatment facilities constitute a possible risk for public health because the related species are prevalent in humans; the results invite for further epidemiological investigations to evaluate the real public health risk in Greece.

Chemical activity-based environmental risk analysis of the plasticizer di-ethylhexyl phthalate and its main metabolite mono-ethylhexyl phthalate.

PubMed

Gobas, Frank A P C; Otton, S Victoria; Tupper-Ring, Laura F; Crawford, Meara A; Clark, Kathryn E; Ikonomou, Michael G

2017-06-01

The present study applies a chemical activity-based approach to: 1) evaluate environmental concentrations of di-ethylhexyl phthalate (DEHP; n = 23 651) and its metabolite mono-ethylhexyl phthalate (MEHP; n = 1232) in 16 environmental media from 1174 studies in the United States, Canada, Europe, and Asia, and in vivo toxicity data from 934 studies in 20 species, as well as in vitro biological activity data from the US Environmental Protection Agency's Toxicity Forecaster and other sources; and 2) conduct a comprehensive environmental risk analysis. The results show that the mean chemical activities of DEHP and MEHP in abiotic environmental samples from locations around the globe are 0.001 and 10 -8 , respectively. This indicates that DEHP has reached on average 0.1% of saturation in the abiotic environment. The mean chemical activity of DEHP in biological samples is on average 100-fold lower than that in abiotic samples, likely because of biotransformation of DEHP in biota. Biological responses in both in vivo and in vitro tests occur at chemical activities between 0.01 to 1 for DEHP and between approximately 10 -6 and 10 -2 for MEHP, suggesting a greater potency of MEHP compared with DEHP. Chemical activities of both DEHP and MEHP in biota samples were less than those causing biological responses in the in vitro bioassays, without exception. A small fraction of chemical activities of DEHP in abiotic environmental samples (i.e., 4-8%) and none (0%) for MEHP were within the range of chemical activities associated with observed toxicological responses in the in vivo tests. The present study illustrates the chemical activity approach for conducting risk analyses. Environ Toxicol Chem 2017;36:1483-1492. © 2016 SETAC. © 2016 SETAC.

High-throughput immunomagnetic scavenging technique for quantitative analysis of live VX nerve agent in water, hamburger, and soil matrixes.

PubMed

Knaack, Jennifer S; Zhou, Yingtao; Abney, Carter W; Prezioso, Samantha M; Magnuson, Matthew; Evans, Ronald; Jakubowski, Edward M; Hardy, Katelyn; Johnson, Rudolph C

2012-11-20

We have developed a novel immunomagnetic scavenging technique for extracting cholinesterase inhibitors from aqueous matrixes using biological targeting and antibody-based extraction. The technique was characterized using the organophosphorus nerve agent VX. The limit of detection for VX in high-performance liquid chromatography (HPLC)-grade water, defined as the lowest calibrator concentration, was 25 pg/mL in a small, 500 μL sample. The method was characterized over the course of 22 sample sets containing calibrators, blanks, and quality control samples. Method precision, expressed as the mean relative standard deviation, was less than 9.2% for all calibrators. Quality control sample accuracy was 102% and 100% of the mean for VX spiked into HPLC-grade water at concentrations of 2.0 and 0.25 ng/mL, respectively. This method successfully was applied to aqueous extracts from soil, hamburger, and finished tap water spiked with VX. Recovery was 65%, 81%, and 100% from these matrixes, respectively. Biologically based extractions of organophosphorus compounds represent a new technique for sample extraction that provides an increase in extraction specificity and sensitivity.

Fiber-based polarization-sensitive Mueller matrix optical coherence tomography with continuous source polarization modulation.

PubMed

Jiao, Shuliang; Todorović, Milos; Stoica, George; Wang, Lihong V

2005-09-10

We report on a new configuration of fiber-based polarization-sensitive Mueller matrix optical coherence tomography that permits the acquisition of the round-trip Jones matrix of a biological sample using only one light source and a single depth scan. In this new configuration, a polarization modulator is used in the source arm to continuously modulate the incident polarization state for both the reference and the sample arms. The Jones matrix of the sample can be calculated from the two frequency terms in the two detection channels. The first term is modulated by the carrier frequency, which is determined by the longitudinal scanning mechanism, whereas the other term is modulated by the beat frequency between the carrier frequency and the second harmonic of the modulation frequency of the polarization modulator. One important feature of this system is that, for the first time to our knowledge, the Jones matrix of the sample can be calculated with a single detection channel and a single measurement when diattenuation is negligible. The system was successfully tested by imaging both standard polarization elements and biological samples.

Life detection systems.

NASA Technical Reports Server (NTRS)

Mitz, M. A.

1972-01-01

Some promising newer approaches for detecting microorganisms are discussed, giving particular attention to the integration of different methods into a single instrument. Life detection methods may be divided into biological, chemical, and cytological methods. Biological methods are based on the biological properties of assimilation, metabolism, and growth. Devices for the detection of organic materials are considered, taking into account an instrument which volatilizes, separates, and analyzes a sample sequentially. Other instrumental systems described make use of a microscope and the cytochemical staining principle.

An assessment of the potential of laser-induced breakdown spectroscopy (LIBS) for the analysis of cesium in liquid samples of biological origin.

PubMed

Metzinger, Anikó; Kovács-Széles, Eva; Almási, István; Galbács, Gábor

2014-01-01

The present study describes the development of an analytical method for the determination of cesium in biological fluid samples (human urine and blood samples) by laser-induced breakdown spectroscopy (LIBS). The developed method is based on sample presentation by liquid-to-solid conversion, enhancing the emission signal by drying the liquid into small "pockets" created in a metal support (zinc plate), and allows the analysis to be carried out on as little as 1 μL of sample volume, in a closed sample cell. Absolute detection limits on the Cs I 852.1 nm spectral line were calculated by the IUPAC 3σ method to be 6 ng in the urine sample and 27 ng in the blood serum sample. It is estimated that LIBS may be used to detect highly elevated concentration levels of Cs in fluid samples taken from people potentially exposed to surges of Cs from non-natural sources.

Paper-based archiving of biological samples from fish for detecting betanodavirus.

PubMed

Navaneeth Krishnan, A; Bhuvaneswari, T; Ezhil Praveena, P; Jithendran, K P

2016-07-01

This study was carried out to evaluate the efficiency of the Flinders Technology Associates (FTA(®)) card (Whatman(®)) as a sampling device and storage platform for RNA from betanodavirus-infected biological samples (viz., larvae, broodstock, cell culture supernatants and rearing seawater spiked with infected materials). The study showed that FTA cards can be used to detect betanodaviruses by reverse transcription-polymerase chain reaction (RT-PCR). The diagnostic efficiency of RT-PCR from all sample types on FTA cards decreased after 21 days of storage at 4 °C, although the virus could be detected up to 28 days by nested RT-PCR. The FTA card protocol thus provides a supplementary method for quick and easy collection of samples, preservation of RNA on a dry storage basis, and detection of betanodavirus-infected fish.

Enzymatic determination of carbon-14 labeled L-alanine in biological samples

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

Serra, F.; Palou, A.; Pons, A.

A method for determination of L-alanine-specific radioactivity in biological samples is presented. This method is based on the specific enzymatic transformation of L-alanine to pyruvic acid hydrazone catalyzed by the enzyme L-alanine dehydrogenase, formation of the pyruvic acid 2,4-dinitrophenylhydrazone derivative, and quantitative trapping in Amberlite XAD-7 columns, followed by radioactivity counting of the lipophilic eluate. No interferences from other UC-labeled materials such as D-glucose, glycerol, L-lactate, L-serine, L-glutamate, L-phenylalanine, glycine, L-leucine, and L-arginine were observed. This inexpensive and high-speed method is applicable to the simultaneous determination of L-alanine-specific radioactivity for a large number of samples.

Correcting for the influence of sampling conditions on biomarkers of exposure to phenols and phthalates: a 2-step standardization method based on regression residuals.

PubMed

Mortamais, Marion; Chevrier, Cécile; Philippat, Claire; Petit, Claire; Calafat, Antonia M; Ye, Xiaoyun; Silva, Manori J; Brambilla, Christian; Eijkemans, Marinus J C; Charles, Marie-Aline; Cordier, Sylvaine; Slama, Rémy

2012-04-26

Environmental epidemiology and biomonitoring studies typically rely on biological samples to assay the concentration of non-persistent exposure biomarkers. Between-participant variations in sampling conditions of these biological samples constitute a potential source of exposure misclassification. Few studies attempted to correct biomarker levels for this error. We aimed to assess the influence of sampling conditions on concentrations of urinary biomarkers of select phenols and phthalates, two widely-produced families of chemicals, and to standardize biomarker concentrations on sampling conditions. Urine samples were collected between 2002 and 2006 among 287 pregnant women from Eden and Pélagie cohorts, from which phthalates and phenols metabolites levels were assayed. We applied a 2-step standardization method based on regression residuals. First, the influence of sampling conditions (including sampling hour, duration of storage before freezing) and of creatinine levels on biomarker concentrations were characterized using adjusted linear regression models. In the second step, the model estimates were used to remove the variability in biomarker concentrations due to sampling conditions and to standardize concentrations as if all samples had been collected under the same conditions (e.g., same hour of urine collection). Sampling hour was associated with concentrations of several exposure biomarkers. After standardization for sampling conditions, median concentrations differed by--38% for 2,5-dichlorophenol to +80 % for a metabolite of diisodecyl phthalate. However, at the individual level, standardized biomarker levels were strongly correlated (correlation coefficients above 0.80) with unstandardized measures. Sampling conditions, such as sampling hour, should be systematically collected in biomarker-based studies, in particular when the biomarker half-life is short. The 2-step standardization method based on regression residuals that we proposed in order to limit the impact of heterogeneity in sampling conditions could be further tested in studies describing levels of biomarkers or their influence on health.

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

PubMed

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

2017-12-15

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

Smooth quantile normalization.

PubMed

Hicks, Stephanie C; Okrah, Kwame; Paulson, Joseph N; Quackenbush, John; Irizarry, Rafael A; Bravo, Héctor Corrada

2018-04-01

Between-sample normalization is a critical step in genomic data analysis to remove systematic bias and unwanted technical variation in high-throughput data. Global normalization methods are based on the assumption that observed variability in global properties is due to technical reasons and are unrelated to the biology of interest. For example, some methods correct for differences in sequencing read counts by scaling features to have similar median values across samples, but these fail to reduce other forms of unwanted technical variation. Methods such as quantile normalization transform the statistical distributions across samples to be the same and assume global differences in the distribution are induced by only technical variation. However, it remains unclear how to proceed with normalization if these assumptions are violated, for example, if there are global differences in the statistical distributions between biological conditions or groups, and external information, such as negative or control features, is not available. Here, we introduce a generalization of quantile normalization, referred to as smooth quantile normalization (qsmooth), which is based on the assumption that the statistical distribution of each sample should be the same (or have the same distributional shape) within biological groups or conditions, but allowing that they may differ between groups. We illustrate the advantages of our method on several high-throughput datasets with global differences in distributions corresponding to different biological conditions. We also perform a Monte Carlo simulation study to illustrate the bias-variance tradeoff and root mean squared error of qsmooth compared to other global normalization methods. A software implementation is available from https://github.com/stephaniehicks/qsmooth.

Assessment of soil biological quality index (QBS-ar) in different crop rotation systems in paddy soils

NASA Astrophysics Data System (ADS)

Nadimi-Goki, Mandana; Bini, Claudio; haefele, Stephan

2013-04-01

New methods, based on soil microarthropods for soil quality evaluation have been proposed by some Authors. Soil microarthropods demonstrated to respond sensitively to land management practices and to be correlated with beneficial soil functions. QBS Index (QBS-ar) is calculated on the basis of microarthropod groups present in a soil sample. Each biological form found in the sample receives a score from 1 to 20 (eco-morphological index, EMI), according to its adaptation to soil environment. The objective of this study was to evaluate the effect of various rotation systems and sampling periods on soil biological quality index, in paddy soils. For the purpose of this study surface soil samples (0-15 cm depth) were collected from different rotation systems (rice-rice-rice, soya-rice-rice, fallow-rice and pea-soya-rice) with three replications, and four sampling times in April (after field preparation), June (after seedling), August (after tillering stage) and October (after rice harvesting). The study area is located in paddy soils of Verona area, Northern Italy. Soil microarthropods from a total of 48 samples were extracted and classified according to the Biological Quality of Soil Index (QBS-ar) method. In addition soil moisture, Cumulative Soil Respiration and pH were measured in each site. More diversity of microarthropod groups was found in June and August sampling times. T-test results between different rotations did not show significant differences while the mean difference between rotation and different sampling times is statistically different. The highest QBS-ar value was found in the fallow-rice rotation in the forth soil sampling time. Similar value was found in soya-rice-rice rotation. Result of linear regression analysis indicated that there is significant correlation between QBS-ar values and Cumulative Soil Respiration. Keywords: soil biological quality index (QBS-ar), Crop Rotation System, paddy soils, Italy

Generation of monodisperse cell-sized microdroplets using a centrifuge-based axisymmetric co-flowing microfluidic device.

PubMed

Yamashita, Hitoyoshi; Morita, Masamune; Sugiura, Haruka; Fujiwara, Kei; Onoe, Hiroaki; Takinoue, Masahiro

2015-04-01

We report an easy-to-use generation method of biologically compatible monodisperse water-in-oil microdroplets using a glass-capillary-based microfluidic device in a tabletop mini-centrifuge. This device does not require complicated microfabrication; furthermore, only a small sample volume is required in experiments. Therefore, we believe that this method will assist biochemical and cell-biological experiments. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Freshwater macroinvertebrate samples from a water quality monitoring network in the Iberian Peninsula

PubMed Central

Escribano, Nora; Oscoz, Javier; Galicia, David; Cancellario, Tommaso; Durán, Concha; Navarro, Patricia; Ariño, Arturo H.

2018-01-01

This dataset gathers information about the macroinvertatebrate samples and environmental variables collected on rivers of the Ebro River Basin (NE Iberian Peninsula), the second largest catchment in the Iberian Peninsula. The collection is composed of 1,776 sampling events carried out between 2005 and 2015 at more than 400 sampling sites. This dataset is part of a monitoring network set up by the Ebro Hydrographic Confederation, the official body entrusted with the care of the basin, to fulfill the requirements of the European Water Framework Directive. Biological indices based on the freshwater macroinvertebrate communities were used to evaluate the ecological status of the water bodies within the basin. Samples were qualitatively screened for all occurring taxa. Then, all individuals from all taxa in a quantitative subsample of each sample were counted. Biological indices were calculated to estimate water quality at each sampling site. All samples are kept at the Museum of Zoology of the University of Navarra. PMID:29870034

Freshwater macroinvertebrate samples from a water quality monitoring network in the Iberian Peninsula.

PubMed

Escribano, Nora; Oscoz, Javier; Galicia, David; Cancellario, Tommaso; Durán, Concha; Navarro, Patricia; Ariño, Arturo H

2018-06-05

This dataset gathers information about the macroinvertatebrate samples and environmental variables collected on rivers of the Ebro River Basin (NE Iberian Peninsula), the second largest catchment in the Iberian Peninsula. The collection is composed of 1,776 sampling events carried out between 2005 and 2015 at more than 400 sampling sites. This dataset is part of a monitoring network set up by the Ebro Hydrographic Confederation, the official body entrusted with the care of the basin, to fulfill the requirements of the European Water Framework Directive. Biological indices based on the freshwater macroinvertebrate communities were used to evaluate the ecological status of the water bodies within the basin. Samples were qualitatively screened for all occurring taxa. Then, all individuals from all taxa in a quantitative subsample of each sample were counted. Biological indices were calculated to estimate water quality at each sampling site. All samples are kept at the Museum of Zoology of the University of Navarra.

75 FR 43150 - Marine Mammals; File Nos. 10018, 13846, 14451, 14585, 14599, 14122, 14296, and 14353

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-23

... of sloughed skin, photogrammetry, biopsy sampling, playback experiments, and/or suction- cup and... to individuals; (6) attachment of suction cup tags; (7) SCUBA observations; and (8) opportunistic.... Research will include vessel-based approaches: (1) to humpback whales for biological sampling, suction cup...

Genetic variation, and biological activity of nucleopolyhedrovirus samples from larvae Heliothis virescens, Helicoverpa zea, and Helicoverpa armigera

USDA-ARS?s Scientific Manuscript database

To assess the diversity and relationships of baculoviruses found in insects of the heliothine pest complex, a PCR-based method was used to classify 90 samples of nucleopolyhedrovirus (NPV; Baculoviridae: Alphabaculovirus) obtained worldwide from larvae of Heliothis virescens (Fabricius), Helicoverpa...

Segment fusion of ToF-SIMS images.

PubMed

Milillo, Tammy M; Miller, Mary E; Fischione, Remo; Montes, Angelina; Gardella, Joseph A

2016-06-08

The imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) have not been used to their full potential in the analysis of polymer and biological samples. Imaging has been limited by the size of the dataset and the chemical complexity of the sample being imaged. Pixel and segment based image fusion algorithms commonly used in remote sensing, ecology, geography, and geology provide a way to improve spatial resolution and classification of biological images. In this study, a sample of Arabidopsis thaliana was treated with silver nanoparticles and imaged with ToF-SIMS. These images provide insight into the uptake mechanism for the silver nanoparticles into the plant tissue, giving new understanding to the mechanism of uptake of heavy metals in the environment. The Munechika algorithm was programmed in-house and applied to achieve pixel based fusion, which improved the spatial resolution of the image obtained. Multispectral and quadtree segment or region based fusion algorithms were performed using ecognition software, a commercially available remote sensing software suite, and used to classify the images. The Munechika fusion improved the spatial resolution for the images containing silver nanoparticles, while the segment fusion allowed classification and fusion based on the tissue types in the sample, suggesting potential pathways for the uptake of the silver nanoparticles.

Fully Automated Sample Preparation for Ultrafast N-Glycosylation Analysis of Antibody Therapeutics.

PubMed

Szigeti, Marton; Lew, Clarence; Roby, Keith; Guttman, Andras

2016-04-01

There is a growing demand in the biopharmaceutical industry for high-throughput, large-scale N-glycosylation profiling of therapeutic antibodies in all phases of product development, but especially during clone selection when hundreds of samples should be analyzed in a short period of time to assure their glycosylation-based biological activity. Our group has recently developed a magnetic bead-based protocol for N-glycosylation analysis of glycoproteins to alleviate the hard-to-automate centrifugation and vacuum-centrifugation steps of the currently used protocols. Glycan release, fluorophore labeling, and cleanup were all optimized, resulting in a <4 h magnetic bead-based process with excellent yield and good repeatability. This article demonstrates the next level of this work by automating all steps of the optimized magnetic bead-based protocol from endoglycosidase digestion, through fluorophore labeling and cleanup with high-throughput sample processing in 96-well plate format, using an automated laboratory workstation. Capillary electrophoresis analysis of the fluorophore-labeled glycans was also optimized for rapid (<3 min) separation to accommodate the high-throughput processing of the automated sample preparation workflow. Ultrafast N-glycosylation analyses of several commercially relevant antibody therapeutics are also shown and compared to their biosimilar counterparts, addressing the biological significance of the differences. © 2015 Society for Laboratory Automation and Screening.

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography.

PubMed

Trépout, Sylvain; Bastin, Philippe; Marco, Sergio

2017-03-12

This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It also describes an imaging method for studying the 3D structure of thick biological specimens by scanning transmission electron tomography. The sample preparation protocol is based on conventional methods in which the sample is fixed using chemical agents, treated with a heavy atom salt contrasting agent, dehydrated in a series of ethanol baths, and embedded in resin. The specific imaging conditions for observing thick samples by scanning transmission electron microscopy are then described. Sections of the sample are observed using a through-focus method involving the collection of several images at various focal planes. This enables the recovery of in-focus information at various heights throughout the sample. This particular collection pattern is performed at each tilt angle during tomography data collection. A single image is then generated, merging the in-focus information from all the different focal planes. A classic tilt-series dataset is then generated. The advantage of the method is that the tilt-series alignment and reconstruction can be performed using standard tools. The collection of through-focal images allows the reconstruction of a 3D volume that contains all of the structural details of the sample in focus.

Revisiting the linkage between ethnomedical use and development of new medicines: A novel plant collection strategy towards the discovery of anticancer agents

PubMed Central

Henkin, Joshua M.; Sydara, Kongmany; Xayvue, Mouachanh; Souliya, Onevilay; Kinghorn, A. Douglas; Burdette, Joanna E.; Chen, Wei-Lun; Elkington, Bethany G.; Soejarto, Djaja D.

2017-01-01

The Vietnam-Laos International Cooperative Biodiversity Group (ICBG) based at the University of Illinois at Chicago (UIC) catalyzed a country-wide network of medicinal plant preserves (MPP) and medicinal biodiversity preserves (MBP) now established in ten provinces of the Lao People’s Democratic Republic (Lao PDR), which are relied upon as protected sources of ethnomedicines for local villagers and traditional healers. In collaboration with the Lao PDR’s Institute of Traditional Medicine (ITM), our ongoing P01 Program Project (Ohio State University) examined the anticancer bioprospecting potential for two of the most exhaustively inventoried of these sites: the Bolikhamxay MPP and the Xiengkhouang MBP. Guided by prior voucher specimens sourced from these preserves with an overwhelming emphasis on plants employed in traditional medicine, 201 distinct samples from 96 species were collected along with proper herbarium documentation. Aliquots of these plant samples were extracted in azeotropic ethanol and evaporated to dryness for initial biological evaluation. In six samples from six different species (2.99% of the collected samples, 6.25% of taxa) it was observed that extracts exhibited notable cytotoxicity against HT-29 colon adenocarcinoma cells. The wisdom behind the utilization of HT-29 cells in this preliminary biological screen is discussed. Furthermore, comparison of screening results based on longstanding considerations and ideological underpinnings of ethnobotanical vs. “random” biodiversity-based collection approaches is detailed herein. The results of this interdisciplinary study support the hypothesis that, by privileging the initial sample set in terms of human safety and pharmacological activity, ethnobotanically driven collection for biological screening efforts can produce leads unprecedented by the strict traditional usages of plants. PMID:29152156

Recommendations for the design, optimization, and qualification of cell-based assays used for the detection of neutralizing antibody responses elicited to biological therapeutics.

PubMed

Gupta, Shalini; Indelicato, Stephen R; Jethwa, Vijay; Kawabata, Thomas; Kelley, Marian; Mire-Sluis, Anthony R; Richards, Susan M; Rup, Bonita; Shores, Elizabeth; Swanson, Steven J; Wakshull, Eric

2007-04-10

The administration of biological therapeutics can evoke some level of immune response to the drug product in the receiving subjects. An immune response comprised of neutralizing antibodies can lead to loss of efficacy or potentially more serious clinical sequelae. Therefore, it is important to monitor the immunogenicity of biological therapeutics throughout the drug product development cycle. Immunoassays are typically used to screen for the presence and development of anti-drug product antibodies. However, in-vitro cell-based assays prove extremely useful for the characterization of immunoassay-positive samples to determine if the detected antibodies have neutralizing properties. This document provides scientific recommendations based on the experience of the authors for the development of cell-based assays for the detection of neutralizing antibodies in non-clinical and clinical studies.

Fiber array based hyperspectral Raman imaging for chemical selective analysis of malaria-infected red blood cells.

PubMed

Brückner, Michael; Becker, Katja; Popp, Jürgen; Frosch, Torsten

2015-09-24

A new setup for Raman spectroscopic wide-field imaging is presented. It combines the advantages of a fiber array based spectral translator with a tailor-made laser illumination system for high-quality Raman chemical imaging of sensitive biological samples. The Gaussian-like intensity distribution of the illuminating laser beam is shaped by a square-core optical multimode fiber to a top-hat profile with very homogeneous intensity distribution to fulfill the conditions of Koehler. The 30 m long optical fiber and an additional vibrator efficiently destroy the polarization and coherence of the illuminating light. This homogeneous, incoherent illumination is an essential prerequisite for stable quantitative imaging of complex biological samples. The fiber array translates the two-dimensional lateral information of the Raman stray light into separated spectral channels with very high contrast. The Raman image can be correlated with a corresponding white light microscopic image of the sample. The new setup enables simultaneous quantification of all Raman spectra across the whole spatial area with very good spectral resolution and thus outperforms other Raman imaging approaches based on scanning and tunable filters. The unique capabilities of the setup for fast, gentle, sensitive, and selective chemical imaging of biological samples were applied for automated hemozoin analysis. A special algorithm was developed to generate Raman images based on the hemozoin distribution in red blood cells without any influence from other Raman scattering. The new imaging setup in combination with the robust algorithm provides a novel, elegant way for chemical selective analysis of the malaria pigment hemozoin in early ring stages of Plasmodium falciparum infected erythrocytes. Copyright © 2015 Elsevier B.V. All rights reserved.

On incomplete sampling under birth-death models and connections to the sampling-based coalescent.

PubMed

Stadler, Tanja

2009-11-07

The constant rate birth-death process is used as a stochastic model for many biological systems, for example phylogenies or disease transmission. As the biological data are usually not fully available, it is crucial to understand the effect of incomplete sampling. In this paper, we analyze the constant rate birth-death process with incomplete sampling. We derive the density of the bifurcation events for trees on n leaves which evolved under this birth-death-sampling process. This density is used for calculating prior distributions in Bayesian inference programs and for efficiently simulating trees. We show that the birth-death-sampling process can be interpreted as a birth-death process with reduced rates and complete sampling. This shows that joint inference of birth rate, death rate and sampling probability is not possible. The birth-death-sampling process is compared to the sampling-based population genetics model, the coalescent. It is shown that despite many similarities between these two models, the distribution of bifurcation times remains different even in the case of very large population sizes. We illustrate these findings on an Hepatitis C virus dataset from Egypt. We show that the transmission times estimates are significantly different-the widely used Gamma statistic even changes its sign from negative to positive when switching from the coalescent to the birth-death process.

A fluorogenic molecular nanoprobe with an engineered internal environment for sensitive and selective detection of biological hydrogen sulfide.

PubMed

Kim, Myung; Seo, Young Hun; Kim, Youngsun; Heo, Jeongyun; Jang, Woo-Dong; Sim, Sang Jun; Kim, Sehoon

2017-02-14

A nanoreactor approach based on the amphiphilic assembly of various molecules offers a chance to finely engineer the internal reaction medium to enable highly selective and sensitive detection of H 2 S in biological media, being useful for microscopic imaging of cellular processes and in vitro diagnostics with blood samples.

Surface Sampling of Spores in Dry-Deposition Aerosols▿

PubMed Central

Edmonds, Jason M.; Collett, Patricia J.; Valdes, Erica R.; Skowronski, Evan W.; Pellar, Gregory J.; Emanuel, Peter A.

2009-01-01

The ability to reliably and reproducibly sample surfaces contaminated with a biological agent is a critical step in measuring the extent of contamination and determining if decontamination steps have been successful. The recovery operations following the 2001 attacks with Bacillus anthracis spores were complicated by the fact that no standard sample collection format or decontamination procedures were established. Recovery efficiencies traditionally have been calculated based upon biological agents which were applied to test surfaces in a liquid format and then allowed to dry prior to sampling tests, which may not be best suited for a real-world event with aerosolized biological agents. In order to ascertain if differences existed between air-dried liquid deposition and biological spores which were allowed to settle on a surface in a dried format, a study was undertaken to determine if differences existed in surface sampling recovery efficiencies for four representative surfaces. Studies were then undertaken to compare sampling efficiencies between liquid spore deposition and aerosolized spores which were allowed to gradually settle under gravity on four different test coupon types. Tests with both types of deposition compared efficiencies of four unique swabbing materials applied to four surfaces with various surface properties. Our studies demonstrate that recovery of liquid-deposited spores differs significantly from recovery of dry aerosol-deposited spores in most instances. Whether the recovery of liquid-deposited spores is overexaggerated or underrepresented with respect to that of aerosol-deposited spores depends upon the surface material being tested. PMID:18997021

RNA-Seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.

PubMed

Auerbach, Scott S; Phadke, Dhiral P; Mav, Deepak; Holmgren, Stephanie; Gao, Yuan; Xie, Bin; Shin, Joo Heon; Shah, Ruchir R; Merrick, B Alex; Tice, Raymond R

2015-07-01

Formalin-fixed, paraffin-embedded (FFPE) pathology specimens represent a potentially vast resource for transcriptomic-based biomarker discovery. We present here a comparison of results from a whole transcriptome RNA-Seq analysis of RNA extracted from fresh frozen and FFPE livers. The samples were derived from rats exposed to aflatoxin B1 (AFB1 ) and a corresponding set of control animals. Principal components analysis indicated that samples were separated in the two groups representing presence or absence of chemical exposure, both in fresh frozen and FFPE sample types. Sixty-five percent of the differentially expressed transcripts (AFB1 vs. controls) in fresh frozen samples were also differentially expressed in FFPE samples (overlap significance: P < 0.0001). Genomic signature and gene set analysis of AFB1 differentially expressed transcript lists indicated highly similar results between fresh frozen and FFPE at the level of chemogenomic signatures (i.e., single chemical/dose/duration elicited transcriptomic signatures), mechanistic and pathology signatures, biological processes, canonical pathways and transcription factor networks. Overall, our results suggest that similar hypotheses about the biological mechanism of toxicity would be formulated from fresh frozen and FFPE samples. These results indicate that phenotypically anchored archival specimens represent a potentially informative resource for signature-based biomarker discovery and mechanistic characterization of toxicity. Copyright © 2014 John Wiley & Sons, Ltd.

Transport of Bacillus thuringiensis var. kurstaki from an outdoor release into buildings: pathways of infiltration and a rapid method to identify contaminated buildings.

PubMed

Van Cuyk, Sheila; Deshpande, Alina; Hollander, Attelia; Franco, David O; Teclemariam, Nerayo P; Layshock, Julie A; Ticknor, Lawrence O; Brown, Michael J; Omberg, Kristin M

2012-06-01

Understanding the fate and transport of biological agents into buildings will be critical to recovery and restoration efforts after a biological attack in an urban area. As part of the Interagency Biological Restoration Demonstration (IBRD), experiments were conducted in Fairfax County, VA, to study whether a biological agent can be expected to infiltrate into buildings following a wide-area release. Bacillus thuringiensis var. kurstaki is a common organic pesticide that has been sprayed in Fairfax County for a number of years to control the gypsy moth. Because the bacterium shares many physical and biological properties with Bacillus anthracis, the results from these studies can be extrapolated to a bioterrorist release. In 2009, samples were collected from inside buildings located immediately adjacent to a spray block. A combined probabilistic and targeted sampling strategy and modeling were conducted to provide insight into likely methods of infiltration. Both the simulations and the experimental results indicate sampling entryways and heating, ventilation, and air conditioning (HVAC) filters are reasonable methods for "ruling in" a building as contaminated. Following a biological attack, this method is likely to provide significant savings in time and labor compared to more rigorous, statistically based characterization. However, this method should never be used to "rule out," or clear, a building.

Screening and identification of antioxidants in biological samples using high-performance liquid chromatography-mass spectrometry and its application on Salacca edulis Reinw.

PubMed

Shui, Guanghou; Leong, Lai Peng

2005-02-23

In this study, a new approach was developed for screening and identifying antioxidants in biological samples. The approach was based on significant decreases of the intensities of ion peaks obtained from high-performance liquid chromatography (HPLC) coupled with mass spectrometry (MS) upon reaction with 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radicals. HPLC-MS/MS was further applied to elucidate structures of antioxidant peaks characterized in a spiking test. The new approach could also be used to monitor the reactivity of antioxidants in biological sample with free radicals. The approach was successfully applied to the identification of antioxidants in salak (Salacca edulis Reinw), a tropical fruit that is reported to be a very good source of natural antioxidants, but it was still not clear which compounds were responsible for its antioxidant property. The antioxidants in salak were identified to be chlorogenic acid, (-)-epicatechin, and singly linked proanthocyanidins that mainly existed as dimers through hexamers of catechin or epicatechin. In salak, chlorogenic acid was identified to be an antioxidant of the slow reaction type as it reacted with free radicals much more slowly than either (-)-epicatechin or proanthocyanidins. The new approach was proved to be useful for the characterization and identification of antioxidants in biological samples as a mass detector combined with an HPLC separation system not only serves as an ideal tool to monitor free radical active components but also provides their possible chemical structures in a biological sample.

Review of in situ derivatization techniques for enhanced bioanalysis using liquid chromatography with mass spectrometry.

PubMed

Baghdady, Yehia Z; Schug, Kevin A

2016-01-01

Accurate and specific analysis of target molecules in complex biological matrices remains a significant challenge, especially when ultra-trace detection limits are required. Liquid chromatography with mass spectrometry is often the method of choice for bioanalysis. Conventional sample preparation and clean-up methods prior to the analysis of biological fluids such as liquid-liquid extraction, solid-phase extraction, or protein precipitation are time-consuming, tedious, and can negatively affect target recovery and detection sensitivity. An alternative or complementary strategy is the use of an off-line or on-line in situ derivatization technique. In situ derivatization can be incorporated to directly derivatize target analytes in their native biological matrices, without any prior sample clean-up methods, to substitute or even enhance the extraction and preconcentration efficiency of these traditional sample preparation methods. Designed appropriately, it can reduce the number of sample preparation steps necessary prior to analysis. Moreover, in situ derivatization can be used to enhance the performance of the developed liquid chromatography with mass spectrometry-based bioanalysis methods regarding stability, chromatographic separation, selectivity, and ionization efficiency. This review presents an overview of the commonly used in situ derivatization techniques coupled to liquid chromatography with mass spectrometry-based bioanalysis to guide and to stimulate future research. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Selecting Feature Subsets Based on SVM-RFE and the Overlapping Ratio with Applications in Bioinformatics.

PubMed

Lin, Xiaohui; Li, Chao; Zhang, Yanhui; Su, Benzhe; Fan, Meng; Wei, Hai

2017-12-26

Feature selection is an important topic in bioinformatics. Defining informative features from complex high dimensional biological data is critical in disease study, drug development, etc. Support vector machine-recursive feature elimination (SVM-RFE) is an efficient feature selection technique that has shown its power in many applications. It ranks the features according to the recursive feature deletion sequence based on SVM. In this study, we propose a method, SVM-RFE-OA, which combines the classification accuracy rate and the average overlapping ratio of the samples to determine the number of features to be selected from the feature rank of SVM-RFE. Meanwhile, to measure the feature weights more accurately, we propose a modified SVM-RFE-OA (M-SVM-RFE-OA) algorithm that temporally screens out the samples lying in a heavy overlapping area in each iteration. The experiments on the eight public biological datasets show that the discriminative ability of the feature subset could be measured more accurately by combining the classification accuracy rate with the average overlapping degree of the samples compared with using the classification accuracy rate alone, and shielding the samples in the overlapping area made the calculation of the feature weights more stable and accurate. The methods proposed in this study can also be used with other RFE techniques to define potential biomarkers from big biological data.

The New Bedford Harbor Superfund Site Long Term ...

EPA Pesticide Factsheets

Background. New Bedford Harbor (NBH), located in southeastern Massachusetts, was designated as a marine Superfund site in 1983 due to sediment contamination by polychlorinated biphenyls (PCBs). Based on risks to human health and the environment, the first two phases of the site cleanup involved dredging PCB-contaminated sediments from the harbor. Therefore, a long-term monitoring program (LTM) was developed to measure spatial and temporal chemical and biological changes in sediment, water, and biota to assess the effects and effectiveness of the remedial activities. Approach. A systematic, probabilistic sampling design was used to select approximately 70 sediment sampling stations. Sediment was collected at each station and chemical (e.g., PCBs, metals), physical (e.g., grain size), and biological (e.g., benthic community) measurements were conducted on all samples. There have been six sample collections to date: 1993-baseline, 1995-post hot spot removal, 1999-prior to full scale dredging, and then at 5 year intervals: 2004, 2009, and 2014. Mussel (Mytilus edulis) bioaccumulation has also been measured twice yearly. Results. There is a decreasing spatial gradient in sediment PCB concentrations from the northern boundary (upper harbor) to the southern boundary (outer harbor) of the site. Along this same transect, there is an increase in biological condition (e.g., benthic community diversity). Temporally, the contaminant and biological gradients have been

A novel method for single sample multi-axial nanoindentation of hydrated heterogeneous tissues based on testing great white shark jaws.

PubMed

Ferrara, Toni L; Boughton, Philip; Slavich, Eve; Wroe, Stephen

2013-01-01

Nanomechanical testing methods that are suitable for a range of hydrated tissues are crucial for understanding biological systems. Nanoindentation of tissues can provide valuable insights into biology, tissue engineering and biomimetic design. However, testing hydrated biological samples still remains a significant challenge. Shark jaw cartilage is an ideal substrate for developing a method to test hydrated tissues because it is a unique heterogeneous composite of both mineralized (hard) and non-mineralized (soft) layers and possesses a jaw geometry that is challenging to test mechanically. The aim of this study is to develop a novel method for obtaining multidirectional nanomechanical properties for both layers of jaw cartilage from a single sample, taken from the great white shark (Carcharodon carcharias). A method for obtaining multidirectional data from a single sample is necessary for examining tissue mechanics in this shark because it is a protected species and hence samples may be difficult to obtain. Results show that this method maintains hydration of samples that would otherwise rapidly dehydrate. Our study is the first analysis of nanomechanical properties of great white shark jaw cartilage. Variation in nanomechanical properties were detected in different orthogonal directions for both layers of jaw cartilage in this species. The data further suggest that the mineralized layer of shark jaw cartilage is less stiff than previously posited. Our method allows multidirectional nanomechanical properties to be obtained from a single, small, hydrated heterogeneous sample. Our technique is therefore suitable for use when specimens are rare, valuable or limited in quantity, such as samples obtained from endangered species or pathological tissues. We also outline a method for tip-to-optic calibration that facilitates nanoindentation of soft biological tissues. Our technique may help address the critical need for a nanomechanical testing method that is applicable to a variety of hydrated biological materials whether soft or hard.

Development of a micro-XRF system for biological samples based on proton-induced quasimonochromatic X-rays

NASA Astrophysics Data System (ADS)

Ploykrachang, K.; Hasegawa, J.; Kondo, K.; Fukuda, H.; Oguri, Y.

2014-07-01

We have developed a micro-XRF system based on a proton-induced quasimonochromatic X-ray (QMXR) microbeam for in vivo measurement of biological samples. A 2.5-MeV proton beam impinged normally on a Cu foil target that was slightly thicker than the proton range. The emitted QMXR behind the Cu target was focused with a polycapillary X-ray half lens. For application to analysis of wet or aquatic samples, we prepared a QMXR beam with an incident angle of 45° with respect to the horizontal plane by using a dipole magnet in order to bend the primary proton beam downward by 45°. The focal spot size of the QMXR microbeam on a horizontal sample surface was evaluated to be 250 × 350 μm by a wire scanning method. A microscope camera with a long working distance was installed perpendicular to the sample surface to identify the analyzed position on the sample. The fluorescent radiation from the sample was collected by a Si-PIN photodiode X-ray detector. Using the setup above, we were able to successfully measure the accumulation and distribution of Co in the leaves of a free-floating aquatic plant on a dilute Co solution surface.

Molecular characterization, biological forms and sporozoite rate of Anopheles stephensi in southern Iran

PubMed Central

Chavshin, Ali Reza; Oshaghi, Mohammad Ali; Vatandoost, Hasan; Hanafi-Bojd, Ahmad Ali; Raeisi, Ahmad; Nikpoor, Fatemeh

2014-01-01

Objective To identify the biological forms, sporozoite rate and molecular characterization of the Anopheles stephensi (An. stephensi) in Hormozgan and Sistan-Baluchistan provinces, the most important malarious areas in Iran. Methods Wild live An. stephensi samples were collected from different malarious areas in southern Iran. The biological forms were identified based on number of egg-ridges. Molecular characterization of biological forms was verified by analysis of the mitochondrial cytochrome oxidase subunit I and II (mtDNA-COI/COII). The Plasmodium infection was examined in the wild female specimens by species-specific nested–PCR method. Results Results showed that all three biological forms including mysorensis, intermediate and type are present in the study areas. Molecular investigations revealed no genetic variation between mtDNA COI/COII sequences of the biological forms and no Plasmodium parasites was detected in the collected mosquito samples. Conclusions Presence of three biological forms with identical sequences showed that the known biological forms belong to a single taxon and the various vectorial capacities reported for these forms are more likely corresponded to other epidemiological factors than to the morphotype of the populations. Lack of malaria parasite infection in An. stephensi, the most important vector of malaria, may be partly due to the success and achievement of ongoing active malaria control program in the region. PMID:24144130

Is it ethical to prevent secondary use of stored biological samples and data derived from consenting research participants? The case of Malawi.

PubMed

Mungwira, Randy G; Nyangulu, Wongani; Misiri, James; Iphani, Steven; Ng'ong'ola, Ruby; Chirambo, Chawanangwa M; Masiye, Francis; Mfutso-Bengo, Joseph

2015-12-02

This paper discusses the contentious issue of reuse of stored biological samples and data obtained from research participants in past clinical research to answer future ethical and scientifically valid research questions. Many countries have regulations and guidelines that guide the use and exportation of stored biological samples and data. However, there are variations in regulations and guidelines governing the reuse of stored biological samples and data in Sub-Saharan Africa including Malawi. The current research ethics regulations and guidelines in Malawi do not allow indefinite storage and reuse of biological samples and data for future unspecified research. This comes even though the country has managed to answer pertinent research questions using stored biological samples and data. We acknowledge the limited technical expertise and equipment unavailable in Malawi that necessitates exportation of biological samples and data and the genuine concern raised by the regulatory authorities about the possible exploitation of biological samples and data by researchers. We also acknowledge that Malawi does not have bio-banks for storing biological samples and data for future research purposes. This creates room for possible exploitation of biological samples and data collected from research participants in primary research projects in Malawi. However, research ethics committees require completion and approval of material transfer agreements and data transfer agreements for biological samples and data collected for research purposes respectively and this requirement may partly address the concern raised by the regulatory authorities. Our concern though is that there is no such requirement for biological samples and data collected from patients for clinical or diagnostic purposes. In conclusion, we propose developing a medical data and material transfer agreement for biological samples and data collected from patients for clinical or diagnostic purposes in both public and private health facilities that may end up in research centers outside Malawi. We also propose revision of the current research ethics regulations and guidelines in Malawi in order to allow secondary use of biological samples and data collected from primary research projects as a way of maximizing the use of collected samples and data. Finally, we call for consultation of all stakeholders within the Malawi research community when regulatory authorities are developing policies that govern research in Malawi.

Surface enhanced Raman spectroscopy in the presence of hydroquinone assisted by gold nanorods

NASA Astrophysics Data System (ADS)

Cabrera Alonso, R.; Guevara, Edgar; Ramírez Elías, Miguel G.; González, Francisco Javier

2017-08-01

Hydroquinone is an aromatic organic molecule found in skin lightening creams for dermatological melasma treatment. The absorbance of this substance at high concentrations can be the cause of skin diseases. Nowadays most of the methods used for medical diagnosis for dermatological diseases consist on invasive methods such as biopsies. In recent years non-invasive techniques based on the properties of light and the interaction with biological samples have come to a new way for medical diagnosis. By means of Raman spectroscopy is of great interest the detection of hydroquinone for future medical applications. Due to the low Raman signal that the biological samples present, it is necessary to make use of nanotechnology. Making biosensors (SERS substrates) that allow us to amplify the electromagnetic field for the biological Raman signals.

Advances in metabolome information retrieval: turning chemistry into biology. Part I: analytical chemistry of the metabolome.

PubMed

Tebani, Abdellah; Afonso, Carlos; Bekri, Soumeya

2018-05-01

Metabolites are small molecules produced by enzymatic reactions in a given organism. Metabolomics or metabolic phenotyping is a well-established omics aimed at comprehensively assessing metabolites in biological systems. These comprehensive analyses use analytical platforms, mainly nuclear magnetic resonance spectroscopy and mass spectrometry, along with associated separation methods to gather qualitative and quantitative data. Metabolomics holistically evaluates biological systems in an unbiased, data-driven approach that may ultimately support generation of hypotheses. The approach inherently allows the molecular characterization of a biological sample with regard to both internal (genetics) and environmental (exosome, microbiome) influences. Metabolomics workflows are based on whether the investigator knows a priori what kind of metabolites to assess. Thus, a targeted metabolomics approach is defined as a quantitative analysis (absolute concentrations are determined) or a semiquantitative analysis (relative intensities are determined) of a set of metabolites that are possibly linked to common chemical classes or a selected metabolic pathway. An untargeted metabolomics approach is a semiquantitative analysis of the largest possible number of metabolites contained in a biological sample. This is part I of a review intending to give an overview of the state of the art of major metabolic phenotyping technologies. Furthermore, their inherent analytical advantages and limits regarding experimental design, sample handling, standardization and workflow challenges are discussed.

X-ray mosaic nanotomography of large microorganisms.

PubMed

Mokso, R; Quaroni, L; Marone, F; Irvine, S; Vila-Comamala, J; Blanke, A; Stampanoni, M

2012-02-01

Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state. Copyright © 2012 Elsevier Inc. All rights reserved.

Electrochemical imaging of cells and tissues

PubMed Central

Lin, Tzu-En; Rapino, Stefania; Girault, Hubert H.

2018-01-01

The technological and experimental progress in electrochemical imaging of biological specimens is discussed with a view on potential applications for skin cancer diagnostics, reproductive medicine and microbial testing. The electrochemical analysis of single cell activity inside cell cultures, 3D cellular aggregates and microtissues is based on the selective detection of electroactive species involved in biological functions. Electrochemical imaging strategies, based on nano/micrometric probes scanning over the sample and sensor array chips, respectively, can be made sensitive and selective without being affected by optical interference as many other microscopy techniques. The recent developments in microfabrication, electronics and cell culturing/tissue engineering have evolved in affordable and fast-sampling electrochemical imaging platforms. We believe that the topics discussed herein demonstrate the applicability of electrochemical imaging devices in many areas related to cellular functions. PMID:29899947

Polymer monolithic capillary microextraction on-line coupled with inductively coupled plasma-mass spectrometry for the determination of trace Au and Pd in biological samples

NASA Astrophysics Data System (ADS)

Liu, Xiaolan; He, Man; Chen, Beibei; Hu, Bin

2014-11-01

A novel method based on on-line polymer monolithic capillary microextraction (CME)-inductively coupled plasma mass spectrometry (ICP-MS) was developed for the determination of trace Au and Pd in biological samples. For this purpose, poly(glycidyl methacrylate-ethylene dimethacrylate) monolith was prepared and functionalized with mercapto groups. The prepared monolith exhibited good selectivity to Au and Pd, and good resistance to strong acid with a long life span. Factors affecting the extraction efficiency of CME, such as sample acidity, sample flow rate, eluent conditions and coexisting ion interference were investigated in detail. Under the optimal conditions, the limits of detection (LODs, 3σ) were 5.9 ng L- 1 for Au and 8.3 ng L- 1 for Pd, and the relative standard deviations (RSDs, c = 50 ng L-1, n = 7) were 6.5% for Au and 1.1% for Pd, respectively. The developed method was successfully applied to the determination of Au and Pd in human urine and serum samples with the recovery in the range of 84-118% for spiked samples. The developed on-line polymer monolithic CME-ICP-MS method has the advantages of rapidity, simplicity, low sample/reagent consumption, high sensitivity and is suitable for the determination of trace Au and Pd in biological samples with limited amount available and complex matrix.

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

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

Scanning electron microscopy (SEM) has been widely used to examine biological specimens of bacteria, viruses and proteins. Until now, atmospheric and/or wet biological specimens have been examined using various atmospheric holders or special equipment involving SEM. Unfortunately, they undergo heavy radiation damage by the direct electron beam. In addition, images of unstained biological samples in water yield poor contrast. We recently developed a new analytical technology involving a frequency transmission electric-field (FTE) method based on thermionic SEM. This method is suitable for high-contrast imaging of unstained biological specimens. Our aim was to optimise the method. Here we describe a high-resolutionmore » FTE system based on field-emission SEM; it allows for imaging and nanoscale examination of various biological specimens in water without radiation damage. The spatial resolution is 8 nm, which is higher than 41 nm of the existing FTE system. Our new method can be easily utilised for examination of unstained biological specimens including bacteria, viruses and protein complexes. Furthermore, our high-resolution FTE system can be used for diverse liquid samples across a broad range of scientific fields, e.g. nanoparticles, nanotubes and organic and catalytic materials. - Highlights: • We developed a high-resolution frequency transmission electric-field (FTE) system. • High-resolution FTE system is introduced in the field-emission SEM. • The spatial resolution of high-resolution FTE method is 8 nm. • High-resolution FTE system enables observation of the intact IgM particles in water.« less

Quantitative Evaluation of Hard X-ray Damage to Biological Samples using EUV Ptychography

NASA Astrophysics Data System (ADS)

Baksh, Peter; Odstrcil, Michal; Parsons, Aaron; Bailey, Jo; Deinhardt, Katrin; Chad, John E.; Brocklesby, William S.; Frey, Jeremy G.

2017-06-01

Coherent diffractive imaging (CDI) has become a standard method on a variety of synchrotron beam lines. The high brilliance short wavelength radiation from these sources can be used to reconstruct attenuation and relative phase of a sample with nanometre resolution via CDI methods. However, the interaction between the sample and high energy ionising radiation can cause degradation to sample structure. We demonstrate, using a laboratory based high harmonic generation (HHG) based extreme ultraviolet (EUV) source, imaging a sample of hippocampal neurons using the ptychography method. The significant increase in contrast of the sample in the EUV light allows identification of damage induced from exposure to 7.3 keV photons, without causing any damage to the sample itself.

Introducing Undergraduate Students to Metabolomics Using a NMR-Based Analysis of Coffee Beans

ERIC Educational Resources Information Center

Sandusky, Peter Olaf

2017-01-01

Metabolomics applies multivariate statistical analysis to sets of high-resolution spectra taken over a population of biologically derived samples. The objective is to distinguish subpopulations within the overall sample population, and possibly also to identify biomarkers. While metabolomics has become part of the standard analytical toolbox in…

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

PubMed Central

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

2016-01-01

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

The role of different sampling methods in improving biological activity prediction using deep belief network.

PubMed

Ghasemi, Fahimeh; Fassihi, Afshin; Pérez-Sánchez, Horacio; Mehri Dehnavi, Alireza

2017-02-05

Thousands of molecules and descriptors are available for a medicinal chemist thanks to the technological advancements in different branches of chemistry. This fact as well as the correlation between them has raised new problems in quantitative structure activity relationship studies. Proper parameter initialization in statistical modeling has merged as another challenge in recent years. Random selection of parameters leads to poor performance of deep neural network (DNN). In this research, deep belief network (DBN) was applied to initialize DNNs. DBN is composed of some stacks of restricted Boltzmann machine, an energy-based method that requires computing log likelihood gradient for all samples. Three different sampling approaches were suggested to solve this gradient. In this respect, the impact of DBN was applied based on the different sampling approaches mentioned above to initialize the DNN architecture in predicting biological activity of all fifteen Kaggle targets that contain more than 70k molecules. The same as other fields of processing research, the outputs of these models demonstrated significant superiority to that of DNN with random parameters. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

A review of microdialysis coupled to microchip electrophoresis for monitoring biological events

PubMed Central

Saylor, Rachel A.; Lunte, Susan M.

2015-01-01

Microdialysis is a powerful sampling technique that enables monitoring of dynamic processes in vitro and in vivo. The combination of microdialysis with chromatographic or electrophoretic methods yields along with selective detection methods yields a “separation-based sensor” capable of monitoring multiple analytes in near real time. Analysis of microdialysis samples requires techniques that are fast (<1 min), have low volume requirements (nL–pL), and, ideally, can be employed on-line. Microchip electrophoresis fulfills these requirements and also permits the possibility of integrating sample preparation and manipulation with detection strategies directly on-chip. Microdialysis coupled to microchip electrophoresis has been employed for monitoring biological events in vivo and in vitro. This review discusses technical considerations for coupling microdialysis sampling and microchip electrophoresis, including various interface designs, and current applications in the field. PMID:25637011

Quantitation of DNA adducts by stable isotope dilution mass spectrometry

PubMed Central

Tretyakova, Natalia; Goggin, Melissa; Janis, Gregory

2012-01-01

Exposure to endogenous and exogenous chemicals can lead to the formation of structurally modified DNA bases (DNA adducts). If not repaired, these nucleobase lesions can cause polymerase errors during DNA replication, leading to heritable mutations potentially contributing to the development of cancer. Due to their critical role in cancer initiation, DNA adducts represent mechanism-based biomarkers of carcinogen exposure, and their quantitation is particularly useful for cancer risk assessment. DNA adducts are also valuable in mechanistic studies linking tumorigenic effects of environmental and industrial carcinogens to specific electrophilic species generated from their metabolism. While multiple experimental methodologies have been developed for DNA adduct analysis in biological samples – including immunoassay, HPLC, and 32P-postlabeling – isotope dilution high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) generally has superior selectivity, sensitivity, accuracy, and reproducibility. As typical DNA adducts concentrations in biological samples are between 0.01 – 10 adducts per 108 normal nucleotides, ultrasensitive HPLC-ESI-MS/MS methodologies are required for their analysis. Recent developments in analytical separations and biological mass spectrometry – especially nanoflow HPLC, nanospray ionization MS, chip-MS, and high resolution MS – have pushed the limits of analytical HPLC-ESI-MS/MS methodologies for DNA adducts, allowing researchers to accurately measure their concentrations in biological samples from patients treated with DNA alkylating drugs and in populations exposed to carcinogens from urban air, drinking water, cooked food, alcohol, and cigarette smoke. PMID:22827593

Evaluation of peak picking quality in LC-MS metabolomics data.

PubMed

Brodsky, Leonid; Moussaieff, Arieh; Shahaf, Nir; Aharoni, Asaph; Rogachev, Ilana

2010-11-15

The output of LC-MS metabolomics experiments consists of mass-peak intensities identified through a peak-picking/alignment procedure. Besides imperfections in biological samples and instrumentation, data accuracy is highly dependent on the applied algorithms and their parameters. Consequently, quality control (QC) is essential for further data analysis. Here, we present a QC approach that is based on discrepancies between replicate samples. First, the quantile normalization of per-sample log-signal distributions is applied to each group of biologically homogeneous samples. Next, the overall quality of each replicate group is characterized by the Z-transformed correlation coefficients between samples. This general QC allows a tuning of the procedure's parameters which minimizes the inter-replicate discrepancies in the generated output. Subsequently, an in-depth QC measure detects local neighborhoods on a template of aligned chromatograms that are enriched by divergences between intensity profiles of replicate samples. These neighborhoods are determined through a segmentation algorithm. The retention time (RT)-m/z positions of the neighborhoods with local divergences are indicative of either: incorrect alignment of chromatographic features, technical problems in the chromatograms, or to a true biological discrepancy between replicates for particular metabolites. We expect this method to aid in the accurate analysis of metabolomics data and in the development of new peak-picking/alignment procedures.

Integration of Microdialysis Sampling and Microchip Electrophoresis with Electrochemical Detection

PubMed Central

Mecker, Laura C.; Martin, R. Scott

2009-01-01

Here we describe the fabrication, optimization, and application of a microfluidic device that integrates microdialysis (MD) sampling, microchip electrophoresis (ME), and electrochemical detection (EC). The manner in which the chip is produced is reproducible and enables the fixed alignment of the MD/ME and ME/EC interfaces. Poly(dimethylsiloxane) (PDMS) -based valves were used for the discrete injection of sample from the hydrodynamic MD dialysate stream into a separation channel for analysis with ME. To enable the integration of ME with EC detection, a palladium decoupler was used to isolate the high voltages associated with electrophoresis from micron-sized carbon ink detection electrodes. Optimization of the ME/EC interface was needed to allow the use of biologically appropriate perfusate buffers containing high salt content. This optimization included changes in the fabrication procedure, increases in the decoupler surface area, and a programmed voltage shutoff. The ability of the MD/ME/EC system to sample a biological system was demonstrated by using a linear probe to monitor the stimulated release of dopamine from a confluent layer of PC 12 cells. To our knowledge, this is the first report of a microchip-based system that couples microdialysis sampling with microchip electrophoresis and electrochemical detection. PMID:19551945

Decline in Interest in Biology among Elementary School Pupils during a Generation

ERIC Educational Resources Information Center

Randler, Christoph; Osti, Janina; Hummel, Eberhard

2012-01-01

A decline in biology interest has often been claimed but seldom with an empirically substantiation. This study was based on a sample of 3rd and 4th grade pupils within the same geographical area as Lowe's (1987, 1992) previous results from southwest Germany from the year 1983. We used a four-point Likert-type questionnaire to assess interest with…

Advances in the analysis of biological samples using ionic liquids.

PubMed

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

2018-02-12

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

Quantitative estimation of global patterns of surface ocean biological productivity and its seasonal variation on timescales from centuries to millennia

NASA Astrophysics Data System (ADS)

Loubere, Paul; Fariduddin, Mohammad

1999-03-01

We present a quantitative method, based on the relative abundances of benthic foraminifera in deep-sea sediments, for estimating surface ocean biological productivity over the timescale of centuries to millennia. We calibrate the method using a global data set composed of 207 samples from the Atlantic, Pacific, and Indian Oceans from a water depth range between 2300 and 3600 m. The sample set was developed so that other, potentially significant, environmental variables would be uncorrelated to overlying surface ocean productivity. A regression of assemblages against productivity yielded an r2 = 0.89 demonstrating a strong productivity signal in the faunal data. In addition, we examined assemblage response to annual variability in biological productivity (seasonality). Our data set included a range of seasonalities which we quantified into a seasonality index using the pigment color bands from the coastal zone color scanner (CZCS). The response of benthic foraminiferal assemblage composition to our seasonality index was tested with regression analysis. We obtained a statistically highly significant r2 = 0.75. Further, discriminant function analysis revealed a clear separation among sample groups based on surface ocean productivity and our seasonality index. Finally, we tested the response of benthic foraminiferal assemblages to three different modes of seasonality. We observed a distinct separation of our samples into groups representing low seasonal variability, strong seasonality with a single main productivity event in the year, and strong seasonality with multiple productivity events in the year. Reconstructing surface ocean biological productivity with benthic foraminifera will aid in modeling marine biogeochemical cycles. Also, estimating mode and range of annual seasonality will provide insight to changing oceanic processes, allowing the examination of the mechanisms causing changes in the marine biotic system over time. This article contains supplementary material.

Single input state, single–mode fiber–based polarization sensitive optical frequency domain imaging by eigenpolarization referencing

PubMed Central

Lippok, Norman; Villiger, Martin; Jun, Chang–Su; Bouma, Brett E.

2015-01-01

Fiber–based polarization sensitive OFDI is more challenging than free–space implementations. Using multiple input states, fiber–based systems provide sample birefringence information with the benefit of a flexible sample arm but come at the cost of increased system and acquisition complexity, and either reduce acquisition speed or require increased acquisition bandwidth. Here we show that with the calibration of a single polarization state, fiber–based configurations can approach the conceptual simplicity of traditional free–space configurations. We remotely control the polarization state of the light incident at the sample using the eigenpolarization states of a wave plate as a reference, and determine the Jones matrix of the output fiber. We demonstrate this method for polarization sensitive imaging of biological samples. PMID:25927775

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

PubMed Central

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.; Burnum-Johnson, Kristin E.; Kim, Young-Mo; Kyle, Jennifer E.; Matzke, Melissa M.; Shukla, Anil K.; Chu, Rosalie K.; Schepmoes, Athena A.; Jacobs, Jon M.; Baric, Ralph S.; Webb-Robertson, Bobbie-Jo; Smith, Richard D.

2016-01-01

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The metabolite, protein, and lipid extraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro, and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample. Author Video: An author video summary of this article is available. PMID:27822525

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.

Gravitational Biology Facility on Space Station: Meeting the needs of space biology

NASA Technical Reports Server (NTRS)

Allen, Katherine; Wade, Charles

1992-01-01

The Gravitational Biology Facility (GBF) is a set of generic laboratory equipment needed to conduct research on Space Station Freedom (SSF), focusing on Space Biology Program science (Cell and Developmental Biology and Plant Biology). The GBF will be functional from the earliest utilization flights through the permanent manned phase. Gravitational biology research will also make use of other Life Sciences equipment on the space station as well as existing equipment developed for the space shuttle. The facility equipment will be developed based on requirements derived from experiments proposed by the scientific community to address critical questions in the Space Biology Program. This requires that the facility have the ability to house a wide variety of species, various methods of observation, and numerous methods of sample collection, preservation, and storage. The selection of the equipment will be done by the members of a scientific working group (5 members representing cell biology, 6 developmental biology, and 6 plant biology) who also provide requirements to design engineers to ensure that the equipment will meet scientific needs. All equipment will undergo extensive ground based experimental validation studies by various investigators addressing a variety of experimental questions. Equipment will be designed to be adaptable to other space platforms. The theme of the Gravitational Biology Facility effort is to provide optimal and reliable equipment to answer the critical questions in Space Biology as to the effects of gravity on living systems.

The search for an identification of amino acids, nucleobases and nucleosides in samples returned from Mars

NASA Technical Reports Server (NTRS)

Gehrke, Charles W.; Ponnamperuma, Cyril; Kuo, Kenneth C.; Stalling, David L.; Zumwalt, Robert W.

1988-01-01

The Mars Sample Return mission will provide us with a unique source of material from our solar system; material which could advance our knowledge of the processes of chemical evolution. As has been pointed out, Mars geological investigations based on the Viking datasets have shown that primordial Mars was in many biologically important ways similar to the primordial Earth; the presence of surface liquid water, moderate surface temperatures, and atmosphere of carbon dioxide and nitrogen, and high geothermal heat flow. Indeed, it would seem that conditions on Earth and Mars were fundamentally similar during the first one billion years or so. As has been pointed out, Mars may well contain the best preserved record of the events that transpired on the early planets. Examination of that early record will involve searching for many things, from microfossils to isotopic abundance data. We propose an investigation of the returned Mars samples for biologically important organic compounds, with emphases on amino acids, the purine and pyrimidine bases, and nucleosides.

Next-generation libraries for robust RNA interference-based genome-wide screens

PubMed Central

Kampmann, Martin; Horlbeck, Max A.; Chen, Yuwen; Tsai, Jordan C.; Bassik, Michael C.; Gilbert, Luke A.; Villalta, Jacqueline E.; Kwon, S. Chul; Chang, Hyeshik; Kim, V. Narry; Weissman, Jonathan S.

2015-01-01

Genetic screening based on loss-of-function phenotypes is a powerful discovery tool in biology. Although the recent development of clustered regularly interspaced short palindromic repeats (CRISPR)-based screening approaches in mammalian cell culture has enormous potential, RNA interference (RNAi)-based screening remains the method of choice in several biological contexts. We previously demonstrated that ultracomplex pooled short-hairpin RNA (shRNA) libraries can largely overcome the problem of RNAi off-target effects in genome-wide screens. Here, we systematically optimize several aspects of our shRNA library, including the promoter and microRNA context for shRNA expression, selection of guide strands, and features relevant for postscreen sample preparation for deep sequencing. We present next-generation high-complexity libraries targeting human and mouse protein-coding genes, which we grouped into 12 sublibraries based on biological function. A pilot screen suggests that our next-generation RNAi library performs comparably to current CRISPR interference (CRISPRi)-based approaches and can yield complementary results with high sensitivity and high specificity. PMID:26080438

Combinatorial Multidomain Mesoporous Chips and a Method for Fractionation, Stabilization, and Storage of Biomolecules

NASA Technical Reports Server (NTRS)

Tasciotti, Ennio (Inventor); Hu, Ye (Inventor); Ferrari, Mauro (Inventor); Bouamrani, Ali (Inventor); Liu, Xuewu (Inventor)

2014-01-01

A new fractionation device shows desirable features for exploratory screening and biomarker discovery. The constituent MSCs may be tailored for desired pore sizes and surface properties and for the sequestration and enrichment of extremely low abundant protein and peptides in desired ranges of the mass/charge spectrum. The MSCs are effective in yielding reproducible extracts from complex biological samples as small as 10 microliter in a time as short as 30 minutes. They are inexpensive to manufacture, and allow for scaled up production to attain the simultaneous processing of a large number of samples. The MSCs are multiplexed, label-free diagnostic tools with the potential of biological recognition moiety modification for enhanced specificity. The MSCs may store, protect and stabilize biological fluids, enabling the simplified and cost-effective collection and transportation of clinical samples. The MSC-based device may serve as a diagnostic tool to complement histopathology, imaging, and other conventional clinical techniques. The MSCs mediated identification of disease-specific protein signatures may help in the selection of personalized therapeutic combinations, in the real-time assessment of therapeutic efficacy and toxicity, and in the rational modulation of therapy based on the changes in the protein networks associated with the prognosis and the drug resistance of the disease.

Development of an Analytical Protocol for Determination of Cyanide in Human Biological Samples Based on Application of Ion Chromatography with Pulsed Amperometric Detection

PubMed Central

Ruman, Marek; Narkowicz, Sylwia; Namieśnik, Jacek

2017-01-01

A simple and accurate ion chromatography (IC) method with pulsed amperometric detection (PAD) was proposed for the determination of cyanide ion in urine, sweat, and saliva samples. The sample pretreatment relies on alkaline digestion and application of Dionex OnGuard II H cartridge. Under the optimized conditions, the method showed good linearity in the range of 1–100 μg/L for urine, 5–100 μg/L for saliva, and 3–100 μg/L for sweat samples with determination coefficients (R) > 0.992. Low detection limits (LODs) in the range of 1.8 μg/L, 5.1 μg/L, and 5.8 μg/L for urine, saliva, and sweat samples, respectively, and good repeatability (CV < 3%, n = 3) were obtained. The proposed method has been successfully applied to the analysis of human biological samples. PMID:29348966

Development of an Analytical Protocol for Determination of Cyanide in Human Biological Samples Based on Application of Ion Chromatography with Pulsed Amperometric Detection.

PubMed

Jaszczak, Ewa; Ruman, Marek; Narkowicz, Sylwia; Namieśnik, Jacek; Polkowska, Żaneta

2017-01-01

A simple and accurate ion chromatography (IC) method with pulsed amperometric detection (PAD) was proposed for the determination of cyanide ion in urine, sweat, and saliva samples. The sample pretreatment relies on alkaline digestion and application of Dionex OnGuard II H cartridge. Under the optimized conditions, the method showed good linearity in the range of 1-100  μ g/L for urine, 5-100  μ g/L for saliva, and 3-100  μ g/L for sweat samples with determination coefficients ( R ) > 0.992. Low detection limits (LODs) in the range of 1.8  μ g/L, 5.1  μ g/L, and 5.8  μ g/L for urine, saliva, and sweat samples, respectively, and good repeatability (CV < 3%, n = 3) were obtained. The proposed method has been successfully applied to the analysis of human biological samples.

Biological tracer method

DOEpatents

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

1998-01-01

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

Biological tracer method

DOEpatents

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

1998-09-15

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

ESDA®-Lite collection of DNA from latent fingerprints on documents.

PubMed

Plaza, Dane T; Mealy, Jamia L; Lane, J Nicholas; Parsons, M Neal; Bathrick, Abigail S; Slack, Donia P

2015-05-01

The ability to detect and non-destructively collect biological samples for DNA processing would benefit the forensic community by preserving the physical integrity of evidentiary items for more thorough evaluations by other forensic disciplines. The Electrostatic Detection Apparatus (ESDA®) was systemically evaluated for its ability to non-destructively collect DNA from latent fingerprints deposited on various paper substrates for short tandem repeat (STR) DNA profiling. Fingerprints were deposited on a variety of paper substrates that included resume paper, cotton paper, magazine paper, currency, copy paper, and newspaper. Three DNA collection techniques were performed: ESDA collection, dry swabbing, and substrate cutting. Efficacy of each collection technique was evaluated by the quantity of DNA present in each sample and the percent profile generated by each sample. Both the ESDA and dry swabbing non-destructive sampling techniques outperformed the destructive methodology of substrate cutting. A greater number of full profiles were generated from samples collected with the non-destructive dry swabbing collection technique than were generated from samples collected with the ESDA; however, the ESDA also allowed the user to visualize the area of interest while non-destructively collecting the biological material. The ability to visualize the biological material made sampling straightforward and eliminated the need for numerous, random swabbings/cuttings. Based on these results, the evaluated non-destructive ESDA collection technique has great potential for real-world forensic implementation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Magnetic induction spectroscopy: non-contact measurement of the electrical conductivity spectra of biological samples

NASA Astrophysics Data System (ADS)

Barai, A.; Watson, S.; Griffiths, H.; Patz, R.

2012-08-01

Measurement of the electrical conductivity of biological tissues as a function of frequency, often termed ‘bioelectrical impedance spectroscopy (BIS)’, provides valuable information on tissue structure and composition. In implementing BIS though, there can be significant practical difficulties arising from the electrode-sample interface which have likely limited its deployment in industrial applications. In magnetic induction spectroscopy (MIS) these difficulties are eliminated through the use of fully non-contacting inductive coupling between the sensors and sample. However, inductive coupling introduces its own set of technical difficulties, primarily related to the small magnitudes of the induced currents and their proportionality with frequency. This paper describes the design of a practical MIS system incorporating new, highly-phase-stable electronics and compares its performance with that of electrode-based BIS in measurements on biological samples including yeast suspensions in saline (concentration 50-400 g l-1) and solid samples of potato, cucumber, tomato, banana and porcine liver. The shapes of the MIS spectra were in good agreement with those for electrode-based BIS, with a residual maximum discrepancy of 28%. The measurement precision of the MIS was 0.05 S m-1 at 200 kHz, improving to 0.01 S m-1 at a frequency of 20 MHz, for a sample volume of 80 ml. The data-acquisition time for each MIS measurement was 52 s. Given the value of spectroscopic conductivity information and the many advantages of obtaining these data in a non-contacting manner, even through electrically-insulating packaging materials if necessary, it is concluded that MIS is a technique with considerable potential for monitoring bio-industrial processes and product quality.

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.

Improving the accuracy of effect-directed analysis: the role of bioavailability.

PubMed

You, Jing; Li, Huizhen

2017-12-13

Aquatic ecosystems have been suffering from contamination by multiple stressors. Traditional chemical-based risk assessment usually fails to explain the toxicity contributions from contaminants that are not regularly monitored or that have an unknown identity. Diagnosing the causes of noted adverse outcomes in the environment is of great importance in ecological risk assessment and in this regard effect-directed analysis (EDA) has been designed to fulfill this purpose. The EDA approach is now increasingly used in aquatic risk assessment owing to its specialty in achieving effect-directed nontarget analysis; however, a lack of environmental relevance makes conventional EDA less favorable. In particular, ignoring the bioavailability in EDA may cause a biased and even erroneous identification of causative toxicants in a mixture. Taking bioavailability into consideration is therefore of great importance to improve the accuracy of EDA diagnosis. The present article reviews the current status and applications of EDA practices that incorporate bioavailability. The use of biological samples is the most obvious way to include bioavailability into EDA applications, but its development is limited due to the small sample size and lack of evidence for metabolizable compounds. Bioavailability/bioaccessibility-based extraction (bioaccessibility-directed and partitioning-based extraction) and passive-dosing techniques are recommended to be used to integrate bioavailability into EDA diagnosis in abiotic samples. Lastly, the future perspectives of expanding and standardizing the use of biological samples and bioavailability-based techniques in EDA are discussed.

Clustering of change patterns using Fourier coefficients.

PubMed

Kim, Jaehee; Kim, Haseong

2008-01-15

To understand the behavior of genes, it is important to explore how the patterns of gene expression change over a time period because biologically related gene groups can share the same change patterns. Many clustering algorithms have been proposed to group observation data. However, because of the complexity of the underlying functions there have not been many studies on grouping data based on change patterns. In this study, the problem of finding similar change patterns is induced to clustering with the derivative Fourier coefficients. The sample Fourier coefficients not only provide information about the underlying functions, but also reduce the dimension. In addition, as their limiting distribution is a multivariate normal, a model-based clustering method incorporating statistical properties would be appropriate. This work is aimed at discovering gene groups with similar change patterns that share similar biological properties. We developed a statistical model using derivative Fourier coefficients to identify similar change patterns of gene expression. We used a model-based method to cluster the Fourier series estimation of derivatives. The model-based method is advantageous over other methods in our proposed model because the sample Fourier coefficients asymptotically follow the multivariate normal distribution. Change patterns are automatically estimated with the Fourier representation in our model. Our model was tested in simulations and on real gene data sets. The simulation results showed that the model-based clustering method with the sample Fourier coefficients has a lower clustering error rate than K-means clustering. Even when the number of repeated time points was small, the same results were obtained. We also applied our model to cluster change patterns of yeast cell cycle microarray expression data with alpha-factor synchronization. It showed that, as the method clusters with the probability-neighboring data, the model-based clustering with our proposed model yielded biologically interpretable results. We expect that our proposed Fourier analysis with suitably chosen smoothing parameters could serve as a useful tool in classifying genes and interpreting possible biological change patterns. The R program is available upon the request.

The York Gospels: a 1000-year biological palimpsest

PubMed Central

Fiddyment, Sarah; Vnouček, Jiří; Mattiangeli, Valeria; Speller, Camilla; Binois, Annelise; Carver, Martin; Dand, Catherine; Newfield, Timothy P.; Webb, Christopher C.; Bradley, Daniel G.; Collins, Matthew J.

2017-01-01

Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object. PMID:29134095

Ethical management guidelines for the shanghai disease-based biobank network.

PubMed

Zhu, Shu; Shen, Mingxian; Qiu, Xiangxing; Gan, Rongxing; Hu, Qingli

2015-02-01

The Ethical Management Guidelines for the Shanghai Disease-Based Biobank Network are intended to safeguard the interests of all the participants, to standardize the construction, management, and resource sharing of the Shanghai Disease-based Biobank Network, to promote the development of medical research, and to improve public health and well-being. The guidelines contain seven chapters: General Principles; Informed Consent; Use of Bio-samples from Persons without the Capacity to Consent; Privacy and Confidentiality; Applications of Use of Biological Samples and Data; Intellectual Property and Resource Sharing; and Conflict of Interest.

Spectral and spatial shaping of a laser-produced ion beam for radiation-biology experiments

NASA Astrophysics Data System (ADS)

Pommarel, L.; Vauzour, B.; Mégnin-Chanet, F.; Bayart, E.; Delmas, O.; Goudjil, F.; Nauraye, C.; Letellier, V.; Pouzoulet, F.; Schillaci, F.; Romano, F.; Scuderi, V.; Cirrone, G. A. P.; Deutsch, E.; Flacco, A.; Malka, V.

2017-03-01

The study of radiation biology on laser-based accelerators is most interesting due to the unique irradiation conditions they can produce, in terms of peak current and duration of the irradiation. In this paper we present the implementation of a beam transport system to transport and shape the proton beam generated by laser-target interaction for in vitro irradiation of biological samples. A set of four permanent magnet quadrupoles is used to transport and focus the beam, efficiently shaping the spectrum and providing a large and relatively uniform irradiation surface. Real time, absolutely calibrated, dosimetry is installed on the beam line, to enable shot-to-shot control of dose deposition in the irradiated volume. Preliminary results of cell sample irradiation are presented to validate the robustness of the full system.

Purification of complex samples: Implementation of a modular and reconfigurable droplet-based microfluidic platform with cascaded deterministic lateral displacement separation modules

PubMed Central

Pudda, Catherine; Boizot, François; Verplanck, Nicolas; Revol-Cavalier, Frédéric; Berthier, Jean; Thuaire, Aurélie

2018-01-01

Particle separation in microfluidic devices is a common problematic for sample preparation in biology. Deterministic lateral displacement (DLD) is efficiently implemented as a size-based fractionation technique to separate two populations of particles around a specific size. However, real biological samples contain components of many different sizes and a single DLD separation step is not sufficient to purify these complex samples. When connecting several DLD modules in series, pressure balancing at the DLD outlets of each step becomes critical to ensure an optimal separation efficiency. A generic microfluidic platform is presented in this paper to optimize pressure balancing, when DLD separation is connected either to another DLD module or to a different microfluidic function. This is made possible by generating droplets at T-junctions connected to the DLD outlets. Droplets act as pressure controllers, which perform at the same time the encapsulation of DLD sorted particles and the balance of output pressures. The optimized pressures to apply on DLD modules and on T-junctions are determined by a general model that ensures the equilibrium of the entire platform. The proposed separation platform is completely modular and reconfigurable since the same predictive model applies to any cascaded DLD modules of the droplet-based cartridge. PMID:29768490

Beyond the proteome: Mass Spectrometry Special Interest Group (MS-SIG) at ISMB/ECCB 2013

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

Ryu, Soyoung; Payne, Samuel H.; Schaab, Christoph

2014-07-02

Mass spectrometry special interest group (MS-SIG) aims to bring together experts from the global research community to discuss highlights and challenges in the field of mass spectrometry (MS)-based proteomics and computational biology. The rapid echnological developments in MS-based proteomics have enabled the generation of a large amount of meaningful information on hundreds to thousands of proteins simultaneously from a biological sample; however, the complexity of the MS data require sophisticated computational algorithms and software for data analysis and interpretation. This year’s MS-SIG meeting theme was ‘Beyond the Proteome’ with major focuses on improving protein identification/quantification and using proteomics data tomore » solve interesting problems in systems biology and clinical research.« less

Making a protein extract from plant pathogenic fungi for gel- and LC-based proteomics.

PubMed

Fernández, Raquel González; Redondo, Inmaculada; Jorrin-Novo, Jesus V

2014-01-01

Proteomic technologies have become a successful tool to provide relevant information on fungal biology. In the case of plant pathogenic fungi, this approach would allow a deeper knowledge of the interaction and the biological cycle of the pathogen, as well as the identification of pathogenicity and virulence factors. These two elements open up new possibilities for crop disease diagnosis and environment-friendly crop protection. Phytopathogenic fungi, due to its particular cellular characteristics, can be considered as a recalcitrant biological material, which makes it difficult to obtain quality protein samples for proteomic analysis. This chapter focuses on protein extraction for gel- and LC-based proteomics with specific protocols of our current research with Botrytis cinerea.

Development of garlic bioactive compounds analytical methodology based on liquid phase microextraction using response surface design. Implications for dual analysis: Cooked and biological fluids samples.

PubMed

Ramirez, Daniela Andrea; Locatelli, Daniela Ana; Torres-Palazzolo, Carolina Andrea; Altamirano, Jorgelina Cecilia; Camargo, Alejandra Beatriz

2017-01-15

Organosulphur compounds (OSCs) present in garlic (Allium sativum L.) are responsible of several biological properties. Functional foods researches indicate the importance of quantifying these compounds in food matrices and biological fluids. For this purpose, this paper introduces a novel methodology based on dispersive liquid-liquid microextraction (DLLME) coupled to high performance liquid chromatography with ultraviolet detector (HPLC-UV) for the extraction and determination of organosulphur compounds in different matrices. The target analytes were allicin, (E)- and (Z)-ajoene, 2-vinyl-4H-1,2-dithiin (2-VD), diallyl sulphide (DAS) and diallyl disulphide (DADS). The microextraction technique was optimized using an experimental design, and the analytical performance was evaluated under optimum conditions. The desirability function presented an optimal value for 600μL of chloroform as extraction solvent using acetonitrile as dispersant. The method proved to be reliable, precise and accurate. It was successfully applied to determine OSCs in cooked garlic samples as well as blood plasma and digestive fluids. Copyright © 2016 Elsevier Ltd. All rights reserved.

Detection of stiff nanoparticles within cellular structures by contact resonance atomic force microscopy subsurface nanomechanical imaging.

PubMed

Reggente, Melania; Passeri, Daniele; Angeloni, Livia; Scaramuzzo, Francesca Anna; Barteri, Mario; De Angelis, Francesca; Persiconi, Irene; De Stefano, Maria Egle; Rossi, Marco

2017-05-04

Detecting stiff nanoparticles buried in soft biological matrices by atomic force microscopy (AFM) based techniques represents a new frontier in the field of scanning probe microscopies, originally developed as surface characterization methods. Here we report the detection of stiff (magnetic) nanoparticles (NPs) internalized in cells by using contact resonance AFM (CR-AFM) employed as a potentially non-destructive subsurface characterization tool. Magnetite (Fe 3 O 4 ) NPs were internalized in microglial cells from cerebral cortices of mouse embryos of 18 days by phagocytosis. Nanomechanical imaging of cells was performed by detecting the contact resonance frequencies (CRFs) of an AFM cantilever held in contact with the sample. Agglomerates of NPs internalized in cells were visualized on the basis of the local increase in the contact stiffness with respect to the surrounding biological matrix. A second AFM-based technique for nanomechanical imaging, i.e., HarmoniX™, as well as magnetic force microscopy and light microscopy were used to confirm the CR-AFM results. Thus, CR-AFM was demonstrated as a promising technique for subsurface imaging of nanomaterials in biological samples.

Secondary Ion Mass Spectrometers (SIMS) for calcium isotope measurements as an application to biological samples

NASA Astrophysics Data System (ADS)

Craven, S. M.; Hoenigman, J. R.; Moddeman, W. E.

1981-11-01

The potential use of secondary ion mass spectroscopy (SIMS) to analyze biological samples for calcium isotopes is discussed. Comparison of UTI and Extranuclear based quadrupole systems is made on the basis of the analysis of CaO and calcium metal. The Extranuclear quadrupole based system is superior in resolution and sensitivity to the UTI system and is recommended. For determination of calcium isotopes to within an accuracy of a few percent a high resolution quadrupole, such as the Extranuclear, and signal averaging capability are required. Charge neutralization will be mandated for calcium oxide, calcium nitrate, or calcium oxalate. SIMS is not capable of the high precision and high accuracy results possible by thermal ionization methods, but where faster analysis is desirable with an accuracy of a few percent, SIMS is a viable alternative.

Biology Procedural Knowledge at Eleventh Grade of Senior High School in West Lampung Based on Curriculum

NASA Astrophysics Data System (ADS)

Sari, T. M.; Paidi; Mercuriani, I. S.

2018-03-01

This study was aim to determine Biology procedural knowledge of senior high school in West Lampung based on curriculum at 11th grade in even semester. This research was descriptive research. The population was all students of senior high school in West Lampung. The sampling technique in this research used purposive sampling technique, so the researcher obtained 3 schools using K13 and 3 schools using KTSP. Data collecting technique used instrument test. Data analysis technique used U-Mann Whitney test. The result showed that p=0.028 (p<0.05), so there was significant differences between school using K13 and KTSP. The procedural knowledge of schools which using K13 is higher than school which using KTSP, with the mean score K13=4.35 and KTSP=4.00

Functional networks inference from rule-based machine learning models.

PubMed

Lazzarini, Nicola; Widera, Paweł; Williamson, Stuart; Heer, Rakesh; Krasnogor, Natalio; Bacardit, Jaume

2016-01-01

Functional networks play an important role in the analysis of biological processes and systems. The inference of these networks from high-throughput (-omics) data is an area of intense research. So far, the similarity-based inference paradigm (e.g. gene co-expression) has been the most popular approach. It assumes a functional relationship between genes which are expressed at similar levels across different samples. An alternative to this paradigm is the inference of relationships from the structure of machine learning models. These models are able to capture complex relationships between variables, that often are different/complementary to the similarity-based methods. We propose a protocol to infer functional networks from machine learning models, called FuNeL. It assumes, that genes used together within a rule-based machine learning model to classify the samples, might also be functionally related at a biological level. The protocol is first tested on synthetic datasets and then evaluated on a test suite of 8 real-world datasets related to human cancer. The networks inferred from the real-world data are compared against gene co-expression networks of equal size, generated with 3 different methods. The comparison is performed from two different points of view. We analyse the enriched biological terms in the set of network nodes and the relationships between known disease-associated genes in a context of the network topology. The comparison confirms both the biological relevance and the complementary character of the knowledge captured by the FuNeL networks in relation to similarity-based methods and demonstrates its potential to identify known disease associations as core elements of the network. Finally, using a prostate cancer dataset as a case study, we confirm that the biological knowledge captured by our method is relevant to the disease and consistent with the specialised literature and with an independent dataset not used in the inference process. The implementation of our network inference protocol is available at: http://ico2s.org/software/funel.html.

Preservation of Liquid Biological Samples

NASA Technical Reports Server (NTRS)

Putcha, Lakshmi (Inventor); Nimmagudda, Ramalingeshwara R. (Inventor)

2000-01-01

The present invention provides a method of preserving a liquid biological sample, comprising the step of: contacting said liquid biological sample with a preservative comprising, sodium benzoate in an amount of at least about 0.15% of the sample (weight/volume) and citric acid in an amount of at least about 0.025% of the sample (weight/volume).

A Novel Hydrogel-Based Biosampling Approach

DTIC Science & Technology

2016-03-01

MONITORING AGENCY NAME(S) AND ADDRESS(ES) U.S. Army Edgewood Chemical Biological Center Seedling Program, APG, MD 21010-5424 10. SPONSOR/MONITOR’S...Std. Z39.18 ii Blank   iii PREFACE The work described in this report was authorized under the U.S. Army Edgewood Chemical Biological...a complex area of intensive, ongoing research. After a biorelease event, sampling is at the core of all pre- and post- decontamination analyses

A robust high resolution reversed-phase HPLC strategy to investigate various metabolic species in different biological models.

PubMed

D'Alessandro, Angelo; Gevi, Federica; Zolla, Lello

2011-04-01

Recent advancements in the field of omics sciences have paved the way for further expansion of metabolomics. Originally tied to NMR spectroscopy, metabolomic disciplines are constantly and growingly involving HPLC and mass spectrometry (MS)-based analytical strategies and, in this context, we hereby propose a robust and efficient extraction protocol for metabolites from four different biological sources which are subsequently analysed, identified and quantified through high resolution reversed-phase fast HPLC and mass spectrometry. To this end, we demonstrate the elevated intra- and inter-day technical reproducibility, ease of an MRM-based MS method, allowing simultaneous detection of up to 10 distinct features, and robustness of multiple metabolite detection and quantification in four different biological samples. This strategy might become routinely applicable to various samples/biological matrices, especially for low-availability ones. In parallel, we compare the present strategy for targeted detection of a representative metabolite, L-glutamic acid, with our previously-proposed chemical-derivatization through dansyl chloride. A direct comparison of the present method against spectrophotometric assays is proposed as well. An application of the proposed method is also introduced, using the SAOS-2 cell line, either induced or non-induced to express the TAp63 isoform of the p63 gene, as a model for determination of variations of glutamate concentrations.

Importance of Data Management in a Long-term Biological Monitoring Program

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

Christensen, Sigurd W; Brandt, Craig C; McCracken, Kitty

2011-01-01

The long-term Biological Monitoring and Abatement Program (BMAP) has always needed to collect and retain high-quality data on which to base its assessments of ecological status of streams and their recovery after remediation. Its formal quality assurance, data processing, and data management components all contribute to this need. The Quality Assurance Program comprehensively addresses requirements from various institutions, funders, and regulators, and includes a data management component. Centralized data management began a few years into the program. An existing relational database was adapted and extended to handle biological data. Data modeling enabled the program's database to process, store, and retrievemore » its data. The data base's main data tables and several key reference tables are described. One of the most important related activities supporting long-term analyses was the establishing of standards for sampling site names, taxonomic identification, flagging, and other components. There are limitations. Some types of program data were not easily accommodated in the central systems, and many possible data-sharing and integration options are not easily accessible to investigators. The implemented relational database supports the transmittal of data to the Oak Ridge Environmental Information System (OREIS) as the permanent repository. From our experience we offer data management advice to other biologically oriented long-term environmental sampling and analysis programs.« less

Cumulative assessment of steroid receptor mediated activity of contaminants in water samples using in vitro bioassays. -EMGS

EPA Science Inventory

Cell-based in vitro assays show promise for water quality monitoring applications due to high sensitivity, the ability to quantitatively detect a biologically relevant effect endpoint such as receptor transactivation (i.e., effect-based monitoring), and the ability to assess comp...

Evaluation of Sampling Methods for Bacillus Spore ...

EPA Pesticide Factsheets

Journal Article Following a wide area release of biological materials, mapping the extent of contamination is essential for orderly response and decontamination operations. HVAC filters process large volumes of air and therefore collect highly representative particulate samples in buildings. HVAC filter extraction may have great utility in rapidly estimating the extent of building contamination following a large-scale incident. However, until now, no studies have been conducted comparing the two most appropriate sampling approaches for HVAC filter materials: direct extraction and vacuum-based sampling.

Banking biological collections: data warehousing, data mining, and data dilemmas in genomics and global health policy.

PubMed

Blatt, R J R

2000-01-01

While DNA databases may offer the opportunity to (1) assess population-based prevalence of specific genes and variants, (2) simplify the search for molecular markers, (3) improve targeted drug discovery and development for disease management, (4) refine strategies for disease prevention, and (5) provide the data necessary for evidence-based decision-making, serious scientific and social questions remain. Whether samples are identified, coded, or anonymous, biological banking raises profound ethical and legal issues pertaining to access, informed consent, privacy and confidentiality of genomic information, civil liberties, patenting, and proprietary rights. This paper provides an overview of key policy issues and questions pertaining to biological banking, with a focus on developments in specimen collection, transnational distribution, and public health and academic-industry research alliances. It highlights the challenges posed by the commercialization of genomics, and proposes the need for harmonization of biological banking policies.

Biological sample collector

DOEpatents

Murphy, Gloria A [French Camp, CA

2010-09-07

A biological sample collector is adapted to a collect several biological samples in a plurality of filter wells. A biological sample collector may comprise a manifold plate for mounting a filter plate thereon, the filter plate having a plurality of filter wells therein; a hollow slider for engaging and positioning a tube that slides therethrough; and a slide case within which the hollow slider travels to allow the tube to be aligned with a selected filter well of the plurality of filter wells, wherein when the tube is aligned with the selected filter well, the tube is pushed through the hollow slider and into the selected filter well to sealingly engage the selected filter well and to allow the tube to deposit a biological sample onto a filter in the bottom of the selected filter well. The biological sample collector may be portable.

Optical-fiber-based Mueller optical coherence tomography.

PubMed

Jiao, Shuliang; Yu, Wurong; Stoica, George; Wang, Lihong V

2003-07-15

An optical-fiber-based multichannel polarization-sensitive Mueller optical coherence tomography (OCT) system was built to acquire the Jones or Mueller matrix of a scattering medium, such as biological tissue. For the first time to our knowledge, fiber-based polarization-sensitive OCT was dynamically calibrated to eliminate the polarization distortion caused by the single-mode optical fiber in the sample arm, thereby overcoming a key technical impediment to the application of optical fibers in this technology. The round-trip Jones matrix of the sampling fiber was acquired from the reflecting surface of the sample for each depth scan (A scan) with our OCT system. A new rigorous algorithm was then used to retrieve the calibrated polarization properties of the sample. This algorithm was validated with experimental data. The skin of a rat was imaged with this fiber-based system.

Reproducibility, stability, and biological variability of thrombin generation using calibrated automated thrombography in healthy dogs.

PubMed

Cuq, Benoît; Blois, Shauna L; Wood, R Darren; Monteith, Gabrielle; Abrams-Ogg, Anthony C; Bédard, Christian; Wood, Geoffrey A

2018-06-01

Thrombin plays a central role in hemostasis and thrombosis. Calibrated automated thrombography (CAT), a thrombin generation assay, may be a useful test for hemostatic disorders in dogs. To describe CAT results in a group of healthy dogs, and assess preanalytical variables and biological variability. Forty healthy dogs were enrolled. Lag time (Lag), time to peak (ttpeak), peak thrombin generation (peak), and endogenous thrombin potential (ETP) were measured. Direct jugular venipuncture and winged-needle catheter-assisted saphenous venipuncture were used to collect samples from each dog, and results were compared between methods. Sample stability at -80°C was assessed over 12 months in a subset of samples. Biological variability of CAT was assessed via nested ANOVA using samples obtained weekly from a subset of 9 dogs for 4 consecutive weeks. Samples for CAT were stable at -80°C over 12 months of storage. Samples collected via winged-needle catheter venipuncture showed poor repeatability compared to direct venipuncture samples; there was also poor agreement between the 2 sampling methods. Intra-individual variability of CAT parameters was below 25%; inter-individual variability ranged from 36.9% to 78.5%. Measurement of thrombin generation using CAT appears to be repeatable in healthy dogs, and samples are stable for at least 12 months when stored at -80°C. Direct venipuncture sampling is recommended for CAT. Low indices of individuality suggest that subject-based reference intervals are more suitable when interpreting CAT results. © 2018 American Society for Veterinary Clinical Pathology.

Water-Quality and Biological Assessment of the Iowa River and Tributaries Within and Contiguous to the Meskwaki Settlement of the Sac and Fox Tribe of the Mississippi in Iowa, 2006-07

USGS Publications Warehouse

Littin, Gregory R.; McVay, Jason C.

2009-01-01

In cooperation with the Sac and Fox Tribe of the Mississippi in Iowa (Meskwaki Nation), the U.S. Geological Survey conducted a 2-year baseline assessment of the chemical and biological quality of streams within the Meskwaki Settlement in central Iowa. The Meskwaki Nation is a federally recognized tribe that wishes to establish water-quality standards to safeguard the integrity of surface waters and aquatic biota within the settlement for the health and welfare of the tribal community. The settlement is drained by the Iowa River and four tributaries (Onion, Cattail, Raven, and Bennett Creeks). Water-quality samples were collected at three sites on the Iowa River, two sites on Onion Creek, and one site each on Cattail, Raven, and Bennett Creeks from April 2006 through July 2007. Biological and habitat assessments were conducted at all three sites on the Iowa River and the downstream-most site on Onion Creek from June through August 2007. Analysis of physical properties, major ions, nutrients, trace compounds, bacteria, and total suspended solids in water, and trace metals and organic compounds in streambed sediment provided information about the effects of anthropogenic (human related) activities on the water quality of settlement streams. Analysis of biological samples collected during the summer of 2007, including fish community, benthic macroinvertebrates, and periphyton samples, as well as physical habitat characteristics, provided information on the effects of water quality on the condition of the aquatic environment. The majority of surface water sampled within the settlement was predominately a calcium bicarbonate type. Nitrates (nitrate plus nitrite as nitrogen) exceeded the U.S. Environmental Protection Agency's (USEPA) primary drinking-water Maximum Contaminant Level of 10 ug/L in 19 of 36 samples from sites on the Iowa River and Raven and Bennett Creeks but not in samples from Onion and Cattail Creeks. None of the samples analyzed for pesticides, trace metals, wastewater, or fuel contaminants were found to exceed drinking-water regulations for the USEPA or State of Iowa targeted constituents. Bacteria densities for Escherichia coli (E. coli) ranged from less than 10 to more than 600,000 colony-forming units per 100 milliliters of water and were largest following intense rainfall runoff. The largest densities were recorded in samples collected from the tributaries, most notably from Cattail Creek downstream from the tribal headquarters area and Onion Creek downstream from the sewage lagoons. Arsenic and nickel concentrations in bottom sediment from Onion Creek exceeded the USEPA threshold effects level in a composite sample collected during the habitat assessment in July 2007. Suspended-sediment concentration was estimated in terms of total suspended solids. Overall, Onion and Bennett Creeks were the least turbid, whereas the ephemeral Cattail Creek had the most turbid samples. Aquatic-community data were collected at four sites on the Meskwaki Settlement during the summer of 2007 to provide a baseline biological assessment of stream conditions. This assessment was based on sampling of the fish, benthic macroinvertebrate, and periphyton communities along with physical habitat characteristics. Individual biological metrics were derived from the data collected during the community surveys. These metrics were used to calculate Indexes of Biological Integrity (IBIs). The calculated values from the IBIs provided a numerical value that was used to provide an assessment of the biological condition at each biological sampling site. The fish community samples indicated that all of the sampling sites would be considered in fair condition, with one exception being a collection site on the Iowa River at Highway 49 near Tama, Iowa, which was classified in poor condition. The benthic macroinvertebrate IBI indicated a classification of good for three of the four biological sampling sites, with the Iowa River near Montour, Iowa,

Biological response in vitro of skeletal muscle cells treated with different intensity continuous and pulsed ultrasound fields

NASA Astrophysics Data System (ADS)

Abrunhosa, Viviane M.; Mermelstein, Claudia S.; Costa, Manoel L.; Costa-Felix, Rodrigo P. B.

2011-02-01

Therapeutic ultrasound has been used in physiotherapy to accelerate tissue healing. Although the ultrasonic wave is widely used in clinical practice, not much is known about the biological effects of ultrasound on cells and tissues. This study aims to evaluate the biological response of ultrasound in primary cultures of chick myogenic cells. To ensure the metrological reliability of whole measurement process, the ultrasound equipment was calibrated in accordance with IEC 61689:2007. The skeletal muscle cells were divided in four samples. One sample was used as a control group and the others were submitted to different time and intensity and operation mode of ultrasound: 1) 0.5 W/cm2 continuous for 5 minutes, 2) 0.5 W/cm2 pulsed for 5 minutes, 3) 1.0 W/cm2 pulsed for 10 minutes. The samples were analyzed with phase contrast optical microscopy before and after the treatment. The results showed alignment of myogenic cells in the sample treated with 0.5 W/cm2 continuous during 5 minutes when compared with the control group and the other samples. This study is a first step towards a metrological and scientific based protocol to cells and tissues treatment under different ultrasound field exposures.

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

PubMed

Gil, F; Hernández, A F

2015-06-01

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

Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

PubMed

Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

2012-03-05

Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

Human metabolic profiles are stably controlled by genetic and environmental variation

PubMed Central

Nicholson, George; Rantalainen, Mattias; Maher, Anthony D; Li, Jia V; Malmodin, Daniel; Ahmadi, Kourosh R; Faber, Johan H; Hallgrímsdóttir, Ingileif B; Barrett, Amy; Toft, Henrik; Krestyaninova, Maria; Viksna, Juris; Neogi, Sudeshna Guha; Dumas, Marc-Emmanuel; Sarkans, Ugis; The MolPAGE Consortium; Silverman, Bernard W; Donnelly, Peter; Nicholson, Jeremy K; Allen, Maxine; Zondervan, Krina T; Lindon, John C; Spector, Tim D; McCarthy, Mark I; Holmes, Elaine; Baunsgaard, Dorrit; Holmes, Chris C

2011-01-01

1H Nuclear Magnetic Resonance spectroscopy (1H NMR) is increasingly used to measure metabolite concentrations in sets of biological samples for top-down systems biology and molecular epidemiology. For such purposes, knowledge of the sources of human variation in metabolite concentrations is valuable, but currently sparse. We conducted and analysed a study to create such a resource. In our unique design, identical and non-identical twin pairs donated plasma and urine samples longitudinally. We acquired 1H NMR spectra on the samples, and statistically decomposed variation in metabolite concentration into familial (genetic and common-environmental), individual-environmental, and longitudinally unstable components. We estimate that stable variation, comprising familial and individual-environmental factors, accounts on average for 60% (plasma) and 47% (urine) of biological variation in 1H NMR-detectable metabolite concentrations. Clinically predictive metabolic variation is likely nested within this stable component, so our results have implications for the effective design of biomarker-discovery studies. We provide a power-calculation method which reveals that sample sizes of a few thousand should offer sufficient statistical precision to detect 1H NMR-based biomarkers quantifying predisposition to disease. PMID:21878913

SAMURAI: Polar AUV-Based Autonomous Dexterous Sampling

NASA Astrophysics Data System (ADS)

Akin, D. L.; Roberts, B. J.; Smith, W.; Roderick, S.; Reves-Sohn, R.; Singh, H.

2006-12-01

While autonomous undersea vehicles are increasingly being used for surveying and mapping missions, as of yet there has been little concerted effort to create a system capable of performing physical sampling or other manipulation of the local environment. This type of activity has typically been performed under teleoperated control from ROVs, which provides high-bandwidth real-time human direction of the manipulation activities. Manipulation from an AUV will require a completely autonomous sampling system, which implies both advanced technologies such as machine vision and autonomous target designation, but also dexterous robot manipulators to perform the actual sampling without human intervention. As part of the NASA Astrobiology Science and Technology for Exploring the Planets (ASTEP) program, the University of Maryland Space Systems Laboratory has been adapting and extending robotics technologies developed for spacecraft assembly and maintenance to the problem of autonomous sampling of biologicals and soil samples around hydrothermal vents. The Sub-polar ice Advanced Manipulator for Universal Sampling and Autonomous Intervention (SAMURAI) system is comprised of a 6000-meter capable six-degree-of-freedom dexterous manipulator, along with an autonomous vision system, multi-level control system, and sampling end effectors and storage mechanisms to allow collection of samples from vent fields. SAMURAI will be integrated onto the Woods Hole Oceanographic Institute (WHOI) Jaguar AUV, and used in Arctic during the fall of 2007 for autonomous vent field sampling on the Gakkel Ridge. Under the current operations concept, the JAGUAR and PUMA AUVs will survey the water column and localize on hydrothermal vents. Early mapping missions will create photomosaics of the vents and local surroundings, allowing scientists on the mission to designate desirable sampling targets. Based on physical characteristics such as size, shape, and coloration, the targets will be loaded into the SAMURAI control system, and JAGUAR (with SAMURAI mounted to the lower forward hull) will return to the designated target areas. Once on site, vehicle control will be turned over to the SAMURAI controller, which will perform vision-based guidance to the sampling site and will then ground the AUV to the sea bottom for stability. The SAMURAI manipulator will collect samples, such as sessile biologicals, geological samples, and (potentially) vent fluids, and store the samples for the return trip. After several hours of sampling operations on one or several sites, JAGUAR control will be returned to the WHOI onboard controller for the return to the support ship. (Operational details of AUV operations on the Gakkel Ridge mission are presented in other papers at this conference.) Between sorties, SAMURAI end effectors can be changed out on the surface for specific targets, such as push cores or larger biologicals such as tube worms. In addition to the obvious challenges in autonomous vision-based manipulator control from a free-flying support vehicle, significant development challenges have been the design of a highly capable robotic arm within the mass limitations (both wet and dry) of the JAGUAR vehicle, the development of a highly robust manipulator with modular maintenance units for extended polar operations, and the creation of a robot-based sample collection and holding system for multiple heterogeneous samples on a single extended sortie.

Local reconstruction in computed tomography of diffraction enhanced imaging

NASA Astrophysics Data System (ADS)

Huang, Zhi-Feng; Zhang, Li; Kang, Ke-Jun; Chen, Zhi-Qiang; Zhu, Pei-Ping; Yuan, Qing-Xi; Huang, Wan-Xia

2007-07-01

Computed tomography of diffraction enhanced imaging (DEI-CT) based on synchrotron radiation source has extremely high sensitivity of weakly absorbing low-Z samples in medical and biological fields. The authors propose a modified backprojection filtration(BPF)-type algorithm based on PI-line segments to reconstruct region of interest from truncated refraction-angle projection data in DEI-CT. The distribution of refractive index decrement in the sample can be directly estimated from its reconstruction images, which has been proved by experiments at the Beijing Synchrotron Radiation Facility. The algorithm paves the way for local reconstruction of large-size samples by the use of DEI-CT with small field of view based on synchrotron radiation source.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

Ensuring Sample Quality for Biomarker Discovery Studies - Use of ICT Tools to Trace Biosample Life-cycle.

PubMed

Riondino, Silvia; Ferroni, Patrizia; Spila, Antonella; Alessandroni, Jhessica; D'Alessandro, Roberta; Formica, Vincenzo; Della-Morte, David; Palmirotta, Raffaele; Nanni, Umberto; Roselli, Mario; Guadagni, Fiorella

2015-01-01

The growing demand of personalized medicine marked the transition from an empirical medicine to a molecular one, aimed at predicting safer and more effective medical treatment for every patient, while minimizing adverse effects. This passage has emphasized the importance of biomarker discovery studies, and has led sample availability to assume a crucial role in biomedical research. Accordingly, a great interest in Biological Bank science has grown concomitantly. In biobanks, biological material and its accompanying data are collected, handled and stored in accordance with standard operating procedures (SOPs) and existing legislation. Sample quality is ensured by adherence to SOPs and sample whole life-cycle can be recorded by innovative tracking systems employing information technology (IT) tools for monitoring storage conditions and characterization of vast amount of data. All the above will ensure proper sample exchangeability among research facilities and will represent the starting point of all future personalized medicine-based clinical trials. Copyright© 2015, International Institute of Anticancer Research (Dr. John G. Delinasios), All rights reserved.

Identifying Ant-Mirid Spatial Interactions to Improve Biological Control in Cacao-Based Agroforestry System.

PubMed

Bagny Beilhe, Leïla; Piou, Cyril; Tadu, Zéphirin; Babin, Régis

2018-06-06

The use of ants for biological control of insect pests was the first reported case of conservation biological control. Direct and indirect community interactions between ants and pests lead to differential spatial pattern. We investigated spatial interactions between mirids, the major cocoa pest in West Africa and numerically dominant ant species, using bivariate point pattern analysis to identify potential biological control agents. We assume that potential biological control agents should display negative spatial interactions with mirids considering their niche overlap. The mirid/ant data were collected in complex cacao-based agroforestry systems sampled in three agroecological areas over a forest-savannah gradient in Cameroon. Three species, Crematogaster striatula Emery (Hymenoptera: Formicidae), Crematogaster clariventris Mayr (Hymenoptera: Formicidae), and Oecophylla longinoda Latreille (Hymenoptera: Formicidae) with high predator and aggressive behaviors were identified as dominant and showed negative spatial relationships with mirids. The weaver ant, O. longinoda was identified as the only potential biological control agent, considering its ubiquity in the plots, the similarity in niche requirements, and the spatial segregation with mirids resulting probably from exclusion mechanisms. Combining bivariate point pattern analysis to good knowledge of insect ecology was an effective method to identify a potentially good biological control agent.

Indices of polarimetric purity for biological tissues inspection

NASA Astrophysics Data System (ADS)

Van Eeckhout, Albert; Lizana, Angel; Garcia-Caurel, Enric; Gil, José J.; Sansa, Adrià; Rodríguez, Carla; Estévez, Irene; González, Emilio; Escalera, Juan C.; Moreno, Ignacio; Campos, Juan

2018-02-01

We highlight the interest of using the Indices of Polarimetric Purity (IPPs) for the biological tissue inspection. These are three polarimetric metrics focused on the study of the depolarizing behaviour of the sample. The IPPs have been recently proposed in the literature and provide different and synthetized information than the commonly used depolarizing indices, as depolarization index (PΔ) or depolarization power (Δ). Compared with the standard polarimetric images of biological samples, IPPs enhance the contrast between different tissues of the sample and show differences between similar tissues which are not observed using the other standard techniques. Moreover, they present further physical information related to the depolarization mechanisms inherent to different tissues. In addition, the algorithm does not require advanced calculations (as in the case of polar decompositions), being the indices of polarimetric purity fast and easy to implement. We also propose a pseudo-coloured image method which encodes the sample information as a function of the different indices weights. These images allow us to customize the visualization of samples and to highlight certain of their constitutive structures. The interest and potential of the IPP approach are experimentally illustrated throughout the manuscript by comparing polarimetric images of different ex-vivo samples obtained with standard polarimetric methods with those obtained from the IPPs analysis. Enhanced contrast and retrieval of new information are experimentally obtained from the different IPP based images.

Biology Factual Knowledge at Eleventh Grade of Senior High School Students in Pacitan based on Favorite Schools

NASA Astrophysics Data System (ADS)

Yustiana, I. A.; Paidi; Mercuriani, I. S.

2018-03-01

This study aimed to determine the Biology factual knowledge at eleventh grade of senior high school students in Pacitan based on favorite schools. This research was a descriptive research by using survey method. The population in this study was all of senior high school students in Pacitan. The sampling technique used purposive sampling technique and obtained 3 favorite schools and 3 non-favorite schools. The technique of collecting data used test form which was as the instrument of the research. Data analysis technique used Mann-Whitney U test. Based on the test, it was obtained p = 0,000 (p <0,05) so there was a significant difference between the factual knowledge of the students in the favorite schools and non-favorite schools in Pacitan. The factual knowledge of students in favorite schools was higher with an average of 5.32 while non-favorite schools were obtained an average of 4.36.

Knockdown of stem cell regulator Oct4A in ovarian cancer reveals cellular reprogramming associated with key regulators of cytoskeleton-extracellular matrix remodelling

PubMed Central

Samardzija, Chantel; Greening, David W.; Escalona, Ruth; Chen, Maoshan; Bilandzic, Maree; Luwor, Rodney; Kannourakis, George; Findlay, Jock K.; Ahmed, Nuzhat

2017-01-01

Oct4A is a master regulator of self-renewal and pluripotency in embryonic stem cells. It is a well-established marker for cancer stem cell (CSC) in malignancies. Recently, using a loss of function studies, we have demonstrated key roles for Oct4A in tumor cell survival, metastasis and chemoresistance in in vitro and in vivo models of ovarian cancer. In an effort to understand the regulatory role of Oct4A in tumor biology, we employed the use of an ovarian cancer shRNA Oct4A knockdown cell line (HEY Oct4A KD) and a global mass spectrometry (MS)-based proteomic analysis to investigate novel biological targets of Oct4A in HEY samples (cell lysates, secretomes and mouse tumor xenografts). Based on significant differential expression, pathway and protein network analyses, and comprehensive literature search we identified key proteins involved with biologically relevant functions of Oct4A in tumor biology. Across all preparations of HEY Oct4A KD samples significant alterations in protein networks associated with cytoskeleton, extracellular matrix (ECM), proliferation, adhesion, metabolism, epithelial-mesenchymal transition (EMT), cancer stem cells (CSCs) and drug resistance was observed. This comprehensive proteomics study for the first time presents the Oct4A associated proteome and expands our understanding on the biological role of this stem cell regulator in carcinomas. PMID:28406185

Imaging Cellular Architecture with X-rays

PubMed Central

Larabell, Carolyn A.; Nugent, Keith A.

2012-01-01

X-ray imaging of biological samples is progressing rapidly. In this paper we review the progress to date in high resolution imaging of cellular architecture. In particular we survey the progress in soft X-ray tomography and argue that the field is coming of age and that important biological insights are starting to emerge. We then review the new ideas based on coherent diffraction. These methods are at a much earlier stage of development but, as they eliminate the need for X-ray optics, have the capacity to provide substantially better spatial resolution than zone plate based methods. PMID:20869868

Testing Silica Fume-Based Concrete Composites under Chemical and Microbiological Sulfate Attacks

PubMed Central

Estokova, Adriana; Kovalcikova, Martina; Luptakova, Alena; Prascakova, Maria

2016-01-01

Current design practices based on descriptive approaches to concrete specification may not be appropriate for the management of aggressive environments. In this study, the durability of cement-based materials with and without the addition of silica fume, subjected to conditions that leach calcium and silicon, were investigated. Chemical corrosion was simulated by employing various H2SO4 and MgSO4 solutions, and biological corrosion was simulated using Acidithiobacillus sp. bacterial inoculation, leading to disrupted and damaged surfaces; the samples’ mass changes were studied following both chemical and biological attacks. Different leaching trends were observed via X-ray fluorescence when comparing chemical with biological leaching. Lower leaching rates were found for concrete samples fortified with silica fume than those without silica fume. X-ray diffraction and scanning electron microscopy confirmed a massive sulfate precipitate formation on the concrete surface due to bacterial exposure. PMID:28773452

Designed Strategies for Fluorescence-Based Biosensors for the Detection of Mycotoxins

PubMed Central

Sharma, Atul; Khan, Reem; Catanante, Gaelle; Sherazi, Tauqir A.; Bhand, Sunil; Hayat, Akhtar; Marty, Jean Louis

2018-01-01

Small molecule toxins such as mycotoxins with low molecular weight are the most widely studied biological toxins. These biological toxins are responsible for food poisoning and have the potential to be used as biological warfare agents at the toxic dose. Due to the poisonous nature of mycotoxins, effective analysis techniques for quantifying their toxicity are indispensable. In this context, biosensors have been emerged as a powerful tool to monitors toxins at extremely low level. Recently, biosensors based on fluorescence detection have attained special interest with the incorporation of nanomaterials. This review paper will focus on the development of fluorescence-based biosensors for mycotoxin detection, with particular emphasis on their design as well as properties such as sensitivity and specificity. A number of these fluorescent biosensors have shown promising results in food samples for the detection of mycotoxins, suggesting their future potential for food applications. PMID:29751687

Designed Strategies for Fluorescence-Based Biosensors for the Detection of Mycotoxins.

PubMed

Sharma, Atul; Khan, Reem; Catanante, Gaelle; Sherazi, Tauqir A; Bhand, Sunil; Hayat, Akhtar; Marty, Jean Louis

2018-05-11

Small molecule toxins such as mycotoxins with low molecular weight are the most widely studied biological toxins. These biological toxins are responsible for food poisoning and have the potential to be used as biological warfare agents at the toxic dose. Due to the poisonous nature of mycotoxins, effective analysis techniques for quantifying their toxicity are indispensable. In this context, biosensors have been emerged as a powerful tool to monitors toxins at extremely low level. Recently, biosensors based on fluorescence detection have attained special interest with the incorporation of nanomaterials. This review paper will focus on the development of fluorescence-based biosensors for mycotoxin detection, with particular emphasis on their design as well as properties such as sensitivity and specificity. A number of these fluorescent biosensors have shown promising results in food samples for the detection of mycotoxins, suggesting their future potential for food applications.

Analysis of host response to bacterial infection using error model based gene expression microarray experiments

PubMed Central

Stekel, Dov J.; Sarti, Donatella; Trevino, Victor; Zhang, Lihong; Salmon, Mike; Buckley, Chris D.; Stevens, Mark; Pallen, Mark J.; Penn, Charles; Falciani, Francesco

2005-01-01

A key step in the analysis of microarray data is the selection of genes that are differentially expressed. Ideally, such experiments should be properly replicated in order to infer both technical and biological variability, and the data should be subjected to rigorous hypothesis tests to identify the differentially expressed genes. However, in microarray experiments involving the analysis of very large numbers of biological samples, replication is not always practical. Therefore, there is a need for a method to select differentially expressed genes in a rational way from insufficiently replicated data. In this paper, we describe a simple method that uses bootstrapping to generate an error model from a replicated pilot study that can be used to identify differentially expressed genes in subsequent large-scale studies on the same platform, but in which there may be no replicated arrays. The method builds a stratified error model that includes array-to-array variability, feature-to-feature variability and the dependence of error on signal intensity. We apply this model to the characterization of the host response in a model of bacterial infection of human intestinal epithelial cells. We demonstrate the effectiveness of error model based microarray experiments and propose this as a general strategy for a microarray-based screening of large collections of biological samples. PMID:15800204

Community-based wastewater treatment systems and water quality of an Indonesian village.

PubMed

Lim, H S; Lee, L Y; Bramono, S E

2014-03-01

This paper examines the impact of community-based water treatment systems on water quality in a peri-urban village in Yogyakarta, Indonesia. Water samples were taken from the wastewater treatment plants (WWTPs), irrigation canals, paddy fields and wells during the dry and wet seasons. The samples were tested for biological and chemical oxygen demand, nutrients (ammonia, nitrate, total nitrogen and total phosphorus) and Escherichia coli. Water quality in this village is affected by the presence of active septic tanks, WWTP effluent discharge, small-scale tempe industries and external sources. We found that the WWTPs remove oxygen-demanding wastes effectively but discharged nutrients, such as nitrate and ammonia, into irrigation canals. Irrigation canals had high levels of E. coli as well as oxygen-demanding wastes. Well samples had high E. coli, nitrate and total nitrogen levels. Rainfall tended to increase concentrations of biological and chemical oxygen demand and some nutrients. All our samples fell within the drinking water standards for nitrate but failed the international and Indonesian standards for E. coli. Water quality in this village can be improved by improving the WWTP treatment of nutrients, encouraging more villagers to be connected to WWTPs and controlling hotspot contamination areas in the village.

Saccharose solid matrix embedded proteins: a new method for sample preparation for X-ray absorption spectroscopy.

PubMed

Ascone, I; Sabatucci, A; Bubacco, L; Di Muro, P; Salvato, B

2000-01-01

In this study, solid samples of hemoglobin and hemocyanin have been prepared by embedding the proteins into a saccharose-based matrix. These materials have been developed specifically for specimens for X-ray absorption spectroscopy (XAS). The preservation of protein conformation and active site organization was tested, making comparisons between the solid and the corresponding liquid samples, using resonance Raman, infra red, fluorescence and XAS. The XAS spectra of irradiated solid and liquid samples were then compared, and the preservation of biological activity of the proteins during both preparation procedure and X-ray irradiation was assessed. In all cases, the measurements clearly demonstrate that protein solid samples are both structurally and functionally quite well preserved, much better than those in the liquid state. The saccharose matrix provides an excellent protection against X-ray damages, allowing for longer exposure to the X-ray beam. Moreover, the demonstrated long-term stability of samples permits their preparation and storage in optimal conditions, allowing for the repetition of data collection with the same sample in several experimental sessions. The very high protein concentration that can be reached results in a significantly better signal-to-noise ratio, particularly useful for high molecular weight proteins with a low metal-to-protein ratio. On the bases of the above-mentioned results, we propose the new method as a standard procedure for the preparation of biological samples to be used for XAS spectroscopy.

Biological method to quantify progressive stages of decay in five commercial woods by Coriolus versicolor.

PubMed

Olfat, A M; Karimi, A N; Parsapajouh, D

2007-04-01

Biologic agar-block method was developed that allowed wood samples to be evaluated and monitored in terms of colonization and development of the decay by Basidiomycetes fungi (Coriolus versicolor) and to be directly classified based on mean mass loss. In this research, the in vitro decay of five commercial woods by Coriolus versicolor was studied by the agar-block method. The selected wood samples were Abies alba, Populus alba, Fagus orientalis, Platanus orientalis and Ulmus glabra. The results demonstrated the strong resistance of Ulmus glabra and the lowest resistance in Fagus orientalis. The mass losses (%) were 16.8 and 42.4%, respectively. There were also a high correlation between the mass loss and apparent damage. Therefore biological evaluation of wood regarding biodegradation and the selection of wood types for various application respects will be of high priority.

Optical sensor for heat conduction measurement in biological tissue

NASA Astrophysics Data System (ADS)

Gutierrez-Arroyo, A.; Sanchez-Perez, C.; Aleman-Garcia, N.

2013-06-01

This paper presents the design of a heat flux sensor using an optical fiber system to measure heat conduction in biological tissues. This optoelectronic device is based on the photothermal beam deflection of a laser beam travelling in an acrylic slab this deflection is measured with a fiber optic angle sensor. We measure heat conduction in biological samples with high repeatability and sensitivity enough to detect differences in tissues from three chicken organs. This technique could provide important information of vital organ function as well as the detect modifications due to degenerative diseases or physical damage caused by medications or therapies.

Highly sensitive dendrimer-based nanoplasmonic biosensor for drug allergy diagnosis.

PubMed

Soler, Maria; Mesa-Antunez, Pablo; Estevez, M-Carmen; Ruiz-Sanchez, Antonio Jesus; Otte, Marinus A; Sepulveda, Borja; Collado, Daniel; Mayorga, Cristobalina; Torres, Maria Jose; Perez-Inestrosa, Ezequiel; Lechuga, Laura M

2015-04-15

A label-free biosensing strategy for amoxicillin (AX) allergy diagnosis based on the combination of novel dendrimer-based conjugates and a recently developed nanoplasmonic sensor technology is reported. Gold nanodisks were functionalized with a custom-designed thiol-ending-polyamido-based dendron (d-BAPAD) peripherally decorated with amoxicilloyl (AXO) groups (d-BAPAD-AXO) in order to detect specific IgE generated in patient's serum against this antibiotic during an allergy outbreak. This innovative strategy, which follows a simple one-step immobilization procedure, shows exceptional results in terms of sensitivity and robustness, leading to a highly-reproducible and long-term stable surface which allows achieving extremely low limits of detection. Moreover, the viability of this biosensor approach to analyze human biological samples has been demonstrated by directly analyzing and quantifying specific anti-AX antibodies in patient's serum without any sample pretreatment. An excellent limit of detection (LoD) of 0.6ng/mL (i.e. 0.25kU/L) has been achieved in the evaluation of clinical samples evidencing the potential of our nanoplasmonic biosensor as an advanced diagnostic tool to quickly identify allergic patients. The results have been compared and validated with a conventional clinical immunofluorescence assay (ImmunoCAP test), confirming an excellent correlation between both techniques. The combination of a novel compact nanoplasmonic platform and a dendrimer-based strategy provides a highly sensitive label free biosensor approach with over two times better detectability than conventional SPR. Both the biosensor device and the carrier structure hold great potential in clinical diagnosis for biomarker analysis in whole serum samples and other human biological samples. Copyright © 2014 Elsevier B.V. All rights reserved.

An in vitro approach for lipolysis measurement using high-resolution mass spectrometry and partial least squares based analysis.

PubMed

Chang, Wen-Qi; Zhou, Jian-Liang; Li, Yi; Shi, Zi-Qi; Wang, Li; Yang, Jie; Li, Ping; Liu, Li-Fang; Xin, Gui-Zhong

2017-01-15

The elevation of free fatty acids (FFAs) has been regarded as a universal metabolic signature of excessive adipocyte lipolysis. Nowadays, in vitro lipolysis assay is generally essential for drug screening prior to the animal study. Here, we present a novel in vitro approach for lipolysis measurement combining UHPLC-Orbitrap and partial least squares (PLS) based analysis. Firstly, the calibration matrix was constructed by serial proportions of mixed samples (blended with control and model samples). Then, lipidome profiling was performed by UHPLC-Orbitrap, and 403 variables were extracted and aligned as dataset. Owing to the high resolution of Orbitrap analyzer and open source lipid identification software, 28 FFAs were further screened and identified. Based on the relative intensity of the screened FFAs, PLS regression model was constructed for lipolysis measurement. After leave-one-out cross-validation, ten principal components have been designated to build the final PLS model with excellent performances (RMSECV, 0.0268; RMSEC, 0.0173; R 2 , 0.9977). In addition, the high predictive accuracy (R 2  = 0.9907 and RMSEP = 0.0345) of the trained PLS model was also demonstrated using test samples. Finally, taking curcumin as a model compound, its antilipolytic effect on palmitic acid-induced lipolysis was successfully predicted as 31.78% by the proposed approach. Besides, supplementary evidences of curcumin induced modification in FFAs compositions as well as lipidome were given by PLS extended methods. Different from general biological assays, high resolution MS-based method provide more sophisticated information included in biological events. Thus, the novel biological evaluation model proposed here showed promising perspectives for drug evaluation or disease diagnosis. Copyright © 2016 Elsevier B.V. All rights reserved.

DNA-based approach to aging martens (Martes americana and M. caurina)

Treesearch

Jonathan N. Pauli; John P. Whiteman; Bruce G. Marcot; Terry M. McClean; Merav Ben-David

2011-01-01

Demographic structure is central to understanding the dynamics of animal populations. However, determining the age of free-ranging mammals is difficult, and currently impossible when sampling with noninvasive, genetic-based approaches. We present a method to estimate age class by combining measures of telomere lengths with other biologically meaningful covariates in a...

Pathway-based personalized analysis of cancer

PubMed Central

Drier, Yotam; Sheffer, Michal; Domany, Eytan

2013-01-01

We introduce Pathifier, an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample. We demonstrate the algorithm’s performance on three colorectal cancer datasets and two glioblastoma multiforme datasets and show that our multipathway-based representation is reproducible, preserves much of the original information, and allows inference of complex biologically significant information. We discovered several pathways that were significantly associated with survival of glioblastoma patients and two whose scores are predictive of survival in colorectal cancer: CXCR3-mediated signaling and oxidative phosphorylation. We also identified a subclass of proneural and neural glioblastoma with significantly better survival, and an EGF receptor-deregulated subclass of colon cancers. PMID:23547110

Differentiation of five body fluids from forensic samples by expression analysis of four microRNAs using quantitative PCR.

PubMed

Sauer, Eva; Reinke, Ann-Kathrin; Courts, Cornelius

2016-05-01

Applying molecular genetic approaches for the identification of forensically relevant body fluids, which often yield crucial information for the reconstruction of a potential crime, is a current topic of forensic research. Due to their body fluid specific expression patterns and stability against degradation, microRNAs (miRNA) emerged as a promising molecular species, with a range of candidate markers published. The analysis of miRNA via quantitative Real-Time PCR, however, should be based on a relevant strategy of normalization of non-biological variances to deliver reliable and biologically meaningful results. The herein presented work is the as yet most comprehensive study of forensic body fluid identification via miRNA expression analysis based on a thoroughly validated qPCR procedure and unbiased statistical decision making to identify single source samples. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Chemical and biological threat-agent detection using electrophoresis-based lab-on-a-chip devices.

PubMed

Borowsky, Joseph; Collins, Greg E

2007-10-01

The ability to separate complex mixtures of analytes has made capillary electrophoresis (CE) a powerful analytical tool since its modern configuration was first introduced over 25 years ago. The technique found new utility with its application to the microfluidics based lab-on-a-chip platform (i.e., microchip), which resulted in ever smaller footprints, sample volumes, and analysis times. These features, coupled with the technique's potential for portability, have prompted recent interest in the development of novel analyzers for chemical and biological threat agents. This article will comment on three main areas of microchip CE as applied to the separation and detection of threat agents: detection techniques and their corresponding limits of detection, sampling protocol and preparation time, and system portability. These three areas typify the broad utility of lab-on-a-chip for meeting critical, present-day security, in addition to illustrating areas wherein advances are necessary.

Secondary ion mass spectrometers (SIMS) for calcium isotope measurements as an application to biological samples

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

Craven, S.M.; Hoenigman, J.R.; Moddeman, W.E.

1981-11-20

The potential use of secondary ion mass spectroscopy (SIMS) to analyze biological samples for calcium isotopes is discussed. Comparison of UTI and Extranuclear based quadrupole systems is made on the basis of the analysis of CaO and calcium metal. The Extranuclear quadrupole based system is superior in resolution and sensitivity to the UTI system and is recommended. For determination of calcium isotopes to within an accuracy of a few percent a high resolution quadrupole, such as the Extranuclear, and signal averaging capability are required. Charge neutralization will be mandated for calcium oxide, calcium nitrate, or calcium oxalate. SIMS is notmore » capable of the high precision and high accuracy results possible by thermal ionization methods, but where faster analysis is desirable with an accuracy of a few percent, SIMS is a viable alternative.« less

Mesoscale Eddies Are Oases for Higher Trophic Marine Life

PubMed Central

Godø, Olav R.; Samuelsen, Annette; Macaulay, Gavin J.; Patel, Ruben; Hjøllo, Solfrid Sætre; Horne, John; Kaartvedt, Stein; Johannessen, Johnny A.

2012-01-01

Mesoscale eddies stimulate biological production in the ocean, but knowledge of energy transfers to higher trophic levels within eddies remains fragmented and not quantified. Increasing the knowledge base is constrained by the inability of traditional sampling methods to adequately sample biological processes at the spatio-temporal scales at which they occur. By combining satellite and acoustic observations over spatial scales of 10 s of km horizontally and 100 s of m vertically, supported by hydrographical and biological sampling we show that anticyclonic eddies shape distribution and density of marine life from the surface to bathyal depths. Fish feed along density structures of eddies, demonstrating that eddies catalyze energy transfer across trophic levels. Eddies create attractive pelagic habitats, analogous to oases in the desert, for higher trophic level aquatic organisms through enhanced 3-D motion that accumulates and redistributes biomass, contributing to overall bioproduction in the ocean. Integrating multidisciplinary observation methodologies promoted a new understanding of biophysical interaction in mesoscale eddies. Our findings emphasize the impact of eddies on the patchiness of biomass in the sea and demonstrate that they provide rich feeding habitat for higher trophic marine life. PMID:22272294

Wavelet data processing of micro-Raman spectra of biological samples

NASA Astrophysics Data System (ADS)

Camerlingo, C.; Zenone, F.; Gaeta, G. M.; Riccio, R.; Lepore, M.

2006-02-01

A wavelet multi-component decomposition algorithm is proposed for processing data from micro-Raman spectroscopy (μ-RS) of biological tissue. The μ-RS has been recently recognized as a promising tool for the biopsy test and in vivo diagnosis of degenerative human tissue pathologies, due to the high chemical and structural information contents of this spectroscopic technique. However, measurements of biological tissues are usually hampered by typically low-level signals and by the presence of noise and background components caused by light diffusion or fluorescence processes. In order to overcome these problems, a numerical method based on discrete wavelet transform is used for the analysis of data from μ-RS measurements performed in vitro on animal (pig and chicken) tissue samples and, in a preliminary form, on human skin and oral tissue biopsy from normal subjects. Visible light μ-RS was performed using a He-Ne laser and a monochromator with a liquid nitrogen cooled charge coupled device equipped with a grating of 1800 grooves mm-1. The validity of the proposed data procedure has been tested on the well-characterized Raman spectra of reference acetylsalicylic acid samples.

Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.

PubMed

Ling, Zhi-Qiang; Wang, Yi; Mukaisho, Kenichi; Hattori, Takanori; Tatsuta, Takeshi; Ge, Ming-Hua; Jin, Li; Mao, Wei-Min; Sugihara, Hiroyuki

2010-06-01

Tests of differentially expressed genes (DEGs) from microarray experiments are based on the null hypothesis that genes that are irrelevant to the phenotype/stimulus are expressed equally in the target and control samples. However, this strict hypothesis is not always true, as there can be several transcriptomic background differences between target and control samples, including different cell/tissue types, different cell cycle stages and different biological donors. These differences lead to increased false positives, which have little biological/medical significance. In this article, we propose a statistical framework to identify DEGs between target and control samples from expression microarray data allowing transcriptomic background differences between these samples by introducing a modified null hypothesis that the gene expression background difference is normally distributed. We use an iterative procedure to perform robust estimation of the null hypothesis and identify DEGs as outliers. We evaluated our method using our own triplicate microarray experiment, followed by validations with reverse transcription-polymerase chain reaction (RT-PCR) and on the MicroArray Quality Control dataset. The evaluations suggest that our technique (i) results in less false positive and false negative results, as measured by the degree of agreement with RT-PCR of the same samples, (ii) can be applied to different microarray platforms and results in better reproducibility as measured by the degree of DEG identification concordance both intra- and inter-platforms and (iii) can be applied efficiently with only a few microarray replicates. Based on these evaluations, we propose that this method not only identifies more reliable and biologically/medically significant DEG, but also reduces the power-cost tradeoff problem in the microarray field. Source code and binaries freely available for download at http://comonca.org.cn/fdca/resources/softwares/deg.zip.

Cellular respiration: replicating in vivo systems biology for in ...

EPA Pesticide Factsheets

This editorial develops a philosophy for expanding the scope of Journal of Breath Research (JBR) into the realm of cellular level study, and links certain topics back to more traditional systemic research for understanding human health based on exhaled breath constituents. The express purpose is to provide a publication outlet for novel breath related research that includes in vitro studies, especially those that explore the biological origin and expression of compounds that may ultimately influence the constituents of exhaled breath. The new topics include all manner of methods and instrumentations for making in vivo and in vitro measurements, the use of different biological media (blood, urine saliva, swabs) including human and microbial cell-lines, in vitro kinetic studies of metabolism, and advances in ex vivo methods for maintaining metabolic competency and viability of biological samples. Traditionally, JBR has published articles on human breath analysis for diagnosing disease, tracking health state, assessing the dose and effect of exogenous chemicals, and contributions of malodorous compounds from the oral/nasal cavity. These have also included research describing novel sampling and analytical technologies, most notably those implementing mass spectrometry, chemical sensors and optical measurement instrumentation (Amann and Smith 2013). The journal’s original scope has also embraced animal models as surrogates for human sampling, new mathematical and

Preparation and characterization of magnetic nanocomposite of Schiff base/silica/magnetite as a preconcentration phase for the trace determination of heavy metal ions in water, food and biological samples using atomic absorption spectrometry.

PubMed

Bagheri, Hasan; Afkhami, Abbas; Saber-Tehrani, Mohammad; Khoshsafar, Hosein

2012-08-15

A versatile and robust solid phase with both magnetic property and a very high adsorption capacity is presented on the basis of modification of iron oxide-silica magnetic particles with a newly synthesized Schiff base (Fe(3)O(4)/SiO(2)/L). The structure of the resulting product was confirmed by Fourier transform infrared (FT-IR) spectra, X-ray diffraction (XRD) spectrometry and transmission electron microscopy (TEM). We developed an efficient and cost-effective method for the preconcentration of trace amounts of Pb(II), Cd(II) and Cu(II) in environmental and biological samples using this novel magnetic solid phase. Prepared magnetic solid phase is an ideal support because it has a large surface area, good selectivity and can be easily retrieved from large volumes of aqueous solutions. The possible parameters affecting the enrichment were optimized. Under the optimal conditions, the method detection limit was 0.14, 0.19 and 0.12 μg L(-1) for Pb(II), Cd(II) and Cu(II) ions, respectively. The established method has been successfully applied to analyze real samples, and satisfactory results were obtained. All these indicated that this magnetic phase had a great potential in environmental and biological fields. Copyright © 2012 Elsevier B.V. All rights reserved.

Simultaneous measurement of NAD metabolome in aged mice tissue using liquid chromatography tandem-mass spectrometry.

PubMed

Yaku, Keisuke; Okabe, Keisuke; Nakagawa, Takashi

2018-06-01

Nicotinamide adenine dinucleotide (NAD) is a major co-factor that mediates multiple biological processes including redox reaction and gene expression. Recently, NAD metabolism has received considerable attention because administration of NAD precursors exhibited beneficial effects against aging-related metabolic disorders in animals. Although numerous studies have reported that NAD levels decline with aging in multiple animal tissues, the pathway and kinetics of NAD metabolism in aged organs are not completely understood. To determine the NAD metabolism upon aging, we developed targeted metabolomics based on an LC/MS/MS system. Our method is simple and applicable to crude biological samples, including culture cells and animal tissues. Unlike a conventional enzymatic cycling assay, our approach can determine NAD and NADH (reduced form of NAD) by performing a single sample preparation. Further, we validated our method using biological samples and investigated the alteration of the NAD metabolome during aging. Consistent with previous reports, the NAD levels in the liver and skeletal muscle decreased with aging. Further, we detected a significant increase in nicotinamide mononucleotide and nicotinamide riboside in the kidney upon aging. The LC/MS/MS-based NAD metabolomics that we have developed is extensively applicable to biomedical studies, and the results will present innovative ideas for the aging studies, especially for that of NAD metabolism. Copyright © 2018 John Wiley & Sons, Ltd.

Head space solid phase microextraction based on nano-structured lead dioxide: application to the speciation of volatile organoselenium in environmental and biological samples.

PubMed

Ghasemi, Ensieh; Farahani, Hadi

2012-10-05

A novel and efficient speciation method based on the nano-structured lead dioxide as stationary phase of head space solid phase microextraction combined with gas chromatography mass spectrometry (GC-MS) was developed for the determination of volatile organoselenium compounds (dimethylselenide (DMSe) and dimethyldiselenide (DMDSe)) in different biological and environmental samples. PbO(2) particles with a diameter in the range of 50-70 nm have been grown on platinum wire via elechtrochemical deposition. The effect of different variables on the extraction efficiency was studied simultaneously using an experimental design. The variables of interest in the HS-SPME were condition of coating preparation, desorption time, stirring rate, desorption temperature, ionic strength, time and temperature of extraction. A Plackett-Burman design was performed for screening in order to determine the significant variables affecting the extraction efficiency. Then, the significant factors were optimized by a Box-Behnken design (BBD) and the response surface equations were derived. The detection limit and relative standard deviation (RSD) (n=5, c=50 μgL(-1)) for DMSe were 16 ngL(-1) and 4.3%, respectively. They were also obtained for DMDSe as 11ngL(-1) and 4.6%, respectively. The developed technique was found to be applicable to spiked environmental and biological samples. Copyright © 2012 Elsevier B.V. All rights reserved.

Electrochemistry and analytical determination of lysergic acid diethylamide (LSD) via adsorptive stripping voltammetry.

PubMed

Merli, Daniele; Zamboni, Daniele; Protti, Stefano; Pesavento, Maria; Profumo, Antonella

2014-12-01

Lysergic acid diethylamide (LSD) is hardly detectable and quantifiable in biological samples because of its low active dose. Although several analytical tests are available, routine analysis of this drug is rarely performed. In this article, we report a simple and accurate method for the determination of LSD, based on adsorptive stripping voltammetry in DMF/tetrabutylammonium perchlorate, with a linear range of 1-90 ng L(-1) for deposition times of 50s. LOD of 1.4 ng L(-1) and LOQ of 4.3 ng L(-1) were found. The method can be also applied to biological samples after a simple extraction with 1-chlorobutane. Copyright © 2014 Elsevier B.V. All rights reserved.

On the Applications of IBA Techniques to Biological Samples Analysis: PIXE and RBS

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

Falcon-Gonzalez, J. M.; Bernal-Alvarado, J.; Sosa, M.

2008-08-11

The analytical techniques based on ion beams or IBA techniques give quantitative information on elemental concentration in samples of a wide variety of nature. In this work, we focus on PIXE technique, analyzing thick target biological specimens (TTPIXE), using 3 MeV protons produced by an electrostatic accelerator. A nuclear microprobe was used performing PIXE and RBS simultaneously, in order to solve the uncertainties produced in the absolute PIXE quantifying. The advantages of using both techniques and a nuclear microprobe are discussed. Quantitative results are shown to illustrate the multielemental resolution of the PIXE technique; for this, a blood standard wasmore » used.« less

In Situ Biological Treatment Test at Kelly Air Force Base. Volume 3. Appendices.

DTIC Science & Technology

1987-07-01

175 B-12 Results of Groundwater Acidity Monitoring. . . . . . . . 176 B-13 Results of Groundwater Alkalinity Monitoring . . . . . . 177 B- 14 ...Oichloroethylene 499 Vinyl chloride 850 1.2-cis dichloroethylene Pam jupe Table A-I. Results of 5/23/85 Groundwater Sampling (Continued) 14 aqualab inc. 9909...Sample No. : 08/134621 Matrix: NATURAL WATER Parameter Result Units CC SPECIAL SCAN 1400 ug/L Client I.D.: 14 ERG Sample No.: 08/134622 Matrix

Comparing conventional Descriptive Analysis and Napping®-UFP against physiochemical measurements: a case study using apples.

PubMed

Pickup, William; Bremer, Phil; Peng, Mei

2018-03-01

The extensive time and cost associated with conventional sensory profiling methods has spurred sensory researchers to develop rapid method alternatives, such as Napping® with Ultra-Flash Profiling (UFP). Napping®-UFP generates sensory maps by requiring untrained panellists to separate samples based on perceived sensory similarities. Evaluations of this method have been restrained to manufactured/formulated food models, and predominantly structured on comparisons against the conventional descriptive method. The present study aims to extend the validation of Napping®-UFP (N = 72) to natural biological products; and to evaluate this method against Descriptive Analysis (DA; N = 8) with physiochemical measurements as an additional evaluative criterion. The results revealed that sample configurations generated by DA and Napping®-UFP were not significantly correlated (RV = 0.425, P = 0.077); however, they were both correlated with the product map generated based on the instrumental measures (P < 0.05). The finding also noted that sample characterisations from DA and Napping®-UFP were driven by different sensory attributes, indicating potential structural differences between these two methods in configuring samples. Overall, these findings lent support for the extended use of Napping®-UFP for evaluations of natural biological products. Although DA was shown to be a better method for establishing sensory-instrumental relationships, Napping®-UFP exhibited strengths in generating informative sample configurations based on holistic perception of products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

The effect of pathological processes on absorption and scattering spectra of samples of bile and pancreatic juice

NASA Astrophysics Data System (ADS)

Giraev, K. M.; Ashurbekov, N. A.; Magomedov, M. A.; Murtazaeva, A. A.; Medzhidov, R. T.

2015-07-01

Spectra of optical transmission coefficients and optical reflectance for bile and pancreatic juice samples were measured experimentally for different forms of pathologies of the pancreas within the range of 250-2500 nm. The absorption and scattering spectra, as well as the spectrum of the anisotropy factor of scattering, were determined based on the results obtained using the reverse Monte Carlo method. The surface morphology for the corresponding samples of the biological media was studied employing electron microscopy. The dynamics of the optical properties of the biological media was determined depending on the stage of the pathology. It has been demonstrated that the results of the study presented are in a good agreement with pathophysiological data and could supplement and broaden the results of conventional methods for diagnostics of the pancreas.

Refractive index measurement for biomaterial samples by total internal reflection.

PubMed

Jin, Y L; Chen, J Y; Xu, L; Wang, P N

2006-10-21

The refractive index of biological tissue is a fundamental parameter in applications of optical diagnosis and laser treatments. In the present work, the refractive indices and thermo-optic coefficients of some basic biomaterials, such as blood plasma, haemoglobin solution and lipid membrane, were studied by the method of total internal reflection at the wavelengths of 532 and 632.8 nm that are the most frequently used laser wavelengths in the biomedical field. The effects of the sample concentration and the temperature on refractive index were measured, and empirical relationships were summarized, accompanied by a theoretical explanation based on molecular polarization theory. The results provide some fundamental data for the refractive indices of these biomaterials under variant conditions, and also demonstrate that the total internal reflection method is a feasible and reliable way to measure the refractive indices of biological samples.

Standard biological parts knowledgebase.

PubMed

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Biological assessments of Appalachian streams based on predictive models for fish, macroinvertebrate, and diatom assemblages

USGS Publications Warehouse

Carlisle, D.M.; Hawkins, C.P.; Meador, M.R.; Potapova, M.; Falcone, J.

2008-01-01

We developed empirical models for fish, macroinvertebrate, and diatom assemblages to assess the biological condition of 268 streams sampled from 1993 to 2002 in 7 major river basins in the Appalachian region of the USA. These models estimate the expected taxonomic composition at each site based on observed variation in taxonomic composition at reference sites. The index, O/E, is the ratio of the number of predicted taxa that were observed (O) to that expected (E) to occur at a site and is a measure of taxonomic completeness. We compared how O/E for each assemblage varied among major landuse settings and whether impaired assemblages were associated with particular physicochemical conditions. We also examined concordance among assemblages in their response to stress. Biological, chemical, and physical data were collected following consistent protocols. We used land-cover criteria, published data, and topographic maps to classify sites by major landuse setting. Fish, macroinvertebrate, and diatom assemblages had been sampled at 73, 108, and 52, respectively, of the least disturbed sites used to establish reference conditions. The models accounted for a substantial portion of the natural variation in taxonomic composition across sites that was associated with biogeographic, climatic, and basin-scale factors and generally were unbiased across the range of environmental gradients observed in the region. Assessments at nonreference sites showed that impairment of fish and macroinvertebrate assemblages was most strongly associated with agriculture and urban land uses, whereas impairment of diatom assemblages was most strongly associated with mining in the basin. Concordance in assessments among assemblages was not strong. Assessments based on 2 assemblages differed in 28 to 57% of cases, and assessments were never concordant for cases where all 3 assemblages were sampled. Furthermore, only 1/2 of these cases would have been assessed as ecologically impaired had only 1 assemblage been sampled. Differences between observed and predicted frequencies of occurrence for individual taxa were generally consistent with known tolerances to environmental stressors and might aid in identifying causes of biological impairment. ?? 2008 by The North American Benthological Society.

Subtyping attention-deficit/hyperactivity disorder using temperament dimensions: toward biologically based nosologic criteria.

PubMed

Karalunas, Sarah L; Fair, Damien; Musser, Erica D; Aykes, Kamari; Iyer, Swathi P; Nigg, Joel T

2014-09-01

Psychiatric nosology is limited by behavioral and biological heterogeneity within existing disorder categories. The imprecise nature of current nosologic distinctions limits both mechanistic understanding and clinical prediction. We demonstrate an approach consistent with the National Institute of Mental Health Research Domain Criteria initiative to identify superior, neurobiologically valid subgroups with better predictive capacity than existing psychiatric categories for childhood attention-deficit/hyperactivity disorder (ADHD). To refine subtyping of childhood ADHD by using biologically based behavioral dimensions (i.e., temperament), novel classification algorithms, and multiple external validators. A total of 437 clinically well-characterized, community-recruited children, with and without ADHD, participated in an ongoing longitudinal study. Baseline data were used to classify children into subgroups based on temperament dimensions and examine external validators including physiological and magnetic resonance imaging measures. One-year longitudinal follow-up data are reported for a subgroup of the ADHD sample to address stability and clinical prediction. Parent/guardian ratings of children on a measure of temperament were used as input features in novel community detection analyses to identify subgroups within the sample. Groups were validated using 3 widely accepted external validators: peripheral physiological characteristics (cardiac measures of respiratory sinus arrhythmia and pre-ejection period), central nervous system functioning (via resting-state functional connectivity magnetic resonance imaging), and clinical outcomes (at 1-year longitudinal follow-up). The community detection algorithm suggested 3 novel types of ADHD, labeled as mild (normative emotion regulation), surgent (extreme levels of positive approach-motivation), and irritable (extreme levels of negative emotionality, anger, and poor soothability). Types were independent of existing clinical demarcations including DSM-5 presentations or symptom severity. These types showed stability over time and were distinguished by unique patterns of cardiac physiological response, resting-state functional brain connectivity, and clinical outcomes 1 year later. Results suggest that a biologically informed temperament-based typology, developed with a discovery-based community detection algorithm, provides a superior description of heterogeneity in the ADHD population than does any current clinical nosologic criteria. This demonstration sets the stage for more aggressive attempts at a tractable, biologically based nosology.

DESIGN OF A SIMPLE SLOW COOLING DEVICE FOR CRYOPRESERVATION OF SMALL BIOLOGICAL SAMPLES.

PubMed

de Paz, Leonardo Juan; Robert, Maria Celeste; Graf, Daniel Adolfo; Guibert, Edgardo Elvio; Rodriguez, Joaquin Valentin

2015-01-01

Slow cooling is a cryopreservation methodology where samples are cooled to its storage temperature at controlled cooling rates. Design, construction and evaluation of a simple and low cost device for slow cooling of small biological samples. The device was constructed based on Pye's freezer idea. A Dewar flask filled with liquid nitrogen was used as heat sink and a methanol bath containing the sample was cooled at constant rates using copper bars as heat conductor. Sample temperature may be lowered at controlled cooling rate (ranging from 0.4°C/min to 6.0°C/min) down to ~-60°C, where it could be conserved at lower temperatures. An example involving the cryopreservation of Neuro-2A cell line showed a marked influence of cooling rate over post preservation cell viability with optimal values between 2.6 and 4.6°C/min. The cooling device proved to be a valuable alternative to more expensive systems allowing the assessment of different cooling rates to evaluate the optimal condition for cryopreservation of such samples.

Personal Exposure to Particulate Matter and Endotoxin in California Dairy Workers

NASA Astrophysics Data System (ADS)

Garcia, Johnny

The average number of cows per dairy has increased over the last thirty years, with little known about how this increase may impact occupational exposure. Thirteen California dairies and 226 workers participated in this study throughout the 2008 summer months. Particulate Matter (PM) and endotoxin concentrations were quantified using ambient area based and personal air samplers. Two size fractions were collected, Total Suspended Particulate matter (TSP) and PM 2.5. Differences across dairies were evaluated by placing area based integrated air samplers in established locations on the dairies, e.g. milking parlor, drylot corral, and freestall barns. The workers occupational exposure was quantified using personal air samplers. We analyzed concentrations along with the time workers spent conducting specific job tasks during their shift to identify high exposure job tasks. Biological and chemical analytical methods were employed to ascertain endotoxin concentrations in personal and area based air samples. Recombinant factor C assays (rFC) were used to analyze biologically active endotoxin and gas chromatography coupled with mass spectrometry in tandem (GC-MS/MS) was used to quantify total endotoxin. The PM2.5 concentrations ranged from 2-116 mug/m3 for ambient area concentration and 7-495 mug/m3 for personal concentrations while TSP concentrations ranged from 74-1690 mug/m3 for area ambient concentrations and 191-4950 mug/m3 for personal concentrations. Biologically active endotoxin concentrations in the TSP size fraction from ambient area based samples ranged from 11-2095 EU/m3 and 45-2061 EU/m3 for personal samples. Total endotoxin in the TSP size fraction ranged from 75-10,166 pmol/m3 for area based samples and 34-11,689 pmol/m3 for personal samples. Drylot corrals were found to have higher sample mean concentrations when compared to other locations on the dairies for PM and endotoxin. Re-bedding, of the freestalls, was found to consistently lead to higher personal sample mean concentrations when compared to other tasks performed on dairies for both endotoxin and PM. In mixed effect regression models, regional ambient concentrations of PM 2.5 helped account for variation in PM2.5 concentration outcomes. We found that while upwind and downwind mean concentrations were not significantly different, central mean concentrations were higher than upwind concentration. Variation in TSP levels was largely explained by dairy-level characteristics such as the age of the dairy and number of animals in the drylot corrals and freestall barns. The different locations within the dairy were found to differ in mean concentrations for TSP. Biologically active and total endotoxin concentration variation was explained by meteorological data, wind speed, relative humidity, and dairy waste management practices. Personal exposure levels where found to be higher than area based concentrations for PM and endotoxin. Endotoxin characteristics differed by particle size and location within the dairy. The chain length proportion for endotoxin in the PM 2.5 size fraction was dominated by C12 and C16 in the TSP size fraction.

Why is infant mortality higher in boys than in girls? A new hypothesis based on preconception environment and evidence from a large sample of twins.

PubMed

Pongou, Roland

2013-04-01

Infant mortality is higher in boys than girls in most parts of the world. This has been explained by sex differences in genetic and biological makeup, with boys being biologically weaker and more susceptible to diseases and premature death. At the same time, recent studies have found that numerous preconception or prenatal environmental factors affect the probability of a baby being conceived male or female. I propose that these environmental factors also explain sex differences in mortality. I contribute a new methodology of distinguishing between child biology and preconception environment by comparing male-female differences in mortality across opposite-sex twins, same-sex twins, and all twins. Using a large sample of twins from sub-Saharan Africa, I find that both preconception environment and child biology increase the mortality of male infants, but the effect of biology is substantially smaller than the literature suggests. I also estimate the interacting effects of biology with some intrauterine and external environmental factors, including birth order within a twin pair, social status, and climate. I find that a twin is more likely to be male if he is the firstborn, born to an educated mother, or born in certain climatic conditions. Male firstborns are more likely to survive than female firstborns, but only during the neonatal period. Finally, mortality is not affected by the interactions between biology and climate or between biology and social status.

An integrated approach for identifying priority contaminant in ...

EPA Pesticide Factsheets

Environmental assessment of complex mixtures typically requires integration of chemical and biological measurements. This study demonstrates the use of a combination of instrumental chemical analyses, effects-based monitoring, and bio-effects prediction approaches to help identify potential hazards and priority contaminants in two Great Lakes Areas of Concern (AOCs), the Lower Green Bay/Fox River located near Green Bay, WI, USA and the Milwaukee River Estuary, located near Milwaukee, WI, USA. Fathead minnows were caged at four sites within each AOC (eight sites total). Following 4 d of in situ exposure, tissues and biofluids were sampled and used for targeted biological effects analyses. Additionally, 4 d composite water samples were collected concurrently at each caged fish site and analyzed for 134 analytes as well as evaluated for total estrogenic and androgenic activity using cell-based bioassays. Of the analytes examined, 75 were detected in composite samples from at least one site. Based on multiple analyses, one site in the East River and another site near a paper mill discharge from lower Green Bay/Fox River AOC, were prioritized due to their estrogenic and androgenic acitvity, respectively. The water samples from other sites generally did not exhibit significant estrogenic or androgenic activity, nor was there evidence for endocrine disruption in the fish exposed at these sites as indicated the the lack of alterations in ex vivo steroid production, c

Mixed hemimicelles solid-phase extraction based on sodium dodecyl sulfate (SDS)-coated nano-magnets for the spectrophotometric determination of Fingolomid in biological fluids

NASA Astrophysics Data System (ADS)

Azari, Zhila; Pourbasheer, Eslam; Beheshti, Abolghasem

2016-01-01

In this study, mixed hemimicelles solid-phase extraction (SPE) based on sodium dodecyl sulfate (SDS)-coated nano-magnets Fe3O4 was investigated as a novel method for the separation and determination of Fingolimod (FLM) in water, urine and plasma samples prior to spectrophotometeric determination. Due to the high surface area of these new sorbents and the excellent adsorption capacity after surface modification by SDS, satisfactory extraction recoveries can be produced. The main factors affecting the adsolubilization of analysts, such as pH, surfactant and adsorbent amounts, ionic strength, extraction time and desorption conditions were studied and optimized. Under the selected conditions, FLM has been quantitatively extracted. The accuracy of the method was evaluated by recovery measurements on spiked samples, and good recoveries of 96%, 95% and 88% were observed for water, urine and plasma respectively. Proper linear behaviors over the investigated concentration ranges of 2-26, 2-17 and 2-13 mg/L with good coefficients of determination, 0.998, 0.997 and 0.995 were achieved for water, urine and plasma samples, respectively. To the best of our knowledge, this is the first time that a mixed hemimicelles SPE method based on magnetic separation and nanoparticles has been used as a simple and sensitive method for monitoring of FLM in water and biological samples.

Advancing microwave technology for dehydration processing of biologics.

PubMed

Cellemme, Stephanie L; Van Vorst, Matthew; Paramore, Elisha; Elliott, Gloria D

2013-10-01

Our prior work has shown that microwave processing can be effective as a method for dehydrating cell-based suspensions in preparation for anhydrous storage, yielding homogenous samples with predictable and reproducible drying times. In the current work an optimized microwave-based drying process was developed that expands upon this previous proof-of-concept. Utilization of a commercial microwave (CEM SAM 255, Matthews, NC) enabled continuous drying at variable low power settings. A new turntable was manufactured from Ultra High Molecular Weight Polyethylene (UHMW-PE; Grainger, Lake Forest, IL) to provide for drying of up to 12 samples at a time. The new process enabled rapid and simultaneous drying of multiple samples in containment devices suitable for long-term storage and aseptic rehydration of the sample. To determine sample repeatability and consistency of drying within the microwave cavity, a concentration series of aqueous trehalose solutions were dried for specific intervals and water content assessed using Karl Fischer Titration at the end of each processing period. Samples were dried on Whatman S-14 conjugate release filters (Whatman, Maidestone, UK), a glass fiber membrane used currently in clinical laboratories. The filters were cut to size for use in a 13 mm Swinnex(®) syringe filter holder (Millipore(™), Billerica, MA). Samples of 40 μL volume could be dehydrated to the equilibrium moisture content by continuous processing at 20% with excellent sample-to-sample repeatability. The microwave-assisted procedure enabled high throughput, repeatable drying of multiple samples, in a manner easily adaptable for drying a wide array of biological samples. Depending on the tolerance for sample heating, the drying time can be altered by changing the power level of the microwave unit.

Development of a highly sensitive and specific ELISA method for the determination of l-corydalmine in SD rats with monoclonal antibody.

PubMed

Zhang, Hongwei; Gao, Lan; Shu, Menglin; Liu, Jihua; Yu, Boyang

2018-01-15

l-Corydalmine (l-CDL) is a potent analgesic constituent of the traditional Chinese medicine, Rhizoma Corydalis. However, the pharmacokinetic process and tissue distribution of l-CDL in vivo are still unknown. Therefore, it is necessary to establish a simple and sensitive method to detect l-CDL, which will be helpful to study its distribution and pharmacokinetic process. To determine this compound in biological samples, a monoclonal antibody (mAb) against l-CDL was produced and a fast and highly sensitive indirect competitive enzyme-linked immunosorbent assay (icELISA) was developed in this study. The icELISA was applied to determine l-CDL in biological samples. The limit of detection (LOD) of the method was 0.015 ng/mL with a liner range of 1-1000 ng/mL (R 2  = 0.9912). The intra- and inter-day precision were below 15% and the recoveries were within 80-117%. Finally, the developed immunoassay was successfully applied to the analysis of the distribution of l-CDL in SD rats. In conclusion, the icELISA based on the anti-l-CDL mAb could be considered as a highly sensitive and rapid method for the determination of l-CDL in biological samples. The ELISA approach may provide a valuable tool for the analysis of small molecules in biological samples. Copyright © 2017. Published by Elsevier B.V.

Optical tweezers and surface plasmon resonance combination system based on the high numerical aperture lens

NASA Astrophysics Data System (ADS)

Shan, Xuchen; Zhang, Bei; Lan, Guoqiang; Wang, Yiqiao; Liu, Shugang

2015-11-01

Biology and medicine sample measurement takes an important role in the microscopic optical technology. Optical tweezer has the advantage of accurate capture and non-pollution of the sample. The SPR(surface plasmon resonance) sensor has so many advantages include high sensitivity, fast measurement, less consumption of sample and label-free detection of biological sample that the SPR sensing technique has been used for surface topography, analysis of biochemical and immune, drug screening and environmental monitoring. If they combine, they will play an important role in the biological, chemical and other subjects. The system we propose use the multi-axis cage system, by using the methods of reflection and transmiss ion to improve the space utilization. The SPR system and optical tweezer were builtup and combined in one system. The cage of multi-axis system gives full play to its accuracy, simplicity and flexibility. The size of the system is 20 * 15 * 40 cm3 and thus the sample can be replaced to switch between the optical tweezers system and the SPR system in the small space. It means that we get the refractive index of the sample and control the particle in the same system. In order to control the revolving stage, get the picture and achieve the data stored automatically, we write a LabVIEW procedure. Then according to the data from the back focal plane calculate the refractive index of the sample. By changing the slide we can trap the particle as optical tweezer, which makes us measurement and trap the sample at the same time.

Salting-out assisted liquid-liquid extraction combined with gas chromatography-mass spectrometry for the determination of pyrethroid insecticides in high salinity and biological samples.

PubMed

Niu, Zongliang; Yu, Chunwei; He, Xiaowen; Zhang, Jun; Wen, Yingying

2017-09-05

A salting-out assisted liquid-liquid extraction (SALLE) combined with gas chromatography-mass spectrometry (GC-MS) method was developed for the determination of four pyrethroid insecticides (PYRs) in high salinity and biological samples. Several parameters including sample pH, salting-out solution volume and salting-out solution pH influencing the extraction efficiency were systematically investigated with the aid of orthogonal design. The optimal extraction conditions of SALLE were: 4mL of salting-out solution with pH=4 and the sample pH=3. Under the optimum extraction and determination conditions, good responses for four PYRs were obtained in a range of 5-5000ng/mL, with linear coefficients greater than 0.998. The recoveries of the four PYRs ranged from 74% to 110%, with standard deviations ranging from 1.8% to 9.8%. The limits of detection based on a signal-to-noise ratio of 3 were between 1.5-60.6ng/mL. The method was applied to the determination of PYRs in urine, seawater and wastewater samples with a satisfactory result. The results demonstrated that this SALLE-GC-MS method was successfully applied to determine PYRs in high salinity and biological samples. SALLE avoided the need for the elimination of salinity and protein in the sample matrix, as well as clean-up of the extractant. Most of all, no centrifugation or any special apparatus are required, make this a promising method for rapid sample preparation procedure. Copyright © 2017 Elsevier B.V. All rights reserved.

Standardized Procedures for Use of Nucleic Acid-Based Tools

EPA Science Inventory

Groundwater and soil samples are frequently analyzed using molecular biological tools (MBTs) to detect unique genetic biomarkers associated with Dehalococcoides (Dhc) and other environmentally relevant microorganisms. The results of these analyses are increasingly used b...

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

PubMed

Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

2016-07-01

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Flexible imaging payload for real-time fluorescent biological imaging in parabolic, suborbital and space analog environments

NASA Astrophysics Data System (ADS)

Bamsey, Matthew T.; Paul, Anna-Lisa; Graham, Thomas; Ferl, Robert J.

2014-10-01

Fluorescent imaging offers the ability to monitor biological functions, in this case biological responses to space-related environments. For plants, fluorescent imaging can include general health indicators such as chlorophyll fluorescence as well as specific metabolic indicators such as engineered fluorescent reporters. This paper describes the Flex Imager a fluorescent imaging payload designed for Middeck Locker deployment and now tested on multiple flight and flight-related platforms. The Flex Imager and associated payload elements have been developed with a focus on 'flexibility' allowing for multiple imaging modalities and change-out of individual imaging or control components in the field. The imaging platform is contained within the standard Middeck Locker spaceflight form factor, with components affixed to a baseplate that permits easy rearrangement and fine adjustment of components. The Flex Imager utilizes standard software packages to simplify operation, operator training, and evaluation by flight provider flight test engineers, or by researchers processing the raw data. Images are obtained using a commercial cooled CCD image sensor, with light-emitting diodes for excitation and a suite of filters that allow biological samples to be imaged over wavelength bands of interest. Although baselined for the monitoring of green fluorescent protein and chlorophyll fluorescence from Arabidopsis samples, the Flex Imager payload permits imaging of any biological sample contained within a standard 10 cm by 10 cm square Petri plate. A sample holder was developed to secure sample plates under different flight profiles while permitting sample change-out should crewed operations be possible. In addition to crew-directed imaging, autonomous or telemetric operation of the payload is also a viable operational mode. An infrared camera has also been integrated into the Flex Imager payload to allow concurrent fluorescent and thermal imaging of samples. The Flex Imager has been utilized to assess, in real-time, the response of plants to novel environments including various spaceflight analogs, including several parabolic flight environments as well as hypobaric plant growth chambers. Basic performance results obtained under these operational environments, as well as laboratory-based tests are described. The Flex Imager has also been designed to be compatible with emerging suborbital platforms.

Primary and secondary organics in the tropical Amazonian rainforest aerosols: chiral analysis of 2-methyltetraols.

PubMed

González, N J D; Borg-Karlson, A-K; Artaxo, P; Guenther, A; Krejci, R; Nozière, B; Noone, K

2014-05-01

This work presents the application of a new method to facilitate the distinction between biologically produced (primary) and atmospherically produced (secondary) organic compounds in ambient aerosols based on their chirality. The compounds chosen for this analysis were the stereomers of 2-methyltetraols, (2R,3S)- and (2S,3R)-methylerythritol, (l- and d-form, respectively), and (2S,3S)- and (2R,3R)-methylthreitol (l- and d-form), shown previously to display some enantiomeric excesses in atmospheric aerosols, thus to have at least a partial biological origin. In this work PM10 aerosol fractions were collected in a remote tropical rainforest environment near Manaus, Brazil, between June 2008 and June 2009 and analysed. Both 2-methylerythritol and 2-methylthreitol displayed a net excess of one enantiomer (either the l- or the d-form) in 60 to 72% of these samples. These net enantiomeric excesses corresponded to compounds entirely biological but accounted for only about 5% of the total 2-methyltetrol mass in all the samples. Further analysis showed that, in addition, a large mass of the racemic fractions (equal mixtures of d- and l-forms) was also biological. Estimating the contribution of secondary reactions from the isomeric ratios measured in the samples (=ratios 2-methylthreitol over 2-methylerythritol), the mass fraction of secondary methyltetrols in these samples was estimated to a maximum of 31% and their primary fraction to a minimum of 69%. Such large primary fractions could have been expected in PM10 aerosols, largely influenced by biological emissions, and would now need to be investigated in finer aerosols. This work demonstrates the effectiveness of chiral and isomeric analyses as the first direct tool to assess the primary and secondary fractions of organic aerosols.

First International Symposium on Nonthermal Medical/Biological Treatments using Electromagnetic Fields and Ionized Gases

DTIC Science & Technology

1999-11-30

Natick Soldier Center. Sample products include spaghetti sauce, orange juice and yogurt - based drinks or puddings. Benefits of PEF treatment compared...Kiel, AFRL, Brooks AFB. Pulsed microwave radiation in the 1.25 to 9.35 GHz range was found to affect the growth of bacteria in the presence of certain...being very effective for biological decontamination. A major US company has already a commercial product on sale. An in-depth analysis of

Determination of antitrypsin activity on agar plates: relationship between antitrypsin and biological value of soybean for trout.

PubMed

Sandholm, M; Smith, R R; Shih, J C; Scott, M L

1976-06-01

A new method is described for determination of antitrypsin activity based on inhibition of trypsin solubilization of calcium caseinate in agar plates. The method was applied to analyze soybeans after graded heat treatments for their antitrypsin content. Biological determination of protein and energy values of the soybean samples showed direct correlation of these values with the destruction of antitrypsin as measured by the new method, using rainbow trout.

Denoising of Raman spectroscopy for biological samples based on empirical mode decomposition

NASA Astrophysics Data System (ADS)

León-Bejarano, Fabiola; Ramírez-Elías, Miguel; Mendez, Martin O.; Dorantes-Méndez, Guadalupe; Rodríguez-Aranda, Ma. Del Carmen; Alba, Alfonso

Raman spectroscopy of biological samples presents undesirable noise and fluorescence generated by the biomolecular excitation. The reduction of these types of noise is a fundamental task to obtain the valuable information of the sample under analysis. This paper proposes the application of the empirical mode decomposition (EMD) for noise elimination. EMD is a parameter-free and adaptive signal processing method useful for the analysis of nonstationary signals. EMD performance was compared with the commonly used Vancouver algorithm (VRA) through artificial data (Teflon), synthetic (Vitamin E and paracetamol) and biological (Mouse brain and human nails) Raman spectra. The correlation coefficient (ρ) was used as performance measure. Results on synthetic data showed a better performance of EMD (ρ=0.52) at high noise levels compared with VRA (ρ=0.19). The methods with simulated fluorescence added to artificial material exhibited a similar shape of fluorescence in both cases (ρ=0.95 for VRA and ρ=0.93 for EMD). For synthetic data, Raman spectra of vitamin E were used and the results showed a good performance comparing both methods (ρ=0.95 for EMD and ρ=0.99 for VRA). Finally, in biological data, EMD and VRA displayed a similar behavior (ρ=0.85 for EMD and ρ=0.96 for VRA), but with the advantage that EMD maintains small amplitude Raman peaks. The results suggest that EMD could be an effective method for denoising biological Raman spectra, EMD is able to retain information and correctly eliminates the fluorescence without parameter tuning.

A high-resolution optical imaging system for obtaining the serial transverse section images of biologic tissue

NASA Astrophysics Data System (ADS)

Wu, Li; Zhang, Bin; Wu, Ping; Liu, Qian; Gong, Hui

2007-05-01

A high-resolution optical imaging system was designed and developed to obtain the serial transverse section images of the biologic tissue, such as the mouse brain, in which new knife-edge imaging technology, high-speed and high-sensitive line-scan CCD and linear air bearing stages were adopted and incorporated with an OLYMPUS microscope. The section images on the tip of the knife-edge were synchronously captured by the reflection imaging in the microscope while cutting the biologic tissue. The biologic tissue can be sectioned at interval of 250 nm with the same resolution of the transverse section images obtained in x and y plane. And the cutting job can be automatically finished based on the control program wrote specially in advance, so we save the mass labor of the registration of the vast images data. In addition, by using this system a larger sample can be cut than conventional ultramicrotome so as to avoid the loss of the tissue structure information because of splitting the tissue sample to meet the size request of the ultramicrotome.

RENEB - Running the European Network of biological dosimetry and physical retrospective dosimetry.

PubMed

Kulka, Ulrike; Abend, Michael; Ainsbury, Elizabeth; Badie, Christophe; Barquinero, Joan Francesc; Barrios, Lleonard; Beinke, Christina; Bortolin, Emanuela; Cucu, Alexandra; De Amicis, Andrea; Domínguez, Inmaculada; Fattibene, Paola; Frøvig, Anne Marie; Gregoire, Eric; Guogyte, Kamile; Hadjidekova, Valeria; Jaworska, Alicja; Kriehuber, Ralf; Lindholm, Carita; Lloyd, David; Lumniczky, Katalin; Lyng, Fiona; Meschini, Roberta; Mörtl, Simone; Della Monaca, Sara; Monteiro Gil, Octávia; Montoro, Alegria; Moquet, Jayne; Moreno, Mercedes; Oestreicher, Ursula; Palitti, Fabrizio; Pantelias, Gabriel; Patrono, Clarice; Piqueret-Stephan, Laure; Port, Matthias; Prieto, María Jesus; Quintens, Roel; Ricoul, Michelle; Romm, Horst; Roy, Laurence; Sáfrány, Géza; Sabatier, Laure; Sebastià, Natividad; Sommer, Sylwester; Terzoudi, Georgia; Testa, Antonella; Thierens, Hubert; Turai, Istvan; Trompier, François; Valente, Marco; Vaz, Pedro; Voisin, Philippe; Vral, Anne; Woda, Clemens; Zafiropoulos, Demetre; Wojcik, Andrzej

2017-01-01

A European network was initiated in 2012 by 23 partners from 16 European countries with the aim to significantly increase individualized dose reconstruction in case of large-scale radiological emergency scenarios. The network was built on three complementary pillars: (1) an operational basis with seven biological and physical dosimetric assays in ready-to-use mode, (2) a basis for education, training and quality assurance, and (3) a basis for further network development regarding new techniques and members. Techniques for individual dose estimation based on biological samples and/or inert personalized devices as mobile phones or smart phones were optimized to support rapid categorization of many potential victims according to the received dose to the blood or personal devices. Communication and cross-border collaboration were also standardized. To assure long-term sustainability of the network, cooperation with national and international emergency preparedness organizations was initiated and links to radiation protection and research platforms have been developed. A legal framework, based on a Memorandum of Understanding, was established and signed by 27 organizations by the end of 2015. RENEB is a European Network of biological and physical-retrospective dosimetry, with the capacity and capability to perform large-scale rapid individualized dose estimation. Specialized to handle large numbers of samples, RENEB is able to contribute to radiological emergency preparedness and wider large-scale research projects.

Out-of-School Experience Categories Influencing Interest in Science of Upper Primary Students by Gender and Locale: Exploration on an Indian Sample

ERIC Educational Resources Information Center

Gafoor, K. Abdul; Narayan, Smitha

2012-01-01

In view of student shift away from science at advanced levels, and gender and locale based divergence in interest in studying physics, chemistry and biology, this study explores experience categories that significantly contribute to interest in science on a sample of upper primary school students from Kerala, India. A series of multiple regression…

Identification of Forensic Samples via Mitochondrial DNA in the Undergraduate Biochemistry Laboratory

NASA Astrophysics Data System (ADS)

Millard, Julie T.; Pilon, André M.

2003-04-01

A recent forensic approach for identification of unknown biological samples is mitochondrial DNA (mtDNA) sequencing. We describe a laboratory exercise suitable for an undergraduate biochemistry course in which the polymerase chain reaction is used to amplify a 440 base pair hypervariable region of human mtDNA from a variety of "crime scene" samples (e.g., teeth, hair, nails, cigarettes, envelope flaps, toothbrushes, and chewing gum). Amplification is verified via agarose gel electrophoresis and then samples are subjected to cycle sequencing. Sequence alignments are made via the program CLUSTAL W, allowing students to compare samples and solve the "crime."

A high-throughput microRNA expression profiling system.

PubMed

Guo, Yanwen; Mastriano, Stephen; Lu, Jun

2014-01-01

As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.

Determination of curcumin in biologically active supplements and food spices using a mesofluidic platform with fluorescence detection.

PubMed

Petrova, Anastasiia; Dar'in, Dmitriy; Ivanov, Aleхander; Moskvin, Leonid; Ishimatsu, Ryoichi; Nakano, Koji; Imato, Toshihiko; Bulatov, Andrey

2016-10-01

A mesofluidic platform (MP) with fluorescence detection based on a stepwise injection analysis (SWIA) was used for the determination of curcumin in biologically active supplements and food spices. The main units of the MP are a mixing chamber (MC) and an optical channel with a quartz capillary inside. The MC provides rapid and complete mixing solutions by gas bubbling. The proposed method is based on the new rapid and sensitive reaction of curcumin with a fluorescence reagent - 4-(2,3,3-trimethyl-3H-indolium-1-yl)butane-1-sulfonate (TIBS). The fluorescence intensity of TIBS is greatly quenched in the presence of curcumin in an alkaline medium. The linear range was from 1 to 10µM of curcumin, and the limit of detection, calculated as 3σ of a blank test (n=5), was found to be 0.3µM. The sample throughput was 24h(-1). The proposed method was successfully applied for the determination of curcumin in biologically active supplements and samples of food spices. The obtained data were in good agreement with those measured by a HPLC-UV method. Copyright © 2016 Elsevier B.V. All rights reserved.

Intuitive web-based experimental design for high-throughput biomedical data.

PubMed

Friedrich, Andreas; Kenar, Erhan; Kohlbacher, Oliver; Nahnsen, Sven

2015-01-01

Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.

Non-target time trend screening: a data reduction strategy for detecting emerging contaminants in biological samples.

PubMed

Plassmann, Merle M; Tengstrand, Erik; Åberg, K Magnus; Benskin, Jonathan P

2016-06-01

Non-targeted mass spectrometry-based approaches for detecting novel xenobiotics in biological samples are hampered by the occurrence of naturally fluctuating endogenous substances, which are difficult to distinguish from environmental contaminants. Here, we investigate a data reduction strategy for datasets derived from a biological time series. The objective is to flag reoccurring peaks in the time series based on increasing peak intensities, thereby reducing peak lists to only those which may be associated with emerging bioaccumulative contaminants. As a result, compounds with increasing concentrations are flagged while compounds displaying random, decreasing, or steady-state time trends are removed. As an initial proof of concept, we created artificial time trends by fortifying human whole blood samples with isotopically labelled standards. Different scenarios were investigated: eight model compounds had a continuously increasing trend in the last two to nine time points, and four model compounds had a trend that reached steady state after an initial increase. Each time series was investigated at three fortification levels and one unfortified series. Following extraction, analysis by ultra performance liquid chromatography high-resolution mass spectrometry, and data processing, a total of 21,700 aligned peaks were obtained. Peaks displaying an increasing trend were filtered from randomly fluctuating peaks using time trend ratios and Spearman's rank correlation coefficients. The first approach was successful in flagging model compounds spiked at only two to three time points, while the latter approach resulted in all model compounds ranking in the top 11 % of the peak lists. Compared to initial peak lists, a combination of both approaches reduced the size of datasets by 80-85 %. Overall, non-target time trend screening represents a promising data reduction strategy for identifying emerging bioaccumulative contaminants in biological samples. Graphical abstract Using time trends to filter out emerging contaminants from large peak lists.

Robotic ecological mapping: Habitats and the search for life in the Atacama Desert

NASA Astrophysics Data System (ADS)

Warren-Rhodes, K.; Weinstein, S.; Piatek, J. L.; Dohm, J.; Hock, A.; Minkley, E.; Pane, D.; Ernst, L. A.; Fisher, G.; Emani, S.; Waggoner, A. S.; Cabrol, N. A.; Wettergreen, D. S.; Grin, E.; Coppin, P.; Diaz, Chong; Moersch, J.; Oril, G. G.; Smith, T.; Stubbs, K.; Thomas, G.; Wagner, M.; Wyatt, M.; Boyle, L. Ng

2007-12-01

As part of the three-year `Life in the Atacama' (LITA) project, plant and microbial abundance were mapped within three sites in the Atacama Desert, Chile, using an automated robotic rover. On-board fluorescence imaging of six biological signatures (e.g., chlorophyll, DNA, proteins) was used to assess abundance, based on a percent positive sample rating system and standardized robotic ecological transects. The percent positive rating system scored each sample based on the measured signal strength (0 for no signal to 2 for strong signal) for each biological signature relative to the total rating possible. The 2005 field experiment results show that percent positive ratings varied significantly across Site D (coastal site with fog), with patchy zones of high abundance correlated with orbital and microscale habitat types (heaved surface crust and gravel bars); alluvial fan habitats generally had lower abundance. Non-random multi-scale biological patchiness also characterized interior desert Sites E and F, with relatively high abundance associated with (paleo)aqueous habitats such as playas. Localized variables, including topography, played an important, albeit complex, role in microbial spatial distribution. Site D biosignature trends correlated with culturable soil bacteria, with MPN ranging from 10-1000 CFU/g-soil, and chlorophyll ratings accurately mapped lichen/moss abundance (Site D) and higher plant (Site F) distributions. Climate also affected biological patchiness, with significant correlation shown between abundance and (rover) air relative humidity, while lichen patterns were linked to the presence of fog. Rover biological mapping results across sites parallel longitudinal W-E wet/dry/wet Atacama climate trends. Overall, the study highlights the success of targeting of aqueous-associated habitats identifiable from orbital geology and mineralogy. The LITA experience also suggests the terrestrial study of life and its distribution, particularly the fields of landscape ecology and ecohydrology, hold critical lessons for the search for life on other planets. Their applications to robotic sampling strategies on Mars should be further exploited.

Cultural interaction and biological distance in postclassic period Mexico.

PubMed

Ragsdale, Corey S; Edgar, Heather J H

2015-05-01

Economic, political, and cultural relationships connected virtually every population throughout Mexico during Postclassic period (AD 900-1520). Much of what is known about population interaction in prehistoric Mexico is based on archaeological or ethnohistoric data. What is unclear, especially for the Postclassic period, is how these data correlate with biological population structure. We address this by assessing biological (phenotypic) distances among 28 samples based upon a comparison of dental morphology trait frequencies, which serve as a proxy for genetic variation, from 810 individuals. These distances were compared with models representing geographic and cultural relationships among the same groups. Results of Mantel and partial Mantel matrix correlation tests show that shared migration and trade are correlated with biological distances, but geographic distance is not. Trade and political interaction are also correlated with biological distance when combined in a single matrix. These results indicate that trade and political relationships affected population structure among Postclassic Mexican populations. We suggest that trade likely played a major role in shaping patterns of interaction between populations. This study also shows that the biological distance data support the migration histories described in ethnohistoric sources. © 2015 Wiley Periodicals, Inc.

Identification of Chiari Type I Malformation subtypes using whole genome expression profiles and cranial base morphometrics

PubMed Central

2014-01-01

Background Chiari Type I Malformation (CMI) is characterized by herniation of the cerebellar tonsils through the foramen magnum at the base of the skull, resulting in significant neurologic morbidity. As CMI patients display a high degree of clinical variability and multiple mechanisms have been proposed for tonsillar herniation, it is hypothesized that this heterogeneous disorder is due to multiple genetic and environmental factors. The purpose of the present study was to gain a better understanding of what factors contribute to this heterogeneity by using an unsupervised statistical approach to define disease subtypes within a case-only pediatric population. Methods A collection of forty-four pediatric CMI patients were ascertained to identify disease subtypes using whole genome expression profiles generated from patient blood and dura mater tissue samples, and radiological data consisting of posterior fossa (PF) morphometrics. Sparse k-means clustering and an extension to accommodate multiple data sources were used to cluster patients into more homogeneous groups using biological and radiological data both individually and collectively. Results All clustering analyses resulted in the significant identification of patient classes, with the pure biological classes derived from patient blood and dura mater samples demonstrating the strongest evidence. Those patient classes were further characterized by identifying enriched biological pathways, as well as correlated cranial base morphological and clinical traits. Conclusions Our results implicate several strong biological candidates warranting further investigation from the dura expression analysis and also identified a blood gene expression profile corresponding to a global down-regulation in protein synthesis. PMID:24962150

50 CFR 679.7 - Prohibitions.

Code of Federal Regulations, 2014 CFR

2014-10-01

... and the collection of scientific data or biological samples from the salmon has been completed. (B... scientific data or biological samples from the previous haul. (5) For the operator of a catcher vessel, to... count of salmon and the collection of scientific data or biological samples from the previous offload...

50 CFR 679.7 - Prohibitions.

Code of Federal Regulations, 2011 CFR

2011-10-01

... collection of scientific data or biological samples from the salmon has been completed. (B) Non-Chinook... scientific data or biological samples from the previous haul. (5) For the operator of a catcher vessel, to... count of salmon and the collection of scientific data or biological samples from the previous offload...

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.

RNA sample preparation applied to gene expression profiling for the horse biological passport.

PubMed

Bailly-Chouriberry, Ludovic; Baudoin, Florent; Cormant, Florence; Glavieux, Yohan; Loup, Benoit; Garcia, Patrice; Popot, Marie-Agnès; Bonnaire, Yves

2017-09-01

The improvement of doping control is an ongoing race. Techniques to fight doping are usually based on the direct detection of drugs or their metabolites by analytical methods such as chromatography hyphenated to mass spectrometry after ad hoc sample preparation. Nowadays, omic methods constitute an attractive development and advances have been achieved particularly by application of molecular biology tools for detection of anabolic androgenic steroids (AAS), erythropoiesis-stimulating agent (ESA), or to control human growth hormone misuses. These interesting results across different animal species have suggested that modification of gene expression offers promising new methods of improving the window of detection of banned substances by targeting their effects on blood cell gene expression. In this context, the present study describes the possibility of using a modified version of the dedicated Human IVD (in vitro Diagnostics) PAXgene® Blood RNA Kit for horse gene expression analysis in blood collected on PAXgene® tubes applied to the horse biological passport. The commercial kit was only approved for human blood samples and has required an optimization of specific technical requirements for equine blood samples. Improvements and recommendations were achieved for sample collection, storage and RNA extraction procedure. Following these developments, RNA yield and quality were demonstrated to be suitable for downstream gene expression analysis by qPCR techniques. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Vitamin D receptor gene and osteoporosis - author`s response

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

Looney, J.E.; Yoon, Hyun Koo; Fischer, M.

1996-04-01

We appreciate the comments of Dr. Nguyen et al. about our recent study, but we disagree with their suggestion that the lack of an association between low bone density and the BB VDR genotype, which we reported, is an artifact generated by the small sample size. Furthermore, our results are consistent with similar conclusions reached by a number of other investigators, as recently reported by Peacock. Peacock states {open_quotes}Taken as a whole, the results of studies outlined ... indicate that VDR alleles, cannot account for the major part of the heritable component of bone density as indicated by Morrison etmore » al.{close_quotes}. The majority of the 17 studies cited in this editorial could not confirm an association between the VDR genotype and the bone phenotype. Surely one cannot criticize this combined work as representing an artifact because of a too small sample size. We do not dispute the suggestion by Nguyen et al. that large sample sizes are required to analyze small biological effects. This is evident in both Peacock`s summary and in their own bone density studies. We did not design our study with a larger sample size because, based on the work of Morrison et al., we had hypothesized a large biological effect; large sample sizes are only needed for small biological effects. 4 refs.« less

Use of Community and School Mental Health Services by Custodial Grandchildren

ERIC Educational Resources Information Center

Montoro-Rodriguez, Julian; Smith, Gregory C.; Palmieri, Patrick A.

2012-01-01

We examined patterns and predictors of perceived need, use, and unmet need for mental health services by custodial grandchildren within the school-based and community-based delivery sectors. Data were from a national sample of 610 grandmothers caring for grandchildren ages 6 to 17 in the absence of biological parents. Overlapping use of services…

Spatially resolved in vivo plant metabolomics by laser ablation-based mass spectrometry imaging (MSI) techniques: LDI-MSI and LAESI

PubMed Central

Bartels, Benjamin; Svatoš, Aleš

2015-01-01

This short review aims to summarize the current developments and applications of mass spectrometry-based methods for in situ profiling and imaging of plants with minimal or no sample pre-treatment or manipulation. Infrared-laser ablation electrospray ionization and UV-laser desorption/ionization methods are reviewed. The underlying mechanisms of the ionization techniques–namely, laser ablation of biological samples and electrospray ionization–as well as variations of the LAESI ion source for specific targets of interest are described. PMID:26217345

Sample Preparation for Mass Spectrometry Imaging of Plant Tissues: A Review

PubMed Central

Dong, Yonghui; Li, Bin; Malitsky, Sergey; Rogachev, Ilana; Aharoni, Asaph; Kaftan, Filip; Svatoš, Aleš; Franceschi, Pietro

2016-01-01

Mass spectrometry imaging (MSI) is a mass spectrometry based molecular ion imaging technique. It provides the means for ascertaining the spatial distribution of a large variety of analytes directly on tissue sample surfaces without any labeling or staining agents. These advantages make it an attractive molecular histology tool in medical, pharmaceutical, and biological research. Likewise, MSI has started gaining popularity in plant sciences; yet, information regarding sample preparation methods for plant tissues is still limited. Sample preparation is a crucial step that is directly associated with the quality and authenticity of the imaging results, it therefore demands in-depth studies based on the characteristics of plant samples. In this review, a sample preparation pipeline is discussed in detail and illustrated through selected practical examples. In particular, special concerns regarding sample preparation for plant imaging are critically evaluated. Finally, the applications of MSI techniques in plants are reviewed according to different classes of plant metabolites. PMID:26904042

Testing the effect of the rock record on diversity: a multidisciplinary approach to elucidating the generic richness of sauropodomorph dinosaurs through time.

PubMed

Mannion, Philip D; Upchurch, Paul; Carrano, Matthew T; Barrett, Paul M

2011-02-01

The accurate reconstruction of palaeobiodiversity patterns is central to a detailed understanding of the macroevolutionary history of a group of organisms. However, there is increasing evidence that diversity patterns observed directly from the fossil record are strongly influenced by fluctuations in the quality of our sampling of the rock record; thus, any patterns we see may reflect sampling biases, rather than genuine biological signals. Previous dinosaur diversity studies have suggested that fluctuations in sauropodomorph palaeobiodiversity reflect genuine biological signals, in comparison to theropods and ornithischians whose diversity seems to be largely controlled by the rock record. Most previous diversity analyses that have attempted to take into account the effects of sampling biases have used only a single method or proxy: here we use a number of techniques in order to elucidate diversity. A global database of all known sauropodomorph body fossil occurrences (2024) was constructed. A taxic diversity curve for all valid sauropodomorph genera was extracted from this database and compared statistically with several sampling proxies (rock outcrop area and dinosaur-bearing formations and collections), each of which captures a different aspect of fossil record sampling. Phylogenetic diversity estimates, residuals and sample-based rarefaction (including the first attempt to capture 'cryptic' diversity in dinosaurs) were implemented to investigate further the effects of sampling. After 'removal' of biases, sauropodomorph diversity appears to be genuinely high in the Norian, Pliensbachian-Toarcian, Bathonian-Callovian and Kimmeridgian-Tithonian (with a small peak in the Aptian), whereas low diversity levels are recorded for the Oxfordian and Berriasian-Barremian, with the Jurassic/Cretaceous boundary seemingly representing a real diversity trough. Observed diversity in the remaining Triassic-Jurassic stages appears to be largely driven by sampling effort. Late Cretaceous diversity is difficult to elucidate and it is possible that this interval remains relatively under-sampled. Despite its distortion by sampling biases, much of sauropodomorph palaeobiodiversity can be interpreted as a reflection of genuine biological signals, and fluctuations in sea level may account for some of these diversity patterns. © 2010 The Authors. Biological Reviews © 2010 Cambridge Philosophical Society.

Development and Experiment in College Teaching.

ERIC Educational Resources Information Center

Committee on Institutional Cooperation.

These reports comprise sample collections of experimental instructional projects seeking new and better arrangements for teaching. The entries in section one, describe department-based projects in accounting, art history, biology, botany, business administration, communication, counseling, dairy science, design, education, engineering, language,…

9 CFR 113.3 - Sampling of biological products.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 1 2011-01-01 2011-01-01 false Sampling of biological products. 113.3 Section 113.3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... Applicability § 113.3 Sampling of biological products. Each licensee and permittee shall furnish representative...

9 CFR 113.3 - Sampling of biological products.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 1 2010-01-01 2010-01-01 false Sampling of biological products. 113.3 Section 113.3 Animals and Animal Products ANIMAL AND PLANT HEALTH INSPECTION SERVICE, DEPARTMENT OF... Applicability § 113.3 Sampling of biological products. Each licensee and permittee shall furnish representative...

Recent advances in stable isotope labeling based techniques for proteome relative quantification.

PubMed

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2014-10-24

The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected. Copyright © 2014 Elsevier B.V. All rights reserved.

Compound parabolic concentrator probe for efficient light collection in spectroscopy of biological tissue

NASA Astrophysics Data System (ADS)

Tanaka, Kazunori; Pacheco, Marcos T. T.; Brennan, James F., III; Itzkan, Irving; Berger, Andrew J.; Dasari, Ramachandra R.; Feld, Michael S.

1996-02-01

We describe a compound parabolic concentrator (CPC)-based probe for enhanced signal collection in the spectroscopy of biological tissues. Theoretical considerations governing signal enhancement compared with conventional collection methods are given. A ray-tracing program was used to analyze the throughput of CPC's with shape deviations and surface imperfections. A modified CPC shape with 99% throughput was discovered. A 4.4-mm-long CPC was manufactured and incorporated into an optical fiber-based near-infrared Raman spectrometer system. For human tissue samples, light collection was enhanced by a factor of 7 compared with collection with 0.29-NA optical fibers.

[Confirming Indicators of Qualitative Results by Chromatography-mass Spectrometry in Biological Samples].

PubMed

Liu, S D; Zhang, D M; Zhang, W; Zhang, W F

2017-04-01

Because of the exist of complex matrix, the confirming indicators of qualitative results for toxic substances in biological samples by chromatography-mass spectrometry are different from that in non-biological samples. Even in biological samples, the confirming indicators are different in various application areas. This paper reviews the similarities and differences of confirming indicators for the analyte in biological samples by chromatography-mass spectrometry in the field of forensic toxicological analysis and other application areas. These confirming indicators include retention time （RT）, relative retention time （RRT）, signal to noise （S/N）, characteristic ions, relative abundance of characteristic ions, parent ion-daughter ion pair and abundance ratio of ion pair, etc. Copyright© by the Editorial Department of Journal of Forensic Medicine.

Selecting islands and shoals for conservation based on biological and aesthetic criteria

USGS Publications Warehouse

Knutson, M.G.; Leopold, D.J.; Smardon, R.C.

1993-01-01

Consideration of biological quality has long been an important component of rating areas for conservation. Often these same areas are highly valued by people for aesthetic reasons, creating demands for housing and recreation that may conflict with protection plans for these habitats. Most methods of selecting land for conservation purposes use biological factors alone. For some land areas, analysis of aesthetic qualities is also important in describing the scenic value of undisturbed land. A method for prioritizing small islands and shoals based on both biological and visual quality factors is presented here. The study included 169 undeveloped islands and shoals a??0.8 ha in the Thousand Islands Region of the St. Lawrence River, New York. Criteria such as critical habitat for uncommon plant and animal species were considered together with visual quality and incorporated into a rating system that ranked the islands and shoals according to their priority for conservation management and protection from development. Biological factors were determined based on previous research and a field survey. Visual quality was determined by visual diagnostic criteria developed from public responses to photographs of a sample of islands. Variables such as elevation, soil depth, and type of plant community can be used to classify islands into different categories of visual quality but are unsuccessful in classifying islands into categories of overall biological quality.

Biological data extraction from imagery - How far can we go? A case study from the Mid-Atlantic Ridge.

PubMed

Cuvelier, Daphne; de Busserolles, Fanny; Lavaud, Romain; Floc'h, Estelle; Fabri, Marie-Claire; Sarradin, Pierre-Marie; Sarrazin, Jozée

2012-12-01

In the past few decades, hydrothermal vent research has progressed immensely, resulting in higher-quality samples and long-term studies. With time, scientists are becoming more aware of the impacts of sampling on the faunal communities and are looking for less invasive ways to investigate the vent ecosystems. In this perspective, imagery analysis plays a very important role. With this study, we test which factors can be quantitatively and accurately assessed based on imagery, through comparison with faunal sampling. Twelve instrumented chains were deployed on the Atlantic Eiffel Tower hydrothermal edifice and the corresponding study sites were subsequently sampled. Discrete, quantitative samples were compared to the imagery recorded during the experiment. An observer-effect was tested, by comparing imagery data gathered by different scientists. Most factors based on image analyses concerning Bathymodiolus azoricus mussels were shown to be valid representations of the corresponding samples. Additional ecological assets, based exclusively on imagery, were included. Copyright © 2012 Elsevier Ltd. All rights reserved.

AOX removal from industrial wastewaters using advanced oxidation processes: assessment of a combined chemical-biological oxidation.

PubMed

Luyten, J; Sniegowski, K; Van Eyck, K; Maertens, D; Timmermans, S; Liers, Sven; Braeken, L

2013-01-01

In this paper, the abatement of adsorbable halogenated organic compounds (AOX) from an industrial wastewater containing relatively high chloride concentrations by a combined chemical and biological oxidation is assessed. For chemical oxidation, the O(3)/UV, H(2)O(2)/UV and photo-Fenton processes are evaluated on pilot scale. Biological oxidation is simulated in a 4 h respirometry experiment with periodic aeration. The results show that a selective degradation of AOX with respect to the matrix compounds (expressed as chemical oxygen demand) could be achieved. For O(3)/UV, lowering the ratio of O(3) dosage to UV intensity leads to a better selectivity for AOX. During O(3)-based experiments, the AOX removal is generally less than during the H(2)O(2)-based experiments. However, after biological oxidation, the AOX levels are comparable. For H(2)O(2)/UV, optimal operating parameters for UV and H(2)O(2) dosage are next determined in a second run with another wastewater sample.

[Study on chemical diversity of volatile oils in Houttuynia cordata and their genetic basis].

PubMed

Wu, Lingshang; Si, Jinping; Zhou, Hui; Zhu, Yan; Lan, Yunlong

2009-01-01

To reveal chemical diversify of volatile oils in Houttuynia cordata from major producing areas in China and their genetic basis, lay a foundation for breeding a quality H. cordata variety. The volatile oils in H. cordata from 22 provenances were determined by GC. And the relationship among the peak areas of volatile oils, biological characteristics and RAPD makers were analyzed. There were common and special volatile oils in H. cordata from different provenances. The peak areas of common volatile oils in samples were significantly different. The clustering figure based on the peak areas or the relative peak areas of common volatile oils was almost agreed with the one based on RAPD makers analysis. And the differences in chromatograms could be distinguished according to the biological characteristics. The diversity of volatile oils exists in H. cordata from different provenances which relate with biological characteristics and has genetic basis. H. cordata can be divided into 2 types according to volatile oils, biological characteristics or RAPD marker.

Biological and Psychosocial Predictors of Postpartum Depression: Systematic Review and Call for Integration

PubMed Central

Tanner Stapleton, Lynlee R.; Guardino, Christine M.; Hahn-Holbrook, Jennifer; Schetter, Christine Dunkel

2017-01-01

Postpartum depression (PPD) adversely affects the health and well being of many new mothers, their infants, and their families. A comprehensive understanding of biopsychosocial precursors to PPD is needed to solidify the current evidence base for best practices in translation. We conducted a systematic review of research published from 2000 through 2013 on biological and psychosocial factors associated with PPD and postpartum depressive symptoms. Two hundred fourteen publications based on 199 investigations of 151,651 women in the first postpartum year met inclusion criteria. The biological and psychosocial literatures are largely distinct, and few studies provide integrative analyses. The strongest PPD risk predictors among biological processes are hypothalamic-pituitary-adrenal dysregulation, inflammatory processes, and genetic vulnerabilities. Among psychosocial factors, the strongest predictors are severe life events, some forms of chronic strain, relationship quality, and support from partner and mother. Fully integrated biopsychosocial investigations with large samples are needed to advance our knowledge of PPD etiology. PMID:25822344

Carbon nanotubes and nanowires for biological sensing

NASA Technical Reports Server (NTRS)

Li, Jun; Ng, Hou Tee; Chen, Hua

2005-01-01

This chapter reviews the recent development in biological sensing using nanotechnologies based on carbon nanotubes and various nanowires. These 1D materials have shown unique properties that are efficient in interacting with biomolecules of similar dimensions, i.e., on a nanometer scale. Various aspects including synthesis, materials properties, device fabrication, biofunctionalization, and biological sensing applications of such materials are reviewed. The potential of such integrated nanobiosensors in providing ultrahigh sensitivity, fast response, and high-degree multiplex detection, yet with minimum sample requirements is demonstrated. This chapter is intended to provide comprehensive updated information for people from a variety of backgrounds but with common interests in the fast-moving interdisciplinary field of nanobiotechnology.

Internet-based recruitment system for HIV and STI screening for men who have sex with men in Estonia, 2013: analysis of preliminary outcomes.

PubMed

Ruutel, K; Lohmus, L; Janes, J

2015-04-16

The aim of the current project was to develop an Internet-based recruitment system for HIV and sexually transmitted infection (STI) screening for men who have sex with men (MSM) in Estonia in order to collect biological samples during behavioural studies. In 2013, an Internet-based HIV risk-behaviour survey was conducted among MSM living in Estonia. After completing the questionnaire, all participants were offered anonymous and free-of-charge STI testing. They could either order a urine sample kit by post to screen for chlamydia infections (including lymphogranuloma venereum (LGV)), trichomoniasis, gonorrhoea and Mycoplasma genitalium infections, or visit a laboratory for HIV, hepatitis A virus, hepatitis B virus,hepatitis C virus and syphilis screening. Of 301 participants who completed the questionnaire, 265 (88%),reported that they were MSM. Of these 265 MSM,68 (26%) underwent various types of testing. In the multiple regression analysis, Russian as the first language,previous HIV testing and living in a city or town increased the odds of testing during the study. Linking Internet-based behavioural data collection with biological sample collection is a promising approach. As there are no specific STI services for MSM in Estonia,this system could also be used as an additional option for anonymous and free-of-charge STI screening.

Rapid Nucleic Acid Extraction and Purification Using a Miniature Ultrasonic Technique

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

Branch, Darren W.; Vreeland, Erika C.; McClain, Jamie L.

Miniature ultrasonic lysis for biological sample preparation is a promising technique for efficient and rapid extraction of nucleic acids and proteins from a wide variety of biological sources. Acoustic methods achieve rapid, unbiased, and efficacious disruption of cellular membranes while avoiding the use of harsh chemicals and enzymes, which interfere with detection assays. In this work, a miniature acoustic nucleic acid extraction system is presented. Using a miniature bulk acoustic wave (BAW) transducer array based on 36° Y-cut lithium niobate, acoustic waves were coupled into disposable laminate-based microfluidic cartridges. To verify the lysing effectiveness, the amount of liberated ATP andmore » the cell viability were measured and compared to untreated samples. The relationship between input power, energy dose, flow-rate, and lysing efficiency were determined. DNA was purified on-chip using three approaches implemented in the cartridges: a silica-based sol-gel silica-bead filled microchannel, nucleic acid binding magnetic beads, and Nafion-coated electrodes. Using E. coli, the lysing dose defined as ATP released per joule was 2.2× greater, releasing 6.1× more ATP for the miniature BAW array compared to a bench-top acoustic lysis system. An electric field-based nucleic acid purification approach using Nafion films yielded an extraction efficiency of 69.2% in 10 min for 50 µL samples.« less

Rapid Nucleic Acid Extraction and Purification Using a Miniature Ultrasonic Technique

DOE PAGES

Branch, Darren W.; Vreeland, Erika C.; McClain, Jamie L.; ...

2017-07-21

Miniature ultrasonic lysis for biological sample preparation is a promising technique for efficient and rapid extraction of nucleic acids and proteins from a wide variety of biological sources. Acoustic methods achieve rapid, unbiased, and efficacious disruption of cellular membranes while avoiding the use of harsh chemicals and enzymes, which interfere with detection assays. In this work, a miniature acoustic nucleic acid extraction system is presented. Using a miniature bulk acoustic wave (BAW) transducer array based on 36° Y-cut lithium niobate, acoustic waves were coupled into disposable laminate-based microfluidic cartridges. To verify the lysing effectiveness, the amount of liberated ATP andmore » the cell viability were measured and compared to untreated samples. The relationship between input power, energy dose, flow-rate, and lysing efficiency were determined. DNA was purified on-chip using three approaches implemented in the cartridges: a silica-based sol-gel silica-bead filled microchannel, nucleic acid binding magnetic beads, and Nafion-coated electrodes. Using E. coli, the lysing dose defined as ATP released per joule was 2.2× greater, releasing 6.1× more ATP for the miniature BAW array compared to a bench-top acoustic lysis system. An electric field-based nucleic acid purification approach using Nafion films yielded an extraction efficiency of 69.2% in 10 min for 50 µL samples.« less

The Effect of Multiple Surface Treatments on Biological Properties of Ti-6Al-4V Alloy

NASA Astrophysics Data System (ADS)

Parsikia, Farhang; Amini, Pupak; Asgari, Sirous

2014-09-01

In this research, the effect of various surface treatments including laser processing, grit blasting and anodizing on chemical structure, surface topography, and bioactivity of Ti-6Al-4V was investigated. Six groups of samples were prepared by a combination of two alternative laser processes, grit blasting and anodizing. Selected samples were first evaluated using microanalysis techniques and contact roughness testing and were then exposed to in vitro environment. Scanning electron microscopy was used to characterize the corresponding final surface morphologies. Weight measurement and atomic absorption tests were employed for determination of bioactivity limits of different surface conditions. Based on the data obtained in this study, low-energy laser processing generally yields a better biological response. The maximum bioactivity was attained in those samples exposed to a three step treatment including low-energy laser treatment followed by grit blasting and anodizing.

Suitability of Commercial Transport Media for Biological Pathogens under Nonideal Conditions

PubMed Central

Hubbard, Kyle; Pellar, Gregory; Emanuel, Peter

2011-01-01

There is extensive data to support the use of commercial transport media as a stabilizer for known clinical samples; however, there is little information to support their use outside of controlled conditions specified by the manufacturer. Furthermore, there is no data to determine the suitability of said media for biological pathogens, specifically those of interest to the US military. This study evaluates commercial off-the-shelf (COTS) transport media based on sample recovery, viability, and quality of nucleic acids and peptides for nonpathogenic strains of Bacillus anthracis, Yersinia pestis, and Venezuelan equine encephalitis virus, in addition to ricin toxin. Samples were stored in COTS, PBST, or no media at various temperatures over an extended test period. The results demonstrate that COTS media, although sufficient for the preservation of nucleic acid and proteinaceous material, are not capable of maintaining an accurate representation of biothreat agents at the time of collection. PMID:22121364

Analytical Methodologies for the Determination of Endocrine Disrupting Compounds in Biological and Environmental Samples

PubMed Central

Sosa-Ferrera, Zoraida; Mahugo-Santana, Cristina; Santana-Rodríguez, José Juan

2013-01-01

Endocrine-disruptor compounds (EDCs) can mimic natural hormones and produce adverse effects in the endocrine functions by interacting with estrogen receptors. EDCs include both natural and synthetic chemicals, such as hormones, personal care products, surfactants, and flame retardants, among others. EDCs are characterised by their ubiquitous presence at trace-level concentrations and their wide diversity. Since the discovery of the adverse effects of these pollutants on wildlife and human health, analytical methods have been developed for their qualitative and quantitative determination. In particular, mass-based analytical methods show excellent sensitivity and precision for their quantification. This paper reviews recently published analytical methodologies for the sample preparation and for the determination of these compounds in different environmental and biological matrices by liquid chromatography coupled with mass spectrometry. The various sample preparation techniques are compared and discussed. In addition, recent developments and advances in this field are presented. PMID:23738329

Microfluidics-based integrated airborne pathogen detection systems

NASA Astrophysics Data System (ADS)

Northrup, M. Allen; Alleman-Sposito, Jennifer; Austin, Todd; Devitt, Amy; Fong, Donna; Lin, Phil; Nakao, Brian; Pourahmadi, Farzad; Vinas, Mary; Yuan, Bob

2006-09-01

Microfluidic Systems is focused on building microfluidic platforms that interface front-end mesofluidics to handle real world sample volumes for optimal sensitivity coupled to microfluidic circuitry to process small liquid volumes for complex reagent metering, mixing, and biochemical analysis, particularly for pathogens. MFSI is the prime contractor on two programs for the US Department of Homeland Security: BAND (Bioagent Autonomous Networked Detector) and IBADS (Instantaneous Bio-Aerosol Detection System). The goal of BAND is to develop an autonomous system for monitoring the air for known biological agents. This consists of air collection, sample lysis, sample purification, detection of DNA, RNA, and toxins, and a networked interface to report the results. For IBADS, MFSI is developing the confirmatory device which must verify the presence of a pathogen with 5 minutes of an air collector/trigger sounding an alarm. Instrument designs and biological assay results from both BAND and IBADS will be presented.

Technical Stability and Biological Variability in MicroRNAs from Dried Blood Spots: A Lung Cancer Therapy-Monitoring Showcase.

PubMed

Kahraman, Mustafa; Laufer, Thomas; Backes, Christina; Schrörs, Hannah; Fehlmann, Tobias; Ludwig, Nicole; Kohlhaas, Jochen; Meese, Eckart; Wehler, Thomas; Bals, Robert; Keller, Andreas

2017-09-01

Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results. We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions. Second, we investigated technical reproducibility by performing 7 replicates of DBS again from 1 person. Third, we investigated DBS samples from 53 patients with lung cancer undergoing different therapies. Across these 3 stages, 108 genome-wide miRNA profiles from DBS were generated and evaluated biostatistically. In the stability analysis, we observed that temperature and humidity had an overall limited influence on the miRNomes (average correlation between the different conditions of 0.993). Usage of a silica gel slightly diminished DBS' technical reproducibility. The 7 technical replicates had an average correlation of 0.996. The correlation with whole-blood PAXGene miRNomes of the same individual was remarkable (correlation of 0.88). Finally, evaluation of the samples from the 53 patients with lung cancer exposed to different therapies showed that the biological variations exceeded the technical variability significantly ( P < 0.0001), yielding 51 dysregulated miRNAs. We present a stable work flow for profiling of whole miRNomes on the basis of samples collected from DBS. Biological variations exceeded technical variations significantly. DBS-based miRNA profiles will potentially further the translational character of miRNA biomarker studies. © 2017 American Association for Clinical Chemistry.

Surface Enhanced Raman Scattering (SERS)-Based Next Generation Commercially Available Substrate: Physical Characterization and Biological Application

DTIC Science & Technology

2011-09-01

the spore and the active areas on the Klarite surface. For these experiments an aliquot of the common bacillus spore B. coagulans was drop...suspension B. coagulans (ATCC SUS-CG) was purchased from Raven Biologicals and used at a log 4 or 6 population per 0.1 mL of solution. For experiments...Klarite substrates were evaluated with the spore sample B. coagulans . In these experiments different substrates and the changes in overall band

Biological Effects of Laser Radiation. Volume I. Review of the Literature on Biological Effects of Laser Radiation-to 1965.

DTIC Science & Technology

1978-10-17

because of the rapid progress made in laser technology to date. The use of the Laser Microprobe in spectrochemical analysis of the elements is based on...spectroscopy to vaporize microscopic amounts of samples for elemental analysis . On the other hand, the intense, highly monochromatic laser beam is being...employed as a light source for Raman spectroscopy to study molecular structure. These two uses of lasers in spectroscopic analysis have been sucessful

An inexpensive and portable microvolumeter for rapid evaluation of biological samples.

PubMed

Douglass, John K; Wcislo, William T

2010-08-01

We describe an improved microvolumeter (MVM) for rapidly measuring volumes of small biological samples, including live zooplankton, embryos, and small animals and organs. Portability and low cost make this instrument suitable for widespread use, including at remote field sites. Beginning with Archimedes' principle, which states that immersing an arbitrarily shaped sample in a fluid-filled container displaces an equivalent volume, we identified procedures that maximize measurement accuracy and repeatability across a broad range of absolute volumes. Crucial steps include matching the overall configuration to the size of the sample, using reflected light to monitor fluid levels precisely, and accounting for evaporation during measurements. The resulting precision is at least 100 times higher than in previous displacement-based methods. Volumes are obtained much faster than by traditional histological or confocal methods and without shrinkage artifacts due to fixation or dehydration. Calibrations using volume standards confirmed accurate measurements of volumes as small as 0.06 microL. We validated the feasibility of evaluating soft-tissue samples by comparing volumes of freshly dissected ant brains measured with the MVM and by confocal reconstruction.

Scalable metagenomic taxonomy classification using a reference genome database

PubMed Central

Ames, Sasha K.; Hysom, David A.; Gardner, Shea N.; Lloyd, G. Scott; Gokhale, Maya B.; Allen, Jonathan E.

2013-01-01

Motivation: Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge. Results: A method is presented to shift computational costs to an off-line computation by creating a taxonomy/genome index that supports scalable metagenomic classification. Scalable performance is demonstrated on real and simulated data to show accurate classification in the presence of novel organisms on samples that include viruses, prokaryotes, fungi and protists. Taxonomic classification of the previously published 150 giga-base Tyrolean Iceman dataset was found to take <20 h on a single node 40 core large memory machine and provide new insights on the metagenomic contents of the sample. Availability: Software was implemented in C++ and is freely available at http://sourceforge.net/projects/lmat Contact: allen99@llnl.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23828782

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

PubMed

Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

2014-01-01

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

Towards the implementation of a spectral database for the detection of biological warfare agents

NASA Astrophysics Data System (ADS)

Carestia, M.; Pizzoferrato, R.; Gelfusa, M.; Cenciarelli, O.; D'Amico, F.; Malizia, A.; Scarpellini, D.; Murari, A.; Vega, J.; Gaudio, P.

2014-10-01

The deliberate use of biological warfare agents (BWA) and other pathogens can jeopardize the safety of population, fauna and flora, and represents a concrete concern from the military and civil perspective. At present, the only commercially available tools for fast warning of a biological attack can perform point detection and require active or passive sampling collection. The development of a stand-off detection system would be extremely valuable to minimize the risk and the possible consequences of the release of biological aerosols in the atmosphere. Biological samples can be analyzed by means of several optical techniques, covering a broad region of the electromagnetic spectrum. Strong evidence proved that the informative content of fluorescence spectra could provide good preliminary discrimination among those agents and it can also be obtained through stand-off measurements. Such a system necessitates a database and a mathematical method for the discrimination of the spectral signatures. In this work, we collected fluorescence emission spectra of the main BWA simulants, to implement a spectral signature database and apply the Universal Multi Event Locator (UMEL) statistical method. Our preliminary analysis, conducted in laboratory conditions with a standard UV lamp source, considers the main experimental setups influencing the fluorescence signature of some of the most commonly used BWA simulants. Our work represents a first step towards the implementation of a spectral database and a laser-based biological stand-off detection and identification technique.

The Cotesia sesamiae story: insight into host-range evolution in a Hymenoptera parasitoid and implication for its use in biological control programs.

PubMed

Kaiser, L; Dupas, S; Branca, A; Herniou, E A; Clarke, C W; Capdevielle Dulac, C; Obonyo, J; Benoist, R; Gauthier, J; Calatayud, P A; Silvain, J F; Le Ru, B P

2017-12-01

This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding. In the second part, we consider the larger ecosystem of wild Poales plant species hosting many Lepidoptera stem borer species that are potential hosts for C. sesamiae. The hypothesis of other host-adapted C. sesamiae populations was investigated based on a large sampling of stem borer larvae on various Poales across sub-Saharan Africa. The sampling provided information on the respective contribution of local hosts, biogeography and Wolbachia in the genetic structure of C. sesamiae populations. Molecular evolution analyses highlighted that several bracovirus genes were under positive selection, some of them being under different selection pressure in C. sesamiae populations adapted to different hosts. This suggests that C. sesamiae host races result from co-evolution acting at the local scale on different bracovirus genes. The third part considers the mechanisms driving specialization. C. sesamiae host races are more or less host-specialized. This character is crucial for efficient and environmentally-safe use of natural enemies for biological control of pests. One method to get an insight in the evolutionary stability of host-parasite associations is to characterize the phylogenetic relationships between the so-called host-races. Based on the construction of a phylogeny of C. sesamiae samples from various host- and plant species, we revealed three main lineages. Mechanisms of differentiation are discussed with regard to the geography and ecology of the samples. One of the lineage presented all the hallmarks of a distinct species, which has been morphologically described and is now studied in the perspective of being used as biological control agent against Sesamia nonagrioides Lefèbvre (Lepidoptera: Noctuidae), a major maize pest in West Africa and Mediterranean countries (see Benoist et al. 2017). The fourth part reviews past and present use of C. sesamiae in biological control, and points out the interest of such molecular ecology studies to reconcile biodiversity and food security stakes in future biological control.

Optimal time points sampling in pathway modelling.

PubMed

Hu, Shiyan

2004-01-01

Modelling cellular dynamics based on experimental data is at the heart of system biology. Considerable progress has been made to dynamic pathway modelling as well as the related parameter estimation. However, few of them gives consideration for the issue of optimal sampling time selection for parameter estimation. Time course experiments in molecular biology rarely produce large and accurate data sets and the experiments involved are usually time consuming and expensive. Therefore, to approximate parameters for models with only few available sampling data is of significant practical value. For signal transduction, the sampling intervals are usually not evenly distributed and are based on heuristics. In the paper, we investigate an approach to guide the process of selecting time points in an optimal way to minimize the variance of parameter estimates. In the method, we first formulate the problem to a nonlinear constrained optimization problem by maximum likelihood estimation. We then modify and apply a quantum-inspired evolutionary algorithm, which combines the advantages of both quantum computing and evolutionary computing, to solve the optimization problem. The new algorithm does not suffer from the morass of selecting good initial values and being stuck into local optimum as usually accompanied with the conventional numerical optimization techniques. The simulation results indicate the soundness of the new method.

Quantum Cascade Lasers-Based Detection of Nitric Oxide.

PubMed

Montilla-Bascón, Gracia; Mandon, Julien; Harren, Frans J M; Mur, Luis A J; Cristescu, Simona M; Prats, Elena

2018-01-01

Despite the established importance of nitric oxide (NO) in many physiological and molecular processes in plants, most methods for quantifying NO are open to criticism This reflects the differing methods either lacking specificity or sensitivity, or even from an undue dependence of results on experimental conditions (i.e., chemical concentrations, pH, etc.). In this chapter we describe a protocol to measure gaseous NO produced by a biological sample using quantum cascade laser (QCL)-based spectroscopy. This technique is based on absorption of the laser light by the NO molecules which have been passed from a biological sample into an optical s cell that is equipped with two mirrors placed at both ends. This design greatly increases the interaction path length with the NO molecules due to multiple reflections of the light coupled inside the cell. Thus, the method is able to provide online, in planta measurements of the dynamics of NO production, being highly selective and sensitive (down to ppbv levels;1 ppbv = part per billion by volume mixing ratio = 1:10 -9 ).

Tissues from population-based cancer registries: a novel approach to increasing research potential.

PubMed

Goodman, Marc T; Hernandez, Brenda Y; Hewitt, Stephen; Lynch, Charles F; Coté, Timothy R; Frierson, Henry F; Moskaluk, Christopher A; Killeen, Jeffrey L; Cozen, Wendy; Key, Charles R; Clegg, Limin; Reichman, Marsha; Hankey, Benjamin F; Edwards, Brenda

2005-07-01

Population-based cancer registries, such as those included in the Surveillance, Epidemiology, and End-Results (SEER) Program, offer tremendous research potential beyond traditional surveillance activities. We describe the expansion of SEER registries to gather formalin-fixed, paraffin-embedded tissue from cancer patients on a population basis. Population-based tissue banks have the advantage of providing an unbiased sampling frame for evaluating the public health impact of genes or protein targets that may be used for therapeutic or diagnostic purposes in defined communities. Such repositories provide a unique resource for testing new molecular classification schemes for cancer, validating new biologic markers of malignancy, prognosis and progression, assessing therapeutic targets, and measuring allele frequencies of cancer-associated genetic polymorphisms or germline mutations in representative samples. The assembly of tissue microarrays will allow for the use of rapid, large-scale protein-expression profiling of tumor samples while limiting depletion of this valuable resource. Access to biologic specimens through SEER registries will provide researchers with demographic, clinical, and risk factor information on cancer patients with assured data quality and completeness. Clinical outcome data, such as disease-free survival, can be correlated with previously validated prognostic markers. Furthermore, the anonymity of the study subject can be protected through rigorous standards of confidentiality. SEER-based tissue resources represent a step forward in true, population-based tissue repositories of tumors from US patients and may serve as a foundation for molecular epidemiology studies of cancer in this country.

Microfluidic-Based Platform for Universal Sample Preparation and Biological Assays Automation for Life-Sciences Research and Remote Medical Applications

NASA Astrophysics Data System (ADS)

Brassard, D.; Clime, L.; Daoud, J.; Geissler, M.; Malic, L.; Charlebois, D.; Buckley, N.; Veres, T.

2018-02-01

An innovative centrifugal microfluidic universal platform for remote bio-analytical assays automation required in life-sciences research and medical applications, including purification and analysis from body fluids of cellular and circulating markers.

Subtyping attention-deficit/hyperactivity disorder using temperament dimensions: toward biologically based nosologic criteria

PubMed Central

Karalunas, Sarah L.; Fair, Damien; Musser, Erica D.; Aykes, Kamari; Iyer, Swathi P.; Nigg, Joel T.

2014-01-01

Importance Psychiatric nosology is limited by behavioral and biological heterogeneity within existing disorder categories. The imprecise nature of current nosological distinctions limits both mechanistic understanding and clinical prediction. Here, we demonstrate an approach consistent with the NIMH Research Domain Criteria (RDoC) initiative to identifying superior, neurobiologically-valid subgroups with better predictive capacity than existing psychiatric categories for childhood Attention-Deficit Hyperactivity Disorder (ADHD). Objective Refine subtyping of childhood ADHD by using biologically-based behavioral dimensions (i.e. temperament), novel classification algorithms, and multiple external validators. In doing so, we demonstrate how refined nosology is capable of improving on current predictive capacity of long-term outcomes relative to current DSM-based nosology. Design, Setting, Participants 437 clinically well-characterized, community-recruited children with and without ADHD participated in an on-going longitudinal study. Baseline data were used to classify children into subgroups based on temperament dimensions and to examine external validators including physiological and MRI measures. One-year longitudinal follow-up data are reported for a subgroup of the ADHD sample to address stability and clinical prediction. Main Outcome Measures Parent/guardian ratings of children on a measure of temperament were used as input features in novel community detection analyses to identify subgroups within the sample. Groups were validated using three widely-accepted external validators: peripheral physiology (cardiac measures of respiratory sinus arrhythmia and pre-ejection period), central nervous system functioning (via resting-state functional connectivity MRI), and clinical outcomes (at one-year longitudinal follow-up). Results The community detection algorithm suggested three novel types of ADHD, labeled as “Mild” (normative emotion regulation); “Surgent” (extreme levels of positive approach-motivation); and “Irritable” (extreme levels of negative emotionality, anger, and poor soothability). Types were independent of existing clinical demarcations, including DSM-5 presentations or symptom severity. These types showed stability over time and were distinguished by unique patterns of cardiac physiological response, resting-state functional brain connectivity, and clinical outcome one year later. Conclusions and Relevance Results suggest that a biologically-informed temperament-based typology, developed with a discovery-based community detection algorithm, provided a superior description of heterogeneity in the ADHD population than any current clinical nosology. This demonstration sets the stage for more aggressive attempts at a tractable, biologically-based nosology. PMID:25006969

Holographic femtosecond laser processing and its application to biological materials (Conference Presentation)

NASA Astrophysics Data System (ADS)

Hayasaki, Yoshio

2017-02-01

Femtosecond laser processing is a promising tool for fabricating novel and useful structures on the surfaces of and inside materials. An enormous number of pulse irradiation points will be required for fabricating actual structures with millimeter scale, and therefore, the throughput of femtosecond laser processing must be improved for practical adoption of this technique. One promising method to improve throughput is parallel pulse generation based on a computer-generated hologram (CGH) displayed on a spatial light modulator (SLM), a technique called holographic femtosecond laser processing. The holographic method has the advantages such as high throughput, high light use efficiency, and variable, instantaneous, and 3D patterning. Furthermore, the use of an SLM gives an ability to correct unknown imperfections of the optical system and inhomogeneity in a sample using in-system optimization of the CGH. Furthermore, the CGH can adaptively compensate in response to dynamic unpredictable mechanical movements, air and liquid disturbances, a shape variation and deformation of the target sample, as well as adaptive wavefront control for environmental changes. Therefore, it is a powerful tool for the fabrication of biological cells and tissues, because they have free form, variable, and deformable structures. In this paper, we present the principle and the experimental setup of holographic femtosecond laser processing, and the effective way for processing the biological sample. We demonstrate the femtosecond laser processing of biological materials and the processing properties.

The use of an integrated molecular-, chemical- and biological-based approach for promoting the better use and conservation of medicinal species: a case study of Brazilian quinas.

PubMed

Palhares, Rafael M; Drummond, Marcela G; Brasil, Bruno S A F; Krettli, Antoniana U; Oliveira, Guilherme C; Brandão, Maria G L

2014-08-08

Quina is a popular name originally attributed to Cinchona pubescens Vahl (=Cinchona succirubra) and Cinchona. calisaya Wedd., species native from Peru that have the antimalarial alkaloid quinine. In Brazil, bitter barks substitutes for the Peruvian species began to be used centuries ago, and they still are sold in popular markets. To assess the authenticity and the conditions on which samples of quinas have been commercialized, using the DNA barcode, chemical and biological assays. Starting with 28 samples of barks acquired on a popular market, 23 had their DNA extracted successfully. The regions matK and rbcL were amplified and sequenced for 15 and 23 samples, respectively. Phytochemical analyses were performed by chromatographic methods, and biological essays were done by antimalarial tests in vitro. The identified species belonged to six different families, many of them endangered or with no correlation with use in traditional medicine as a Brazilian quina. The absence of typical bitter chemical substances indicated that barks have been collected from other species or from very young trees. The results of biological essays confirm the lack of standardization of the sold materials. The integrated approaches proved to be efficient to evaluate medicinal plants sold in popular markets and can be useful for promoting their better use and conservation. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Lensfree diffractive tomography for the imaging of 3D cell cultures

NASA Astrophysics Data System (ADS)

Berdeu, Anthony; Momey, Fabien; Dinten, Jean-Marc; Gidrol, Xavier; Picollet-D'hahan, Nathalie; Allier, Cédric

2017-02-01

New microscopes are needed to help reaching the full potential of 3D organoid culture studies by gathering large quantitative and systematic data over extended periods of time while preserving the integrity of the living sample. In order to reconstruct large volumes while preserving the ability to catch every single cell, we propose new imaging platforms based on lens-free microscopy, a technic which is addressing these needs in the context of 2D cell culture, providing label-free and non-phototoxic acquisition of large datasets. We built lens-free diffractive tomography setups performing multi-angle acquisitions of 3D organoid cultures embedded in Matrigel and developed dedicated 3D holographic reconstruction algorithms based on the Fourier diffraction theorem. Nonetheless, holographic setups do not record the phase of the incident wave front and the biological samples in Petri dish strongly limit the angular coverage. These limitations introduce numerous artefacts in the sample reconstruction. We developed several methods to overcome them, such as multi-wavelength imaging or iterative phase retrieval. The most promising technic currently developed is based on a regularised inverse problem approach directly applied on the 3D volume to reconstruct. 3D reconstructions were performed on several complex samples such as 3D networks or spheroids embedded in capsules with large reconstructed volumes up to 25 mm3 while still being able to identify single cells. To our knowledge, this is the first time that such an inverse problem approach is implemented in the context of lens-free diffractive tomography enabling to reconstruct large fully 3D volumes of unstained biological samples.

Interlaboratory trial for the measurement of total cobalt in equine urine and plasma by ICP-MS.

PubMed

Popot, Marie-Agnes; Ho, Emmie N M; Stojiljkovic, Natali; Bagilet, Florian; Remy, Pierre; Maciejewski, Pascal; Loup, Benoit; Chan, George H M; Hargrave, Sabine; Arthur, Rick M; Russo, Charlie; White, James; Hincks, Pamela; Pearce, Clive; Ganio, George; Zahra, Paul; Batty, David; Jarrett, Mark; Brooks, Lydia; Prescott, Lise-Anne; Bailly-Chouriberry, Ludovic; Bonnaire, Yves; Wan, Terence S M

2017-09-01

Cobalt is an essential mineral micronutrient and is regularly present in equine nutritional and feed supplements. Therefore, cobalt is naturally present at low concentrations in biological samples. The administration of cobalt chloride is considered to be blood doping and is thus prohibited. To control the misuse of cobalt, it was mandatory to establish an international threshold for cobalt in plasma and/or in urine. To achieve this goal, an international collaboration, consisting of an interlaboratory comparison between 5 laboratories for the urine study and 8 laboratories for the plasma study, has been undertaken. Quantification of cobalt in the biological samples was performed by inductively coupled plasma-mass spectrometry (ICP-MS). Ring tests were based on the analysis of 5 urine samples supplemented at concentrations ranging from 5 up to 500 ng/mL and 5 plasma samples spiked at concentrations ranging from 0.5 up to 25 ng/mL. The results obtained from the different laboratories were collected, compiled, and compared to assess the reproducibility and robustness of cobalt quantification measurements. The statistical approach for the ring test for total cobalt in urine was based on the determination of percentage deviations from the calculated means, while robust statistics based on the calculated median were applied to the ring test for total cobalt in plasma. The inter-laboratory comparisons in urine and in plasma were successful so that 97.6% of the urine samples and 97.5% of the plasma samples gave satisfactory results. Threshold values for cobalt in plasma and urine were established from data only obtained by laboratories involved in the ring test. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Availability of MudPIT data for classification of biological samples.

PubMed

Silvestre, Dario Di; Zoppis, Italo; Brambilla, Francesca; Bellettato, Valeria; Mauri, Giancarlo; Mauri, Pierluigi

2013-01-14

Mass spectrometry is an important analytical tool for clinical proteomics. Primarily employed for biomarker discovery, it is increasingly used for developing methods which may help to provide unambiguous diagnosis of biological samples. In this context, we investigated the classification of phenotypes by applying support vector machine (SVM) on experimental data obtained by MudPIT approach. In particular, we compared the performance capabilities of SVM by using two independent collection of complex samples and different data-types, such as mass spectra (m/z), peptides and proteins. Globally, protein and peptide data allowed a better discriminant informative content than experimental mass spectra (overall accuracy higher than 87% in both collection 1 and 2). These results indicate that sequencing of peptides and proteins reduces the experimental noise affecting the raw mass spectra, and allows the extraction of more informative features available for the effective classification of samples. In addition, proteins and peptides features selected by SVM matched for 80% with the differentially expressed proteins identified by the MAProMa software. These findings confirm the availability of the most label-free quantitative methods based on processing of spectral count and SEQUEST-based SCORE values. On the other hand, it stresses the usefulness of MudPIT data for a correct grouping of sample phenotypes, by applying both supervised and unsupervised learning algorithms. This capacity permit the evaluation of actual samples and it is a good starting point to translate proteomic methodology to clinical application.

Standard Biological Parts Knowledgebase

PubMed Central

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

SERS-based inverse molecular sentinel (iMS) nanoprobes for multiplexed detection of microRNA cancer biomarkers in biological samples

NASA Astrophysics Data System (ADS)

Crawford, Bridget M.; Wang, Hsin-Neng; Fales, Andrew M.; Bowie, Michelle L.; Seewaldt, Victoria L.; Vo-Dinh, Tuan

2017-02-01

The development of sensitive and selective biosensing techniques is of great interest for clinical diagnostics. Here, we describe the development and application of a surface enhanced Raman scattering (SERS) sensing technology, referred to as "inverse Molecular Sentinel (iMS)" nanoprobes, for the detection of nucleic acid biomarkers in biological samples. This iMS nanoprobe involves the use of plasmonic-active nanostars as the sensing platform for a homogenous assay for multiplexed detection of nucleic acid biomarkers, including DNA, RNA and microRNA (miRNA). The "OFF-to-ON" signal switch is based on a non-enzymatic strand-displacement process and the conformational change of stem-loop (hairpin) oligonucleotide probes upon target binding. Here, we demonstrate the development of iMS nanoprobes for the detection of DNA sequences as well as a modified design of the nanoprobe for the detection of short (22-nt) microRNA sequences. The application of iMS nanoprobes to detect miRNAs in real biological samples was performed with total small RNA extracted from breast cancer cell lines. The multiplex capability of the iMS technique was demonstrated using a mixture of the two differently labeled nanoprobes to detect miR-21 and miR-34a miRNA biomarkers for breast cancer. The results of this study demonstrate the feasibility of applying the iMS technique for multiplexed detection of nucleic acid biomarkers, including short miRNAs molecules.

Gaussian graphical modeling reveals specific lipid correlations in glioblastoma cells

NASA Astrophysics Data System (ADS)

Mueller, Nikola S.; Krumsiek, Jan; Theis, Fabian J.; Böhm, Christian; Meyer-Bäse, Anke

2011-06-01

Advances in high-throughput measurements of biological specimens necessitate the development of biologically driven computational techniques. To understand the molecular level of many human diseases, such as cancer, lipid quantifications have been shown to offer an excellent opportunity to reveal disease-specific regulations. The data analysis of the cell lipidome, however, remains a challenging task and cannot be accomplished solely based on intuitive reasoning. We have developed a method to identify a lipid correlation network which is entirely disease-specific. A powerful method to correlate experimentally measured lipid levels across the various samples is a Gaussian Graphical Model (GGM), which is based on partial correlation coefficients. In contrast to regular Pearson correlations, partial correlations aim to identify only direct correlations while eliminating indirect associations. Conventional GGM calculations on the entire dataset can, however, not provide information on whether a correlation is truly disease-specific with respect to the disease samples and not a correlation of control samples. Thus, we implemented a novel differential GGM approach unraveling only the disease-specific correlations, and applied it to the lipidome of immortal Glioblastoma tumor cells. A large set of lipid species were measured by mass spectrometry in order to evaluate lipid remodeling as a result to a combination of perturbation of cells inducing programmed cell death, while the other perturbations served solely as biological controls. With the differential GGM, we were able to reveal Glioblastoma-specific lipid correlations to advance biomedical research on novel gene therapies.

Integrated quantification and identification of aldehydes and ketones in biological samples.

PubMed

Siegel, David; Meinema, Anne C; Permentier, Hjalmar; Hopfgartner, Gérard; Bischoff, Rainer

2014-05-20

The identification of unknown compounds remains to be a bottleneck of mass spectrometry (MS)-based metabolomics screening experiments. Here, we present a novel approach which facilitates the identification and quantification of analytes containing aldehyde and ketone groups in biological samples by adding chemical information to MS data. Our strategy is based on rapid autosampler-in-needle-derivatization with p-toluenesulfonylhydrazine (TSH). The resulting TSH-hydrazones are separated by ultrahigh-performance liquid chromatography (UHPLC) and detected by electrospray ionization-quadrupole-time-of-flight (ESI-QqTOF) mass spectrometry using a SWATH (Sequential Window Acquisition of all Theoretical Fragment-Ion Spectra) data-independent high-resolution mass spectrometry (HR-MS) approach. Derivatization makes small, poorly ionizable or retained analytes amenable to reversed phase chromatography and electrospray ionization in both polarities. Negatively charged TSH-hydrazone ions furthermore show a simple and predictable fragmentation pattern upon collision induced dissociation, which enables the chemo-selective screening for unknown aldehydes and ketones via a signature fragment ion (m/z 155.0172). By means of SWATH, targeted and nontargeted application scenarios of the suggested derivatization route are enabled in the frame of a single UHPLC-ESI-QqTOF-HR-MS workflow. The method's ability to simultaneously quantify and identify molecules containing aldehyde and ketone groups is demonstrated using 61 target analytes from various compound classes and a (13)C labeled yeast matrix. The identification of unknowns in biological samples is detailed using the example of indole-3-acetaldehyde.

Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization.

PubMed

Glaser, Joshua I; Zamft, Bradley M; Church, George M; Kording, Konrad P

2015-01-01

Current high-resolution imaging techniques require an intact sample that preserves spatial relationships. We here present a novel approach, "puzzle imaging," that allows imaging a spatially scrambled sample. This technique takes many spatially disordered samples, and then pieces them back together using local properties embedded within the sample. We show that puzzle imaging can efficiently produce high-resolution images using dimensionality reduction algorithms. We demonstrate the theoretical capabilities of puzzle imaging in three biological scenarios, showing that (1) relatively precise 3-dimensional brain imaging is possible; (2) the physical structure of a neural network can often be recovered based only on the neural connectivity matrix; and (3) a chemical map could be reproduced using bacteria with chemosensitive DNA and conjugative transfer. The ability to reconstruct scrambled images promises to enable imaging based on DNA sequencing of homogenized tissue samples.

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

PubMed

duVerle, David A; Yotsukura, Sohiya; Nomura, Seitaro; Aburatani, Hiroyuki; Tsuda, Koji

2016-09-13

Single-cell RNA sequencing is fast becoming one the standard method for gene expression measurement, providing unique insights into cellular processes. A number of methods, based on general dimensionality reduction techniques, have been suggested to help infer and visualise the underlying structure of cell populations from single-cell expression levels, yet their models generally lack proper biological grounding and struggle at identifying complex differentiation paths. Here we introduce cellTree: an R/Bioconductor package that uses a novel statistical approach, based on document analysis techniques, to produce tree structures outlining the hierarchical relationship between single-cell samples, while identifying latent groups of genes that can provide biological insights. With cellTree, we provide experimentalists with an easy-to-use tool, based on statistically and biologically-sound algorithms, to efficiently explore and visualise single-cell RNA data. The cellTree package is publicly available in the online Bionconductor repository at: http://bioconductor.org/packages/cellTree/ .

The effect on cadaver blood DNA identification by the use of targeted and whole body post-mortem computed tomography angiography.

PubMed

Rutty, Guy N; Barber, Jade; Amoroso, Jasmin; Morgan, Bruno; Graham, Eleanor A M

2013-12-01

Post-mortem computed tomography angiography (PMCTA) involves the injection of contrast agents. This could have both a dilution effect on biological fluid samples and could affect subsequent post-contrast analytical laboratory processes. We undertook a small sample study of 10 targeted and 10 whole body PMCTA cases to consider whether or not these two methods of PMCTA could affect post-PMCTA cadaver blood based DNA identification. We used standard methodology to examine DNA from blood samples obtained before and after the PMCTA procedure. We illustrate that neither of these PMCTA methods had an effect on the alleles called following short tandem repeat based DNA profiling, and therefore the ability to undertake post-PMCTA blood based DNA identification.

Clinically relevant advances in on-chip affinity-based electrophoresis and electrochromatography.

PubMed

Hou, Chenlu; Herr, Amy E

2008-08-01

Clinical and point-of-care disease diagnostics promise to play an important role in personalized medicine, new approaches to global health, and health monitoring. Emerging instrument platforms based on lab-on-a-chip technology can confer performance advantages successfully exploited in electrophoresis and electrochromatography to affinity-based electrokinetic separations. This review surveys lab-on-a-chip diagnostic developments in affinity-based electrokinetic separations for quantitation of proteins, integration of preparatory functions needed for subsequent analysis of diverse biological samples, and initial forays into multiplexed analyses. The technologies detailed here underpin new clinical and point-of-care diagnostic strategies. The techniques and devices promise to advance translation of until now laboratory-based sample preparation and analytical assays to near-patient settings.

An algal model for predicting attainment of tiered biological criteria of Maine's streams and rivers

USGS Publications Warehouse

Danielson, Thomas J.; Loftin, Cyndy; Tsomides, Leonidas; DiFranco, Jeanne L.; Connors, Beth; Courtemanch, David L.; Drummond, Francis; Davies, Susan

2012-01-01

State water-quality professionals developing new biological assessment methods often have difficulty relating assessment results to narrative criteria in water-quality standards. An alternative to selecting index thresholds arbitrarily is to include the Biological Condition Gradient (BCG) in the development of the assessment method. The BCG describes tiers of biological community condition to help identify and communicate the position of a water body along a gradient of water quality ranging from natural to degraded. Although originally developed for fish and macroinvertebrate communities of streams and rivers, the BCG is easily adapted to other habitats and taxonomic groups. We developed a discriminant analysis model with stream algal data to predict attainment of tiered aquatic-life uses in Maine's water-quality standards. We modified the BCG framework for Maine stream algae, related the BCG tiers to Maine's tiered aquatic-life uses, and identified appropriate algal metrics for describing BCG tiers. Using a modified Delphi method, 5 aquatic biologists independently evaluated algal community metrics for 230 samples from streams and rivers across the state and assigned a BCG tier (1–6) and Maine water quality class (AA/A, B, C, nonattainment of any class) to each sample. We used minimally disturbed reference sites to approximate natural conditions (Tier 1). Biologist class assignments were unanimous for 53% of samples, and 42% of samples differed by 1 class. The biologists debated and developed consensus class assignments. A linear discriminant model built to replicate a priori class assignments correctly classified 95% of 150 samples in the model training set and 91% of 80 samples in the model validation set. Locally derived metrics based on BCG taxon tolerance groupings (e.g., sensitive, intermediate, tolerant) were more effective than were metrics developed in other regions. Adding the algal discriminant model to Maine's existing macroinvertebrate discriminant model will broaden detection of biological impairment and further diagnose sources of impairment. The algal discriminant model is specific to Maine, but our approach of explicitly tying an assessment tool to tiered aquatic-life goals is widely transferrable to other regions, taxonomic groups, and waterbody types.

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Associations of benthic macroinvertebrate assemblages with environmental variables in the upper Clear Creek watershed, California

USGS Publications Warehouse

Brown, Larry R.; May, Jason T.; Wulff, Marissa

2012-01-01

Benthic macroinvertebrates are integral components of stream ecosystems and are often used to assess the ecological integrity of streams. We sampled streams in the upper Clear Creek drainage in the Klamath—Siskiyou Ecoregion of northwestern California in fall 2004 (17 sites) and 2005 (original 17 plus 4 new sites) with the objectives of documenting the benthic macroinvertebrate assemblages supported by the streams in the area, determining how those assemblages respond to environmental variables, assessing the biological condition of the streams using a benthic index of biotic integrity (IBI), and understanding the assemblages in the context of biodiversity of the ecoregion. We collected both reach-wide (RW) and targeted-riffle (TR) macroinvertebrate samples at each site. The macroinvertebrate assemblages were diverse, with over 150 genera collected for each sampling protocol. The macroinvertebrate assemblages appeared to be most responsive to a general habitat gradient based on stream size, gradient, flow, and dominance of riffles. A second important habitat gradient was based on elevation and dominance of riffles. A gradient in water quality based on concentrations of dissolved ions and metals was also important. Models based on these 3 gradients had Spearman's rank correlations with macroinvertebrate taxonomic composition of 0.60 and 0.50 for the TR and RW samples, respectively. The majority (>50%) of the sites were in good or very good biological condition based on IBI scores. The diversity of macroinvertebrate assemblages is associated with the diversity of habitats available in the Klamath—Siskiyou Ecoregion. Maintaining the aquatic habitats in good condition is important in itself but is also vital to maintaining biodiversity in this diverse and unique ecoregion.

NBIT Program Phase I (2007-2010). Part 1, Chapters 1 Through 4

DTIC Science & Technology

2009-08-27

2 schematically shows the sample prepared before hydrothermal synthesis . The thin layer of Zn was convered to ZnO nanowires during hydrothermal ... Nanoparticle -Based Magnetically Amplified Surface Plasmon Resonance (Mag-SPR) Techniques; Jinwoo Cheon (Yonsei University, Korea) and A. Paul...Ion; Chapter 3 ? Ultra-Sensitive Biological Detection via Nanoparticle -Based Magnetically Amplified Surface Plasmon Resonance (Mag-SPR) Techniques

Fission neutron source in Rome

NASA Astrophysics Data System (ADS)

Coppola, Mario; Di Majo, V.; Ingrao, G.; Rebessi, S.; Testa, A.

1997-02-01

A fission neutron source is operating in Rome at the ENEA Casaccia Research Center since 1971, consisting of a low power fast reactor named RSV-Tapiro. it is employed for a variety of experiments, including dosimetry, material testing, radiation protection and biology. In particular, application to experimental radiobiology includes studies of the biological action of neutrons in the whole-body irradiated animal, or in specialized systems in vivo or in vitro. For his purpose a vertical irradiation facility was originally constructed. Recently, a new horizontal irradiation facility has been designed to allow the exposure of larger samples or larger sample batches at one time. Dosimetry at the sample irradiation positions is routinely carried out by the conventional method of using two ion chambers. This physical dosimetry has recently been compared with the results of biological dosimetry based on the detection of chromosomal aberrations in peripheral blood human lymphocytes irradiated in vitro. A characterization of the radiation quality in the two configurations has been carried out by tissue equivalent proportional counter microdosimetry measurements. Information about the main characteristics of the reactor and the two irradiation facilities is provided and relevant results of the various measurements are summarized. Radiobiological results obtained using this neutron source are also briefly outlined.

Placental Proteomics: A Shortcut to Biological Insight

PubMed Central

Robinson, John M.; Vandré, Dale D.; Ackerman, William E.

2012-01-01

Proteomics analysis of biological samples has the potential to identify novel protein expression patterns and/or changes in protein expression patterns in different developmental or disease states. An important component of successful proteomics research, at least in its present form, is to reduce the complexity of the sample if it is derived from cells or tissues. One method to simplify complex tissues is to focus on a specific, highly purified sub-proteome. Using this approach we have developed methods to prepare highly enriched fractions of the apical plasma membrane of the syncytiotrophoblast. Through proteomics analysis of this fraction we have identified over five hundred proteins several of which were previously not known to reside in the syncytiotrophoblast. Herein, we focus on two of these, dysferlin and myoferlin. These proteins, largely known from studies of skeletal muscle, may not have been found in the human placenta were it not for discovery-based proteomics analysis. This new knowledge, acquired through a discovery-driven approach, can now be applied for the generation of hypothesis-based experimentation. Thus discovery-based and hypothesis-based research are complimentary approaches that when coupled together can hasten scientific discoveries. PMID:19070895

The New Bedford Harbor Superfund site long-term monitoring program (1993-2009).

PubMed

Nelson, William G; Bergen, Barbara J

2012-12-01

New Bedford Harbor (NBH), located in southeastern Massachusetts, was designated as a marine Superfund site in 1983 due to sediment contamination by polychlorinated biphenyls (PCBs). Based on risks to human health and the environment, the first two phases of the site cleanup involved dredging PCB-contaminated sediments from the harbor. Therefore, a long-term monitoring program (LTM) was developed to measure spatial and temporal chemical and biological changes in sediment, water, and biota to assess the effects and effectiveness of the remedial activities. A systematic, probabilistic sampling design was used to select sediment sampling stations. This unbiased design allowed the three segments of the harbor to be compared spatially and temporally to quantify changes resulting from dredging the contaminated sediments. Sediment was collected at each station, and chemical (e.g., PCBs and metals), physical (e.g., grain size), and biological (e.g., benthic community) measurements were conducted on all samples. This paper describes the overall NBH-LTM approach and the results from the five rounds of sample collections. There is a decreasing spatial gradient in sediment PCB concentrations from the northern boundary (upper harbor) to the southern boundary (outer harbor) of the site. Along this same transect, there is an increase in biological condition (e.g., benthic community diversity). Temporally, the contaminant and biological gradients have been maintained since the 1993 baseline collection; however, since the onset of full-scale remediation, PCB concentrations have decreased throughout the site, and one of the benthic community indices has shown significant improvement in the lower and outer harbor areas.

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

PubMed

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

2015-02-21

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

Paleolakes and life on early Mars

NASA Technical Reports Server (NTRS)

Meyer, M. A.; Wharton, Robert A., Jr.; Mckay, C. P.

1991-01-01

Two distinct directions have begun to elucidate key parameters in the search for extinct life on Mars. Carbonate sediments, deposited about 10,000 years ago in association with biological activity, have been sampled from the paleolake beds of Lake Vanda and Meirs in the McMurdo Dry Valleys in Antarctica. These samples are being analyzed for simple biological signatures that remain in cold and dry paleolake sediments, namely microfossils, percent carbonate, and total organic carbon. Our second initiative is the study of Colour Lake, in the Canadian Arctic, that periodically maintains a perennial ice cover. Physical measurements started this year will be used to determine one end point for ice covered lake environments and will be compared to continuous measurements from Antarctic lakes started in November 1985. Interestingly, Colour Lake also supports benthic mat communities, but the low pH precludes carbonate deposition. This research will broaden our knowledge base for what conditions are necessary for ice covered lake formation and what biological signatures will remain in paleolake deposits.

Spectrophotometric determination of 4-acetamidophenyl N'-(sulphanilamide) acetate in biological fluids.

PubMed

Shah, Bhavna; Patil, Pravin; Shah, Hirva

2014-01-01

A simple, accurate and low cost spectrophotometric method is proposed for the determination of the synthesized paracetamol derivative; 4-acetamidophenyl N'-(sulphanilamide) acetate (APSA) in biological fluids. The spectrophotometric method is based on a condensation reaction between the alcoholic solution of APSA and acidic solution of p-dimethylaminobenzaldeyde (DPMK) to generate a yellow colored product. The linear range for the determination of APSA was 1-10 µg mL(-1) with molar absorptivity of 3.6877 × 10(4) L mol(-1) cm(-1) and Sandell's sensitivity of 0.001 µg cm-2/0.001 absorbance unit. During the inter-day and intra-day analysis, the relative standard deviation for replicated determination of APSA was found to be less than 2.0% and accuracy was 99.20-101.60% and 99.10-101.30% in blood and urine samples, respectively. There was no interference with commonly used blood and urine sample. The developed spectrophotometric method was successfully applied to assess APSA in biological fluids.

The validation of forensic DNA extraction systems to utilize soil contaminated biological evidence.

PubMed

Kasu, Mohaimin; Shires, Karen

2015-07-01

The production of full DNA profiles from biological evidence found in soil has a high failure rate due largely to the inhibitory substance humic acid (HA). Abundant in various natural soils, HA co-extracts with DNA during extraction and inhibits DNA profiling by binding to the molecular components of the genotyping assay. To successfully utilize traces of soil contaminated evidence, such as that found at many murder and rape crime scenes in South Africa, a reliable HA removal extraction system would often be selected based on previous validation studies. However, for many standard forensic DNA extraction systems, peer-reviewed publications detailing the efficacy on soil evidence is either lacking or is incomplete. Consequently, these sample types are often not collected or fail to yield suitable DNA material due to the use of unsuitable methodology. The aim of this study was to validate the common forensic DNA collection and extraction systems used in South Africa, namely DNA IQ, FTA elute and Nucleosave for processing blood and saliva contaminated with HA. A forensic appropriate volume of biological evidence was spiked with HA (0, 0.5, 1.5 and 2.5 mg/ml) and processed through each extraction protocol for the evaluation of HA removal using QPCR and STR-genotyping. The DNA IQ magnetic bead system effectively removed HA from highly contaminated blood and saliva, and generated consistently acceptable STR profiles from both artificially spiked samples and crude soil samples. This system is highly recommended for use on soil-contaminated evidence over the cellulose card-based systems currently being preferentially used for DNA sample collection. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Water-quality assessment of the Ozark Plateaus study unit, Arkansas, Kansas, Missouri, and Oklahoma- summary of information on pesticides, 1970-90

USGS Publications Warehouse

Bell, Richard W.; Joseph, Robert L.; Freiwald, David A.

1996-01-01

Historical pesticide data from 1970-90 were compiled for 140 surface-water, 92 ground-water, 55 streambed-sediment, and 120 biological-tissue sampling sites within the Ozark Plateaus National Water-Quality Assessment Program study unit. Surface-water, bed-sediment, and biological-tissue sites have drainage basins predominantly in the Springfield and Salem Plateaus; ground-water sites are predominantly located in the Osage Plains and Mississippi Alluvial Plain. Many sites were sampled only once or twice during this period. A large percentage of the samples were collected in the mid-1970's and early 1980's for surface water, 1990 for ground water, the late 1980's for surface water, 1990 for ground water, the late 1980's for bed sediment, and the early 1980's for biological tissue. Pesticide use was approximately 4.2 million pounds per year of active ingredients from 1982-85 in the study unit and was generally greatest in the Springfield and Salem Plateaus pasturelands and in the Osage Plains and Mississippi Alluvial Plain cropland areas. The most frequently applied pesticide in the study unit was 2,4-D. Alachlor was the second most applied pesticide. Corn, pasture, rice, sorghum, and soybeans received approximately 90 percent of the pesticides applied within the study unit. The highest pesticide application rate per acre occurred on these crops in the Osage Plains and Mississippi Alluvial Plain. Pastureland was the predominant crop type in 50 of the 94 counties in the study unit. Toxaphene, the pesticide having the most number of detections in surface water, was found in 17 of 866 samples from 5 of 112 sites. Concentrations ranged from 0.1 to 6.0 micrograms per liter. Six other pesticides or pesticide metabolites were detected in 12 or more surface-water samples: DDE, dieldrin, DDT, aldrin, 2,4-D, and lindane. The maximum concentration for these pesticides was less than 1.0 micrograms per liter. Atrazine, the pesticide having the most number of detections in ground water, was found in 15 of 95 samples from 15 of 79 wells with concentrations ranging from 0.1 to 8.2 micrograms per liter. Metolachlor, alachlor, and prometon were detected more than once with maximum concentrations less than 1.0 micrograms per liter, except for prometon (2.4 micrograms per liter). Chlordane was the pesticide having the most number of detections in bed sediment and biological tissue. Chlordane was detected in 12 of 73 samples from 10 of 45 bed-sediment sites with concentrations ranging from 2.0 to 240 micrograms per kilogram. In biological tissue, chlordane was found in 93 of 151 samples from 39 of 53 sites with concentrations ranging from 0.009 to 8.6 milligrams per kilogram. Other pesticides or pesticide metabolites detected more than once in bed sediment include DDT, DDD, p,p'-DDE, DDE, and hexachlorobenzene and in biological tissue include DDT, p,p'-DDE, and hexachlorobenzene. Quality criteria or standards have been established for 15 of the pesticides detected in the study unit. For surface-water samples, the drinking water maximum contaminant level for alachlor was exceeded in one sample from one site in 1982. For ground-water samples, the drinking water maximum contaminant level for atrazine was exceeded in four samples from four wells in 1990. For biological-tissue samples collected during the years 1982-89, the fish tissue action levels for chlordane (19 sites; 26 samples), heptachlor epoxide (3 sites; 3 samples), p,p'-DDE (2 sites; 2 samples), dieldrin (2 sites, 2 samples), and mirex (1 site; 1 sample) were exceeded. For bed-sediment samples, quality criteria or standards were not exceeded for any pesticide. Pesticides do not pose any widespread or persistent problems in the study unit, based on the limited number of samples that exceeded quality criteria and standards.

Remote sensing of life: polarimetric signatures of photosynthetic pigments as sensitive biomarkers

NASA Astrophysics Data System (ADS)

Berdyugina, Svetlana V.; Kuhn, Jeff R.; Harrington, David M.; Šantl-Temkiv, Tina; Messersmith, E. John

2016-01-01

We develop a polarimetry-based remote-sensing method for detecting and identifying life forms in distant worlds and distinguishing them from non-biological species. To achieve this we have designed and built a bio-polarimetric laboratory experiment BioPol for measuring optical polarized spectra of various biological and non-biological samples. Here we focus on biological pigments, which are common in plants and bacteria that employ them either for photosynthesis or for protection against reactive oxygen species. Photosynthesis, which provides organisms with the ability to use light as a source of energy, emerged early in the evolution of life on Earth. The ability to harvest such a significant energy resource could likely also develop on habited exoplanets. Thus, we investigate the detectability of biomolecules that can capture photons of particular wavelengths and contribute to storing their energy in chemical bonds. We have carried out laboratory spectropolarimetric measurements of a representative sample of plants containing various amounts of pigments such as chlorophyll, carotenoids and others. We have also measured a variety of non-biological samples (sands, rocks). Using our lab measurements, we have modelled intensity and polarized spectra of Earth-like planets having different surface coverage by photosynthetic organisms, deserted land and ocean, as well as clouds. Our results demonstrate that linearly polarized spectra provide very sensitive and rather unambiguous detection of photosynthetic pigments of various kinds. Our work paves the path towards analogous measurements of microorganisms and remote sensing of microbial ecology on the Earth and of extraterrestrial life on other planets and moons.

Fast vaporization solid phase microextraction and ion mobility spectrometry: A new approach for determination of creatinine in biological fluids.

PubMed

Jafari, Mostafa; Ebrahimzadeh, Homeira; Banitaba, Mohamma Hossein

2015-11-01

In this work a rapid and simple method for creatinine determination in urine and plasma samples based on aqueous derivatization of creatinine and complete vaporization of sample (as low as 10 µL), followed by ion mobility spectrometry analysis has been proposed. The effect of four important parameters (extraction temperature, total volume of solution, desorption temperature and extraction time) on ion mobility signal has been studied. Under the optimized conditions, the quantitative response of ion mobility spectrometry for creatinine was linear in the range of 0-500 mg L(-1) with a detection limit of 0.6 mg L(-1) in urine and 0-250 mg L(-1) with a detection limit of 2.6 mg L(-1) in plasma sample. The limit of quantitation of creatinine was 2.1 mg L(-1) and 8.7 mg L(-1) in urine and plasma samples, respectively. The relative standard deviation of the method was found to be 13%. The method was successfully applied to the analysis of creatinine in biological samples, showing recoveries from 92% to 104% in urine and 101-110% in plasma samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Variability in stream chemistry in relation to urban development and biological condition in seven metropolitan areas of the United States, 1999-2004

USGS Publications Warehouse

Beaulieu, Karen M.; Bell, Amanda H.; Coles, James F.

2012-01-01

Beginning in 1999, the U.S. Geological Survey National Water Quality Assessment Program investigated the effects of urban development on stream ecosystems in nine metropolitan study areas across the United States. In seven of these study areas, stream-chemistry samples were collected every other month for 1 year at 6 to 10 sites. Within a study area, the sites collectively represented a gradient of urban development from minimally to highly developed watersheds, based on the percentage of urban land cover; depending on study area, the land cover before urban development was either forested or agricultural. The stream-chemistry factors measured in the samples were total nitrogen, total phosphorus, chloride, and pesticide toxicity. These data were used to characterize the stream-chemistry factors in four ways (hereafter referred to as characterizations)—seasonal high-flow value, seasonal low-flow value, the median value (representing a single integrated value of the factor over the year), and the standard deviation of values (representing the variation of the factor over the year). Aquatic macroinvertebrate communities were sampled at each site to infer the biological condition of the stream based on the relative sensitivity of the community to environmental stressors. A Spearman correlation analysis was used to evaluate relations between (1) urban development and each characterization of the stream-chemistry factors and (2) the biological condition of a stream and the different characterizations of chloride and pesticide toxicity. Overall, the study areas where the land cover before urban development was primarily forested had a greater number of moderate and strong relations compared with the study areas where the land cover before urban development was primarily agriculture; this was true when urban development was correlated with the stream-chemistry factors (except chloride) and when chloride and pesticide toxicity was correlated with the biological condition. Except for primarily phosphorus in two study areas, stream-chemistry factors generally increased with urban development, and among the different characterizations, the median value typically indicated the strongest relations. The variation in stream-chemistry factors throughout the year generally increased with urban development, indicating that water quality became less consistent as watersheds were developed. In study areas with high annual snow fall, the variation in chloride concentrations throughout the year was particularly strongly related to urban development, likely a result of road salt applications during the winter. The relations of the biological condition to chloride and pesticide toxicity were calculated irrespective of urban development, but the overall results indicated that the relations were still stronger in the study areas that had been forested before urban development. The weaker relations in the study areas that had been agricultural before urban development were likely the results of biological communities having been degraded from agricultural practices in the watersheds. Collectively, these results indicated that, compared with sampling a stream at a single point in time, sampling at regular intervals during a year may provide a more representative measure of water quality, especially in the areas of high urban development where water quality fluctuated more widely between samples. Furthermore, the use of "integrated" values of stream chemistry factors may be more appropriate when assessing relations to the biological condition of a stream because the taxa composition of a biological community typically reflects the water-quality conditions over time.

Same-Sex Behavior and its Relationship with Sexual and Health-Related Practices Among a Population-Based Sample of Women in Puerto Rico: Implications for Cancer Prevention and Control.

PubMed

Soto-Salgado, Marievelisse; Colón-López, Vivian; Perez, Cynthia; Muñoz-Masso, Cristina; Marrero, Edmir; Suárez, Erick; Ortiz, Ana P

2016-01-01

This secondary data analysis aimed to estimate the prevalence of same-sex behavior and sexual and health-related practices of a population-based sample (n=560) of women aged 16-64 years in Puerto Rico (PR). Data collection included interviews and biologic samples. Seven percent of the sample had had sex with other women (WSW). Age-adjusted logistic regression models indicated that WSW had higher odds of history of cancer, having ≥ 7 lifetime sexual partners, using sex toys and sharing them, and use of tobacco and illicit drugs. Future research is needed to address the health needs of WSW, including cancer-related risk factors and sexual practices.

A two-step electrodialysis method for DNA purification from polluted metallic environmental samples.

PubMed

Rodríguez-Mejía, José Luis; Martínez-Anaya, Claudia; Folch-Mallol, Jorge Luis; Dantán-González, Edgar

2008-08-01

Extracting DNA from samples of polluted environments using standard methods often results in low yields of poor-quality material unsuited to subsequent manipulation and analysis by molecular biological techniques. Here, we report a novel two-step electrodialysis-based method for the extraction of DNA from environmental samples. This technique permits the rapid and efficient isolation of high-quality DNA based on its acidic nature, and without the requirement for phenol-chloroform-isoamyl alcohol cleanup and ethanol precipitation steps. Subsequent PCR, endonuclease restriction, and cloning reactions were successfully performed utilizing DNA obtained by electrodialysis, whereas some or all of these techniques failed using DNA extracted with two alternative methods. We also show that his technique is applicable to purify DNA from a range of polluted and nonpolluted samples.

Machine vision for digital microfluidics

NASA Astrophysics Data System (ADS)

Shin, Yong-Jun; Lee, Jeong-Bong

2010-01-01

Machine vision is widely used in an industrial environment today. It can perform various tasks, such as inspecting and controlling production processes, that may require humanlike intelligence. The importance of imaging technology for biological research or medical diagnosis is greater than ever. For example, fluorescent reporter imaging enables scientists to study the dynamics of gene networks with high spatial and temporal resolution. Such high-throughput imaging is increasingly demanding the use of machine vision for real-time analysis and control. Digital microfluidics is a relatively new technology with expectations of becoming a true lab-on-a-chip platform. Utilizing digital microfluidics, only small amounts of biological samples are required and the experimental procedures can be automatically controlled. There is a strong need for the development of a digital microfluidics system integrated with machine vision for innovative biological research today. In this paper, we show how machine vision can be applied to digital microfluidics by demonstrating two applications: machine vision-based measurement of the kinetics of biomolecular interactions and machine vision-based droplet motion control. It is expected that digital microfluidics-based machine vision system will add intelligence and automation to high-throughput biological imaging in the future.

Field-deployed Metabolomics for Assessing Waters Impacted by Point and Non-Point Sources of Contamination

EPA Science Inventory

Metabolomics is becoming well-established for studying chemical contaminant-induced alterations to normal biological function. For example, the literature contains a wealth of laboratory-based studies involving analysis of samples from organisms exposed to individual chemical tox...

NASA Research Announcement

NASA Technical Reports Server (NTRS)

Chiaramonte, Fran

2002-01-01

This paper presents viewgraphs of NASA's strategic and fundamental research program at the Office of Biological and Physical Research (OBPR). The topics include: 1) Colloid-Polymer Samples; 2) Pool Boiling Experiment; 3) The Dynamics of Miscible Interfaces: A Space Flight Experiment (MIDAS); and 4) ISS and Ground-based Facilities.

Field-deployed Metabolomics for Assessing Surface Waters Impacted by Point and Non-Point Sources of Contamination

EPA Science Inventory

Metabolomics has become well-established for studying chemical contaminant-induced alterations to normal biological function. For example, the literature contains a wealth of laboratory-based studies involving analysis of samples from organisms exposed to individual chemical toxi...

Nanoimaging using soft X-ray and EUV laser-plasma sources

NASA Astrophysics Data System (ADS)

Wachulak, Przemyslaw; Torrisi, Alfio; Ayele, Mesfin; Bartnik, Andrzej; Czwartos, Joanna; Węgrzyński, Łukasz; Fok, Tomasz; Fiedorowicz, Henryk

2018-01-01

In this work we present three experimental, compact desk-top imaging systems: SXR and EUV full field microscopes and the SXR contact microscope. The systems are based on laser-plasma EUV and SXR sources based on a double stream gas puff target. The EUV and SXR full field microscopes, operating at 13.8 nm and 2.88 nm wavelengths are capable of imaging nanostructures with a sub-50 nm spatial resolution and short (seconds) exposure times. The SXR contact microscope operates in the "water-window" spectral range and produces an imprint of the internal structure of the imaged sample in a thin layer of SXR sensitive photoresist. Applications of such desk-top EUV and SXR microscopes, mostly for biological samples (CT26 fibroblast cells and Keratinocytes) are also presented. Details about the sources, the microscopes as well as the imaging results for various objects will be presented and discussed. The development of such compact imaging systems may be important to the new research related to biological, material science and nanotechnology applications.

Review of Detection of Brucella sp. by Polymerase Chain Reaction

PubMed Central

Yu, Wei Ling; Nielsen, Klaus

2010-01-01

Here we present a review of most of the currently used polymerase chain reaction (PCR)-based methods for identification of Brucella bacteria in biological samples. We focused in particular on methods using single-pair primers, multiplex primers, real-time PCRs, PCRs for marine Brucella, and PCRs for molecular biotyping. These methods are becoming very important tools for the identification of Brucella, at the species level and recently also at the biovar level. These techniques require minimum biological containment and can provide results in a very short time. In addition, genetic fingerprinting of isolates aid in epidemiological studies of the disease and its control. PCR-based methods are more useful and practical than conventional methods used to identify Brucella spp., and new methods for Brucella spp identification and typing are still being developed. However, the sensitivity, specificity, and issues of quality control and quality assurance using these methods must be fully validated on clinical samples before PCR can be used in routine laboratory testing for brucellosis. PMID:20718083

Functionalized Gold Nanoparticles for the Detection of C-Reactive Protein

PubMed Central

António, Maria

2018-01-01

C-reactive protein (CRP) is a very important biomarker of infection and inflammation for a number of diseases. Routine CRP measurements with high sensitivity and reliability are highly relevant to the assessment of states of inflammation and the efficacy of treatment intervention, and require the development of very sensitive, selective, fast, robust and reproducible assays. Gold nanoparticles (Au NPs) are distinguished for their unique electrical and optical properties and the ability to conjugate with biomolecules. Au NP-based probes have attracted considerable attention in the last decade in the analysis of biological samples due to their simplicity, high sensitivity and selectivity. Thus, this article aims to be a critical and constructive analysis of the literature of the last three years regarding the advances made in the development of bioanalytical assays based on gold nanoparticles for the in vitro detection and quantification of C-reactive protein from biological samples. Current methods for Au NP synthesis and the strategies for surface modification aiming at selectivity towards CRP are highlighted. PMID:29597295

Bayesian approach to MSD-based analysis of particle motion in live cells.

PubMed

Monnier, Nilah; Guo, Syuan-Ming; Mori, Masashi; He, Jun; Lénárt, Péter; Bathe, Mark

2012-08-08

Quantitative tracking of particle motion using live-cell imaging is a powerful approach to understanding the mechanism of transport of biological molecules, organelles, and cells. However, inferring complex stochastic motion models from single-particle trajectories in an objective manner is nontrivial due to noise from sampling limitations and biological heterogeneity. Here, we present a systematic Bayesian approach to multiple-hypothesis testing of a general set of competing motion models based on particle mean-square displacements that automatically classifies particle motion, properly accounting for sampling limitations and correlated noise while appropriately penalizing model complexity according to Occam's Razor to avoid over-fitting. We test the procedure rigorously using simulated trajectories for which the underlying physical process is known, demonstrating that it chooses the simplest physical model that explains the observed data. Further, we show that computed model probabilities provide a reliability test for the downstream biological interpretation of associated parameter values. We subsequently illustrate the broad utility of the approach by applying it to disparate biological systems including experimental particle trajectories from chromosomes, kinetochores, and membrane receptors undergoing a variety of complex motions. This automated and objective Bayesian framework easily scales to large numbers of particle trajectories, making it ideal for classifying the complex motion of large numbers of single molecules and cells from high-throughput screens, as well as single-cell-, tissue-, and organism-level studies. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Head and facial anthropometry of mixed-race US Army male soldiers for military design and sizing: a pilot study.

PubMed

Yokota, Miyo

2005-05-01

In the United States, the biologically admixed population is increasing. Such demographic changes may affect the distribution of anthropometric characteristics, which are incorporated into the design of equipment and clothing for the US Army and other large organizations. The purpose of this study was to examine multivariate craniofacial anthropometric distributions between biologically admixed male populations and single racial groups of Black and White males. Multivariate statistical results suggested that nose breadth and lip length were different between Blacks and Whites. Such differences may be considered for adjustments to respirators and chemical-biological protective masks. However, based on this pilot study, multivariate anthropometric distributions of admixed individuals were within the distributions of single racial groups. Based on the sample reported, sizing and designing for the admixed groups are not necessary if anthropometric distributions of single racial groups comprising admixed groups are known.

MStern Blotting-High Throughput Polyvinylidene Fluoride (PVDF) Membrane-Based Proteomic Sample Preparation for 96-Well Plates.

PubMed

Berger, Sebastian T; Ahmed, Saima; Muntel, Jan; Cuevas Polo, Nerea; Bachur, Richard; Kentsis, Alex; Steen, Judith; Steen, Hanno

2015-10-01

We describe a 96-well plate compatible membrane-based proteomic sample processing method, which enables the complete processing of 96 samples (or multiples thereof) within a single workday. This method uses a large-pore hydrophobic PVDF membrane that efficiently adsorbs proteins, resulting in fast liquid transfer through the membrane and significantly reduced sample processing times. Low liquid transfer speeds have prevented the useful 96-well plate implementation of FASP as a widely used membrane-based proteomic sample processing method. We validated our approach on whole-cell lysate and urine and cerebrospinal fluid as clinically relevant body fluids. Without compromising peptide and protein identification, our method uses a vacuum manifold and circumvents the need for digest desalting, making our processing method compatible with standard liquid handling robots. In summary, our new method maintains the strengths of FASP and simultaneously overcomes one of the major limitations of FASP without compromising protein identification and quantification. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Reduced electron exposure for energy-dispersive spectroscopy using dynamic sampling

DOE PAGES

Zhang, Yan; Godaliyadda, G. M. Dilshan; Ferrier, Nicola; ...

2017-10-23

Analytical electron microscopy and spectroscopy of biological specimens, polymers, and other beam sensitive materials has been a challenging area due to irradiation damage. There is a pressing need to develop novel imaging and spectroscopic imaging methods that will minimize such sample damage as well as reduce the data acquisition time. The latter is useful for high-throughput analysis of materials structure and chemistry. Here, in this work, we present a novel machine learning based method for dynamic sparse sampling of EDS data using a scanning electron microscope. Our method, based on the supervised learning approach for dynamic sampling algorithm and neuralmore » networks based classification of EDS data, allows a dramatic reduction in the total sampling of up to 90%, while maintaining the fidelity of the reconstructed elemental maps and spectroscopic data. In conclusion, we believe this approach will enable imaging and elemental mapping of materials that would otherwise be inaccessible to these analysis techniques.« less

Label-Free Nanopore Biosensor for Rapid and Highly Sensitive Cocaine Detection in Complex Biological Fluids.

PubMed

Rauf, Sana; Zhang, Ling; Ali, Asghar; Liu, Yang; Li, Jinghong

2017-02-24

Detection of very low amounts of illicit drugs such as cocaine in clinical fluids like serum continues to be important for many areas in the fight against drug trafficking. Herein, we constructed a label-free nanopore biosensor for rapid and highly sensitive detection of cocaine in human serum and saliva samples based on target-induced strand release strategy. In this bioassay, an aptamer for cocaine was prehybridized with a short complementary DNA. Owing to cocaine specific binding with aptamer, the short DNA strand was displaced from aptamer and translocation of this output DNA through α-hemolysin nanopore generated distinct spike-like current blockages. When plotted in double-logarithmic scale, a linear relationship between target cocaine concentration and output DNA event frequency was obtained in a wide concentration range from 50 nM to 100 μM of cocaine, with the limit of detection down to 50 nM. In addition, this aptamer-based sensor method was successfully applied for cocaine detection in complex biological fluids like human saliva and serum samples with great selectivity. Simple preparation, low cost, rapid, label-free, and real sample detection are the motivating factors for practical application of the proposed biosensor.

Next-Generation Proteomics and Its Application to Clinical Breast Cancer Research.

PubMed

Mardamshina, Mariya; Geiger, Tamar

2017-10-01

Proteomics technology aims to map the protein landscapes of biological samples, and it can be applied to a variety of samples, including cells, tissues, and body fluids. Because the proteins are the main functional molecules in the cells, their levels reflect much more accurately the cellular phenotype and the regulatory processes within them than gene levels, mutations, and even mRNA levels. With the advancement in the technology, it is possible now to obtain comprehensive views of the biological systems and to study large patient cohorts in a streamlined manner. In this review we discuss the technological advancements in mass spectrometry-based proteomics, which allow analysis of breast cancer tissue samples, leading to the first large-scale breast cancer proteomics studies. Furthermore, we discuss the technological developments in blood-based biomarker discovery, which provide the basis for future development of assays for routine clinical use. Although these are only the first steps in implementation of proteomics into the clinic, extensive collaborative work between these worlds will undoubtedly lead to major discoveries and advances in clinical practice. Copyright © 2017 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Optofluidic bioimaging platform for quantitative phase imaging of lab on a chip devices using digital holographic microscopy.

PubMed

Pandiyan, Vimal Prabhu; John, Renu

2016-01-20

We propose a versatile 3D phase-imaging microscope platform for real-time imaging of optomicrofluidic devices based on the principle of digital holographic microscopy (DHM). Lab-on-chip microfluidic devices fabricated on transparent polydimethylsiloxane (PDMS) and glass substrates have attained wide popularity in biological sensing applications. However, monitoring, visualization, and characterization of microfluidic devices, microfluidic flows, and the biochemical kinetics happening in these devices is difficult due to the lack of proper techniques for real-time imaging and analysis. The traditional bright-field microscopic techniques fail in imaging applications, as the microfluidic channels and the fluids carrying biological samples are transparent and not visible in bright light. Phase-based microscopy techniques that can image the phase of the microfluidic channel and changes in refractive indices due to the fluids and biological samples present in the channel are ideal for imaging the fluid flow dynamics in a microfluidic channel at high resolutions. This paper demonstrates three-dimensional imaging of a microfluidic device with nanometric depth precisions and high SNR. We demonstrate imaging of microelectrodes of nanometric thickness patterned on glass substrate and the microfluidic channel. Three-dimensional imaging of a transparent PDMS optomicrofluidic channel, fluid flow, and live yeast cell flow in this channel has been demonstrated using DHM. We also quantify the average velocity of fluid flow through the channel. In comparison to any conventional bright-field microscope, the 3D depth information in the images illustrated in this work carry much information about the biological system under observation. The results demonstrated in this paper prove the high potential of DHM in imaging optofluidic devices; detection of pathogens, cells, and bioanalytes on lab-on-chip devices; and in studying microfluidic dynamics in real time based on phase changes.

Quality of Streams in Johnson County, Kansas, and Relations to Environmental Variables, 2003-07

USGS Publications Warehouse

Rasmussen, Teresa J.; Poulton, Barry C.; Graham, Jennifer L.

2009-01-01

The quality of streams and relations to environmental variables in Johnson County, northeastern Kansas, were evaluated using water, streambed sediment, land use, streamflow, habitat, algal periphyton (benthic algae), and benthic macroinvertebrate data. Water, streambed sediment, and macroinvertebrate samples were collected in March 2007 during base flow at 20 stream sites that represent 11 different watersheds in the county. In addition, algal periphyton samples were collected twice (spring and summer 2007) at one-half of the sites. Environmental data including water and streambed-sediment chemistry data (primarily nutrients, fecal-indicator bacteria, and organic wastewater compounds), land use, streamflow, and habitat data were used in statistical analyses to evaluate relations between biological conditions and variables that may affect them. This report includes an evaluation of water and streambed-sediment chemistry, assessment of habitat conditions, comparison of biological community attributes (such as composition, diversity, and abundance) among sampling sites, placement of sampling sites into impairment categories, evaluation of biological data relative to environmental variables, and evaluation of changes in biological communities and effects of urbanization. This evaluation is useful for understanding factors that affect stream quality, for improving water-quality management programs, and for documenting changing conditions over time. The information will become increasingly important for protecting streams in the future as urbanization continues. Results of this study indicate that the biological quality at nearly all biological sampling sites in Johnson County has some level of impairment. Periphyton taxa generally were indicative of somewhat degraded conditions with small to moderate amounts of organic enrichment. Camp Branch in the Blue River watershed was the only site that met State criteria for full support of aquatic life in 2007. Since 2003, biological quality improved at one rural sampling site, possibly because of changes in wastewater affecting the site, and declined at three urban sites possibly because of the combined effects of ongoing development. Rural streams in the western and southern parts of the county, with land-use conditions similar to those found at the State reference site (Captain Creek), continue to support some organisms normally associated with healthy streams. Several environmental factors contribute to biological indicators of stream quality. The primary factor explaining biological quality at sites in Johnson County was the amount of urbanization upstream in the watershed. Specific conductance of stream water, which is a measure of dissolved solids in water and is determined primarily by the amount of groundwater contributing to streamflow, the amount of urbanization, and discharges from wastewater and industrial sites, was strongly negatively correlated with biological stream quality as indicated by macroinvertebrate metrics. Concentration of polycyclic aromatic hydrocarbons (PAHs) in streambed sediment also was negatively correlated with biological stream quality. Individual habitat variables that most commonly were positively correlated with biological indicators included stream sinuosity, buffer length, and substrate cover diversity. Riffle substrate embeddedness and sediment deposition commonly were negatively correlated with favorable metric scores. Statistical analysis indicated that specific conductance, impervious surface area (a measure of urbanization), and stream sinuosity explained 85 percent of the variance in macroinvertebrate communities. Management practices affecting environmental variables that appear to be most important for Johnson County streams include protection of stream corridors, measures that reduce the effects of impervious surfaces associated with urbanization, reduction of dissolved solids in stream water, reduction of PAHs entering streams and

Comparability among four invertebrate sampling methods, Fountain Creek Basin, Colorado, 2010-2012

USGS Publications Warehouse

Zuellig, Robert E.; Bruce, James F.; Stogner, Sr., Robert W.; Brown, Krystal D.

2014-01-01

The U.S. Geological Survey, in cooperation with Colorado Springs City Engineering and Colorado Springs Utilities, designed a study to determine if sampling method and sample timing resulted in comparable samples and assessments of biological condition. To accomplish this task, annual invertebrate samples were collected concurrently using four sampling methods at 15 U.S. Geological Survey streamflow gages in the Fountain Creek basin from 2010 to 2012. Collectively, the four methods are used by local (U.S. Geological Survey cooperative monitoring program) and State monitoring programs (Colorado Department of Public Health and Environment) in the Fountain Creek basin to produce two distinct sample types for each program that target single-and multiple-habitats. This study found distinguishable differences between single-and multi-habitat sample types using both community similarities and multi-metric index values, while methods from each program within sample type were comparable. This indicates that the Colorado Department of Public Health and Environment methods were compatible with the cooperative monitoring program methods within multi-and single-habitat sample types. Comparisons between September and October samples found distinguishable differences based on community similarities for both sample types, whereas only differences were found for single-habitat samples when multi-metric index values were considered. At one site, differences between September and October index values from single-habitat samples resulted in opposing assessments of biological condition. Direct application of the results to inform the revision of the existing Fountain Creek basin U.S. Geological Survey cooperative monitoring program are discussed.

SU-F-J-193: Efficient Dose Extinction Method for Water Equivalent Path Length (WEPL) of Real Tissue Samples for Validation of CT HU to Stopping Power Conversion

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

Zhang, R; Baer, E; Jee, K

Purpose: For proton therapy, an accurate model of CT HU to relative stopping power (RSP) conversion is essential. In current practice, validation of these models relies solely on measurements of tissue substitutes with standard compositions. Validation based on real tissue samples would be much more direct and can address variations between patients. This study intends to develop an efficient and accurate system based on the concept of dose extinction to measure WEPL and retrieve RSP in biological tissue in large number of types. Methods: A broad AP proton beam delivering a spread out Bragg peak (SOBP) is used to irradiatemore » the samples with a Matrixx detector positioned immediately below. A water tank was placed on top of the samples, with the water level controllable in sub-millimeter by a remotely controlled dosing pump. While gradually lowering the water level with beam on, the transmission dose was recorded at 1 frame/sec. The WEPL were determined as the difference between the known beam range of the delivered SOBP (80%) and the water level corresponding to 80% of measured dose profiles in time. A Gammex 467 phantom was used to test the system and various types of biological tissue was measured. Results: RSP for all Gammex inserts, expect the one made with lung-450 material (<2% error), were determined within ±0.5% error. Depends on the WEPL of investigated phantom, a measurement takes around 10 min, which can be accelerated by a faster pump. Conclusion: Based on the concept of dose extinction, a system was explored to measure WEPL efficiently and accurately for a large number of samples. This allows the validation of CT HU to stopping power conversions based on large number of samples and real tissues. It also allows the assessment of beam uncertainties due to variations over patients, which issue has never been sufficiently studied before.« less

Method of and apparatus for determining the similarity of a biological analyte from a model constructed from known biological fluids

DOEpatents

Robinson, Mark R.; Ward, Kenneth J.; Eaton, Robert P.; Haaland, David M.

1990-01-01

The characteristics of a biological fluid sample having an analyte are determined from a model constructed from plural known biological fluid samples. The model is a function of the concentration of materials in the known fluid samples as a function of absorption of wideband infrared energy. The wideband infrared energy is coupled to the analyte containing sample so there is differential absorption of the infrared energy as a function of the wavelength of the wideband infrared energy incident on the analyte containing sample. The differential absorption causes intensity variations of the infrared energy incident on the analyte containing sample as a function of sample wavelength of the energy, and concentration of the unknown analyte is determined from the thus-derived intensity variations of the infrared energy as a function of wavelength from the model absorption versus wavelength function.

[The present study situation and application prospect of nail analysis for abused drugs].

PubMed

Chen, Hang; Xiang, Ping; Shen, Min

2010-10-01

In forensic toxicology analysis, various types of biological samples have their own special characteristics and scope of applications. In this article, the physiological structure of nails, methods for collecting and pre-processing samples, and for analyzing some poisons and drugs in the nails are reviewed with details. This paper introduces the influence factors of drug abuse of the nails. The prospects of its further applications are concluded based on the research results. Nails, as an unconventional bio-sample without general application, show great potential and advantages in forensic toxicology.

Microfluidics Integrated Biosensors: A Leading Technology towards Lab-on-a-Chip and Sensing Applications

PubMed Central

Luka, George; Ahmadi, Ali; Najjaran, Homayoun; Alocilja, Evangelyn; DeRosa, Maria; Wolthers, Kirsten; Malki, Ahmed; Aziz, Hassan; Althani, Asmaa; Hoorfar, Mina

2015-01-01

A biosensor can be defined as a compact analytical device or unit incorporating a biological or biologically derived sensitive recognition element immobilized on a physicochemical transducer to measure one or more analytes. Microfluidic systems, on the other hand, provide throughput processing, enhance transport for controlling the flow conditions, increase the mixing rate of different reagents, reduce sample and reagents volume (down to nanoliter), increase sensitivity of detection, and utilize the same platform for both sample preparation and detection. In view of these advantages, the integration of microfluidic and biosensor technologies provides the ability to merge chemical and biological components into a single platform and offers new opportunities for future biosensing applications including portability, disposability, real-time detection, unprecedented accuracies, and simultaneous analysis of different analytes in a single device. This review aims at representing advances and achievements in the field of microfluidic-based biosensing. The review also presents examples extracted from the literature to demonstrate the advantages of merging microfluidic and biosensing technologies and illustrate the versatility that such integration promises in the future biosensing for emerging areas of biological engineering, biomedical studies, point-of-care diagnostics, environmental monitoring, and precision agriculture. PMID:26633409

A review of sensors, samplers and methods for marine biological observations.

NASA Astrophysics Data System (ADS)

Simmons, S. E.; Chavez, F.; Pearlman, J.; Working Group, T B S

2016-02-01

Physical scientists now have Argo floats, gliders and AUVs to supplement satellites to provide a 3-D view of the time-varying global ocean temperature and salinity structure. Biogeochemists are catching up with evolving sensors for nitrate, optical properties, oxygen and pH that can now be added to these autonomous systems. Biologists are still lagging, although some promising sensor systems based on but not limited to acoustic, chemical, genomic or imaging techniques, that can sense from microbes to whales, are on the horizon. These techniques can not only be applied in situ but also on samples returned to the laboratory using the autonomous systems. The number of samples is limiting, requiring adaptive and smart systems. Given the importance of biology to ocean health and the future earth, and the present reliance on humans and ships for observing species and abundance it is paramount that new biological sensor systems be developed. This abstract will review recent efforts to identify core biological variables for the US Integrated Ocean Observing System and address new sensors and innovations for observing these variables, particularly focused on availability and maturity of sensors. The relevance of this work in a global context will also be touched on.

Determination of selenium in biological samples with an energy-dispersive X-ray fluorescence spectrometer.

PubMed

Li, Xiaoli; Yu, Zhaoshui

2016-05-01

Selenium is both a nutrient and a toxin. Selenium-especially organic selenium-is a core component of human nutrition. Thus, it is very important to measure selenium in biological samples. The limited sensitivity of conventional XRF hampers its widespread use in biological samples. Here, we describe the use of high-energy (100kV, 600W) linearly polarized beam energy-dispersive X-Ray fluorescence spectroscopy (EDXRF) in tandem with a three-dimensional optics design to determine 0.1-5.1μgg(-1) levels of selenium in biological samples. The effects of various experimental parameters such as applied voltage, acquisition time, secondary target and various filters were thoroughly investigated. The detection limit of selenium in biological samples via high-energy (100kV, 600W) linearly polarized beam energy-dispersive X-ray fluorescence spectroscopy was decreased by one order of magnitude versus conventional XRF (Paltridge et al., 2012) and found to be 0.1μg/g. To the best of our knowledge, this is the first report to describe EDXRF measurements of Se in biological samples with important implications for the nutrition and analytical chemistry communities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Ambient Molecular Analysis of Biological Tissue Using Low-Energy, Femtosecond Laser Vaporization and Nanospray Postionization Mass Spectrometry

NASA Astrophysics Data System (ADS)

Shi, Fengjian; Flanigan, Paul M.; Archer, Jieutonne J.; Levis, Robert J.

2016-03-01

Direct analysis of plant and animal tissue samples by laser electrospray mass spectrometry (LEMS) was investigated using low-energy, femtosecond duration laser vaporization at wavelengths of 800 and 1042 nm followed by nanospray postionization. Low-energy (<50 μJ), fiber-based 1042 nm LEMS (F-LEMS) allowed interrogation of the molecular species in fresh flower petal and leaf samples using 435 fs, 10 Hz bursts of 20 pulses from a Ytterbium-doped fiber laser and revealed comparable results to high energy (75-1120 μJ), 45 fs, 800 nm Ti:Sapphire-based LEMS (Ti:Sapphire-LEMS) measurements. Anthocyanins, sugars, and other metabolites were successfully detected and revealed the anticipated metabolite profile for the petal and leaf samples. Phospholipids, especially phosphatidylcholine, were identified from a fresh mouse brain section sample using Ti:Sapphire-LEMS without the application of matrix. These lipid features were suppressed in both the fiber-based and Ti:Sapphire-based LEMS measurements when the brain sample was prepared using the optimal cutting temperature compounds that are commonly used in animal tissue cryosections.

Diagnosis of neonatal group B Streptococcus sepsis by nested-PCR of residual urine samples

PubMed Central

Cezarino, Bruno Nicolino; Yamamoto, Lidia; Del Negro, Gilda Maria Barbaro; Rocha, Daisy; Okay, Thelma Suely

2008-01-01

Group B streptococcus (GBS) remains the most common cause of early-onset sepsis in newborns. Laboratory gold-standard, broth culture methods are highly specific, but lack sensitivity. The aim of this study was to validate a nested-PCR and to determine whether residue volumes of urine samples obtained by non invasive, non sterile methods could be used to confirm neonatal GBS sepsis. The nested-PCR was performed with primers of the major GBS surface antigen. Unavailability of biological samples to perform life supporting exams, as well as others to elucidate the etiology of infections is a frequent problem concerning newborn patients. Nevertheless, we decided to include cases according to strict criteria: newborns had to present with signs and symptoms compatible with GBS infection; at least one of the following biological samples had to be sent for culture: blood, urine, or cerebrospinal fluid; availability of residue volumes of the samples sent for cultures, or of others collected on the day of hospitalization, prior to antibiotic therapy prescription, to be analyzed by PCR; favorable outcome after GBS empiric treatment. In only one newborn GBS infection was confirmed by cultures, while infection was only presumptive in the other three patients (they fulfilled inclusion criteria but were GBS-culture negative). From a total of 12 biological samples (5 blood, 3 CSF and 4 urine specimen), eight were tested by culture methods (2/8 were positive), and 8 were tested by PCR (7/8 were positive), and only 4 samples were simultaneously tested by both methods (1 positive by culture and 3 by PCR). In conclusion, although based on a restricted number of neonates and samples, our results suggest that the proposed nested-PCR might be used to diagnose GBS sepsis as it has successfully amplified the three types of biological samples analyzed (blood, urine and cerebrospinal fluid), and was more sensitive than culture methods as PCR in urine confirmed diagnosis in all four patients. Moreover, PCR has enabled us to use residue volumes of urine samples collected by non invasive, non sterile methods, what is technically adequate as GBS is not part of the normal urine flora, thus avoiding invasive procedures such as suprapubic bladder punction or transurethral catheterization. At the same time, the use of urine instead of blood samples could help preventing newborns blood spoliation. PMID:24031170

Topological study of nanomaterials using surface-enhanced ellipsometric contrast microscopy (SEEC)

NASA Astrophysics Data System (ADS)

Muckenhirn, Sylvain

2016-03-01

Innovations in nanotechnology are empowering scientists to deepen their understanding of physical, chemical and biological mechanisms. Powerful and precise characterization systems are essential to meet researchers' requirements. SEEC (Surface Enhanced Ellipsometric Contrast) microscopy is an innovative advanced optical technique based on ellipsometric and interference fringes of Fizeau principles. This technique offers live and label-free topographic imaging of organic, inorganic and biological samples with high Z resolution (down to 0.1nm thickness), and enhanced X-Y detection limit (down to 1.5nm width). This technique has been successfully applied to the study of nanometric films and structures, biological layers, and nano-objects. We applied SEEC technology to different applications explored below.

Marine Antifreeze Proteins: Structure, Function, and Application to Cryopreservation as a Potential Cryoprotectant

PubMed Central

Kim, Hak Jun; Lee, Jun Hyuck; Hur, Young Baek; Lee, Chang Woo; Park, Sun-Ha; Koo, Bon-Won

2017-01-01

Antifreeze proteins (AFPs) are biological antifreezes with unique properties, including thermal hysteresis (TH), ice recrystallization inhibition (IRI), and interaction with membranes and/or membrane proteins. These properties have been utilized in the preservation of biological samples at low temperatures. Here, we review the structure and function of marine-derived AFPs, including moderately active fish AFPs and hyperactive polar AFPs. We also survey previous and current reports of cryopreservation using AFPs. Cryopreserved biological samples are relatively diverse ranging from diatoms and reproductive cells to embryos and organs. Cryopreserved biological samples mainly originate from mammals. Most cryopreservation trials using marine-derived AFPs have demonstrated that addition of AFPs can improve post-thaw viability regardless of freezing method (slow-freezing or vitrification), storage temperature, and types of biological sample type. PMID:28134801

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

PubMed

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

2011-01-01

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

Infrared microspectroscopy of live cells in microfluidic devices (MD-IRMS): toward a powerful label-free cell-based assay.

PubMed

Vaccari, L; Birarda, G; Businaro, L; Pacor, S; Grenci, G

2012-06-05

Until nowadays most infrared microspectroscopy (IRMS) experiments on biological specimens (i.e., tissues or cells) have been routinely carried out on fixed or dried samples in order to circumvent water absorption problems. In this paper, we demonstrate the possibility to widen the range of in-vitro IRMS experiments to vibrational analysis of live cellular samples, thanks to the development of novel biocompatible IR-visible transparent microfluidic devices (MD). In order to highlight the biological relevance of IRMS in MD (MD-IRMS), we performed a systematic exploration of the biochemical alterations induced by different fixation protocols, ethanol 70% and formaldehyde solution 4%, as well as air-drying on U937 leukemic monocytes by comparing their IR vibrational features with the live U937 counterpart. Both fixation and air-drying procedures affected lipid composition and order as well as protein structure at a different extent while they both induced structural alterations in nucleic acids. Therefore, only IRMS of live cells can provide reliable information on both DNA and RNA structure and on their cellular dynamic. In summary, we show that MD-IRMS of live cells is feasible, reliable, and biologically relevant to be recognized as a label-free cell-based assay.

Mass spectrometry-based targeted quantitative proteomics: achieving sensitive and reproducible detection of proteins.

PubMed

Boja, Emily S; Rodriguez, Henry

2012-04-01

Traditional shotgun proteomics used to detect a mixture of hundreds to thousands of proteins through mass spectrometric analysis, has been the standard approach in research to profile protein content in a biological sample which could lead to the discovery of new (and all) protein candidates with diagnostic, prognostic, and therapeutic values. In practice, this approach requires significant resources and time, and does not necessarily represent the goal of the researcher who would rather study a subset of such discovered proteins (including their variations or posttranslational modifications) under different biological conditions. In this context, targeted proteomics is playing an increasingly important role in the accurate measurement of protein targets in biological samples in the hope of elucidating the molecular mechanism of cellular function via the understanding of intricate protein networks and pathways. One such (targeted) approach, selected reaction monitoring (or multiple reaction monitoring) mass spectrometry (MRM-MS), offers the capability of measuring multiple proteins with higher sensitivity and throughput than shotgun proteomics. Developing and validating MRM-MS-based assays, however, is an extensive and iterative process, requiring a coordinated and collaborative effort by the scientific community through the sharing of publicly accessible data and datasets, bioinformatic tools, standard operating procedures, and well characterized reagents. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Suppression of Botrytis cinerea on necrotic grapevine tissues by early-season applications of natural products and biological control agents.

PubMed

Calvo-Garrido, Carlos; Viñas, Inmaculada; Elmer, Philip A G; Usall, Josep; Teixidó, Neus

2014-04-01

Necrotic tissues within grape (Vitis vinifera) bunches represent an important source of Botrytis cinerea inoculum for Botrytis bunch rot (BBR) at harvest in vineyards. This research quantified the incidence of B. cinerea on necrotic floral and fruit tissues and the efficacy of biologically based treatments for suppression of B. cinerea secondary inoculum within developing bunches. At veraison (2009 and 2010), samples of aborted flowers, aborted fruits and calyptras were collected, and the incidence and sporulation of B. cinerea were determined. Aborted fruits presented significantly higher incidence in untreated samples. Early-season applications of Candida sake plus Fungicover®, Fungicover alone or Ulocladium oudemansii significantly reduced B. cinerea incidence on aborted flowers and calyptras by 46-85%. Chitosan treatment significantly reduced B. cinerea incidence on calyptras. None of the treatments reduced B. cinerea incidence on aborted fruits. Treatments significantly reduced sporulation severity by 48% or more. Treatments were effective at reducing B. cinerea secondary inoculum on necrotic tissues, in spite of the variable control on aborted fruits. This is the first report to quantify B. cinerea on several tissues of bunch trash and to describe the effective suppression of saprophytic B. cinerea inoculum by biologically based treatments. © 2013 Society of Chemical Industry.

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

PubMed Central

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

2011-01-01

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

Gamma-hydroxybutyric acid endogenous production and post-mortem behaviour - the importance of different biological matrices, cut-off reference values, sample collection and storage conditions.

PubMed

Castro, André L; Dias, Mário; Reis, Flávio; Teixeira, Helena M

2014-10-01

Gamma-Hydroxybutyric Acid (GHB) is an endogenous compound with a story of clinical use, since the 1960's. However, due to its secondary effects, it has become a controlled substance, entering the illicit market for recreational and "dance club scene" use, muscle enhancement purposes and drug-facilitated sexual assaults. Its endogenous context can bring some difficulties when interpreting, in a forensic context, the analytical values achieved in biological samples. This manuscript reviewed several crucial aspects related to GHB forensic toxicology evaluation, such as its post-mortem behaviour in biological samples; endogenous production values, whether in in vivo and in post-mortem samples; sampling and storage conditions (including stability tests); and cut-off reference values evaluation for different biological samples, such as whole blood, plasma, serum, urine, saliva, bile, vitreous humour and hair. This revision highlights the need of specific sampling care, storage conditions, and cut-off reference values interpretation in different biological samples, essential for proper practical application in forensic toxicology. Copyright © 2014 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture

DOEpatents

Lassahn, Gordon D.; Lancaster, Gregory D.; Apel, William A.; Thompson, Vicki S.

2013-01-08

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture are described. According to one embodiment, an image portion identification method includes accessing data regarding an image depicting a plurality of biological substrates corresponding to at least one biological sample and indicating presence of at least one biological indicator within the biological sample and, using processing circuitry, automatically identifying a portion of the image depicting one of the biological substrates but not others of the biological substrates.

Apparatus and methods for manipulation and optimization of biological systems

NASA Technical Reports Server (NTRS)

Sun, Ren (Inventor); Ho, Chih-Ming (Inventor); Wong, Pak Kin (Inventor); Yu, Fuqu (Inventor)

2012-01-01

The invention provides systems and methods for manipulating, e.g., optimizing and controlling, biological systems, e.g., for eliciting a more desired biological response of biological sample, such as a tissue, organ, and/or a cell. In one aspect, systems and methods of the invention operate by efficiently searching through a large parametric space of stimuli and system parameters to manipulate, control, and optimize the response of biological samples sustained in the system, e.g., a bioreactor. In alternative aspects, systems include a device for sustaining cells or tissue samples, one or more actuators for stimulating the samples via biochemical, electromagnetic, thermal, mechanical, and/or optical stimulation, one or more sensors for measuring a biological response signal of the samples resulting from the stimulation of the sample. In one aspect, the systems and methods of the invention use at least one optimization algorithm to modify the actuator's control inputs for stimulation, responsive to the sensor's output of response signals. The compositions and methods of the invention can be used, e.g., to for systems optimization of any biological manufacturing or experimental system, e.g., bioreactors for proteins, e.g., therapeutic proteins, polypeptides or peptides for vaccines, and the like, small molecules (e.g., antibiotics), polysaccharides, lipids, and the like. Another use of the apparatus and methods includes combination drug therapy, e.g. optimal drug cocktail, directed cell proliferations and differentiations, e.g. in tissue engineering, e.g. neural progenitor cells differentiation, and discovery of key parameters in complex biological systems.

Acquiring 3-D information about thick objects from differential interference contrast images using texture extraction

NASA Astrophysics Data System (ADS)

Sierra, Heidy; Brooks, Dana; Dimarzio, Charles

2010-07-01

The extraction of 3-D morphological information about thick objects is explored in this work. We extract this information from 3-D differential interference contrast (DIC) images by applying a texture detection method. Texture extraction methods have been successfully used in different applications to study biological samples. A 3-D texture image is obtained by applying a local entropy-based texture extraction method. The use of this method to detect regions of blastocyst mouse embryos that are used in assisted reproduction techniques such as in vitro fertilization is presented as an example. Results demonstrate the potential of using texture detection methods to improve morphological analysis of thick samples, which is relevant to many biomedical and biological studies. Fluorescence and optical quadrature microscope phase images are used for validation.

Phase-contrast x-ray computed tomography for biological imaging

NASA Astrophysics Data System (ADS)

Momose, Atsushi; Takeda, Tohoru; Itai, Yuji

1997-10-01

We have shown so far that 3D structures in biological sot tissues such as cancer can be revealed by phase-contrast x- ray computed tomography using an x-ray interferometer. As a next step, we aim at applications of this technique to in vivo observation, including radiographic applications. For this purpose, the size of view field is desired to be more than a few centimeters. Therefore, a larger x-ray interferometer should be used with x-rays of higher energy. We have evaluated the optimal x-ray energy from an aspect of does as a function of sample size. Moreover, desired spatial resolution to an image sensor is discussed as functions of x-ray energy and sample size, basing on a requirement in the analysis of interference fringes.

Non-contact multi-frequency magnetic induction spectroscopy system for industrial-scale bio-impedance measurement

NASA Astrophysics Data System (ADS)

O'Toole, M. D.; Marsh, L. A.; Davidson, J. L.; Tan, Y. M.; Armitage, D. W.; Peyton, A. J.

2015-03-01

Biological tissues have a complex impedance, or bio-impedance, profile which changes with respect to frequency. This is caused by dispersion mechanisms which govern how the electromagnetic field interacts with the tissue at the cellular and molecular level. Measuring the bio-impedance spectra of a biological sample can potentially provide insight into the sample’s properties and its cellular structure. This has obvious applications in the medical, pharmaceutical and food-based industrial domains. However, measuring the bio-impedance spectra non-destructively and in a way which is practical at an industrial scale presents substantial challenges. The low conductivity of the sample requires a highly sensitive instrument, while the demands of industrial-scale operation require a fast high-throughput sensor of rugged design. In this paper, we describe a multi-frequency magnetic induction spectroscopy (MIS) system suitable for industrial-scale, non-contact, spectroscopic bio-impedance measurement over a bandwidth of 156 kHz-2.5 MHz. The system sensitivity and performance are investigated using calibration and known reference samples. It is shown to yield rapid and consistently sensitive results with good long-term stability. The system is then used to obtain conductivity spectra of a number of biological test samples, including yeast suspensions of varying concentration and a range of agricultural produce, such as apples, pears, nectarines, kiwis, potatoes, oranges and tomatoes.

Implementation of a Multiplex and Quantitative Proteomics Platform for Assessing Protein Lysates Using DNA-Barcoded Antibodies.

PubMed

Lee, Jinho; Geiss, Gary K; Demirkan, Gokhan; Vellano, Christopher P; Filanoski, Brian; Lu, Yiling; Ju, Zhenlin; Yu, Shuangxing; Guo, Huifang; Bogatzki, Lisa Y; Carter, Warren; Meredith, Rhonda K; Krishnamurthy, Savitri; Ding, Zhiyong; Beechem, Joseph M; Mills, Gordon B

2018-06-01

Molecular analysis of tumors forms the basis for personalized cancer medicine and increasingly guides patient selection for targeted therapy. Future opportunities for personalized medicine are highlighted by the measurement of protein expression levels via immunohistochemistry, protein arrays, and other approaches; however, sample type, sample quantity, batch effects, and "time to result" are limiting factors for clinical application. Here, we present a development pipeline for a novel multiplexed DNA-labeled antibody platform which digitally quantifies protein expression from lysate samples. We implemented a rigorous validation process for each antibody and show that the platform is amenable to multiple protocols covering nitrocellulose and plate-based methods. Results are highly reproducible across technical and biological replicates, and there are no observed "batch effects" which are common for most multiplex molecular assays. Tests from basal and perturbed cancer cell lines indicate that this platform is comparable to orthogonal proteomic assays such as Reverse-Phase Protein Array, and applicable to measuring the pharmacodynamic effects of clinically-relevant cancer therapeutics. Furthermore, we demonstrate the potential clinical utility of the platform with protein profiling from breast cancer patient samples to identify molecular subtypes. Together, these findings highlight the potential of this platform for enhancing our understanding of cancer biology in a clinical translation setting. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

INDICATORS OF ECOLOGICAL STRESS AND THEIR EXTENT IN THE POPULATION OF NORTHEASTERN LAKES

EPA Science Inventory

The Environmental Monitoring and Assessment Program (EMAP) surveyed 345 northeastern lakes, during 1991-1996, in the first regional-scale survey to use a probability-based sampling design to collect biological assemblage data along with a broad range of physical and chemical indi...

Metabolite profiling of fish skin mucus: a novel approach for minimally-invasive environmental exposure monitoring and surveillance

EPA Science Inventory

The application of 'omics tools to biologically based monitoring and surveillance of aquatic environments shows considerable promise for complementing chemical monitoring in ecological risk assessments. However, few of the current approaches offer the ability to sample ecological...

The Analysis of Cyanide and Its Breakdown Products in Biological Samples

DTIC Science & Technology

2010-01-01

simultaneous GC-mass spectrometric (MS) analysis of cyanide and thiocyanate, and Funazo et al. (53) quantita- tively methylated cyanide and thiocyanate for...selective membrane electrode for thiocyanate ion based on a bis-taurine- salicylic binuclear copper(II) complex as ionophore. Chinese Journal of Chemistry

Cell purification: a new challenge for biobanks.

PubMed

Almeida, Maria; García-Montero, Andres C; Orfao, Alberto

2014-01-01

Performing '-omics' analyses on heterogeneous biological tissue samples, such as blood or bone marrow, can lead to biased or even erroneous results, particularly when the targeted cells and/or molecules are present at relatively low percentages/amounts. In such cases, whole sample analysis will most probably dilute and mask the features of the cell and/or molecules of interest, and this will negatively impact the results and their interpretation. Therefore, frequently it is critically important to have well-characterized and high-quality purified cell populations for the reliable detection of subtle variations in their specific features, such as gene expression profile, protein expression pattern and metabolic status. Biobanks are technological platforms which aim to provide researchers access to a large number of high-quality biological samples and their associated data, particularly to support high-quality scientific and clinical research projects, and such projects will benefit enormously by having access to high-quality purified cell populations or their biological components (e.g. DNA, RNA, proteins). Therefore, a clear opportunity exists for preparative cell sorting techniques in biobanks. Although multiple different cell purification approaches exist or are under development (e.g. cell purification techniques based on cell adherence, density and/or cell size properties, methods based on antibody binding as well as new lab-on-a-chip purification techniques), the choice for a specific technology depends on multiple variables, including cell recovery, purity and yield, among others. In addition, most cell purification approaches are not well suited for high-throughput (HT) purification of multiple cell populations coexisting in a sample. Here we review the most (currently) used cell sorting methods that may be applied for sample preparation in biobanks. For the different approaches, technical considerations about their advantages and limitations are highlighted, and the requirements to be met by a HT cell sorting technology to be used in biobanks are also discussed.

Molecularly imprinted polymer coupled with dispersive liquid-liquid microextraction and injector port silylation: a novel approach for the determination of 3-phenoxybenzoic acid in complex biological samples using gas chromatography-tandem mass spectrometry.

PubMed

Mudiam, Mohana Krishna Reddy; Chauhan, Abhishek; Jain, Rajeev; Dhuriya, Yogesh Kumar; Saxena, Prem Narain; Khanna, Vinay Kumar

2014-01-15

A novel analytical approach based on molecularly imprinted solid phase extraction (MISPE) coupled with dispersive liquid-liquid microextraction (DLLME), and injector port silylation (IPS) has been developed for the selective preconcentration, derivatization and analysis of 3-phenoxybenzoic acid (3-PBA) using gas chromatography-tandem mass spectrometry (GC-MS/MS) in complex biological samples such as rat blood and liver. Factors affecting the synthesis of MIP were evaluated and the best monomer and cross-linker were selected based on binding affinity studies. Various parameters of MISPE, DLLME and IPS were optimized for the selective preconcentration and derivatization of 3-PBA. The developed method offers a good linearity over the calibration range of 0.02-2.5ngmg(-1) and 7.5-2000ngmL(-1) for liver and blood respectively. Under optimized conditions, the recovery of 3-PBA in liver and blood samples were found to be in the range of 83-91%. The detection limit was found to be 0.0045ngmg(-1) and 1.82ngmL(-1) in liver and blood respectively. SRM transition of 271→227 and 271→197 has been selected as quantifier and qualifier transition for 3-PBA derivative. Intra and inter-day precision for five replicates in a day and for five, successive days was found to be less than 8%. The method developed was successfully applied to real samples, i.e. rat blood and tissue for quantitative evaluation of 3-PBA. The analytical approach developed is rapid, economic, simple, eco-friendly and possess immense utility for the analysis of analytes with polar functional groups in complex biological samples by GC-MS/MS. Copyright © 2013 Elsevier B.V. All rights reserved.

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.

PubMed

Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I; Brazma, Alvis; Krestyaninova, Maria

2011-02-15

The Sample avAILability system-SAIL-is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. SAIL is available under Aferro-GPL open source license: https://github.com/sail.

Fast, reagentless and reliable screening of "white powders" during the bioterrorism hoaxes.

PubMed

Włodarski, Maksymilian; Kaliszewski, Miron; Trafny, Elżbieta Anna; Szpakowska, Małgorzata; Lewandowski, Rafał; Bombalska, Aneta; Kwaśny, Mirosław; Kopczyński, Krzysztof; Mularczyk-Oliwa, Monika

2015-03-01

The classification of dry powder samples is an important step in managing the consequences of terrorist incidents. Fluorescence decays of these samples (vegetative bacteria, bacterial endospores, fungi, albumins and several flours) were measured with stroboscopic technique using an EasyLife LS system PTI. Three pulsed nanosecond LED sources, generating 280, 340 and 460nm were employed for samples excitation. The usefulness of a new 460nm light source for fluorescence measurements of dry microbial cells has been demonstrated. The principal component analysis (PCA) and hierarchical cluster analysis (HCA) have been used for classification of dry biological samples. It showed that the single excitation wavelength was not sufficient for differentiation of biological samples of diverse origin. However, merging fluorescence decays from two or three excitation wavelengths allowed classification of these samples. An experimental setup allowing the practical implementation of this method for the real time fluorescence decay measurement was designed. It consisted of the LED emitting nanosecond pulses at 280nm and two fast photomultiplier tubes (PMTs) for signal detection in two fluorescence bands simultaneously. The positive results of the dry powder samples measurements confirmed that the fluorescence decay-based technique could be a useful tool for fast classification of the suspected "white powders" performed by the first responders. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

One Sample, One Shot - Evaluation of sample preparation protocols for the mass spectrometric proteome analysis of human bile fluid without extensive fractionation.

PubMed

Megger, Dominik A; Padden, Juliet; Rosowski, Kristin; Uszkoreit, Julian; Bracht, Thilo; Eisenacher, Martin; Gerges, Christian; Neuhaus, Horst; Schumacher, Brigitte; Schlaak, Jörg F; Sitek, Barbara

2017-02-10

The proteome analysis of bile fluid represents a promising strategy to identify biomarker candidates for various diseases of the hepatobiliary system. However, to obtain substantive results in biomarker discovery studies large patient cohorts necessarily need to be analyzed. Consequently, this would lead to an unmanageable number of samples to be analyzed if sample preparation protocols with extensive fractionation methods are applied. Hence, the performance of simple workflows allowing for "one sample, one shot" experiments have been evaluated in this study. In detail, sixteen different protocols implying modifications at the stages of desalting, delipidation, deglycosylation and tryptic digestion have been examined. Each method has been individually evaluated regarding various performance criteria and comparative analyses have been conducted to uncover possible complementarities. Here, the best performance in terms of proteome coverage has been assessed for a combination of acetone precipitation with in-gel digestion. Finally, a mapping of all obtained protein identifications with putative biomarkers for hepatocellular carcinoma (HCC) and cholangiocellular carcinoma (CCC) revealed several proteins easily detectable in bile fluid. These results can build the basis for future studies with large and well-defined patient cohorts in a more disease-related context. Human bile fluid is a proximal body fluid and supposed to be a potential source of disease markers. However, due to its biochemical composition, the proteome analysis of bile fluid still represents a challenging task and is therefore mostly conducted using extensive fractionation procedures. This in turn leads to a high number of mass spectrometric measurements for one biological sample. Considering the fact that in order to overcome the biological variability a high number of biological samples needs to be analyzed in biomarker discovery studies, this leads to the dilemma of an unmanageable number of necessary MS-based analyses. Hence, easy sample preparation protocols are demanded representing a compromise between proteome coverage and simplicity. In the presented study, such protocols have been evaluated regarding various technical criteria (e.g. identification rates, missed cleavages, chromatographic separation) uncovering the strengths and weaknesses of various methods. Furthermore, a cumulative bile proteome list has been generated that extends the current bile proteome catalog by 248 proteins. Finally, a mapping with putative biomarkers for hepatocellular carcinoma (HCC) and cholangiocellular carcinoma (CCC) derived from tissue-based studies, revealed several of these proteins being easily and reproducibly detectable in human bile. Therefore, the presented technical work represents a solid base for future disease-related studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization

PubMed Central

Glaser, Joshua I.; Zamft, Bradley M.; Church, George M.; Kording, Konrad P.

2015-01-01

Current high-resolution imaging techniques require an intact sample that preserves spatial relationships. We here present a novel approach, “puzzle imaging,” that allows imaging a spatially scrambled sample. This technique takes many spatially disordered samples, and then pieces them back together using local properties embedded within the sample. We show that puzzle imaging can efficiently produce high-resolution images using dimensionality reduction algorithms. We demonstrate the theoretical capabilities of puzzle imaging in three biological scenarios, showing that (1) relatively precise 3-dimensional brain imaging is possible; (2) the physical structure of a neural network can often be recovered based only on the neural connectivity matrix; and (3) a chemical map could be reproduced using bacteria with chemosensitive DNA and conjugative transfer. The ability to reconstruct scrambled images promises to enable imaging based on DNA sequencing of homogenized tissue samples. PMID:26192446

Semiautomated Device for Batch Extraction of Metabolites from Tissue Samples

PubMed Central

2012-01-01

Metabolomics has become a mainstream analytical strategy for investigating metabolism. The quality of data derived from these studies is proportional to the consistency of the sample preparation. Although considerable research has been devoted to finding optimal extraction protocols, most of the established methods require extensive sample handling. Manual sample preparation can be highly effective in the hands of skilled technicians, but an automated tool for purifying metabolites from complex biological tissues would be of obvious utility to the field. Here, we introduce the semiautomated metabolite batch extraction device (SAMBED), a new tool designed to simplify metabolomics sample preparation. We discuss SAMBED’s design and show that SAMBED-based extractions are of comparable quality to extracts produced through traditional methods (13% mean coefficient of variation from SAMBED versus 16% from manual extractions). Moreover, we show that aqueous SAMBED-based methods can be completed in less than a quarter of the time required for manual extractions. PMID:22292466

MASS SPECTROMETRY-BASED METABOLOMICS

PubMed Central

Dettmer, Katja; Aronov, Pavel A.; Hammock, Bruce D.

2007-01-01

This review presents an overview of the dynamically developing field of mass spectrometry-based metabolomics. Metabolomics aims at the comprehensive and quantitative analysis of wide arrays of metabolites in biological samples. These numerous analytes have very diverse physico-chemical properties and occur at different abundance levels. Consequently, comprehensive metabolomics investigations are primarily a challenge for analytical chemistry and specifically mass spectrometry has vast potential as a tool for this type of investigation. Metabolomics require special approaches for sample preparation, separation, and mass spectrometric analysis. Current examples of those approaches are described in this review. It primarily focuses on metabolic fingerprinting, a technique that analyzes all detectable analytes in a given sample with subsequent classification of samples and identification of differentially expressed metabolites, which define the sample classes. To perform this complex task, data analysis tools, metabolite libraries, and databases are required. Therefore, recent advances in metabolomics bioinformatics are also discussed. PMID:16921475

Establishment and evaluation of a bead-based luminex assay allowing simultaneous quantification of equine IL-12 and IFN-γ.

PubMed

Duran, Maria Carolina; Willenbrock, Saskia; Müller, Jessika-M V; Nolte, Ingo; Feige, Karsten; Murua Escobar, Hugo

2013-04-01

Interleukin-12 (IL-12) and interferon gamma (IFN-γ) are key cytokines in immunemediated equine melanoma therapy. Currently, a method for accurate simultaneous quantification of these equine cytokines is lacking. Therefore, we sought to establish an assay that allows for accurate and simultaneous quantification of equine IL-12 (eIL-12) and IFN-γ (eIFN-γ). Several antibodies were evaluated for cross-reactivity to eIL-12 and eIFN-γ and were used to establish a bead-based Luminex assay, which was subsequently applied to quantify cytokine concentrations in biological samples. Cytokine detection ranged from 31.5-5,000 pg/ml and 15-10,000 pg/ml for eIL-12 and eIFN-γ, respectively. eIL-12 was detected in supernatants of stimulated peripheral blood mononuclear cells (PBMCs) and supernatants/cell lysates of eIL-12 expression plasmid-transfected cells. Low or undetectable cytokine concentrations were measured in negative controls. In equine serum samples, the mean measured eIL-12 concentration was 1,374 ± 8 pg/ml. The bead-based assay and ELISA for eIFN-γ used to measure eIFN-γ concentrations, showed similar concentrations. Results demonstrate, to our knowledge for the first time, that cross-reactive antibody pairs to eIL-12 and eIFN-γ and Luminex bead-based technology allow for accurate, simultaneous and multiplexed quantification of these key cytokines in biological samples.

Application of ribonucleoside vanadyl complex (RVC) for developing a multifunctional tissue preservative solution

PubMed Central

Yu, Cheng-Chia; Chen, Chin-Chuan

2018-01-01

The quality of biological samples greatly affects the accuracy of scientific results. However, RNA in cryopreserved tissues gradually degrades during storage, leading to errors in the results of subsequent experiments. A suitable sample preservative solution can prolong storage and enhance the research value of samples. Here, we developed a sample preservative solution using the properties of the ribonucleoside vanadyl complex (RVC) and compared its effects on RNA and DNA quality, protein activity, and tissue morphology with the commercially available and widely used RNAlater® Stabilization Solution. The results showed that both the RVC-based preservative solution and RNAlater can effectively delay RNA degradation in tissue samples stored at 4°C or −80°C compared with samples stored without any preservative solution. In contrast to RNAlater, the RVC-based preservative solution did not result in damage to the tissue morphology or a loss of protein activity. Additionally, the RVC-based preservative solution did not affect the RNA and genomic DNA contents of the tissue samples or the results of subsequent experimental analyses. An RVC-based reagent can be used as a multifunctional yet relatively inexpensive tissue preservative solution to provide a comprehensive and cost-effective method for preserving samples for tissue banks. PMID:29538436

On-chip wavelength multiplexed detection of cancer DNA biomarkers in blood

PubMed Central

Cai, H.; Stott, M. A.; Ozcelik, D.; Parks, J. W.; Hawkins, A. R.; Schmidt, H.

2016-01-01

We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip. Specifically, we extract two types of melanoma biomarkers, mutated cell-free nucleic acids —BRAFV600E and NRAS, from whole blood. We detect and identify these two targets simultaneously using the spectral multiplexing approach with up to a 96% success rate. These results point the way toward a full front-to-back chip-based optofluidic compact system for high-performance analysis of complex biological samples. PMID:28058082

Studying the dynamics of interbeat interval time series of healthy and congestive heart failure subjects using scale based symbolic entropy analysis

PubMed Central

Awan, Imtiaz; Aziz, Wajid; Habib, Nazneen; Alowibdi, Jalal S.; Saeed, Sharjil; Nadeem, Malik Sajjad Ahmed; Shah, Syed Ahsin Ali

2018-01-01

Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects. Recently the multiscale entropy (MSE) algorithm was introduced for precise description of the complexity of biological signals, which was used in numerous fields since its inception. The original MSE quantified the complexity of coarse-grained time series using sample entropy. The original MSE may be unreliable for short signals because the length of the coarse-grained time series decreases with increasing scaling factor τ, however, MSE works well for long signals. To overcome the drawback of original MSE, various variants of this method have been proposed for evaluating complexity efficiently. In this study, we have proposed multiscale normalized corrected Shannon entropy (MNCSE), in which instead of using sample entropy, symbolic entropy measure NCSE has been used as an entropy estimate. The results of the study are compared with traditional MSE. The effectiveness of the proposed approach is demonstrated using noise signals as well as interbeat interval signals from healthy and pathological subjects. The preliminary results of the study indicate that MNCSE values are more stable and reliable than original MSE values. The results show that MNCSE based features lead to higher classification accuracies in comparison with the MSE based features. PMID:29771977

Direct analysis of intact biological macromolecules by low-energy, fiber-based femtosecond laser vaporization at 1042 nm wavelength with nanospray postionization mass spectrometry.

PubMed

Shi, Fengjian; Flanigan, Paul M; Archer, Jieutonne J; Levis, Robert J

2015-03-17

A fiber-based laser with a pulse duration of 435 fs and a wavelength of 1042 nm was used to vaporize biological macromolecules intact from the condensed phase into the gas phase for nanospray postionization and mass analysis. Laser vaporization of dried standard protein samples from a glass substrate by 10 Hz bursts of 20 pulses having 10 μs pulse separation and <50 μJ pulse energy resulted in signal comparable to a metal substrate. The protein signal observed from an aqueous droplet on a glass substrate was negligible compared to either a droplet on metal or a thin film on glass. The mass spectra generated from dried and aqueous protein samples by the low-energy, fiber laser were similar to the results from high-energy (500 μJ), 45-fs, 800-nm Ti:sapphire-based femtosecond laser electrospray mass spectrometry (LEMS) experiments, suggesting that the fiber-based femtosecond laser desorption mechanism involves a nonresonant, multiphoton process, rather than thermal- or photoacoustic-induced desorption. Direct analysis of whole blood performed without any pretreatment resulted in features corresponding to hemoglobin subunit-heme complex ions. The observation of intact molecular ions with low charge states from protein, and the tentatively assigned hemoglobin α subunit-heme complex from blood suggests that fiber-based femtosecond laser vaporization is a "soft" desorption source at a laser intensity of 2.39 × 10(12) W/cm(2). The low-energy, turnkey fiber laser demonstrates the potential of a more robust and affordable laser for femtosecond laser vaporization to deliver biological macromolecules into the gas phase for mass analysis.

Studying the dynamics of interbeat interval time series of healthy and congestive heart failure subjects using scale based symbolic entropy analysis.

PubMed

Awan, Imtiaz; Aziz, Wajid; Shah, Imran Hussain; Habib, Nazneen; Alowibdi, Jalal S; Saeed, Sharjil; Nadeem, Malik Sajjad Ahmed; Shah, Syed Ahsin Ali

2018-01-01

Considerable interest has been devoted for developing a deeper understanding of the dynamics of healthy biological systems and how these dynamics are affected due to aging and disease. Entropy based complexity measures have widely been used for quantifying the dynamics of physical and biological systems. These techniques have provided valuable information leading to a fuller understanding of the dynamics of these systems and underlying stimuli that are responsible for anomalous behavior. The single scale based traditional entropy measures yielded contradictory results about the dynamics of real world time series data of healthy and pathological subjects. Recently the multiscale entropy (MSE) algorithm was introduced for precise description of the complexity of biological signals, which was used in numerous fields since its inception. The original MSE quantified the complexity of coarse-grained time series using sample entropy. The original MSE may be unreliable for short signals because the length of the coarse-grained time series decreases with increasing scaling factor τ, however, MSE works well for long signals. To overcome the drawback of original MSE, various variants of this method have been proposed for evaluating complexity efficiently. In this study, we have proposed multiscale normalized corrected Shannon entropy (MNCSE), in which instead of using sample entropy, symbolic entropy measure NCSE has been used as an entropy estimate. The results of the study are compared with traditional MSE. The effectiveness of the proposed approach is demonstrated using noise signals as well as interbeat interval signals from healthy and pathological subjects. The preliminary results of the study indicate that MNCSE values are more stable and reliable than original MSE values. The results show that MNCSE based features lead to higher classification accuracies in comparison with the MSE based features.

Detection of trace fluoride in serum and urine by online membrane-based distillation coupled with ion chromatography.

PubMed

Lou, Chaoyan; Guo, Dandan; Wang, Nani; Wu, Shuchao; Zhang, Peimin; Zhu, Yan

2017-06-02

An online membrane-based distillation (MBD) coupled with ion chromatography (IC) method was proposed for automatic detection of trace fluoride (F - ) in serum and urine samples. The system consisted of a sample vessel, a lab-made membrane module and an ion chromatograph. Hydrophobic polytetrafluoroethylene (PTFE) hollow fiber membrane was used in MBD which was directly performed in serum and urine samples to eliminate the matrix interferences and enrich fluoride, while enabling automation. The determination of fluoride in biological samples was carried out by IC with suppressed conductometric detection. The proposed method feasibly determined trace fluoride in serum and urine matrices with the optimized parameters, such as acid concentration, distillation temperature, and distillation time, etc. Fluoride exhibited satisfactory linearity in the range of 0.01-5.0mg/L with a correlation coefficient of 0.9992. The limit of detection (LOD, S/N=3) and limit of quantification (LOQ, S/N=10) were 0.78μg/L and 2.61μg/L, respectively. The relative standard deviations of peak area and peak height were all less than 5.15%. The developed method was validated for the determination of fluoride in serum and urine with good spiked recoveries ranging between 97.1-101.9%. This method also can be proposed as a suitable alternative for the analysis of fluoride in other complex biological samples. Copyright © 2017. Published by Elsevier B.V.

Detection of bovine viral diarrhoea virus nucleic acid, but not infectious virus, in bovine serum used for human vaccine manufacture.

PubMed

Laassri, Majid; Mee, Edward T; Connaughton, Sarah M; Manukyan, Hasmik; Gruber, Marion; Rodriguez-Hernandez, Carmen; Minor, Philip D; Schepelmann, Silke; Chumakov, Konstantin; Wood, David J

2018-06-22

Bovine viral diarrhoea virus (BVDV) is a cattle pathogen that has previously been reported to be present in bovine raw materials used in the manufacture of biological products for human use. Seven lots of trivalent measles, mumps and rubella (MMR) vaccine and 1 lot of measles vaccine from the same manufacturer, together with 17 lots of foetal bovine serum (FBS) from different vendors, 4 lots of horse serum, 2 lots of bovine trypsin and 5 lots of porcine trypsin were analysed for BVDV using recently developed techniques, including PCR assays for BVDV detection, a qRT-PCR and immunofluorescence-based virus replication assays, and deep sequencing to identify and genotype BVDV genomes. All FBS lots and one lot of bovine-derived trypsin were PCR-positive for the presence of BVDV genome; in contrast all vaccine lots and the other samples were negative. qRT-PCR based virus replication assay and immunofluorescence-based infection assay detected no infectious BVDV in the PCR-positive samples. Complete BVDV genomes were generated from FBS samples by deep sequencing, and all were BVDV type 1. These data confirmed that BVDV nucleic acid may be present in bovine-derived raw materials, but no infectious virus or genomic RNA was detected in the final vaccine products. Copyright © 2018 International Alliance for Biological Standardization. All rights reserved.

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

DOE PAGES

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne; ...

2015-12-30

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, withmore » an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.« less

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

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

Stelpflug, Scott C.; Sekhon, Rajandeep S.; Vaillancourt, Brieanne

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( Zea mays L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, withmore » an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in Arabidopsis thaliana (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. As a result, this comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.« less

Strategies for de-identification and anonymization of electronic health record data for use in multicenter research studies.

PubMed

Kushida, Clete A; Nichols, Deborah A; Jadrnicek, Rik; Miller, Ric; Walsh, James K; Griffin, Kara

2012-07-01

De-identification and anonymization are strategies that are used to remove patient identifiers in electronic health record data. The use of these strategies in multicenter research studies is paramount in importance, given the need to share electronic health record data across multiple environments and institutions while safeguarding patient privacy. Systematic literature search using keywords of de-identify, deidentify, de-identification, deidentification, anonymize, anonymization, data scrubbing, and text scrubbing. Search was conducted up to June 30, 2011 and involved 6 different common literature databases. A total of 1798 prospective citations were identified, and 94 full-text articles met the criteria for review and the corresponding articles were obtained. Search results were supplemented by review of 26 additional full-text articles; a total of 120 full-text articles were reviewed. A final sample of 45 articles met inclusion criteria for review and discussion. Articles were grouped into text, images, and biological sample categories. For text-based strategies, the approaches were segregated into heuristic, lexical, and pattern-based systems versus statistical learning-based systems. For images, approaches that de-identified photographic facial images and magnetic resonance image data were described. For biological samples, approaches that managed the identifiers linked with these samples were discussed, particularly with respect to meeting the anonymization requirements needed for Institutional Review Board exemption under the Common Rule. Current de-identification strategies have their limitations, and statistical learning-based systems have distinct advantages over other approaches for the de-identification of free text. True anonymization is challenging, and further work is needed in the areas of de-identification of datasets and protection of genetic information.

A genome-wide approach to children's aggressive behavior: The EAGLE consortium.

PubMed

Pappa, Irene; St Pourcain, Beate; Benke, Kelly; Cavadino, Alana; Hakulinen, Christian; Nivard, Michel G; Nolte, Ilja M; Tiesler, Carla M T; Bakermans-Kranenburg, Marian J; Davies, Gareth E; Evans, David M; Geoffroy, Marie-Claude; Grallert, Harald; Groen-Blokhuis, Maria M; Hudziak, James J; Kemp, John P; Keltikangas-Järvinen, Liisa; McMahon, George; Mileva-Seitz, Viara R; Motazedi, Ehsan; Power, Christine; Raitakari, Olli T; Ring, Susan M; Rivadeneira, Fernando; Rodriguez, Alina; Scheet, Paul A; Seppälä, Ilkka; Snieder, Harold; Standl, Marie; Thiering, Elisabeth; Timpson, Nicholas J; Veenstra, René; Velders, Fleur P; Whitehouse, Andrew J O; Smith, George Davey; Heinrich, Joachim; Hypponen, Elina; Lehtimäki, Terho; Middeldorp, Christel M; Oldehinkel, Albertine J; Pennell, Craig E; Boomsma, Dorret I; Tiemeier, Henning

2016-07-01

Individual differences in aggressive behavior emerge in early childhood and predict persisting behavioral problems and disorders. Studies of antisocial and severe aggression in adulthood indicate substantial underlying biology. However, little attention has been given to genome-wide approaches of aggressive behavior in children. We analyzed data from nine population-based studies and assessed aggressive behavior using well-validated parent-reported questionnaires. This is the largest sample exploring children's aggressive behavior to date (N = 18,988), with measures in two developmental stages (N = 15,668 early childhood and N = 16,311 middle childhood/early adolescence). First, we estimated the additive genetic variance of children's aggressive behavior based on genome-wide SNP information, using genome-wide complex trait analysis (GCTA). Second, genetic associations within each study were assessed using a quasi-Poisson regression approach, capturing the highly right-skewed distribution of aggressive behavior. Third, we performed meta-analyses of genome-wide associations for both the total age-mixed sample and the two developmental stages. Finally, we performed a gene-based test using the summary statistics of the total sample. GCTA quantified variance tagged by common SNPs (10-54%). The meta-analysis of the total sample identified one region in chromosome 2 (2p12) at near genome-wide significance (top SNP rs11126630, P = 5.30 × 10(-8) ). The separate meta-analyses of the two developmental stages revealed suggestive evidence of association at the same locus. The gene-based analysis indicated association of variation within AVPR1A with aggressive behavior. We conclude that common variants at 2p12 show suggestive evidence for association with childhood aggression. Replication of these initial findings is needed, and further studies should clarify its biological meaning. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

A web-based system for neural network based classification in temporomandibular joint osteoarthritis.

PubMed

de Dumast, Priscille; Mirabel, Clément; Cevidanes, Lucia; Ruellas, Antonio; Yatabe, Marilia; Ioshida, Marcos; Ribera, Nina Tubau; Michoud, Loic; Gomes, Liliane; Huang, Chao; Zhu, Hongtu; Muniz, Luciana; Shoukri, Brandon; Paniagua, Beatriz; Styner, Martin; Pieper, Steve; Budin, Francois; Vimort, Jean-Baptiste; Pascal, Laura; Prieto, Juan Carlos

2018-07-01

The purpose of this study is to describe the methodological innovations of a web-based system for storage, integration and computation of biomedical data, using a training imaging dataset to remotely compute a deep neural network classifier of temporomandibular joint osteoarthritis (TMJOA). This study imaging dataset consisted of three-dimensional (3D) surface meshes of mandibular condyles constructed from cone beam computed tomography (CBCT) scans. The training dataset consisted of 259 condyles, 105 from control subjects and 154 from patients with diagnosis of TMJ OA. For the image analysis classification, 34 right and left condyles from 17 patients (39.9 ± 11.7 years), who experienced signs and symptoms of the disease for less than 5 years, were included as the testing dataset. For the integrative statistical model of clinical, biological and imaging markers, the sample consisted of the same 17 test OA subjects and 17 age and sex matched control subjects (39.4 ± 15.4 years), who did not show any sign or symptom of OA. For these 34 subjects, a standardized clinical questionnaire, blood and saliva samples were also collected. The technological methodologies in this study include a deep neural network classifier of 3D condylar morphology (ShapeVariationAnalyzer, SVA), and a flexible web-based system for data storage, computation and integration (DSCI) of high dimensional imaging, clinical, and biological data. The DSCI system trained and tested the neural network, indicating 5 stages of structural degenerative changes in condylar morphology in the TMJ with 91% close agreement between the clinician consensus and the SVA classifier. The DSCI remotely ran with a novel application of a statistical analysis, the Multivariate Functional Shape Data Analysis, that computed high dimensional correlations between shape 3D coordinates, clinical pain levels and levels of biological markers, and then graphically displayed the computation results. The findings of this study demonstrate a comprehensive phenotypic characterization of TMJ health and disease at clinical, imaging and biological levels, using novel flexible and versatile open-source tools for a web-based system that provides advanced shape statistical analysis and a neural network based classification of temporomandibular joint osteoarthritis. Published by Elsevier Ltd.

Using machine learning tools to model complex toxic interactions with limited sampling regimes.

PubMed

Bertin, Matthew J; Moeller, Peter; Guillette, Louis J; Chapman, Robert W

2013-03-19

A major impediment to understanding the impact of environmental stress, including toxins and other pollutants, on organisms, is that organisms are rarely challenged by one or a few stressors in natural systems. Thus, linking laboratory experiments that are limited by practical considerations to a few stressors and a few levels of these stressors to real world conditions is constrained. In addition, while the existence of complex interactions among stressors can be identified by current statistical methods, these methods do not provide a means to construct mathematical models of these interactions. In this paper, we offer a two-step process by which complex interactions of stressors on biological systems can be modeled in an experimental design that is within the limits of practicality. We begin with the notion that environment conditions circumscribe an n-dimensional hyperspace within which biological processes or end points are embedded. We then randomly sample this hyperspace to establish experimental conditions that span the range of the relevant parameters and conduct the experiment(s) based upon these selected conditions. Models of the complex interactions of the parameters are then extracted using machine learning tools, specifically artificial neural networks. This approach can rapidly generate highly accurate models of biological responses to complex interactions among environmentally relevant toxins, identify critical subspaces where nonlinear responses exist, and provide an expedient means of designing traditional experiments to test the impact of complex mixtures on biological responses. Further, this can be accomplished with an astonishingly small sample size.

Towards advanced biological detection using surface enhanced raman scattering (SERS)-based sensors

NASA Astrophysics Data System (ADS)

Hankus, Mikella E.; Stratis-Cullum, Dimitra N.; Pellegrino, Paul M.

2010-08-01

The Army has a need for an accurate, fast, reliable and robust means to identify and quantify defense related materials. Raman spectroscopy is a form of vibrational spectroscopy that is rapidly becoming a valuable tool for homeland defense applications, as it is well suited for the molecular identification of a variety of compounds, including explosives and chemical and biological hazards. To measure trace levels of these types of materials, surface enhanced Raman scattering (SERS), a specialized form of Raman scattering, can be employed. The SERS enhancements are produced on, or in close proximity to, a nanoscale roughened metal surface and are typically associated with increased local electromagnetic field strengths. However, before application of SERS in the field and in particular to biological and other hazard sensing applications, significant improvements in substrate performance are needed. In this work, we will report the use of several SERS substrate architectures (colloids, film-over-nanospheres (FONs) and commercially available substrates) for detecting and differentiating numerous endospore samples. The variance in spectra as obtained using different sensing architectures will also be discussed. Additionally, the feasibility of using a modified substrate architecture that is tailored with molecular recognition probe system for detecting biological samples will be explored. We will discuss the progress towards an advanced, hybrid molecular recognition with a SERS/Fluorescence nanoprobe system including the optimization, fabrication, and spectroscopic analysis of samples on a commercially available substrate. Additionally, the feasibility of using this single-step switching architecture for hazard material detection will also be explored.

Standoff detection of chemical and biological threats using laser-induced breakdown spectroscopy.

PubMed

Gottfried, Jennifer L; De Lucia, Frank C; Munson, Chase A; Miziolek, Andrzej W

2008-04-01

Laser-induced breakdown spectroscopy (LIBS) is a promising technique for real-time chemical and biological warfare agent detection in the field. We have demonstrated the detection and discrimination of the biological warfare agent surrogates Bacillus subtilis (BG) (2% false negatives, 0% false positives) and ovalbumin (0% false negatives, 1% false positives) at 20 meters using standoff laser-induced breakdown spectroscopy (ST-LIBS) and linear correlation. Unknown interferent samples (not included in the model), samples on different substrates, and mixtures of BG and Arizona road dust have been classified with reasonable success using partial least squares discriminant analysis (PLS-DA). A few of the samples tested such as the soot (not included in the model) and the 25% BG:75% dust mixture resulted in a significant number of false positives or false negatives, respectively. Our preliminary results indicate that while LIBS is able to discriminate biomaterials with similar elemental compositions at standoff distances based on differences in key intensity ratios, further work is needed to reduce the number of false positives/negatives by refining the PLS-DA model to include a sufficient range of material classes and carefully selecting a detection threshold. In addition, we have demonstrated that LIBS can distinguish five different organophosphate nerve agent simulants at 20 meters, despite their similar stoichiometric formulas. Finally, a combined PLS-DA model for chemical, biological, and explosives detection using a single ST-LIBS sensor has been developed in order to demonstrate the potential of standoff LIBS for universal hazardous materials detection.

Hemlock woolly adelgid biological control: molecular methods to distinguish Laricobius nigrinus, L. rubidus, and their hybrids

Treesearch

Nathan P. Havill; Gina Davis; Joanne Klein; Adalgisa Caccone; Scott Salom

2011-01-01

Molecular diagnostics use DNA-based methods to assign unknown organisms to species. As such, they rely on a priori species designation by taxonomists and require validation with enough samples to capture the variation within species for accurately selecting diagnostic characters.

Parallel Curriculum Units for Science, Grades 6-12

ERIC Educational Resources Information Center

Leppien, Jann H.; Purcell, Jeanne H.

2011-01-01

Based on the best-selling book "The Parallel Curriculum", this professional development resource gives multifaceted examples of rigorous learning opportunities for science students in Grades 6-12. The four sample units revolve around genetics, the convergence of science and society, the integration of language arts and biology, and the periodic…

Estimating Methylmercury Intake for the General Population of South Korea Using Physiologically Based Pharmacokinetic Modeling

EPA Science Inventory

The Korean National Environmental Health Survey (KoNEHS 2009–2011) tracks levels of environmental pollutants in biological samples from the adult Korean population (age 19–88). Recent survey results for blood mercury (Hg) suggest some exceedance above existing blood H...

Biosensor and chemical sensor probes for calcium and other metal ions

DOEpatents

Vo-Dinh, Tuan; Viallet, Pierre

1996-01-01

The present invention relates to chemical sensor and biosensor probes for measuring low concentration of metals and metal ions in complex samples such as biological fluids, living cells, and environmental samples. More particularly the present invention relates to a gel-based Indo-1 and Fura-2 chemical sensor probes for the measurement of low concentrations of calcium, cadmium, magnesium and the like. Also disclosed is a detector device using the sensors of the present invention.

Combination of atomic force microscopy and mass spectrometry for the detection of target protein in the serum samples of children with autism spectrum disorders

NASA Astrophysics Data System (ADS)

Kaysheva, A. L.; Pleshakova, T. O.; Kopylov, A. T.; Shumov, I. D.; Iourov, I. Y.; Vorsanova, S. G.; Yurov, Y. B.; Ziborov, V. S.; Archakov, A. I.; Ivanov, Y. D.

2017-10-01

Possibility of detection of target proteins associated with development of autistic disorders in children with use of combined atomic force microscopy and mass spectrometry (AFM/MS) method is demonstrated. The proposed method is based on the combination of affine enrichment of proteins from biological samples and visualization of these proteins by AFM and MS analysis with quantitative detection of target proteins.

Massively parallel nanowell-based single-cell gene expression profiling.

PubMed

Goldstein, Leonard D; Chen, Ying-Jiun Jasmine; Dunne, Jude; Mir, Alain; Hubschle, Hermann; Guillory, Joseph; Yuan, Wenlin; Zhang, Jingli; Stinson, Jeremy; Jaiswal, Bijay; Pahuja, Kanika Bajaj; Mann, Ishminder; Schaal, Thomas; Chan, Leo; Anandakrishnan, Sangeetha; Lin, Chun-Wah; Espinoza, Patricio; Husain, Syed; Shapiro, Harris; Swaminathan, Karthikeyan; Wei, Sherry; Srinivasan, Maithreyan; Seshagiri, Somasekar; Modrusan, Zora

2017-07-07

Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. Here we report a novel nanowell-based single-cell RNA sequencing system, ICELL8, which enables processing of thousands of cells per sample. The system employs a 5,184-nanowell-containing microchip to capture ~1,300 single cells and process them. Each nanowell contains preprinted oligonucleotides encoding poly-d(T), a unique well barcode, and a unique molecular identifier. The ICELL8 system uses imaging software to identify nanowells containing viable single cells and only wells with single cells are processed into sequencing libraries. Here, we report the performance and utility of ICELL8 using samples of increasing complexity from cultured cells to mouse solid tissue samples. Our assessment of the system to discriminate between mixed human and mouse cells showed that ICELL8 has a low cell multiplet rate (< 3%) and low cross-cell contamination. We characterized single-cell transcriptomes of more than a thousand cultured human and mouse cells as well as 468 mouse pancreatic islets cells. We were able to identify distinct cell types in pancreatic islets, including alpha, beta, delta and gamma cells. Overall, ICELL8 provides efficient and cost-effective single-cell expression profiling of thousands of cells, allowing researchers to decipher single-cell transcriptomes within complex biological samples.

Protein Detection Using the Multiplexed Proximity Extension Assay (PEA) from Plasma and Vaginal Fluid Applied to the Indicating FTA Elute Micro Card™

PubMed Central

Berggrund, Malin; Ekman, Daniel; Gustavsson, Inger; Sundfeldt, Karin; Olovsson, Matts; Enroth, Stefan; Gyllensten, Ulf

2016-01-01

The indicating FTA elute micro card™ has been developed to collect and stabilize the nucleic acid in biological samples and is widely used in human and veterinary medicine and other disciplines. This card is not recommended for protein analyses, since surface treatment may denature proteins. We studied the ability to analyse proteins in human plasma and vaginal fluid as applied to the indicating FTA elute micro card™ using the sensitive proximity extension assay (PEA). Among 92 proteins in the Proseek Multiplex Oncology Iv2 panel, 87 were above the limit of detection (LOD) in liquid plasma and 56 among 92 above LOD in plasma applied to FTA cards. Washing and protein elution protocols were compared to identify an optimal method. Liquid-based cytology samples showed a lower number of proteins above LOD than FTA cards with vaginal fluid samples applied. Our results demonstrate that samples applied to the indicating FTA elute micro card™ are amendable to protein analyses, given that a sensitive protein detection assay is used. The results imply that biological samples applied to FTA cards can be used for DNA, RNA and protein detection. PMID:28936257

Protein Detection Using the Multiplexed Proximity Extension Assay (PEA) from Plasma and Vaginal Fluid Applied to the Indicating FTA Elute Micro Card™.

PubMed

Berggrund, Malin; Ekman, Daniel; Gustavsson, Inger; Sundfeldt, Karin; Olovsson, Matts; Enroth, Stefan; Gyllensten, Ulf

2016-01-01

The indicating FTA elute micro card™ has been developed to collect and stabilize the nucleic acid in biological samples and is widely used in human and veterinary medicine and other disciplines. This card is not recommended for protein analyses, since surface treatment may denature proteins. We studied the ability to analyse proteins in human plasma and vaginal fluid as applied to the indicating FTA elute micro card™ using the sensitive proximity extension assay (PEA). Among 92 proteins in the Proseek Multiplex Oncology Iv2 panel, 87 were above the limit of detection (LOD) in liquid plasma and 56 among 92 above LOD in plasma applied to FTA cards. Washing and protein elution protocols were compared to identify an optimal method. Liquid-based cytology samples showed a lower number of proteins above LOD than FTA cards with vaginal fluid samples applied. Our results demonstrate that samples applied to the indicating FTA elute micro card™ are amendable to protein analyses, given that a sensitive protein detection assay is used. The results imply that biological samples applied to FTA cards can be used for DNA, RNA and protein detection.

Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including early detection of cancers

DOEpatents

Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Shively, John E [Arcadia, CA; Li, Lin [Monrovia, CA

2009-06-02

An assay element is described including recognition ligands adapted for binding to carcinoembryonic antigen (CEA) bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of CEA is described including injecting a possible CEA-containing sample into a sensor cell including the assay element, maintaining the sample within the sensor cell for time sufficient for binding to occur between CEA present within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

Conductive resins improve charging and resolution of acquired images in electron microscopic volume imaging

PubMed Central

Nguyen, Huy Bang; Thai, Truc Quynh; Saitoh, Sei; Wu, Bao; Saitoh, Yurika; Shimo, Satoshi; Fujitani, Hiroshi; Otobe, Hirohide; Ohno, Nobuhiko

2016-01-01

Recent advances in serial block-face imaging using scanning electron microscopy (SEM) have enabled the rapid and efficient acquisition of 3-dimensional (3D) ultrastructural information from a large volume of biological specimens including brain tissues. However, volume imaging under SEM is often hampered by sample charging, and typically requires specific sample preparation to reduce charging and increase image contrast. In the present study, we introduced carbon-based conductive resins for 3D analyses of subcellular ultrastructures, using serial block-face SEM (SBF-SEM) to image samples. Conductive resins were produced by adding the carbon black filler, Ketjen black, to resins commonly used for electron microscopic observations of biological specimens. Carbon black mostly localized around tissues and did not penetrate cells, whereas the conductive resins significantly reduced the charging of samples during SBF-SEM imaging. When serial images were acquired, embedding into the conductive resins improved the resolution of images by facilitating the successful cutting of samples in SBF-SEM. These results suggest that improving the conductivities of resins with a carbon black filler is a simple and useful option for reducing charging and enhancing the resolution of images obtained for volume imaging with SEM. PMID:27020327

Determination of Iodate in Food, Environmental, and Biological Samples after Solid-Phase Extraction with Ni-Al-Zr Ternary Layered Double Hydroxide as a Nanosorbent

PubMed Central

Abdolmohammad-Zadeh, Hossein; Tavarid, Keyvan; Talleb, Zeynab

2012-01-01

Nanostructured nickel-aluminum-zirconium ternary layered double hydroxide was successfully applied as a solid-phase extraction sorbent for the separation and pre-concentration of trace levels of iodate in food, environmental and biological samples. An indirect method was used for monitoring of the extracted iodate ions. The method is based on the reaction of the iodate with iodide in acidic solution to produce iodine, which can be spectrophotometrically monitored at 352 nm. The absorbance is directly proportional to the concentration of iodate in the sample. The effect of several parameters such as pH, sample flow rate, amount of nanosorbent, elution conditions, sample volume, and coexisting ions on the recovery was investigated. In the optimum experimental conditions, the limit of detection (3s) and enrichment factor were 0.12 μg mL−1 and 20, respectively. The calibration graph using the preconcentration system was linear in the range of 0.2–2.8 μg mL−1 with a correlation coefficient of 0.998. In order to validate the presented method, a certified reference material, NIST SRM 1549, was also analyzed. PMID:22619590

Multi-center feasibility study evaluating recruitment, variability in risk factors and biomarkers for a diet and cancer cohort in India

PubMed Central

2011-01-01

Background India's population exhibits diverse dietary habits and chronic disease patterns. Nutritional epidemiologic studies in India are primarily of cross-sectional or case-control design and subject to biases, including differential recall of past diet. The aim of this feasibility study was to evaluate whether a diet-focused cohort study of cancer could be established in India, providing insight into potentially unique diet and lifestyle exposures. Methods Field staff contacted 7,064 households within three regions of India (New Delhi, Mumbai, and Trivandrum) and found 4,671 eligible adults aged 35-69 years. Participants completed interviewer-administered questionnaires (demographic, diet history, physical activity, medical/reproductive history, tobacco/alcohol use, and occupational history), and staff collected biological samples (blood, urine, and toenail clippings), anthropometric measurements (weight, standing and sitting height; waist, hip, and thigh circumference; triceps, sub-scapula and supra-patella skin fold), and blood pressure measurements. Results Eighty-eight percent of eligible subjects completed all questionnaires and 67% provided biological samples. Unique protein sources by region were fish in Trivandrum, dairy in New Delhi, and pulses (legumes) in Mumbai. Consumption of meat, alcohol, fast food, and soft drinks was scarce in all three regions. A large percentage of the participants were centrally obese and had elevated blood glucose levels. New Delhi participants were also the least physically active and had elevated lipids levels, suggesting a high prevalence of metabolic syndrome. Conclusions A high percentage of participants complied with study procedures including biological sample collection. Epidemiologic expertise and sufficient infrastructure exists at these three sites in India to successfully carry out a modest sized population-based study; however, we identified some potential problems in conducting a cohort study, such as limited number of facilities to handle biological samples. PMID:21619649

Evaluation of hierarchical models for integrative genomic analyses.

PubMed

Denis, Marie; Tadesse, Mahlet G

2016-03-01

Advances in high-throughput technologies have led to the acquisition of various types of -omic data on the same biological samples. Each data type gives independent and complementary information that can explain the biological mechanisms of interest. While several studies performing independent analyses of each dataset have led to significant results, a better understanding of complex biological mechanisms requires an integrative analysis of different sources of data. Flexible modeling approaches, based on penalized likelihood methods and expectation-maximization (EM) algorithms, are studied and tested under various biological relationship scenarios between the different molecular features and their effects on a clinical outcome. The models are applied to genomic datasets from two cancer types in the Cancer Genome Atlas project: glioblastoma multiforme and ovarian serous cystadenocarcinoma. The integrative models lead to improved model fit and predictive performance. They also provide a better understanding of the biological mechanisms underlying patients' survival. Source code implementing the integrative models is freely available at https://github.com/mgt000/IntegrativeAnalysis along with example datasets and sample R script applying the models to these data. The TCGA datasets used for analysis are publicly available at https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp marie.denis@cirad.fr or mgt26@georgetown.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Sampling stored product insect pests: a comparison of four statistical sampling models for probability of pest detection

USDA-ARS?s Scientific Manuscript database

Statistically robust sampling strategies form an integral component of grain storage and handling activities throughout the world. Developing sampling strategies to target biological pests such as insects in stored grain is inherently difficult due to species biology and behavioral characteristics. ...

Nanomaterial-based electrochemical sensors for arsenic - A review.

PubMed

Kempahanumakkagari, Sureshkumar; Deep, Akash; Kim, Ki-Hyun; Kumar Kailasa, Suresh; Yoon, Hye-On

2017-09-15

The existence of arsenic in the environment poses severe global health threats. Considering its toxicity, the sensing of arsenic is extremely important. Due to the complexity of environmental and biological samples, many of the available detection methods for arsenic have serious limitations on selectivity and sensitivity. To improve sensitivity and selectivity and to circumvent interferences, different electrode systems have been developed based on surface modification with nanomaterials including carbonaceous nanomaterials, metallic nanoparticles (MNPs), metal nanotubes (MNTs), and even enzymes. Despite the progress made in electrochemical sensing of arsenic, some issues still need to be addressed to realize cost effective, portable, and flow-injection type sensor systems. The present review provides an in-depth evaluation of the nanoparticle-modified electrode (NME) based methods for the electrochemical sensing of arsenic. NME based sensing systems are projected to become an important option for monitoring hazardous pollutants in both environmental and biological media. Copyright © 2017 Elsevier B.V. All rights reserved.

Contaminants of emerging concern presence and adverse effects in fish: A case study in the Laurentian Great Lakes.

PubMed

Jorgenson, Zachary G; Thomas, Linnea M; Elliott, Sarah M; Cavallin, Jenna E; Randolph, Eric C; Choy, Steven J; Alvarez, David A; Banda, Jo A; Gefell, Daniel J; Lee, Kathy E; Furlong, Edward T; Schoenfuss, Heiko L

2018-05-01

The Laurentian Great Lakes are a valuable natural resource that is affected by contaminants of emerging concern (CECs), including sex steroid hormones, personal care products, pharmaceuticals, industrial chemicals, and new generation pesticides. However, little is known about the fate and biological effects of CECs in tributaries to the Great Lakes. In the current study, 16 sites on three rivers in the Great Lakes basin (Fox, Cuyahoga, and Raquette Rivers) were assessed for CEC presence using polar organic chemical integrative samplers (POCIS) and grab water samplers. Biological activity was assessed through a combination of in vitro bioassays (focused on estrogenic activity) and in vivo assays with larval fathead minnows. In addition, resident sunfish, largemouth bass, and white suckers were assessed for changes in biological endpoints associated with CEC exposure. CECs were present in all water samples and POCIS extracts. A total of 111 and 97 chemicals were detected in at least one water sample and POCIS extract, respectively. Known estrogenic chemicals were detected in water samples at all 16 sites and in POCIS extracts at 13 sites. Most sites elicited estrogenic activity in bioassays. Ranking sites and rivers based on water chemistry, POCIS chemistry, or total in vitro estrogenicity produced comparable patterns with the Cuyahoga River ranking as most and the Raquette River as least affected by CECs. Changes in biological responses grouped according to physiological processes, and differed between species but not sex. The Fox and Cuyahoga Rivers often had significantly different patterns in biological response Our study supports the need for multiple lines of evidence and provides a framework to assess CEC presence and effects in fish in the Laurentian Great Lakes basin. Copyright © 2018 Elsevier Ltd. All rights reserved.

Correlation of liquid chromatographic and biological assay for potency assessment of filgrastim and related impurities.

PubMed

Skrlin, Ana; Kosor Krnic, Ela; Gosak, Darko; Prester, Berislav; Mrsa, Vladimir; Vuletic, Marko; Runac, Domagoj

2010-11-02

In vivo and in vitro potency assays have always been a critical tool for confirmation of protein activity. However, due to their complexity and time consuming procedures, it remains a challenge to find an alternative analytical approach that would enable their replacement with no impact on the quality of provided information. The goal of this research was to determine if a correlation between liquid chromatography assays and in vitro biological assay could be established for filgrastim (recombinant human granulocyte-colony stimulating factor, rhG-CSF) samples containing various amounts of related impurities. For that purpose, relevant filgrastim related impurities were purified to homogeneity and characterized by liquid chromatography and mass spectrometry. A significant correlation (R(2)>0.90) between the two types of assays was revealed. Potency of oxidized filgrastim was determined to be approximately 25% of filgrastim stated potency (1 x 10(8)IU/mg of protein). Formyl-methionine filgrastim had potency of 89% of the filgrastim stated potency, while filgrastim dimer had 67% of filgrastim stated potency. A mathematical model for the estimation of biological activity of filgrastim samples from chromatography data was established and a significant correlation between experimental potency values and potency values estimated by the mathematical model was obtained (R(2)=0.92). Based on these results a conclusion was made that reversed phase high performance liquid chromatography could be used as an alternative for the in vitro biological assay for potency assessment of filgrastim samples. Such an alternative model would enable substitution of a complex and time consuming biological assay with a robust and precise instrumental method in many practical cases. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Manipulation of the osteoblast response to a Ti 6Al 4V titanium alloy using a high power diode laser

NASA Astrophysics Data System (ADS)

Hao, L.; Lawrence, J.; Li, L.

2005-07-01

To improve the bone integration of titanium-based implants a high power diode laser (HPDL) was used to modify the material for improved osteoblast cell response. The surface properties of un-treated and HPDL treated samples were characterized. Contact angles for the un-treated and the HPDL modified titanium alloy (Ti-6Al-4V) were determined with selected biological liquids by the sessile drop technique. The analysis revealed that the wettability of the Ti-6Al-4V improved after HPDL laser treatment, indicating that better interaction with the biological liquids occurred. Moreover, an in vitro human fetal osteoblast cells (hFOB 1.19) evaluation revealed a more favourable cell response on the HPDL laser treated Ti-6Al-4V alloy than on either un-treated sample or a mechanically roughened sample. It was consequently determined that the HPDL provides more a controllable and effective technique to improve the biocompatibility of bio-metals.

Determination of total concentration of chemically labeled metabolites as a means of metabolome sample normalization and sample loading optimization in mass spectrometry-based metabolomics.

PubMed

Wu, Yiman; Li, Liang

2012-12-18

For mass spectrometry (MS)-based metabolomics, it is important to use the same amount of starting materials from each sample to compare the metabolome changes in two or more comparative samples. Unfortunately, for biological samples, the total amount or concentration of metabolites is difficult to determine. In this work, we report a general approach of determining the total concentration of metabolites based on the use of chemical labeling to attach a UV absorbent to the metabolites to be analyzed, followed by rapid step-gradient liquid chromatography (LC) UV detection of the labeled metabolites. It is shown that quantification of the total labeled analytes in a biological sample facilitates the preparation of an appropriate amount of starting materials for MS analysis as well as the optimization of the sample loading amount to a mass spectrometer for achieving optimal detectability. As an example, dansylation chemistry was used to label the amine- and phenol-containing metabolites in human urine samples. LC-UV quantification of the labeled metabolites could be optimally performed at the detection wavelength of 338 nm. A calibration curve established from the analysis of a mixture of 17 labeled amino acid standards was found to have the same slope as that from the analysis of the labeled urinary metabolites, suggesting that the labeled amino acid standard calibration curve could be used to determine the total concentration of the labeled urinary metabolites. A workflow incorporating this LC-UV metabolite quantification strategy was then developed in which all individual urine samples were first labeled with (12)C-dansylation and the concentration of each sample was determined by LC-UV. The volumes of urine samples taken for producing the pooled urine standard were adjusted to ensure an equal amount of labeled urine metabolites from each sample was used for the pooling. The pooled urine standard was then labeled with (13)C-dansylation. Equal amounts of the (12)C-labeled individual sample and the (13)C-labeled pooled urine standard were mixed for LC-MS analysis. This way of concentration normalization among different samples with varying concentrations of total metabolites was found to be critical for generating reliable metabolome profiles for comparison.

Watershed-based survey designs

USGS Publications Warehouse

Detenbeck, N.E.; Cincotta, D.; Denver, J.M.; Greenlee, S.K.; Olsen, A.R.; Pitchford, A.M.

2005-01-01

Watershed-based sampling design and assessment tools help serve the multiple goals for water quality monitoring required under the Clean Water Act, including assessment of regional conditions to meet Section 305(b), identification of impaired water bodies or watersheds to meet Section 303(d), and development of empirical relationships between causes or sources of impairment and biological responses. Creation of GIS databases for hydrography, hydrologically corrected digital elevation models, and hydrologic derivatives such as watershed boundaries and upstream–downstream topology of subcatchments would provide a consistent seamless nationwide framework for these designs. The elements of a watershed-based sample framework can be represented either as a continuous infinite set defined by points along a linear stream network, or as a discrete set of watershed polygons. Watershed-based designs can be developed with existing probabilistic survey methods, including the use of unequal probability weighting, stratification, and two-stage frames for sampling. Case studies for monitoring of Atlantic Coastal Plain streams, West Virginia wadeable streams, and coastal Oregon streams illustrate three different approaches for selecting sites for watershed-based survey designs.

Optimization of techniques for multiple platform testing in small, precious samples such as human chorionic villus sampling.

PubMed

Pisarska, Margareta D; Akhlaghpour, Marzieh; Lee, Bora; Barlow, Gillian M; Xu, Ning; Wang, Erica T; Mackey, Aaron J; Farber, Charles R; Rich, Stephen S; Rotter, Jerome I; Chen, Yii-der I; Goodarzi, Mark O; Guller, Seth; Williams, John

2016-11-01

Multiple testing to understand global changes in gene expression based on genetic and epigenetic modifications is evolving. Chorionic villi, obtained for prenatal testing, is limited, but can be used to understand ongoing human pregnancies. However, optimal storage, processing and utilization of CVS for multiple platform testing have not been established. Leftover CVS samples were flash-frozen or preserved in RNAlater. Modifications to standard isolation kits were performed to isolate quality DNA and RNA from samples as small as 2-5 mg. RNAlater samples had significantly higher RNA yields and quality and were successfully used in microarray and RNA-sequencing (RNA-seq). RNA-seq libraries generated using 200 versus 800-ng RNA showed similar biological coefficients of variation. RNAlater samples had lower DNA yields and quality, which improved by heating the elution buffer to 70 °C. Purification of DNA was not necessary for bisulfite-conversion and genome-wide methylation profiling. CVS cells were propagated and continue to express genes found in freshly isolated chorionic villi. CVS samples preserved in RNAlater are superior. Our optimized techniques provide specimens for genetic, epigenetic and gene expression studies from a single small sample which can be used to develop diagnostics and treatments using a systems biology approach in the prenatal period. © 2016 John Wiley & Sons, Ltd. © 2016 John Wiley & Sons, Ltd.

Laser nanocomposites based on proteins and carbon nanotubes for restoration of biological tissues

NASA Astrophysics Data System (ADS)

Gerasimenko, A.; Kurilova, U.; Zhurbina, N.; Ignatov, D.; Fedorova, J.; Privalova, P.; Polokhin, A.; Ryabkin, D.; Savelyev, M.; Ichkitidze, L.; Podgaetskiy, V.

2018-04-01

The study of structural properties of nanocomposites, based on different types of single walled carbon nanotubes (SWCNTs) and proteins (albumin, collagen), was carried out. The binding of protein molecules to the carbon component was described by Raman spectroscopy. Complex analysis of the structure and microporosity of nanocomposites was performed by the X-ray microtomography. The nanoporosity study was carried out using the low-temperature nitrogen porosimetry method. Samples based on SWCNTs with smaller size had the most homogeneity. With an increase in the concentration from 0.01 to 0.1 %, the mean micropore size increased from 45 to 93 μm, porosity in general increased from 16 to 28 %. The percentage of open pores was the same for all samples and was 0.02. As it was shown by Raman spectroscopy the protein component in nanocomposites has undergone irreversible denaturation and can act as a biocompatible binder and serve as a source of amino acids for biological tissues. These nanocomposites are bioresorbable and can be used to repair cartilage and bone tissue. This is especially important in the treatment of diseases of hyaline cartilage and subchondral bone.

Direct, Label-Free, and Rapid Transistor-Based Immunodetection in Whole Serum.

PubMed

Gutiérrez-Sanz, Óscar; Andoy, Nesha M; Filipiak, Marcin S; Haustein, Natalie; Tarasov, Alexey

2017-09-22

Transistor-based biosensors fulfill many requirements posed upon transducers for future point-of-care diagnostic devices such as scalable fabrication and label-free and real-time quantification of chemical and biological species with high sensitivity. However, the short Debye screening length in physiological samples (<1 nm) has been a major drawback so far, preventing direct measurements in serum. In this work, we demonstrate how tailoring the sensing surface with short specific biological receptors and a polymer polyethylene glycol (PEG) can strongly enhance the sensor response. In addition, the sensor performance can be dramatically improved if the measurements are performed at elevated temperatures (37 °C instead of 21 °C). With this novel approach, highly sensitive and selective detection of a representative immunosensing parameter-human thyroid-stimulating hormone-is shown over a wide measuring range with subpicomolar detection limits in whole serum. To the best of our knowledge, this is the first demonstration of direct immunodetection in whole serum using transistor-based biosensors, without the need for sample pretreatment, labeling, or washing steps. The presented sensor is low-cost, can be easily integrated into portable diagnostics devices, and offers a competitive performance compared to state-of-the-art central laboratory analyzers.

A compact "water-window" microscope with 60-nm spatial resolution based on a double stream gas-puff target and Fresnel zone plate optics

NASA Astrophysics Data System (ADS)

Wachulak, Przemyslaw; Torrisi, Alfio; Nawaz, Muhammad F.; Adjei, Daniel; Bartnik, Andrzej; Kostecki, Jerzy; Wegrzynski, Łukasz; Vondrová, Šárka; Turňová, Jana; Fok, Tomasz; Jančarek, Alexandr; Fiedorowicz, Henryk

2015-05-01

Radiation with shorter illumination wavelength allows for extension of the diffraction limit towards nanometer scale, which is a straightforward way to significantly improve a spatial resolution in photon based microscopes. Soft X-ray (SXR) radiation, from the so called "water window" spectral range, λ=2.3-4.4 nm, which is particularly suitable for biological imaging due to natural optical contrast, providing much better spatial resolution than one obtained with visible light microscopes. The high contrast is obtained because of selective absorption of radiation by carbon and water, being constituents of the biological samples. We present a desk-top system, capable of resolving 60 nm features in few seconds exposure time. We exploit the advantages of a compact, laser-plasma SXR source, based on a double stream nitrogen gas puff target, developed at the Institute of Optoelectronics, Military University of Technology. The source, emitting quasi-monochromatic, incoherent radiation, in the "water widow" spectral range at λ = 2.88 nm, is coupled with ellipsoidal, grazing incidence condenser and Fresnel zone plate objective. The construction of the microscope with some recent images of test and real samples will be presented and discussed.

Laser-initiated decomposition products of indocyanine green (ICG) and carbon black sensitized biological tissues

NASA Astrophysics Data System (ADS)

Kokosa, John M.; Przyjazny, Andrzej; Bartels, Kenneth E.; Motamedi, Massoud; Hayes, Donald J.; Wallace, David B.; Frederickson, Christopher J.

1997-05-01

Organic dyes have found increasing use a s sensitizers in laser surgical procedures, due to their high optical absorbances. Little is known, however, about the nature of the degradation products formed when these dyes are irradiated with a laser. Previous work in our laboratories has shown that irradiation of polymeric and biological tissues with CO2 and Nd:YAG lasers produces a host of volatile and semivolatile by-products, some of which are known to be potential carcinogens. This work focuses on the identification of the chemical by-products formed by diode laser and Nd:YAG laser irradiation of indocyanine green (ICG) and carbon black based ink sensitized tissues, including bone, tendon and sheep's teeth. Samples were mounted in a 0.5-L Pyrex sample chamber equipped with quartz optical windows, charcoal filtered air inlet and an outlet attached to an appropriate sample trap and a constant flow pump. By-products were analyzed by GC/MS and HPLC. Volatiles identified included benzene and formaldehyde. Semi-volatiles included traces of polycyclic aromatics, arising from the biological matrix and inks, as well as fragments of ICG and the carbon ink components. The significance of these results will be discussed, including the necessity of using appropriate evacuation devices when utilizing lasers for surgical procedures.

KRAS and BRAF Mutation Detection: Is Immunohistochemistry a Possible Alternative to Molecular Biology in Colorectal Cancer?

PubMed Central

Borrini, Francesco; Bolognese, Antonio; Lamy, Aude; Sabourin, Jean-Christophe

2015-01-01

KRAS genotyping is mandatory in metastatic colorectal cancer treatment prior to undertaking antiepidermal growth factor receptor (EGFR) monoclonal antibody therapy. BRAF V600E mutation is often present in colorectal carcinoma with CpG island methylator phenotype and microsatellite instability. Currently, KRAS and BRAF evaluation is based on molecular biology techniques such as SNaPshot or Sanger sequencing. As molecular testing is performed on formalin-fixed paraffin-embedded (FFPE) samples, immunodetection would appear to be an attractive alternative for detecting mutations. Thus, our objective was to assess the validity of KRAS and BRAF immunodetection of mutations compared with the genotyping reference method in colorectal adenocarcinoma. KRAS and BRAF genotyping was assessed by SNaPshot. A rabbit anti-human KRAS polyclonal antibody was tested on 33 FFPE colorectal tumor samples with known KRAS status. Additionally, a mouse anti-human BRAF monoclonal antibody was tested on 30 FFPE tumor samples with known BRAF status. KRAS immunostaining demonstrated both poor sensitivity (27%) and specificity (64%) in detecting KRAS mutation. Conversely, BRAF immunohistochemistry showed perfect sensitivity (100%) and specificity (100%) in detecting V600E mutation. Although molecular biology remains the reference method for detecting KRAS mutation, immunohistochemistry could be an attractive method for detecting BRAF V600E mutation in colorectal cancer. PMID:25983749

Coupling of metal-organic frameworks-containing monolithic capillary-based selective enrichment with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry for efficient analysis of protein phosphorylation.

PubMed

Li, Daojin; Yin, Danyang; Chen, Yang; Liu, Zhen

2017-05-19

Protein phosphorylation is a major post-translational modification, which plays a vital role in cellular signaling of numerous biological processes. Mass spectrometry (MS) has been an essential tool for the analysis of protein phosphorylation, for which it is a key step to selectively enrich phosphopeptides from complex biological samples. In this study, metal-organic frameworks (MOFs)-based monolithic capillary has been successfully prepared as an effective sorbent for the selective enrichment of phosphopeptides and has been off-line coupled with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) for efficient analysis of phosphopeptides. Using š-casein as a representative phosphoprotein, efficient phosphorylation analysis by this off-line platform was verified. Phosphorylation analysis of a nonfat milk sample was also demonstrated. Through introducing large surface areas and highly ordered pores of MOFs into monolithic column, the MOFs-based monolithic capillary exhibited several significant advantages, such as excellent selectivity toward phosphopeptides, superb tolerance to interference and simple operation procedure. Because of these highly desirable properties, the MOFs-based monolithic capillary could be a useful tool for protein phosphorylation analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

Metamaterial Absorber Based Multifunctional Sensor Application

NASA Astrophysics Data System (ADS)

Ozer, Z.; Mamedov, A. M.; Ozbay, E.

2017-02-01

In this study metamaterial based (MA) absorber sensor, integrated with an X-band waveguide, is numerically and experimentally suggested for important application including pressure, density sensing and marble type detecting applications based on rectangular split ring resonator, sensor layer and absorber layer that measures of changing in the dielectric constant and/or the thickness of a sensor layer. Changing of physical, chemical or biological parameters in the sensor layer can be detected by measuring the resonant frequency shifting of metamaterial absorber based sensor. Suggested MA based absorber sensor can be used for medical, biological, agricultural and chemical detecting applications in microwave frequency band. We compare the simulation and experimentally obtained results from the fabricated sample which are good agreement. Simulation results show that the proposed structure can detect the changing of the refractive indexes of different materials via special resonance frequencies, thus it could be said that the MA-based sensors have high sensitivity. Additionally due to the simple and tiny structures it could be adapted to other electronic devices in different sizes.

Evaluating levels and health risk of heavy metals in exposed workers from surgical instrument manufacturing industries of Sialkot, Pakistan.

PubMed

Junaid, Muhammad; Hashmi, Muhammad Zaffar; Malik, Riffat Naseem

2016-09-01

The study aimed to monitor heavy metal (chromium, Cr; cadmium, Cd; nickel, Ni; copper, Cu; lead, Pb; iron, Fe; manganese, Mn; and zinc, Zn) footprints in biological matrices (urine, whole blood, saliva, and hair), as well as in indoor industrial dust samples, and their toxic effects on oxidative stress and health risks in exposed workers. Overall, blood, urine, and saliva samples exhibited significantly higher concentrations of toxic metals in exposed workers (Cr; blood 16.30 μg/L, urine 58.15 μg/L, saliva 5.28 μg/L) than the control samples (Cr; blood 5.48 μg/L, urine 4.47 μg/L, saliva 2.46 μg/L). Indoor industrial dust samples also reported to have elevated heavy metal concentrations, as an example, Cr quantified with concentration of 299 mg/kg of dust, i.e., more than twice the level of Cr in household dust (136 mg/kg). Superoxide dismutase (SOD) level presented significant positive correlation (p ≤ 0.01) with Cr, Zn, and Cd (Cr > Zn > Cd) which is an indication of heavy metal's associated raised oxidative stress in exposed workers. Elevated average daily intake (ADI) of heavy metals resulted in cumulative hazard quotient (HQ) range of 2.97-18.88 in workers of different surgical units; this is an alarming situation of health risk implications. Principal component analysis-multiple linear regression (PCA-MLR)-based pie charts represent that polishing and cutting sections exhibited highest metal inputs to the biological and environmental matrices than other sources. Heavy metal concentrations in biological matrices and dust samples showed a significant positive correlation between Cr in dust, urine, and saliva samples. Current study will help to generate comprehensive base line data of heavy metal status in biomatrices and dust from scientifically ignored industrial sector. Our findings can play vital role for health departments and industrial environmental management system (EMS) authorities in policy making and implementation.

Rapid ionic liquid-based ultrasound assisted dual magnetic microextraction to preconcentrate and separate cadmium-4-(2-thiazolylazo)-resorcinol complex from environmental and biological samples.

PubMed

Khan, Sumaira; Kazi, Tasneem Gul; Soylak, Mustafa

2014-04-05

A rapid and innovative microextraction technique named as, ionic liquid-based ultrasound-assisted dual magnetic microextraction (IL-UA-DMME) was developed for the preconcentration and extraction of trace cadmium from environmental and biological samples, prior to analyzed by flame atomic absorption spectrometry (FAAS). The proposed method has many obvious advantages, including evading the use of organic solvents and achieved high extraction yields by the combination of dispersive liquid-liquid microextraction (DLLME) and magnetic mediated-solid phase extraction (MM-SPE). In this approach ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate [C4mim][PF6] play an important role to extract the cadmium-4-(2-thiazolylazo)-resorcinol (Cd-TAR) complex from acid digested sample solutions and ultrasonic irradiation was applied to assist emulsification. After then, dispersed small amount of Fe3O4 magnetic nanoparticles (MNPs) in sample solutions to salvaged the IL and complete phase separation was attained. Some analytical parameters that influencing the efficiency of proposed (IL-UA-DMME) method, such as pH, volume of IL, ligand concentration, ultra-sonication time, amount of Fe3O4 MNPs, sample volume and matrix effect were optimized. Limit of detection (LOD) and enrichment factor (EF) of the method under optimal experimental conditions were found to be 0.40μgL(-1) and 100, respectively. The relative standard deviation (RSD) of 50μgL(-1) Cd was 4.29%. The validity and accuracy of proposed method, was assessed to analyzed certified reference materials of fortified lake water TMDA-54.4, SPS-WW2 waste water, spinach leaves 1570a and also checked by standard addition method. The obtained values showed good agreement with the certified values and sufficiently high recovery were found in the range of 98.1-101% for Cd. The proposed method was facile, rapid and successfully applied for the determination of Cd in environmental and different biological samples. Copyright © 2013 Elsevier B.V. All rights reserved.

Rapid and Efficient Filtration-Based Procedure for Separation and Safe Analysis of CBRN Mixed Samples

PubMed Central

Bentahir, Mostafa; Laduron, Frederic; Irenge, Leonid; Ambroise, Jérôme; Gala, Jean-Luc

2014-01-01

Separating CBRN mixed samples that contain both chemical and biological warfare agents (CB mixed sample) in liquid and solid matrices remains a very challenging issue. Parameters were set up to assess the performance of a simple filtration-based method first optimized on separate C- and B-agents, and then assessed on a model of CB mixed sample. In this model, MS2 bacteriophage, Autographa californica nuclear polyhedrosis baculovirus (AcNPV), Bacillus atrophaeus and Bacillus subtilis spores were used as biological agent simulants whereas ethyl methylphosphonic acid (EMPA) and pinacolyl methylphophonic acid (PMPA) were used as VX and soman (GD) nerve agent surrogates, respectively. Nanoseparation centrifugal devices with various pore size cut-off (30 kD up to 0.45 µm) and three RNA extraction methods (Invisorb, EZ1 and Nuclisens) were compared. RNA (MS2) and DNA (AcNPV) quantification was carried out by means of specific and sensitive quantitative real-time PCRs (qPCR). Liquid chromatography coupled to time-of-flight mass spectrometry (LC/TOFMS) methods was used for quantifying EMPA and PMPA. Culture methods and qPCR demonstrated that membranes with a 30 kD cut-off retain more than 99.99% of biological agents (MS2, AcNPV, Bacillus Atrophaeus and Bacillus subtilis spores) tested separately. A rapid and reliable separation of CB mixed sample models (MS2/PEG-400 and MS2/EMPA/PMPA) contained in simple liquid or complex matrices such as sand and soil was also successfully achieved on a 30 kD filter with more than 99.99% retention of MS2 on the filter membrane, and up to 99% of PEG-400, EMPA and PMPA recovery in the filtrate. The whole separation process turnaround-time (TAT) was less than 10 minutes. The filtration method appears to be rapid, versatile and extremely efficient. The separation method developed in this work constitutes therefore a useful model for further evaluating and comparing additional separation alternative procedures for a safe handling and preparation of CB mixed samples. PMID:24505375

Separate and interactive contributions of weak inhibitory control and threat sensitivity to prediction of suicide risk.

PubMed

Venables, Noah C; Sellbom, Martin; Sourander, Andre; Kendler, Kenneth S; Joiner, Thomas E; Drislane, Laura E; Sillanmäki, Lauri; Elonheimo, Henrik; Parkkola, Kai; Multimaki, Petteri; Patrick, Christopher J

2015-04-30

Biobehavioral dispositions can serve as valuable referents for biologically oriented research on core processes with relevance to many psychiatric conditions. The present study examined two such dispositional variables-weak response inhibition (or disinhibition; INH-) and threat sensitivity (or fearfulness; THT+)-as predictors of the serious transdiagnostic problem of suicide risk in two samples: male and female outpatients from a U.S. clinic (N=1078), and a population-based male military cohort from Finland (N=3855). INH- and THT+ were operationalized through scores on scale measures of disinhibition and fear/fearlessness, known to be related to DSM-defined clinical conditions and brain biomarkers. Suicide risk was assessed by clinician ratings (clinic sample) and questionnaires (both samples). Across samples and alternative suicide indices, INH- and THT+ each contributed uniquely to prediction of suicide risk-beyond internalizing and externalizing problems in the case of the clinic sample where diagnostic data were available. Further, in both samples, INH- and THT+ interactively predicted suicide risk, with individuals scoring concurrently high on both dispositions exhibiting markedly augmented risk. Findings demonstrate that dispositional constructs of INH- and THT+ are predictive of suicide risk, and hold potential as referents for biological research on suicidal behavior. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

PCR-based detection of Toxoplasma gondii DNA in blood and ocular samples for diagnosis of ocular toxoplasmosis.

PubMed

Bourdin, C; Busse, A; Kouamou, E; Touafek, F; Bodaghi, B; Le Hoang, P; Mazier, D; Paris, L; Fekkar, A

2014-11-01

PCR detection of Toxoplasma gondii in blood has been suggested as a possibly efficient method for the diagnosis of ocular toxoplasmosis (OT) and furthermore for genotyping the strain involved in the disease. To assess this hypothesis, we performed PCR with 121 peripheral blood samples from 104 patients showing clinical and/or biological evidence of ocular toxoplasmosis and from 284 (258 patients) controls. We tested 2 different extraction protocols, using either 200 μl (small volume) or 2 ml (large volume) of whole blood. Sensitivity was poor, i.e., 4.1% and 25% for the small- and large-volume extractions, respectively. In comparison, PCR with ocular samples yielded 35.9% sensitivity, while immunoblotting and calculation of the Goldmann-Witmer coefficient yielded 47.6% and 72.3% sensitivities, respectively. Performing these three methods together provided 89.4% sensitivity. Whatever the origin of the sample (ocular or blood), PCR provided higher sensitivity for immunocompromised patients than for their immunocompetent counterparts. Consequently, PCR detection of Toxoplasma gondii in blood samples cannot currently be considered a sufficient tool for the diagnosis of OT, and ocular sampling remains necessary for the biological diagnosis of OT. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Superresolution Imaging using Single-Molecule Localization

PubMed Central

Patterson, George; Davidson, Michael; Manley, Suliana; Lippincott-Schwartz, Jennifer

2013-01-01

Superresolution imaging is a rapidly emerging new field of microscopy that dramatically improves the spatial resolution of light microscopy by over an order of magnitude (∼10–20-nm resolution), allowing biological processes to be described at the molecular scale. Here, we discuss a form of superresolution microscopy based on the controlled activation and sampling of sparse subsets of photoconvertible fluorescent molecules. In this single-molecule based imaging approach, a wide variety of probes have proved valuable, ranging from genetically encodable photoactivatable fluorescent proteins to photoswitchable cyanine dyes. These have been used in diverse applications of superresolution imaging: from three-dimensional, multicolor molecule localization to tracking of nanometric structures and molecules in living cells. Single-molecule-based superresolution imaging thus offers exciting possibilities for obtaining molecular-scale information on biological events occurring at variable timescales. PMID:20055680

Fluorometric imaging methods for palladium and platinum and the use of palladium for imaging biomolecules.

PubMed

Tracey, Matthew P; Pham, Dianne; Koide, Kazunori

2015-07-21

Neither palladium nor platinum is an endogenous biological metal. Imaging palladium in biological samples, however, is becoming increasingly important because bioorthogonal organometallic chemistry involves palladium catalysis. In addition to being an imaging target, palladium has been used to fluorometrically image biomolecules. In these cases, palladium species are used as imaging-enabling reagents. This review article discusses these fluorometric methods. Platinum-based drugs are widely used as anticancer drugs, yet their mechanism of action remains largely unknown. We discuss fluorometric methods for imaging or quantifying platinum in cells or biofluids. These methods include the use of chemosensors to directly detect platinum, fluorescently tagging platinum-based drugs, and utilizing post-labeling to elucidate distribution and mode of action.

SPR Biosensors in Direct Molecular Fishing: Implications for Protein Interactomics.

PubMed

Florinskaya, Anna; Ershov, Pavel; Mezentsev, Yuri; Kaluzhskiy, Leonid; Yablokov, Evgeniy; Medvedev, Alexei; Ivanov, Alexis

2018-05-18

We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands. Applicability of this approach has been demonstrated within the frame of the Human Proteome Project (HPP) and PPI regulation by a small non-peptide biologically active compound, isatin.

Microsystem strategies for sample preparation in biological detection.

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

James, Conrad D.; Galambos, Paul C.; Bennett, Dawn Jonita

2005-03-01

The objective of this LDRD was to develop microdevice strategies for dealing with samples to be examined in biological detection systems. This includes three sub-components: namely, microdevice fabrication, sample delivery to the microdevice, and sample processing within the microdevice. The first component of this work focused on utilizing Sandia's surface micromachining technology to fabricate small volume (nanoliter) fluidic systems for processing small quantities of biological samples. The next component was to develop interfaces for the surface-micromachined silicon devices. We partnered with Micronics, a commercial company, to produce fluidic manifolds for sample delivery to our silicon devices. Pressure testing was completedmore » to examine the strength of the bond between the pressure-sensitive adhesive layer and the silicon chip. We are also pursuing several other methods, both in house and external, to develop polymer-based fluidic manifolds for packaging silicon-based microfluidic devices. The second component, sample processing, is divided into two sub-tasks: cell collection and cell lysis. Cell collection was achieved using dielectrophoresis, which employs AC fields to collect cells at energized microelectrodes, while rejecting non-cellular particles. Both live and dead Staph. aureus bacteria have been collected using RF frequency dielectrophoresis. Bacteria have been separated from polystyrene microspheres using frequency-shifting dielectrophoresis. Computational modeling was performed to optimize device separation performance, and to predict particle response to the dielectrophoretic traps. Cell lysis is continuing to be pursued using microactuators to mechanically disrupt cell membranes. Novel thermal actuators, which can generate larger forces than previously tested electrostatic actuators, have been incorporated with and tested with cell lysis devices. Significant cell membrane distortion has been observed, but more experiments need to be conducted to determine the effects of the observed distortion on membrane integrity and cell viability. Finally, we are using a commercial PCR DNA amplification system to determine the limits of detectable sample size, and to examine the amplification of DNA bound to microspheres. Our objective is to use microspheres as capture-and-carry chaperones for small molecules such as DNA and proteins, enabling the capture and concentration of the small molecules using dielectrophoresis. Current tests demonstrated amplification of DNA bound to micron-sized polystyrene microspheres using 20-50 microliter volume size reactions.« less

Enzyme-regulated the changes of pH values for assembling a colorimetric and multistage interconnection logic network with multiple readouts.

PubMed

Huang, Yanyan; Ran, Xiang; Lin, Youhui; Ren, Jinsong; Qu, Xiaogang

2015-04-22

Based on enzymatic reactions-triggered changes of pH values and biocomputing, a novel and multistage interconnection biological network with multiple easy-detectable signal outputs has been developed. Compared with traditional chemical computing, the enzyme-based biological system could overcome the interference between reactions or the incompatibility of individual computing gates and offer a unique opportunity to assemble multicomponent/multifunctional logic circuitries. Our system included four enzyme inputs: β-galactosidase (β-gal), glucose oxidase (GOx), esterase (Est) and urease (Ur). With the assistance of two signal transducers (gold nanoparticles and acid-base indicators) or pH meter, the outputs of the biological network could be conveniently read by the naked eyes. In contrast to current methods, the approach present here could realize cost-effective, label-free and colorimetric logic operations without complicated instrument. By designing a series of Boolean logic operations, we could logically make judgment of the compositions of the samples on the basis of visual output signals. Our work offered a promising paradigm for future biological computing technology and might be highly useful in future intelligent diagnostics, prodrug activation, smart drug delivery, process control, and electronic applications. Copyright © 2015 Elsevier B.V. All rights reserved.

On the optimal design of molecular sensing interfaces with lipid bilayer assemblies - A knowledge based approach

NASA Astrophysics Data System (ADS)

Siontorou, Christina G.

2012-12-01

Biosensors are analytic devices that incorporate a biochemical recognition system (biological, biologicalderived or biomimic: enzyme, antibody, DNA, receptor, etc.) in close contact with a physicochemical transducer (electrochemical, optical, piezoelectric, conductimetric, etc.) that converts the biochemical information, produced by the specific biological recognition reaction (analyte-biomolecule binding), into a chemical or physical output signal, related to the concentration of the analyte in the measuring sample. The biosensing concept is based on natural chemoreception mechanisms, which are feasible over/within/by means of a biological membrane, i.e., a structured lipid bilayer, incorporating or attached to proteinaceous moieties that regulate molecular recognition events which trigger ion flux changes (facilitated or passive) through the bilayer. The creation of functional structures that are similar to natural signal transduction systems, correlating and interrelating compatibly and successfully the physicochemical transducer with the lipid film that is self-assembled on its surface while embedding the reconstituted biological recognition system, and at the same time manage to satisfy the basic conditions for measuring device development (simplicity, easy handling, ease of fabrication) is far from trivial. The aim of the present work is to present a methodological framework for designing such molecular sensing interfaces, functioning within a knowledge-based system built on an ontological platform for supplying sub-systems options, compatibilities, and optimization parameters.

Numerical examination of like-honeycomb structures

NASA Astrophysics Data System (ADS)

John, Małgorzata; John, Antoni; Skarka, Wojciech

2018-01-01

In the paper based on the analogy with the biological tissue of bones, it was decided to examine more homogenous structure and also a heterogeneous structure too. Here, a new approach is proposed based on results from literature obtained using topology optimization 2D and 3D structures like beam, girder and cantilever. Proposed model of structure is similar to spatial trusses with honeycomb-shape porous. Parameters varied not only uniformly throughout the volume of the sample, but also be modified depending on various factors. They underwent a change in cell dimensions, among other things, the thickness of the wall. The obtained results were compared with those obtained previously for homogeneous samples.

Method of assessing a lipid-related health risk based on ion mobility analysis of lipoproteins

DOEpatents

Benner, W. Henry; Krauss, Ronald M.; Blanche, Patricia J.

2010-12-14

A medical diagnostic method and instrumentation system for analyzing noncovalently bonded agglomerated biological particles is described. The method and system comprises: a method of preparation for the biological particles; an electrospray generator; an alpha particle radiation source; a differential mobility analyzer; a particle counter; and data acquisition and analysis means. The medical device is useful for the assessment of human diseases, such as cardiac disease risk and hyperlipidemia, by rapid quantitative analysis of lipoprotein fraction densities. Initially, purification procedures are described to reduce an initial blood sample to an analytical input to the instrument. The measured sizes from the analytical sample are correlated with densities, resulting in a spectrum of lipoprotein densities. The lipoprotein density distribution can then be used to characterize cardiac and other lipid-related health risks.

Relationships Among Perceived Stress, Bullying, Cortisol, and Depressive Symptoms in Ninth-Grade Adolescents: A Pilot Study.

PubMed

Williams, Susan G; Turner-Henson, Anne; Davis, Sara; Soistmann, Heather C

2016-06-29

Adolescence is considered a critical period for risk of depressive symptoms, with prevalence ranging from 13% to 34%. Few studies have examined the relationships among perceived stress, bullying, and depressive symptoms accompanied by a biological marker of stress (cortisol). The purpose of this pilot study was to determine the feasibility of collecting biological specimens in a high school setting, including a morning and afternoon sample of salivary cortisol as well as computer-based survey data in order to examine the relationships among these variables in ninth-grade adolescents. A convenience sample of 31 ninth-grade students from a Southern suburban high school participated in this cross-sectional, correlational study. Perceived stress contributed the most toward the variance in depressive symptoms (F = 29.379, df = 1, p < .001, partial eta square [[Formula: see text

Observations on White Grubs Affecting Sugar Cane at the Juba Sugar Project, South-Western Somalia, in the 1980s, and Implications for Their Management

PubMed Central

Cock, Matthew J. W.; Allard, Gillian B.

2013-01-01

The authors made two visits to the Juba Sugar Project in south-west Somalia, at the beginning of the minor rains in October 1986, and at the beginning of the main rains in March 1987. Observations were made on morphospecies of scarabaeid white grub larvae, the adults, and the two associated for the key economic species, Cochliotis melolonthoides and Brachylepis werneri. Sampling larvae and adults by digging soil quadrats and adults by light trapping gave useful information on their biology and phenology. Sampling methods were evaluated and economic thresholds were extrapolated based on earlier work. Natural enemies were surveyed, and entomopathogenic nematodes and a cordyceps fungus (Ophiocordyceps barnesii) were considered to have potential to be used as biological control interventions. PMID:26464389

Observations on White Grubs Affecting Sugar Cane at the Juba Sugar Project, South-Western Somalia, in the 1980s, and Implications for Their Management.

PubMed

Cock, Matthew J W; Allard, Gillian B

2013-06-18

The authors made two visits to the Juba Sugar Project in south-west Somalia, at the beginning of the minor rains in October 1986, and at the beginning of the main rains in March 1987. Observations were made on morphospecies of scarabaeid white grub larvae, the adults, and the two associated for the key economic species, Cochliotis melolonthoides and Brachylepis werneri. Sampling larvae and adults by digging soil quadrats and adults by light trapping gave useful information on their biology and phenology. Sampling methods were evaluated and economic thresholds were extrapolated based on earlier work. Natural enemies were surveyed, and entomopathogenic nematodes and a cordyceps fungus (Ophiocordyceps barnesii) were considered to have potential to be used as biological control interventions.

Humidity-controlled preparation of frozen-hydrated biological samples for cryogenic coherent x-ray diffraction microscopy

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

Takayama, Yuki; Nakasako, Masayoshi; RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo 679-5148

2012-05-15

Coherent x-ray diffraction microscopy (CXDM) has the potential to visualize the structures of micro- to sub-micrometer-sized biological particles, such as cells and organelles, at high resolution. Toward advancing structural studies on the functional states of such particles, here, we developed a system for the preparation of frozen-hydrated biological samples for cryogenic CXDM experiments. The system, which comprised a moist air generator, microscope, micro-injector mounted on a micromanipulator, custom-made sample preparation chamber, and flash-cooling device, allowed for the manipulation of sample particles in the relative humidity range of 20%-94%rh at 293 K to maintain their hydrated and functional states. Here, wemore » report the details of the system and the operation procedure, including its application to the preparation of a frozen-hydrated chloroplast sample. Sample quality was evaluated through a cryogenic CXDM experiment conducted at BL29XUL of SPring-8. Taking the performance of the system and the quality of the sample, the system was suitable to prepare frozen-hydrated biological samples for cryogenic CXDM experiments.« less

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.

Application of Biologically Based Lumping To Investigate the Toxicokinetic Interactions of a Complex Gasoline Mixture.

PubMed

Jasper, Micah N; Martin, Sheppard A; Oshiro, Wendy M; Ford, Jermaine; Bushnell, Philip J; El-Masri, Hisham

2016-03-15

People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate the performance of our PBPK model and chemical lumping method. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course toxicokinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 nontarget chemicals. The same biologically based lumping approach can be used to simplify any complex mixture with tens, hundreds, or thousands of constituents.

Can current analytical quality performance of UK clinical laboratories support evidence-based guidelines for diabetes and ischaemic heart disease?--A pilot study and a proposal.

PubMed

Jassam, Nuthar; Yundt-Pacheco, John; Jansen, Rob; Thomas, Annette; Barth, Julian H

2013-08-01

The implementation of national and international guidelines is beginning to standardise clinical practice. However, since many guidelines have decision limits based on laboratory tests, there is an urgent need to ensure that different laboratories obtain the same analytical result on any sample. A scientifically-based quality control process will be a pre-requisite to provide this level of analytical performance which will support evidence-based guidelines and movement of patients across boundaries while maintaining standardised outcomes. We discuss the finding of a pilot study performed to assess UK clinical laboratories readiness to work to a higher grade quality specifications such as biological variation-based quality specifications. Internal quality control (IQC) data for HbA1c, glucose, creatinine, cholesterol and high density lipoprotein (HDL)-cholesterol were collected from UK laboratories participating in the Bio-Rad Unity QC programme. The median of the coefficient of variation (CV%) of the participating laboratories was evaluated against the CV% based on biological variation. Except creatinine, the other four analytes had a variable degree of compliance with the biological variation-based quality specifications. More than 75% of the laboratories met the biological variation-based quality specifications for glucose, cholesterol and HDL-cholesterol. Slightly over 50% of the laboratories met the analytical goal for HBA1c. Only one analyte (cholesterol) had a performance achieving the higher quality specifications consistent with 5σ. Our data from IQC do not consistently demonstrate that the results from clinical laboratories meet evidence-based quality specifications. Therefore, we propose that a graded scale of quality specifications may be needed at this stage.

Molecular-based rapid inventories of sympatric diversity: a comparison of DNA barcode clustering methods applied to geography-based vs clade-based sampling of amphibians.

PubMed

Paz, Andrea; Crawford, Andrew J

2012-11-01

Molecular markers offer a universal source of data for quantifying biodiversity. DNA barcoding uses a standardized genetic marker and a curated reference database to identify known species and to reveal cryptic diversity within wellsampled clades. Rapid biological inventories, e.g. rapid assessment programs (RAPs), unlike most barcoding campaigns, are focused on particular geographic localities rather than on clades. Because of the potentially sparse phylogenetic sampling, the addition of DNA barcoding to RAPs may present a greater challenge for the identification of named species or for revealing cryptic diversity. In this article we evaluate the use of DNA barcoding for quantifying lineage diversity within a single sampling site as compared to clade-based sampling, and present examples from amphibians. We compared algorithms for identifying DNA barcode clusters (e.g. species, cryptic species or Evolutionary Significant Units) using previously published DNA barcode data obtained from geography-based sampling at a site in Central Panama, and from clade-based sampling in Madagascar. We found that clustering algorithms based on genetic distance performed similarly on sympatric as well as clade-based barcode data, while a promising coalescent-based method performed poorly on sympatric data. The various clustering algorithms were also compared in terms of speed and software implementation. Although each method has its shortcomings in certain contexts, we recommend the use of the ABGD method, which not only performs fairly well under either sampling method, but does so in a few seconds and with a user-friendly Web interface.

Biological surveys on the Savannah River in the vicinity of the Savannah River Plant (1951-1976)

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

Matthews, R. A.

In 1951, the Academy of Natural Sciences of Philadelphia was contracted by the Savannah River Plant to initiate a long-term monitoring program in the Savannah River. The purpose of this program was to determine the effect of the Savannah River Plant on the Savannah River aquatic ecosystem. The data from this monitoring program have been computerized by the Savannah River Laboratory, and are summarized in this report. During the period from 1951-1976, 16 major surveys were conducted by the Academy in the Savannah River. Water chemistry analyses were made, and all major biological communities were sampled qualitatively during the springmore » and fall of each survey year. In addition, quantitative diatom data have been collected quarterly since 1953. Major changes in the Savannah River basin, in the Savannah River Plant's activities, and in the Academy sampling patterns are discussed to provide a historical overview of the biomonitoring program. Appendices include a complete taxonomic listing of species collected from the Savannah River, and summaries of the entire biological and physicochemical data base.« less

A data-independent acquisition workflow for qualitative screening of new psychoactive substances in biological samples.

PubMed

Kinyua, Juliet; Negreira, Noelia; Ibáñez, María; Bijlsma, Lubertus; Hernández, Félix; Covaci, Adrian; van Nuijs, Alexander L N

2015-11-01

Identification of new psychoactive substances (NPS) is challenging. Developing targeted methods for their analysis can be difficult and costly due to their impermanence on the drug scene. Accurate-mass mass spectrometry (AMMS) using a quadrupole time-of-flight (QTOF) analyzer can be useful for wide-scope screening since it provides sensitive, full-spectrum MS data. Our article presents a qualitative screening workflow based on data-independent acquisition mode (all-ions MS/MS) on liquid chromatography (LC) coupled to QTOFMS for the detection and identification of NPS in biological matrices. The workflow combines and structures fundamentals of target and suspect screening data processing techniques in a structured algorithm. This allows the detection and tentative identification of NPS and their metabolites. We have applied the workflow to two actual case studies involving drug intoxications where we detected and confirmed the parent compounds ketamine, 25B-NBOMe, 25C-NBOMe, and several predicted phase I and II metabolites not previously reported in urine and serum samples. The screening workflow demonstrates the added value for the detection and identification of NPS in biological matrices.

Ontology based molecular signatures for immune cell types via gene expression analysis

PubMed Central

2013-01-01

Background New technologies are focusing on characterizing cell types to better understand their heterogeneity. With large volumes of cellular data being generated, innovative methods are needed to structure the resulting data analyses. Here, we describe an ‘Ontologically BAsed Molecular Signature’ (OBAMS) method that identifies novel cellular biomarkers and infers biological functions as characteristics of particular cell types. This method finds molecular signatures for immune cell types based on mapping biological samples to the Cell Ontology (CL) and navigating the space of all possible pairwise comparisons between cell types to find genes whose expression is core to a particular cell type’s identity. Results We illustrate this ontological approach by evaluating expression data available from the Immunological Genome project (IGP) to identify unique biomarkers of mature B cell subtypes. We find that using OBAMS, candidate biomarkers can be identified at every strata of cellular identity from broad classifications to very granular. Furthermore, we show that Gene Ontology can be used to cluster cell types by shared biological processes in order to find candidate genes responsible for somatic hypermutation in germinal center B cells. Moreover, through in silico experiments based on this approach, we have identified genes sets that represent genes overexpressed in germinal center B cells and identify genes uniquely expressed in these B cells compared to other B cell types. Conclusions This work demonstrates the utility of incorporating structured ontological knowledge into biological data analysis – providing a new method for defining novel biomarkers and providing an opportunity for new biological insights. PMID:24004649

Review of sampling hard-to-reach and hidden populations for HIV surveillance.

PubMed

Magnani, Robert; Sabin, Keith; Saidel, Tobi; Heckathorn, Douglas

2005-05-01

Adequate surveillance of hard-to-reach and 'hidden' subpopulations is crucial to containing the HIV epidemic in low prevalence settings and in slowing the rate of transmission in high prevalence settings. For a variety of reasons, however, conventional facility and survey-based surveillance data collection strategies are ineffective for a number of key subpopulations, particularly those whose behaviors are illegal or illicit. This paper critically reviews alternative sampling strategies for undertaking behavioral or biological surveillance surveys of such groups. Non-probability sampling approaches such as facility-based sentinel surveillance and snowball sampling are the simplest to carry out, but are subject to a high risk of sampling/selection bias. Most of the probability sampling methods considered are limited in that they are adequate only under certain circumstances and for some groups. One relatively new method, respondent-driven sampling, an adaptation of chain-referral sampling, appears to be the most promising for general applications. However, as its applicability to HIV surveillance in resource-poor settings has yet to be established, further field trials are needed before a firm conclusion can be reached.

Using Genotype Abundance to Improve Phylogenetic Inference

PubMed Central

Mesin, Luka; Victora, Gabriel D; Minin, Vladimir N; Matsen, Frederick A

2018-01-01

Abstract Modern biological techniques enable very dense genetic sampling of unfolding evolutionary histories, and thus frequently sample some genotypes multiple times. This motivates strategies to incorporate genotype abundance information in phylogenetic inference. In this article, we synthesize a stochastic process model with standard sequence-based phylogenetic optimality, and show that tree estimation is substantially improved by doing so. Our method is validated with extensive simulations and an experimental single-cell lineage tracing study of germinal center B cell receptor affinity maturation. PMID:29474671

The analytical change in plasma creatinine that constitutes a biologic/physiologic change.

PubMed

Toffaletti, John G; Hammett-Stabler, Catherine A; Gearhart, Margaret; Roy Choudhury, Kingshuk; Handel, Elizabeth A

2016-08-01

Accurate and precise measurements of creatinine are necessary to evaluate changes in kidney function related to a decreased glomerular filtration rate (GFR). When serial measurements of creatinine are monitored in an individual, it is useful to know what magnitude of an analytical change in creatinine indicates a true physiologic/biologic change in plasma creatinine that might warrant clinical intervention. We compared results between three different methods for creatinine using large chemistry analyzers, two based on alkaline picrate (AP1 and AP2), and one based on dry-slide enzymatic conversion (ENZ). On each of three different segments or days of the study spaced 1-2months apart, we selected 10 different plasma samples having creatinine concentrations ranging from about 0.5mg/dL to 4.5mg/dL (44 to 400μmol/L). Each sample was analyzed in triplicate on each of two same-model analyzers at each institution, then from this data we determined the precision of each model of analyzer. The within-instrument precision of each analyzer was evaluated from the differences between the triplicate results on each sample by each analyzer (mean and SD of the differences). The between-instrument precision was evaluated as the differences between results on the same sample (1, 2, 3, etc.) analyzed on different analyzers of the same model (A and B). This between-analyzer precision data was used to determine both the range and mean±2SD of the differences that could be used to indicate that greater changes in creatinine concentrations would represent a biologic change. The within-instrument precision was best for the ENZ method in comparison to the two alkaline picrate rate methods. The between-instrument precision of the 90 consecutive measurements (30 samples×triplicate analyses) between the same-model analyzers were (mean and SD of differences in mg/dL): -0.018 and 0.029 (ENZ); 0.016 and 0.11 (AP1), and -0.058 and 0.071 (AP2). While all three of the creatinine methods studied had good precision, the ENZ method had the best precision, such that a change of 0.07mg/dL (6μmol/L) in serial creatinine concentrations up to 1.5mg/dL on a patient could indicate a biologic change had occurred. For the alkaline picrate methods, a measured change of creatinine of 0.23mg/dL for AP1 or 0.11mg/dL for AP2 would indicate that a physiologic change in serum/plasma creatinine has occurred. While a definite biologic change may simply represent daily variations, detecting a biologic change in creatinine more rapidly could impact the ability of creatinine to detect early and clinically significant changes in renal function. Copyright © 2016 Elsevier B.V. All rights reserved.

Size distributions of organic nitrogen and carbon in remote marine aerosols: Evidence of marine biological origin based on their isotopic ratios

NASA Astrophysics Data System (ADS)

Miyazaki, Yuzo; Kawamura, Kimitaka; Sawano, Maki

2010-03-01

Size-segregated aerosol samples were collected over the western North Pacific in summer 2008 for the measurements of organic nitrogen (ON) and organic carbon (OC). ON and OC showed bimodal size distributions. Their concentrations showed positive correlation with those of biogenic tracers, methanesulfonic acid (MSA) and azelaic acid (C9). We found that average ON and OC concentrations were twice greater in aerosols collected in the oceanic region with higher biological productivity than in the regions with lower productivity. The average ON/OC ratios are higher (0.49 ± 0.11) in more biologically influenced aerosols than those (0.35 ± 0.10) in less influenced aerosols. Stable carbon isotopic analysis indicates that marine-derived carbon accounted for ˜46-72% of total carbon in more biologically influenced aerosols. These results provide evidence that organic aerosols in this region are enriched in ON that is linked to oceanic biological activity and the subsequent emissions to the atmosphere.

A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system.

PubMed

Govender, Nisha; Senan, Siju; Mohamed-Hussein, Zeti-Azura; Wickneswari, Ratnam

2018-06-15

The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.

Water-quality and biologic data for the Blue River basin, Kansas City metropolitan area, Missouri and Kansas, October 2000 to October 2004

USGS Publications Warehouse

Wilkison, Donald H.; Armstrong, Daniel J.; Brown, Rebecca E.; Poulton, Barry C.; Cahill, Jeffrey D.; Zaugg, Steven D.

2005-01-01

This report presents water-quality and biologic data collected in the Blue River Basin, metropolitan Kansas City, Missouri and Kansas, from October 2000 to October 2004. Data were collected in cooperation with the city of Kansas City, Missouri, Water Services Department as part of an ongoing study designed to characterize long-term water-quality trends in the basin and to provide data to support a strategy for combined sewer overflow control. These data include values of physical properties, fecal indicator bacteria densities, suspended sediment, and concentrations of major ions, nutrients, trace elements, organic wastewater compounds, and pharmaceutical compounds in base-flow and stormflow stream samples and bottom sediments. Six surface-water sites in the basin were sampled 13 times during base-flow conditions and during a minimum of 7 storms. Benthic macroinvertebrate communities are described at 10 sites in the basin and 1 site outside the basin. Water-column and bottom-sediment data from impounded reaches of Brush Creek are provided. Continuous specific conductance, pH, water-quality temperature, turbidity, and dissolved oxygen data are provided for two streams-the Blue River and Brush Creek. Sampling, analytical, and quality assurance methods used in data collection during the study also are described in the report.

Short-Term Effect of Vermicompost Application on Biological Properties of an Alkaline Soil with High Lime Content from Mediterranean Region of Turkey

PubMed Central

Uz, Ilker; Tavali, Ismail Emrah

2014-01-01

This study was conducted to investigate direct short-term impact of vermicompost on some soil biological properties by monitoring changes after addition of vermicompost as compared to farmyard manure in an alkaline soil with high lime content from semiarid Mediterranean region of Turkey. For this purpose, mixtures of soil and organic fertilizers in different doses were incubated under greenhouse condition. Soil samples collected in regular intervals were analyzed for biological parameters including dehydrogenase, β-glucosidase, urease, alkaline phosphatase activities, and total number of aerobic mesophilic bacteria. Even though soil dehydrogenase activity appeared to be dose-independent based on overall evaluation, organic amendments were found to elevate dehydrogenase activity when sampling periods are evaluated individually. β-glucosidase, urease, alkaline phosphatase activity, and aerobic mesophilic bacterial numbers in vermicompost treatments fluctuated but remained significantly above the control. A slight but statistically significant difference was detected between organic amendments in terms of urease activity. Vermicompost appeared to more significantly increase bacterial number in soil. Clearly, vermicompost has a potential to be used as an alternative to farmyard manure to improve and maintain soil biological activity in alkaline calcareous soils from the Mediterranean region of Turkey. Further studies are needed to assess its full potential for these soils. PMID:25254238

Emission of nitrous acid from soil and biological soil crusts represents an important source of HONO in the remote atmosphere in Cyprus

NASA Astrophysics Data System (ADS)

Meusel, Hannah; Tamm, Alexandra; Kuhn, Uwe; Wu, Dianming; Lena Leifke, Anna; Fiedler, Sabine; Ruckteschler, Nina; Yordanova, Petya; Lang-Yona, Naama; Pöhlker, Mira; Lelieveld, Jos; Hoffmann, Thorsten; Pöschl, Ulrich; Su, Hang; Weber, Bettina; Cheng, Yafang

2018-01-01

Soil and biological soil crusts can emit nitrous acid (HONO) and nitric oxide (NO). The terrestrial ground surface in arid and semiarid regions is anticipated to play an important role in the local atmospheric HONO budget, deemed to represent one of the unaccounted-for HONO sources frequently observed in field studies. In this study HONO and NO emissions from a representative variety of soil and biological soil crust samples from the Mediterranean island Cyprus were investigated under controlled laboratory conditions. A wide range of fluxes was observed, ranging from 0.6 to 264 ng m-2 s-1 HONO-N at optimal soil water content (20-30 % of water holding capacity, WHC). Maximum NO-N fluxes at this WHC were lower (0.8-121 ng m-2 s-1). The highest emissions of both reactive nitrogen species were found from bare soil, followed by light and dark cyanobacteria-dominated biological soil crusts (biocrusts), correlating well with the sample nutrient levels (nitrite and nitrate). Extrapolations of lab-based HONO emission studies agree well with the unaccounted-for HONO source derived previously for the extensive CYPHEX field campaign, i.e., emissions from soil and biocrusts may essentially close the Cyprus HONO budget.

Biological Sex Differences in Depression: A Systematic Review.

PubMed

Labaka, Ainitze; Goñi-Balentziaga, Olatz; Lebeña, Andrea; Pérez-Tejada, Joana

2018-07-01

Depression is the leading cause of disability worldwide, and its prevalence is 2 times higher in women than in men. There is, however, a lack of data on sex-specific pathophysiology of this disorder. The purpose of this systematic review is to identify the biological sex differences found in major depressive disorder (MDD) in studies published in the last 10 years. We conducted a literature search using the Medline, PsycInfo, PubMed, and Web of Science databases, selecting English-language studies that included physiological measures compared by sex in addition to MDD. We identified 20 relevant studies, which consisted primarily of mixed methodology and samples. The reported physiological measures comprised a variety of serum biomarkers, gene mRNA expression, and brain activity. Findings suggest different biological patterns in those with MDD depending on sex. Specifically, women presented higher levels of inflammatory, neurotrophic, and serotonergic markers and a stronger correlation between levels of some inflammatory and neurotrophic factors and the severity of symptoms. This review provides information about possible different biological patterns for women and men with depressive disorder and may have important implications for treatment. Future research should include homogeneous samples; make comparisons based on sex, control sex hormone fluctuations and pharmacological treatment; and use consistent criteria for evaluating psychobiological changes in MDD.

Importance of Data Management in a Long-Term Biological Monitoring Program

NASA Astrophysics Data System (ADS)

Christensen, Sigurd W.; Brandt, Craig C.; McCracken, Mary K.

2011-06-01

The long-term Biological Monitoring and Abatement Program (BMAP) has always needed to collect and retain high-quality data on which to base its assessments of ecological status of streams and their recovery after remediation. Its formal quality assurance, data processing, and data management components all contribute to meeting this need. The Quality Assurance Program comprehensively addresses requirements from various institutions, funders, and regulators, and includes a data management component. Centralized data management began a few years into the program when an existing relational database was adapted and extended to handle biological data. The database's main data tables and several key reference tables are described. One of the most important related activities supporting long-term analyses was the establishing of standards for sampling site names, taxonomic identification, flagging, and other components. The implemented relational database supports the transmittal of data to the Oak Ridge Environmental Information System (OREIS) as the permanent repository. We also discuss some limitations to our implementation. Some types of program data were not easily accommodated in the central systems, and many possible data-sharing and integration options are not easily accessible to investigators. From our experience we offer data management advice to other biologically oriented long-term environmental sampling and analysis programs.

miR2Pathway: A novel analytical method to discover MicroRNA-mediated dysregulated pathways involved in hepatocellular carcinoma.

PubMed

Li, Chaoxing; Dinu, Valentin

2018-05-01

MicroRNAs (miRNAs) are small, non-coding RNAs involved in the regulation of gene expression at a post-transcriptional level. Recent studies have shown miRNAs as key regulators of a variety of biological processes, such as proliferation, differentiation, apoptosis, metabolism, etc. Aberrantly expressed miRNAs influence individual gene expression level, but rewired miRNA-mRNA connections can influence the activity of biological pathways. Here, we define rewired miRNA-mRNA connections as the differential (rewiring) effects on the activity of biological pathways between hepatocellular carcinoma (HCC) and normal phenotypes. Our work presented here uses a PageRank-based approach to measure the degree of miRNA-mediated dysregulation of biological pathways between HCC and normal samples based on rewired miRNA-mRNA connections. In our study, we regard the degree of miRNA-mediated dysregulation of biological pathways as disease risk of biological pathways. Therefore, we propose a new method, miR2Pathway, to measure and rank the degree of miRNA-mediated dysregulation of biological pathways by measuring the total differential influence of miRNAs on the activity of pathways between HCC and normal states. miR2Pathway proposed here systematically shows the first evidence for a mechanism of biological pathways being dysregulated by rewired miRNA-mRNA connections, and provides new insight into exploring mechanisms behind HCC. Thus, miR2Pathway is a novel method to identify and rank miRNA-dysregulated pathways in HCC. Copyright © 2018 Elsevier Inc. All rights reserved.

Studies on the Presence of Mycotoxins in Biological Samples: An Overview

PubMed Central

Escrivá, Laura; Font, Guillermina; Manyes, Lara

2017-01-01

Mycotoxins are fungal secondary metabolites with bioaccumulation levels leading to their carry-over into animal fluids, organs, and tissues. As a consequence, mycotoxin determination in biological samples from humans and animals has been reported worldwide. Since most mycotoxins show toxic effects at low concentrations and considering the extremely low levels present in biological samples, the application of reliable detection methods is required. This review summarizes the information regarding the studies involving mycotoxin determination in biological samples over the last 10 years. Relevant data on extraction methodology, detection techniques, sample size, limits of detection, and quantitation are presented herein. Briefly, liquid-liquid extraction followed by LC-MS/MS determination was the most common technique. The most analyzed mycotoxin was ochratoxin A, followed by zearalenone and deoxynivalenol—including their metabolites, enniatins, fumonisins, aflatoxins, T-2 and HT-2 toxins. Moreover, the studies were classified by their purpose, mainly focused on the development of analytical methodologies, mycotoxin biomonitoring, and exposure assessment. The study of tissue distribution, bioaccumulation, carry-over, persistence and transference of mycotoxins, as well as, toxicokinetics and ADME (absorption, distribution, metabolism and excretion) were other proposed goals for biological sample analysis. Finally, an overview of risk assessment was discussed. PMID:28820481

A reverse engineering approach to optimize experiments for the construction of biological regulatory networks.

PubMed

Zhang, Xiaomeng; Shao, Bin; Wu, Yangle; Qi, Ouyang

2013-01-01

One of the major objectives in systems biology is to understand the relation between the topological structures and the dynamics of biological regulatory networks. In this context, various mathematical tools have been developed to deduct structures of regulatory networks from microarray expression data. In general, from a single data set, one cannot deduct the whole network structure; additional expression data are usually needed. Thus how to design a microarray expression experiment in order to get the most information is a practical problem in systems biology. Here we propose three methods, namely, maximum distance method, trajectory entropy method, and sampling method, to derive the optimal initial conditions for experiments. The performance of these methods is tested and evaluated in three well-known regulatory networks (budding yeast cell cycle, fission yeast cell cycle, and E. coli. SOS network). Based on the evaluation, we propose an efficient strategy for the design of microarray expression experiments.

Detection and differentiation of biological species using microcalorimetric spectroscopy.

PubMed

Arakawa, E T; Lavrik, N V; Rajic, S; Datskos, P G

2003-01-01

We report on the application of infrared (IR) microcalorimetric spectroscopy ( micro -CalSpec) to the identification and detection of trace amounts of biological species. Our approach combines principles of photothermal IR spectroscopy with ultrasensitive microcantilever (MC) thermal detectors. We have obtained photothermal IR spectra for DNA and RNA bases and for Bacillus Cereus (an anthrax simulant) in the wavelength range of 2.5-14.5 micro m (4000-690 cm(-1)). The measurements are accomplished by absorbing biological materials directly on a MC thermal detector. The main advantage of the developed micro -CalSpec is its unprecedented sensitivity as compared to any of the previously explored IR techniques, including FTIR and photothermal FTIR methods. Our results demonstrate that <10(-9)g of a biological sample is sufficient to obtain its characteristic micro -CalSpec spectrum that contains information-rich chemical (vibrational) signatures. This opens up a new opportunity to create inexpensive high-throughput analytical systems for biochemical detection.

Mass spectrometry for the detection of bioterrorism agents: from environmental to clinical applications.

PubMed

Duriez, Elodie; Armengaud, Jean; Fenaille, François; Ezan, Eric

2016-03-01

In the current context of international conflicts and localized terrorist actions, there is unfortunately a permanent threat of attacks with unconventional warfare agents. Among these, biological agents such as toxins, microorganisms, and viruses deserve particular attention owing to their ease of production and dissemination. Mass spectrometry (MS)-based techniques for the detection and quantification of biological agents have a decisive role to play for countermeasures in a scenario of biological attacks. The application of MS to every field of both organic and macromolecular species has in recent years been revolutionized by the development of soft ionization techniques (MALDI and ESI), and by the continuous development of MS technologies (high resolution, accurate mass HR/AM instruments, novel analyzers, hybrid configurations). New possibilities have emerged for exquisite specific and sensitive detection of biological warfare agents. MS-based strategies for clinical application can now address a wide range of analytical questions mainly including issues related to the complexity of biological samples and their available volume. Multiplexed toxin detection, discovery of new markers through omics approaches, and identification of untargeted microbiological or of novel molecular targets are examples of applications. In this paper, we will present these technological advances along with the novel perspectives offered by omics approaches to clinical detection and follow-up. Copyright © 2016 John Wiley & Sons, Ltd.

Experimental design and modeling of a microscale differential thermal calorimeter for the purposes of cryopreservation

NASA Astrophysics Data System (ADS)

Armes, James L.

In order to develop successful cryopreservation protocols for various biological materials, it is necessary to determine the thermodynamic properties of nanoliter- scale biological samples: ranging from heat capacity to heat of fusion. Differential thermal analysis is a calorimetric technique which is efficacious at determining these thermodynamic properties and will help lend insight into the formation of intracellular ice which depends heavily on the rate at which the sample is cooled. If too much intracellular ice is formed during the cooling process, the biological material can be destroyed. To investigate the effects of a range of cooling and warming rates on a cell, a control system and data acquisition software has been developed for use with a custom microfabricated differential thermal analyzer (muDTA). Utilizing either an a-priori prediction of the muDTA's thermal response or an integrated software-based PID control system, the program developed allows for precise control over the cooling and warming rate of the muDTA. In order to enhance the accuracy of the a-priori predicted current profile, a 2D numeric model was developed of the muDTA. This model also has allowed for geometric optimization to be performed on the next generation prototype of the muDTA. The muDTA has been shown to accurately measure the freezing point and heat of fusion of deionized water samples, with sample volumes on the order of nanoliters. The heat capacity of dimethyl sulfoxide (DMSO) has also been experimentally determined.

Predicting Droplet Formation on Centrifugal Microfluidic Platforms

NASA Astrophysics Data System (ADS)

Moebius, Jacob Alfred

Centrifugal microfluidics is a widely known research tool for biological sample and water quality analysis. Currently, the standard equipment used for such diagnostic applications include slow, bulky machines controlled by multiple operators. These machines can be condensed into a smaller, faster benchtop sample-to-answer system. Sample processing is an important step taken to extract, isolate, and convert biological factors, such as nucleic acids or proteins, from a raw sample to an analyzable solution. Volume definition is one such step. The focus of this thesis is the development of a model predicting monodispersed droplet formation and the application of droplets as a technique for volume definition. First, a background of droplet microfluidic platforms is presented, along with current biological analysis technologies and the advantages of integrating such technologies onto microfluidic platforms. Second, background and theories of centrifugal microfluidics is given, followed by theories relevant to droplet emulsions. Third, fabrication techniques for centrifugal microfluidic designs are discussed. Finally, the development of a model for predicting droplet formation on the centrifugal microfluidic platform are presented for the rest of the thesis. Predicting droplet formation analytically based on the volumetric flow rates of the continuous and dispersed phases, the ratios of these two flow rates, and the interfacial tension between the continuous and dispersed phases presented many challenges, which will be discussed in this work. Experimental validation was completed using continuous phase solutions of different interfacial tensions. To conclude, prospective applications are discussed with expected challenges.

Conjugation of glucose oxidase onto Mn-doped ZnS quantum dots for phosphorescent sensing of glucose in biological fluids.

PubMed

Wu, Peng; He, Yu; Wang, He-Fang; Yan, Xiu-Ping

2010-02-15

Integrating various enzymes with nanomaterials provides various nanohybrids with new possibilities in biosensor applications. Furthermore, the enzymatic activity and stability are also improved due to the large surface area of nanomaterials. Here we report the conjugation of glucose oxidase (GOD) onto phosphorescent Mn-doped ZnS quantum dots (QDs) using 1-ethyl-3-(3-dimethylaminopropy)carbodiimide (EDC)/N-hydroxysuccinimide (NHS) as coupling reagents for glucose biosensing based on the effective quenching of the room temperature phosphorescence (RTP) of Mn-doped ZnS QDs by the H(2)O(2) generated from GOD-catalyzed oxidation of glucose. The obtained bioconjugate not only provided improved enzymatic performance with Michaelis-Menten constant of 0.70 mM but also favored biological applications because the phosphorescent detection mode avoided the interference from autofluorescence and scattering light from the biological matrix. In addition, the GOD-conjugated Mn-doped ZnS QDs showed better thermal stability in the temperature range of 20-80 degrees C. The GOD-Mn-doped ZnS QDs based RTP sensor for glucose gave a detection limit of 3 microM and two linear ranges from 10 microM to 0.1 mM and from 0.1 to 1 mM. The developed biosensor was successfully applied to the determination of glucose in real serum samples without the need for any complicated sample pretreatments.

INDICATORS OF ECOLOGICAL STRESS AND THEIR EXTENT IN THE POPULATION OF NORTHEASTERN LAKES: A REGIONAL-SCALE ASSESSMENT

EPA Science Inventory

One of the Environmental Monitoring and Assessment Program's first projects was a survey of 345 lakes in the eight states of the Northeast, during summers of 1991-1996. This survey was the first regional-scale attempt to use a probability-based sampling design to collect biolog...

The Preservation of Two Infant Temperaments into Adolescence

ERIC Educational Resources Information Center

Kagan, Jerome; Snidman, Nancy; Kahn, Vali; Towsley, Sara

2007-01-01

This "Monograph" reports theoretically relevant behavioral, biological, and self-report assessments of a sample of 14-17-year-olds who had been classified into one of four temperamental groups at 4 months of age. The infant temperamental categories were based on observed behavior to a battery of unfamiliar stimuli. The infants classified as high…

Comparison of Monterey pine stress in urban and natural forests

Treesearch

David J. Nowak; Joe R. McBride

1991-01-01

Monterey pine street trees within Carmel, California and its immediate vicinity, as well as forest-grown Monterey pine within adjacent natural stands, were sampled with regard to visual stress characteristics, and various environmental and biological variables. Two stress indices were computed, one hypothesized before data collection was based on relative foliage...

Performance-Based Task Assessment of Higher-Order Proficiencies in Redesigned STEM High Schools

ERIC Educational Resources Information Center

Ernst, Jeremy V.; Glennie, Elizabeth; Li, Songze

2017-01-01

This study explored student abilities in applying conceptual knowledge when presented with structured performance tasks. Specifically, the study gauged proficiency in higher-order applications of students enrolled in earth and environmental science or biology. The student sample was drawn from a Redesigned STEM high school model where a tested…

Classification, genetic variation, and biological activity of nucleopolyhedrovirus samples from larvae of the heliothine pests heliothis virescens, helicoverpa zea, and helicoverpa armigera

USDA-ARS?s Scientific Manuscript database

A PCR-based method was used to classify 109 isolates of nucleopolyhedrovirus (NPV; Baculoviridae: Alphabaculovirus) collected worldwide from larvae of Heliothis virescens, Helicoverpa zea, and Helicoverpa armigera. Partial nucleotide sequencing and phylogenetic analysis of three highly conserved ge...

A Digital Gene Expression-Based Bovine Gene Atlas Evaluating 92 Adult, Juvenile and Fetal Cattle Tissues

USDA-ARS?s Scientific Manuscript database

A comprehensive transcriptome survey, or “Gene Atlas,” provides information essential for a complete understanding of the genomic biology of an organism. Using a digital gene expression approach, we developed a Gene Atlas of RNA abundance in 92 adult, juvenile and fetal cattle tissues. The samples...

Nanoscale imaging with table-top coherent extreme ultraviolet source based on high harmonic generation

NASA Astrophysics Data System (ADS)

Ba Dinh, Khuong; Le, Hoang Vu; Hannaford, Peter; Van Dao, Lap

2017-08-01

A table-top coherent diffractive imaging experiment on a sample with biological-like characteristics using a focused narrow-bandwidth high harmonic source around 30 nm is performed. An approach involving a beam stop and a new reconstruction algorithm to enhance the quality of reconstructed the image is described.

Mapping local anisotropy axis for scattering media using backscattering Mueller matrix imaging

NASA Astrophysics Data System (ADS)

He, Honghui; Sun, Minghao; Zeng, Nan; Du, E.; Guo, Yihong; He, Yonghong; Ma, Hui

2014-03-01

Mueller matrix imaging techniques can be used to detect the micro-structure variations of superficial biological tissues, including the sizes and shapes of cells, the structures in cells, and the densities of the organelles. Many tissues contain anisotropic fibrous micro-structures, such as collagen fibers, elastin fibers, and muscle fibers. Changes of these fibrous structures are potentially good indicators for some pathological variations. In this paper, we propose a quantitative analysis technique based on Mueller matrix for mapping local anisotropy axis of scattering media. By conducting both experiments on silk sample and Monte Carlo simulation based on the sphere-cylinder scattering model (SCSM), we extract anisotropy axis parameters from different backscattering Mueller matrix elements. Moreover, we testify the possible applications of these parameters for biological tissues. The preliminary experimental results of human cancerous samples show that, these parameters are capable to map the local axis of fibers. Since many pathological changes including early stage cancers affect the well aligned structures for tissues, the experimental results indicate that these parameters can be used as potential tools in clinical applications for biomedical diagnosis purposes.

Recommended Immunological Assays to Screen for Ricin-Containing Samples

PubMed Central

Simon, Stéphanie; Worbs, Sylvia; Avondet, Marc-André; Tracz, Dobryan M.; Dano, Julie; Schmidt, Lisa; Volland, Hervé; Dorner, Brigitte G.; Corbett, Cindi R.

2015-01-01

Ricin, a toxin from the plant Ricinus communis, is one of the most toxic biological agents known. Due to its availability, toxicity, ease of production and absence of curative treatments, ricin has been classified by the Centers for Disease Control and Prevention (CDC) as category B biological weapon and it is scheduled as a List 1 compound in the Chemical Weapons Convention. An international proficiency test (PT) was conducted to evaluate detection and quantification capabilities of 17 expert laboratories. In this exercise one goal was to analyse the laboratories’ capacity to detect and differentiate ricin and the less toxic, but highly homologuous protein R. communis agglutinin (RCA120). Six analytical strategies are presented in this paper based on immunological assays (four immunoenzymatic assays and two immunochromatographic tests). Using these immunological methods “dangerous” samples containing ricin and/or RCA120 were successfully identified. Based on different antibodies used the detection and quantification of ricin and RCA120 was successful. The ricin PT highlighted the performance of different immunological approaches that are exemplarily recommended for highly sensitive and precise quantification of ricin. PMID:26703725

Recommended Immunological Assays to Screen for Ricin-Containing Samples.

PubMed

Simon, Stéphanie; Worbs, Sylvia; Avondet, Marc-André; Tracz, Dobryan M; Dano, Julie; Schmidt, Lisa; Volland, Hervé; Dorner, Brigitte G; Corbett, Cindi R

2015-11-26

Ricin, a toxin from the plant Ricinus communis, is one of the most toxic biological agents known. Due to its availability, toxicity, ease of production and absence of curative treatments, ricin has been classified by the Centers for Disease Control and Prevention (CDC) as category B biological weapon and it is scheduled as a List 1 compound in the Chemical Weapons Convention. An international proficiency test (PT) was conducted to evaluate detection and quantification capabilities of 17 expert laboratories. In this exercise one goal was to analyse the laboratories' capacity to detect and differentiate ricin and the less toxic, but highly homologuous protein R. communis agglutinin (RCA120). Six analytical strategies are presented in this paper based on immunological assays (four immunoenzymatic assays and two immunochromatographic tests). Using these immunological methods "dangerous" samples containing ricin and/or RCA120 were successfully identified. Based on different antibodies used the detection and quantification of ricin and RCA120 was successful. The ricin PT highlighted the performance of different immunological approaches that are exemplarily recommended for highly sensitive and precise quantification of ricin.

Chromatography/Mass Spectrometry-Based Biomarkers in the Field of Obstructive Sleep Apnea

PubMed Central

Xu, Huajun; Zheng, Xiaojiao; Jia, Wei; Yin, Shankai

2015-01-01

Abstract Biomarker assessment is based on quantifying several proteins and metabolites. Recent developments in proteomics and metabolomics have enabled detection of these small molecules in biological samples and exploration of the underlying disease mechanisms in obstructive sleep apnea (OSA). This systemic review was performed to identify biomarkers, which were only detected by chromatography and/or mass spectrometry (MS) and to discuss the role of these biomarkers in the field of OSA. We systemically reviewed relevant articles from PubMed and EMBASE referring to proteins and metabolite profiles of biological samples in patients with OSA. The analytical platforms in this review were focused on chromatography and/or MS. In total, 30 studies evaluating biomarkers in patients with OSA using chromatography and/or MS methods were included. Numerous proteins and metabolites, including lipid profiles, adrenergic/dopaminergic biomarkers and derivatives, amino acids, oxidative stress biomarkers, and other micromolecules were identified in patients with OSA. Applying chromatography and/or MS methods to detect biomarkers helps develop an understanding of OSA mechanisms. More proteomic and metabolomic studies are warranted to develop potential diagnostic and clinical monitoring methods for OSA. PMID:26448002

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

PubMed

Thijssen, Bram; Dijkstra, Tjeerd M H; Heskes, Tom; Wessels, Lodewyk F A

2016-10-21

Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and disadvantages. It is typically unclear, before starting an analysis, which algorithm will perform well on a given computational model. We present BCM, a toolkit for the Bayesian analysis of Computational Models using samplers. It provides efficient, multithreaded implementations of eleven algorithms for sampling from posterior probability distributions and for calculating marginal likelihoods. BCM includes tools to simplify the process of model specification and scripts for visualizing the results. The flexible architecture allows it to be used on diverse types of biological computational models. In an example inference task using a model of the cell cycle based on ordinary differential equations, BCM is significantly more efficient than existing software packages, allowing more challenging inference problems to be solved. BCM represents an efficient one-stop-shop for computational modelers wishing to use sampler-based Bayesian statistics.

Kernel-PCA data integration with enhanced interpretability

PubMed Central

2014-01-01

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge. PMID:25032747

Hydrogel microparticles for biosensing

PubMed Central

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

2015-01-01

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

Chemical derivatization for enhancing sensitivity during LC/ESI-MS/MS quantification of steroids in biological samples: a review.

PubMed

Higashi, Tatsuya; Ogawa, Shoujiro

2016-09-01

Sensitive and specific methods for the detection, characterization and quantification of endogenous steroids in body fluids or tissues are necessary for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) has been widely used for these purposes due to its specificity and versatility. However, the ESI efficiency and fragmentation behavior of some steroids are poor, which lead to a low sensitivity. Chemical derivatization is one of the most effective methods to improve the detection characteristics of steroids in ESI-MS/MS. Based on this background, this article reviews the recent advances in chemical derivatization for the trace quantification of steroids in biological samples by LC/ESI-MS/MS. The derivatization in ESI-MS/MS is based on tagging a proton-affinitive or permanently charged moiety on the target steroid. Introduction/formation of a fragmentable moiety suitable for the selected reaction monitoring by the derivatization also enhances the sensitivity. The stable isotope-coded derivatization procedures for the steroid analysis are also described. Copyright © 2015 Elsevier Ltd. All rights reserved.