Gas chromatography-mass spectrometry of biofluids and extracts.

PubMed

Emwas, Abdul-Hamid M; Al-Talla, Zeyad A; Yang, Yang; Kharbatia, Najeh M

2015-01-01

Gas chromatography-mass spectrometry (GC-MS) has been widely used in metabonomics analyses of biofluid samples. Biofluids provide a wealth of information about the metabolism of the whole body and from multiple regions of the body that can be used to study general health status and organ function. Blood serum and blood plasma, for example, can provide a comprehensive picture of the whole body, while urine can be used to monitor the function of the kidneys, and cerebrospinal fluid (CSF) will provide information about the status of the brain and central nervous system (CNS). Different methods have been developed for the extraction of metabolites from biofluids, these ranging from solvent extracts, acids, heat denaturation, and filtration. These methods vary widely in terms of efficiency of protein removal and in the number of metabolites extracted. Consequently, for all biofluid-based metabonomics studies, it is vital to optimize and standardize all steps of sample preparation, including initial extraction of metabolites. In this chapter, recommendations are made of the optimum experimental conditions for biofluid samples for GC-MS, with a particular focus on blood serum and plasma samples.

Gold nanoparticle chemiresistors operating in biological fluids.

PubMed

Hubble, Lee J; Chow, Edith; Cooper, James S; Webster, Melissa; Müller, Karl-Heinz; Wieczorek, Lech; Raguse, Burkhard

2012-09-07

Functionalised gold nanoparticle (Au(NP)) chemiresistors are investigated for direct sensing of small organic molecules in biological fluids. The principle reason that Au(NP) chemiresistors, and many other sensing devices, have limited operation in biological fluids is due to protein and lipid fouling deactivating the sensing mechanism. In order to extend the capability of such chemiresistor sensors to operate directly in biofluids, it is essential to minimise undesirable matrix effects due to protein and lipidic components. Ultrafiltration membranes were investigated as semi-permeable size-selective barriers to prevent large biomolecule interactions with Au(NP) chemiresistors operating in protein-loaded biofluids. All of the ultrafiltration membranes protected the Au(NP) chemiresistors from fouling by the globular biomolecules, with the 10 kDa molecular weight cut-off size being optimum for operation in biofluids. Titrations of toluene in different protein-loaded fluids indicated that small molecule detection was possible. A sensor array consisting of six different thiolate-functionalised Au(NP) chemiresistors protected with a size-selective ultrafiltration membrane successfully identified, and discriminated the spoilage of pasteurised bovine milk. This proof-of-principle study demonstrates the on-chip protein separation and small metabolite detection capability, illustrating the potential for this technology in the field of microbial metabolomics. Overall, these results demonstrate that a sensor array can be protected from protein fouling with the use of a membrane, significantly increasing the possible application areas of Au(NP) chemiresistors ranging from the food industry to health services.

Bioaccessibility of metals in alloys: Evaluation of three surrogate biofluids

PubMed Central

Hillwalker, Wendy E.; Anderson, Kim A.

2014-01-01

Bioaccessibility in vitro tests measure the solubility of materials in surrogate biofluids. However, the lack of uniform methods and the effects of variable test parameters on material solubility limit interpretation. One aim of this study was to measure and compare bioaccessibility of selected economically important alloys and metals in surrogate physiologically based biofluids representing oral, inhalation and dermal exposures. A second aim was to experimentally test different biofluid formulations and residence times in vitro. A third aim was evaluation of dissolution behavior of alloys with in vitro lung and dermal biofluid surrogates. This study evaluated the bioaccessibility of sixteen elements in six alloys and 3 elemental/metal powders. We found that the alloys/metals, the chemical properties of the surrogate fluid, and residence time all had major impacts on metal solubility. The large variability of bioaccessibility indicates the relevancy of assessing alloys as toxicologically distinct relative to individual metals. PMID:24212234

Advances of Proteomic Sciences in Dentistry.

PubMed

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-05-13

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

BEAMing and Droplet Digital PCR Analysis of Mutant IDH1 mRNA in Glioma Patient Serum and Cerebrospinal Fluid Extracellular Vesicles.

PubMed

Chen, Walter W; Balaj, Leonora; Liau, Linda M; Samuels, Michael L; Kotsopoulos, Steve K; Maguire, Casey A; Loguidice, Lori; Soto, Horacio; Garrett, Matthew; Zhu, Lin Dan; Sivaraman, Sarada; Chen, Clark; Wong, Eric T; Carter, Bob S; Hochberg, Fred H; Breakefield, Xandra O; Skog, Johan

2013-07-23

Development of biofluid-based molecular diagnostic tests for cancer is an important step towards tumor characterization and real-time monitoring in a minimally invasive fashion. Extracellular vesicles (EVs) are released from tumor cells into body fluids and can provide a powerful platform for tumor biomarkers because they carry tumor proteins and nucleic acids. Detecting rare point mutations in the background of wild-type sequences in biofluids such as blood and cerebrospinal fluid (CSF) remains a major challenge. Techniques such as BEAMing (beads, emulsion, amplification, magnetics) PCR and droplet digital PCR (ddPCR) are substantially more sensitive than many other assays for mutant sequence detection. Here, we describe a novel approach that combines biofluid EV RNA and BEAMing RT-PCR (EV-BEAMing), as well droplet digital PCR to interrogate mutations from glioma tumors. EVs from CSF of patients with glioma were shown to contain mutant IDH1 transcripts, and we were able to reliably detect and quantify mutant and wild-type IDH1 RNA transcripts in CSF of patients with gliomas. EV-BEAMing and EV-ddPCR represent a valuable new strategy for cancer diagnostics, which can be applied to a variety of biofluids and neoplasms.Molecular Therapy-Nucleic Acids (2013) 2, e109; doi:10.1038/mtna.2013.28; published online 23 July 2013.

Modeling electro-magneto-hydrodynamic thermo-fluidic transport of biofluids with new trend of fractional derivative without singular kernel

NASA Astrophysics Data System (ADS)

Abdulhameed, M.; Vieru, D.; Roslan, R.

2017-10-01

This paper investigates the electro-magneto-hydrodynamic flow of the non-Newtonian behavior of biofluids, with heat transfer, through a cylindrical microchannel. The fluid is acted by an arbitrary time-dependent pressure gradient, an external electric field and an external magnetic field. The governing equations are considered as fractional partial differential equations based on the Caputo-Fabrizio time-fractional derivatives without singular kernel. The usefulness of fractional calculus to study fluid flows or heat and mass transfer phenomena was proven. Several experimental measurements led to conclusion that, in such problems, the models described by fractional differential equations are more suitable. The most common time-fractional derivative used in Continuum Mechanics is Caputo derivative. However, two disadvantages appear when this derivative is used. First, the definition kernel is a singular function and, secondly, the analytical expressions of the problem solutions are expressed by generalized functions (Mittag-Leffler, Lorenzo-Hartley, Robotnov, etc.) which, generally, are not adequate to numerical calculations. The new time-fractional derivative Caputo-Fabrizio, without singular kernel, is more suitable to solve various theoretical and practical problems which involve fractional differential equations. Using the Caputo-Fabrizio derivative, calculations are simpler and, the obtained solutions are expressed by elementary functions. Analytical solutions of the biofluid velocity and thermal transport are obtained by means of the Laplace and finite Hankel transforms. The influence of the fractional parameter, Eckert number and Joule heating parameter on the biofluid velocity and thermal transport are numerically analyzed and graphic presented. This fact can be an important in Biochip technology, thus making it possible to use this analysis technique extremely effective to control bioliquid samples of nanovolumes in microfluidic devices used for biological analysis and medical diagnosis.

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

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

Wu, Chaochao; Duan, Jicheng; Liu, Tao

2016-05-01

Human biofluids, especially blood plasma or serum, hold great potential as the sources of potential biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge to detect promising low-abundance protein biomarkers. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high and moderate-abundance proteins, thus enabling more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomics applications of different human biofluids. The limitations and future perspective of immunoaffinity separationmore » methods are also discussed.« less

Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids

DOE PAGES

Wu, Chaochao; Duan, Jicheng; Liu, Tao; ...

2016-01-12

Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methodsmore » are also discussed.« less

High-throughput analysis using non-depletive SPME: challenges and applications to the determination of free and total concentrations in small sample volumes.

PubMed

Boyacı, Ezel; Bojko, Barbara; Reyes-Garcés, Nathaly; Poole, Justen J; Gómez-Ríos, Germán Augusto; Teixeira, Alexandre; Nicol, Beate; Pawliszyn, Janusz

2018-01-18

In vitro high-throughput non-depletive quantitation of chemicals in biofluids is of growing interest in many areas. Some of the challenges facing researchers include the limited volume of biofluids, rapid and high-throughput sampling requirements, and the lack of reliable methods. Coupled to the above, growing interest in the monitoring of kinetics and dynamics of miniaturized biosystems has spurred the demand for development of novel and revolutionary methodologies for analysis of biofluids. The applicability of solid-phase microextraction (SPME) is investigated as a potential technology to fulfill the aforementioned requirements. As analytes with sufficient diversity in their physicochemical features, nicotine, N,N-Diethyl-meta-toluamide, and diclofenac were selected as test compounds for the study. The objective was to develop methodologies that would allow repeated non-depletive sampling from 96-well plates, using 100 µL of sample. Initially, thin film-SPME was investigated. Results revealed substantial depletion and consequent disruption in the system. Therefore, new ultra-thin coated fibers were developed. The applicability of this device to the described sampling scenario was tested by determining the protein binding of the analytes. Results showed good agreement with rapid equilibrium dialysis. The presented method allows high-throughput analysis using small volumes, enabling fast reliable free and total concentration determinations without disruption of system equilibrium.

An ATMND/SGI based label-free and fluorescence ratiometric aptasensor for rapid and highly sensitive detection of cocaine in biofluids.

PubMed

Wang, Jiamian; Song, Jie; Wang, Xiuyun; Wu, Shuo; Zhao, Yanqiu; Luo, Pinchen; Meng, Changgong

2016-12-01

A label-free ratiometric fluorescence aptasensor has been developed for the rapid and sensitive detection of cocaine in complex biofluids. The fluorescent aptasensor is composed of a non-labeled GC-38 cocaine aptamer which serves as a basic sensing unit and two fluorophores, 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) and SYBR Green I (SGI) which serves as a signal reporter and a build-in reference, respectively. The detection principle is based on a specific cocaine mediated ATMND displacement reaction and the corresponding change in the fluorescence ratio of ATMND to SGI. Due to the high affinity of the non-labeled aptamer, the good precision originated from the ratiometric method, and the good fluorescence quantum yield of the fluorophore, the aptasensor shows good analytical performance with respect to cocaine detection. Under optimal conditions, the aptasensor shows a linear range of 0.10-10μM and a low limit of detection of 56nM, with a fast response of 20s. The low limit of detection is comparable to most of the fluorescent aptasensors with signal amplification strategies and much lower than all of the unamplified cocaine aptasensors. Practical sample analysis in a series of complex biofluids, including urine, saliva and serum, also indicates the good precision, stability, and high sensitivity of the aptasensor, which may have great potential for the point-of-care screening of cocaine in complex biofluids. Copyright © 2016 Elsevier B.V. All rights reserved.

High-throughput and targeted in-depth mass spectrometry-based approaches for biofluid profiling and biomarker discovery.

PubMed

Jimenez, Connie R; Piersma, Sander; Pham, Thang V

2007-12-01

Proteomics aims to create a link between genomic information, biological function and disease through global studies of protein expression, modification and protein-protein interactions. Recent advances in key proteomics tools, such as mass spectrometry (MS) and (bio)informatics, provide tremendous opportunities for biomarker-related clinical applications. In this review, we focus on two complementary MS-based approaches with high potential for the discovery of biomarker patterns and low-abundant candidate biomarkers in biofluids: high-throughput matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy-based methods for peptidome profiling and label-free liquid chromatography-based methods coupled to MS for in-depth profiling of biofluids with a focus on subproteomes, including the low-molecular-weight proteome, carrier-bound proteome and N-linked glycoproteome. The two approaches differ in their aims, throughput and sensitivity. We discuss recent progress and challenges in the analysis of plasma/serum and proximal fluids using these strategies and highlight the potential of liquid chromatography-MS-based proteomics of cancer cell and tumor secretomes for the discovery of candidate blood-based biomarkers. Strategies for candidate validation are also described.

Biofluid Mechanics Education at U Michigan

NASA Astrophysics Data System (ADS)

Grotberg, James

2007-11-01

At the University of Michigan, biofluid mechanics is taught in the Department of Biomedical Engineering with cross-listing in Mechanical Engineering. The course has evolved over 25 years and serves advanced undergraduates and graduate students. The course description is as follows: BiomedE/MechE 476 Biofluid Mechanics. CATALOG DESCRIPTION: This is an intermediate level fluid mechanics course which uses examples from biotechnology processes and physiologic applications including cellular, cardiovascular, respiratory, ocular, renal, orthopedic, and gastrointestinal systems. COURSE TOPICS: 1. Dimensional analysis (gastrointestinal, renal) 2. Approximation methods, numerical methods (biotechnology, respiratory) 3. Particle kinematics in Eulerian and Lagrangian references frames (biotechnology, respiratory) 4. Conservation of mass and momentum 5. Constitutive equations (blood, mucus) 6. Kinematic and stress boundary conditions: rigid, flexible, porous (cardio-pulmonary, cellular) 7. Surface tension phenomena (pulmonary, ocular) 8. Flow and wave propagation in flexible tubes (cardio-pulmonary) 9. Oscillatory and pulsatile flows (cardio-pulmonary, orthopedic) 10. High Reynolds number flows (cardio-pulmonary) 11. Low Reynolds number flows (biotechnology, cellular, vascular) 12. Lubrication theory (vascular, orthopedic) 13. Flow in poroelastic media (orthopedic, pulmonary, ocular) 14. Video presentations of laboratory experiments.

Detection and quantification of extracellular microRNAs in murine biofluids

PubMed Central

2014-01-01

Background MicroRNAs (miRNAs) are short RNA molecules which regulate gene expression in eukaryotic cells, and are abundant and stable in biofluids such as blood serum and plasma. As such, there has been heightened interest in the utility of extracellular miRNAs as minimally invasive biomarkers for diagnosis and monitoring of a wide range of human pathologies. However, quantification of extracellular miRNAs is subject to a number of specific challenges, including the relatively low RNA content of biofluids, the possibility of contamination with serum proteins (including RNases and PCR inhibitors), hemolysis, platelet contamination/activation, a lack of well-established reference miRNAs and the biochemical properties of miRNAs themselves. Protocols for the detection and quantification of miRNAs in biofluids are therefore of high interest. Results The following protocol was validated by quantifying miRNA abundance in C57 (wild-type) and dystrophin-deficient (mdx) mice. Important differences in miRNA abundance were observed depending on whether blood was taken from the jugular or tail vein. Furthermore, efficiency of miRNA recovery was reduced when sample volumes greater than 50 μl were used. Conclusions Here we describe robust and novel procedures to harvest murine serum/plasma, extract biofluid RNA, amplify specific miRNAs by RT-qPCR and analyze the resulting data, enabling the determination of relative and absolute miRNA abundance in extracellular biofluids with high accuracy, specificity and sensitivity. PMID:24629058

Advances of Proteomic Sciences in Dentistry

PubMed Central

Khurshid, Zohaib; Zohaib, Sana; Najeeb, Shariq; Zafar, Muhammad Sohail; Rehman, Rabia; Rehman, Ihtesham Ur

2016-01-01

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed. PMID:27187379

Sample collection and preparation of biofluids and extracts for gas chromatography-mass spectrometry.

PubMed

Emwas, Abdul-Hamid M; Al-Talla, Zeyad A; Kharbatia, Najeh M

2015-01-01

To maximize the utility of gas chromatography-mass spectrometry (GC-MS) in metabonomics research, all stages of the experimental design should be standardized, including sample collection, storage, preparation, and sample separation. Moreover, the prerequisite for any GC-MS analysis is that a compound must be volatile and thermally stable if it is to be analyzed using this technique. Since many metabolites are nonvolatile and polar in nature, they are not readily amenable to analysis by GC-MS and require initial chemical derivatization of the polar functional groups in order to reduce the polarity and to increase the thermal stability and volatility of the analytes. In this chapter, an overview is presented of the optimum approach to sample collection, storage, and preparation for gas chromatography-mass spectrometry-based metabonomics with particular focus on urine samples as example of biofluids.

Bile acid profiling and quantification in biofluids using ultra-performance liquid chromatography tandem mass spectrometry.

PubMed

Sarafian, Magali H; Lewis, Matthew R; Pechlivanis, Alexandros; Ralphs, Simon; McPhail, Mark J W; Patel, Vishal C; Dumas, Marc-Emmanuel; Holmes, Elaine; Nicholson, Jeremy K

2015-10-06

Bile acids are important end products of cholesterol metabolism. While they have been identified as key factors in lipid emulsification and absorption due to their detergent properties, bile acids have also been shown to act as signaling molecules and intermediates between the host and the gut microbiota. To further the investigation of bile acid functions in humans, an advanced platform for high throughput analysis is essential. Herein, we describe the development and application of a 15 min UPLC procedure for the separation of bile acid species from human biofluid samples requiring minimal sample preparation. High resolution time-of-flight mass spectrometry was applied for profiling applications, elucidating rich bile acid profiles in both normal and disease state plasma. In parallel, a second mode of detection was developed utilizing tandem mass spectrometry for sensitive and quantitative targeted analysis of 145 bile acid (BA) species including primary, secondary, and tertiary bile acids. The latter system was validated by testing the linearity (lower limit of quantification, LLOQ, 0.25-10 nM and upper limit of quantification, ULOQ, 2.5-5 μM), precision (≈6.5%), and accuracy (81.2-118.9%) on inter- and intraday analysis achieving good recovery of bile acids (serum/plasma 88% and urine 93%). The ultra performance liquid chromatography-mass spectrometry (UPLC-MS)/MS targeted method was successfully applied to plasma, serum, and urine samples in order to compare the bile acid pool compositional difference between preprandial and postprandial states, demonstrating the utility of such analysis on human biofluids.

Visual detection of nucleic acids based on Mie scattering and the magnetophoretic effect.

PubMed

Zhao, Zichen; Chen, Shan; Ho, John Kin Lim; Chieng, Ching-Chang; Chen, Ting-Hsuan

2015-12-07

Visual detection of nucleic acid biomarkers is a simple and convenient approach to point-of-care applications. However, issues of sensitivity and the handling of complex bio-fluids have posed challenges. Here we report on a visual method detecting nucleic acids using Mie scattering of polystyrene microparticles and the magnetophoretic effect. Magnetic microparticles (MMPs) and polystyrene microparticles (PMPs) were surface-functionalised with oligonucleotide probes, which can hybridise with target oligonucleotides in juxtaposition and lead to the formation of MMPs-targets-PMPs sandwich structures. Using an externally applied magnetic field, the magnetophoretic effect attracts the sandwich structure to the sidewall, which reduces the suspended PMPs and leads to a change in the light transmission via the Mie scattering. Based on the high extinction coefficient of the Mie scattering (∼3 orders of magnitude greater than that of the commonly used gold nanoparticles), our results showed the limit of detection to be 4 pM using a UV-Vis spectrometer or 10 pM by direct visual inspection. Meanwhile, we also demonstrated that this method is compatible with multiplex assays and detection in complex bio-fluids, such as whole blood or a pool of nucleic acids, without purification in advance. With a simplified operation procedure, low instrumentation requirement, high sensitivity and compatibility with complex bio-fluids, this method provides an ideal solution for visual detection of nucleic acids in resource-limited settings.

Quantitative Lateral Flow Assays for Salivary Biomarker Assessment: A Review

PubMed Central

Miočević, Olga; Cole, Craig R.; Laughlin, Mary J.; Buck, Robert L.; Slowey, Paul D.; Shirtcliff, Elizabeth A.

2017-01-01

Saliva is an emerging biofluid with a significant number of applications in use across research and clinical settings. The present paper explores the reasons why saliva has grown in popularity in recent years, balancing both the potential strengths and weaknesses of this biofluid. Focusing on reasons why saliva is different from other common biological fluids such as blood, urine, or tears, we review how saliva is easily obtained, with minimal risk to the donor, and reduced costs for collection, transportation, and analysis. We then move on to a brief review of the history and progress in rapid salivary testing, again reviewing the strengths and weaknesses of rapid immunoassays (e.g., lateral flow immunoassay) compared to more traditional immunoassays. We consider the potential for saliva as an alternative biofluid in a setting where rapid results are important. We focus the review on salivary tests for small molecule biomarkers using cortisol as an example. Such salivary tests can be applied readily in a variety of settings and for specific measurement purposes, providing researchers and clinicians with opportunities to assess biomarkers in real time with lower transportation, collection, and analysis costs, faster turnaround time, and minimal training requirements. We conclude with a note of cautious optimism that the field will soon gain the ability to collect and analyze salivary specimens at any location and return viable results within minutes. PMID:28660183

Cells and biofluids analyzed in aqueous environment by infrared spectroscopy

NASA Astrophysics Data System (ADS)

Naumann, D.; Lasch, P.; Fabian, H.

2006-02-01

Infrared transmission/absorption measurements of cells and biofluids in water are restricted to very short optical pathlengths. When the amide I and amide II bands of protein constituents have to be analysed, path-lengths of less than 8 μm are necessary. Infrared spectra of cancer cells were collected from physiological buffer solutions utilizing custom-made mid-infrared compatible IR-cuvettes. The technology permitted to obtain cell-type specific spectral signatures and probe biochemical changes induced by varying temperatures or cell-drug interaction. Optical path-lengths of 8-30 μm were used on a set of microbial test strains to evaluate, whether the methodology can also be used to discriminate and identify micro-organisms. A semi-automatic methodology was developed for the analysis of liquid serum samples, which combines simple sample handling with high sample throughput and extreme measurement reproducibility. The applicability of this infrared technology to the analysis of liquid serum samples from cattle and human beings suffering from various acute viral or bacterial infections was explored testing the interrelationship between α-helical and β-sheet specific spectral signatures in the amide I band contour and total albumin and globulin content in serum. The technical details, advantages, and limitations of the new technology are described in the context of developing a routine, IR-based biodiagnostic technique for biofluids and biological cells.

Analysis of biofluids in aqueous environment based on mid-infrared spectroscopy.

PubMed

Fabian, Heinz; Lasch, Peter; Naumann, Dieter

2005-01-01

In this study we describe a semiautomatic Fourier transform infrared spectroscopic methodology for the analysis of liquid serum samples, which combines simple sample introduction with high sample throughput. The applicability of this new infrared technology to the analysis of liquid serum samples from a cohort of cattle naturally infected with bovine spongiform encephalopathy and from controls was explored in comparison to the conventional approach based on transmission infrared spectroscopy of dried serum films. Artifical neural network analysis of the infrared data was performed to differentiate between bovine spongiform encephalopathy-negative controls and animals in the late stage of the disease. After training of artifical neural network classifiers, infrared spectra of sera from an independent external validation data set were analyzed. In this way, sensitivities between 90 and 96% and specificities between 84 and 92% were achieved, respectively, depending upon the strategy of data collection and data analysis. Based on these results, the advantages and limitations of the liquid sample technique and the dried film approach for routine analysis of biofluids are discussed. 2005 Society of Photo-Optical Instrumentation Engineers.

Microfluidic Exosome Analysis toward Liquid Biopsy for Cancer.

PubMed

He, Mei; Zeng, Yong

2016-08-01

Assessment of a tumor's molecular makeup using biofluid samples, known as liquid biopsy, is a prominent research topic in precision medicine for cancer, due to its noninvasive property allowing repeat sampling for monitoring molecular changes of tumors over time. Circulating exosomes recently have been recognized as promising tumor surrogates because they deliver enriched biomarkers, such as proteins, RNAs, and DNA. However, purification and characterization of these exosomes are technically challenging. Microfluidic lab-on-a-chip technology effectively addresses these challenges owing to its inherent advantages in integration and automation of multiple functional modules, enhancing sensing performance, and expediting analysis processes. In this article, we review the state-of-the-art development of microfluidic technologies for exosome isolation and molecular characterization with emphasis on their applications toward liquid biopsy-based analysis of cancer. Finally, we share our perspectives on current challenges and future directions of microfluidic exosome analysis. © 2016 Society for Laboratory Automation and Screening.

Study of sample preparation for quantitative analysis of amino acids in human sweat by liquid chromatography-tandem mass spectrometry.

PubMed

Delgado-Povedano, M M; Calderón-Santiago, M; Priego-Capote, F; Luque de Castro, M D

2016-01-01

The determination of physiological levels of amino acids is important to aid in the diagnosis and treatment of several diseases and nutritional status of individuals. Amino acids are frequently determined in biofluids such as blood (serum or plasma) and urine; however, there are less common biofluids with different concentration profiles of amino acids that could be of interest. One of these biofluids is sweat that can be obtained in a non-invasive manner and is characterized by low complex composition. The analysis of amino acids in human sweat requires the development of sample preparation strategies according to the sample matrix and small collected volume. The influence of sample preparation on the quantitative analysis of amino acids in sweat by LC-MS/MS has been assessed through a comparison between two strategies: dilution of sweat and centrifugal microsolid-phase extraction (c-μSPE). In both cases, several dilution factors were assayed for in-depth knowledge of the matrix effects, and the use of c-μSPE provided the best results in terms of accuracy. The behavior of the target analytes was a function of the dilution factor, thus providing a pattern for sample preparation that depended on the amino acid to be determined. The concentration of amino acids in sweat ranges between 6.20 ng mL(-1) (for homocysteine) and 259.77 µg mL(-1) (for serine) with precision, expressed as relative standard deviation, within 1.1-21.4%. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Wu, Chaochao; Duan, Jicheng; Liu, Tao

Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methodsmore » are also discussed.« less

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

DOE PAGES

Zhang, Xing; Romm, Michelle; Zheng, Xueyun; ...

2016-12-29

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here in this article, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with highmore » reproducibility (CV ≤ 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. Lastly, this SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.« less

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids.

PubMed

Zhang, Xing; Romm, Michelle; Zheng, Xueyun; Zink, Erika M; Kim, Young-Mo; Burnum-Johnson, Kristin E; Orton, Daniel J; Apffel, Alex; Ibrahim, Yehia M; Monroe, Matthew E; Moore, Ronald J; Smith, Jordan N; Ma, Jian; Renslow, Ryan S; Thomas, Dennis G; Blackwell, Anne E; Swinford, Glenn; Sausen, John; Kurulugama, Ruwan T; Eno, Nathan; Darland, Ed; Stafford, George; Fjeldsted, John; Metz, Thomas O; Teeguarden, Justin G; Smith, Richard D; Baker, Erin S

2016-12-01

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure.

SPE-IMS-MS: An automated platform for sub-sixty second surveillance of endogenous metabolites and xenobiotics in biofluids

PubMed Central

Zhang, Xing; Romm, Michelle; Zheng, Xueyun; Zink, Erika M.; Kim, Young-Mo; Burnum-Johnson, Kristin E.; Orton, Daniel J.; Apffel, Alex; Ibrahim, Yehia M.; Monroe, Matthew E.; Moore, Ronald J.; Smith, Jordan N.; Ma, Jian; Renslow, Ryan S.; Thomas, Dennis G.; Blackwell, Anne E.; Swinford, Glenn; Sausen, John; Kurulugama, Ruwan T.; Eno, Nathan; Darland, Ed; Stafford, George; Fjeldsted, John; Metz, Thomas O.; Teeguarden, Justin G.; Smith, Richard D.; Baker, Erin S.

2017-01-01

Characterization of endogenous metabolites and xenobiotics is essential to deconvoluting the genetic and environmental causes of disease. However, surveillance of chemical exposure and disease-related changes in large cohorts requires an analytical platform that offers rapid measurement, high sensitivity, efficient separation, broad dynamic range, and application to an expansive chemical space. Here, we present a novel platform for small molecule analyses that addresses these requirements by combining solid-phase extraction with ion mobility spectrometry and mass spectrometry (SPE-IMS-MS). This platform is capable of performing both targeted and global measurements of endogenous metabolites and xenobiotics in human biofluids with high reproducibility (CV 6 3%), sensitivity (LODs in the pM range in biofluids) and throughput (10-s sample-to-sample duty cycle). We report application of this platform to the analysis of human urine from patients with and without type 1 diabetes, where we observed statistically significant variations in the concentration of disaccharides and previously unreported chemical isomers. This SPE-IMS-MS platform overcomes many of the current challenges of large-scale metabolomic and exposomic analyses and offers a viable option for population and patient cohort screening in an effort to gain insights into disease processes and human environmental chemical exposure. PMID:29276770

Development of C60-based labeling reagents for the determination of low-molecular-weight compounds by matrix assisted laser desorption ionization mass (I): Determination of amino acids in microliter biofluids.

PubMed

Wu, Pin; Xiao, Hua-Ming; Ding, Jun; Deng, Qian-Yun; Zheng, Fang; Feng, Yu-Qi

2017-04-01

Quantification of low molecular weight compounds (<800 Da) using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI MS) is challenging due to the matrix signal interference at low m/z region and poor reproducibility of MS responses. In this study, a C60 labeling-MALDI MS strategy was proposed for the fast, sensitive and reliable determination of amino acids (AAs) in biofluids. An N-hydroxysuccinimide functionalized C60 was synthesized as the labeling reagent and added as an 880 Da tag to AAs; a carboxyl acid containing C60 was employed as the internal standards to normalize MS variations. This solved the inherent problems of MALDI MS for small molecule analysis. The entire analytical procedure-which consisted of simple protein precipitation and 10 min of derivatization in a microwave prior to the MALDI MS analysis-could be accomplished within 20 min with high throughput and great sample matrix tolerance. AA quantification showed good linearity from 0.7 to 70.0 μM with correlation coefficients (R) larger than 0.9954. The limits of detection were 70.0-300.0 fmol. Good reproducibility and reliability of the method were demonstrated by intra-day and inter-day precision with relative standard deviations less than 13.8%, and the recovery in biofluid ranged from 80.4% to 106.8%. This approach could be used in 1 μL of urine, serum, plasma, whole blood, and cerebrospinal fluid. Most importantly, the C60 labeling strategy is a universal approach for MALDI MS analysis of various LMW compounds because functionalized C60 is now available on demand. Copyright © 2017 Elsevier B.V. All rights reserved.

Biofluid metabotyping of occupationally exposed subjects to air pollution demonstrates high oxidative stress and deregulated amino acid metabolism

NASA Astrophysics Data System (ADS)

Pradhan, Surya Narayan; Das, Aleena; Meena, Ramovatar; Nanda, Ranjan Kumar; Rajamani, Paulraj

2016-10-01

Occupational exposure to air pollution induces oxidative stress and prolonged exposure increases susceptibility to cardiovascular and respiratory diseases in several working groups. Biofluid of these subjects may reflect perturbed metabolic phenotypes. In this study we carried out a comparative molecular profiling study using parallel biofluids collected from subjects (n = 85) belonging to auto rickshaw drivers (ARD), traffic cops (TC) and office workers (OW). Higher levels of oxidative stress and inflammation markers in serum of ARD subjects were observed as compared to OW and TC. Uni and multivariate analyses of metabolites identified in urine by 1H NMR revealed 11 deregulated molecules in ARD subjects and involved in phenylalanine, histidine, arginine and proline metabolism. Despite contribution of confounding factors like exposure period, dietary factors including smoking and alcohol status, our results demonstrate existence of exposure specific metabotypes in biofluids of ARD, OW and TC groups. Monitoring serum oxidative stress and inflammation markers and urine metabolites by NMR may be useful to characterize perturbed metabolic phenotypes in populations exposed to urban traffic air pollution.

Identification of circulating miRNA involved in meat yield of Korean cattle.

PubMed

Lee, Surim; Park, Seung-Ju; Cheong, Jae-Kyoung; Ko, Jong-Youl; Bong, Jinjong; Baik, Myunggi

2017-07-01

Cattle plays an important role in providing essential nutrients through meat production. Thus, we focused on epigenetic factors associated with meat yield. To investigate circulating miRNAs that are involved with meat yield and connect biofluids and longissimus dorsi (LD) muscle in Korean cattle, we performed analyses of the carcass characteristics, miRNA array, qPCR, and bioinformatics. Carcass characteristics relative to the yield grade (YG) showed that the yield index and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A (equal to high YG) cattle among the three YGs. miRNA array sorted the circulating miRNAs that connect biofluids and LD muscle. miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with biofluids and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting biofluids and LD muscle because the target genes of miR-26b were more involved with myogenesis. Then, miR-26b-targeted genes, DIAPH3 and YOD1, were downregulated in YG A cattle. Our results suggest that miR-15a, miR-26b, and miR-29c are upregulated in biofluids and LD muscle, whereas DIAPH3 and YOD1 are downregulated in the LD muscle of finishing cattle steers. © 2017 International Federation for Cell Biology.

Synthesis of Biofluidic Microsystems (SYNBIOSYS)

DTIC Science & Technology

2007-10-01

reaction system. 58 FIGURE 41. The micro reactor is represented by a PFR network model. The calculation of reaction and convection is conducted in...one column of PFRs and the calculation of diffusional mixing is conducted between two columns of PFRs. 59 FIGURE 42. Apply the numerical method of...lines to calculate the diffusion in the channel width direction. Here, we take 10 discretized concentration points in the channel: ci1 - ci10. Points

Biomarker metabolite signatures pave the way for electronic-nose applications in early clinical disease diagnoses

Treesearch

Alphus Dan Wilson

2017-01-01

Background: Analysis of volatile metabolites derived from the human breath or biofluids provides noninvasive means of detecting and monitoring diseases that occur throughout the body. Diseases arise from different mechanisms that cause alterations in normal physiological processes. Mechanisms of disease (pathogenesis) result in the...

Determination of fluoroquinolones in fish tissues, biological fluids, and environmental waters by liquid chromatography tandem mass spectrometry.

PubMed

Ziarrusta, Haizea; Val, Nahia; Dominguez, Haizea; Mijangos, Leire; Prieto, Ailette; Usobiaga, Aresatz; Etxebarria, Nestor; Zuloaga, Olatz; Olivares, Maitane

2017-11-01

This work describes the optimization, validation, and application in real samples of accurate and precise analytical methods to determine ten fluoroquinolones (FQs) (norfloxacin, enoxacin, pefloxacin, ofloxacin, levofloxacin, ciprofloxacin, danofloxacin, lomefloxacin, enrofloxacin, and sparfloxacin) in different environmental matrices, such as water (estuarine, seawater, and wastewater treatment plant effluent), fish tissues (muscle and liver), and fish biofluids (plasma and bile). The analysis step performed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) was fully optimized to improve the separation and detection steps. The extraction of analytes from fish tissues was accomplished using focused ultrasound solid-liquid extraction using methanol/acetic acid (95:5 v/v) as extractant. The preconcentration and clean-up steps were optimized in terms of extraction efficiency and cleanliness and the best strategy for each matrix was selected: (i) Oasis HLB for seawater and muscle, (ii) liquid-liquid extraction combined with Oasis HLB for the lipid-rich liver, (iii) the combination of Evolute-WAX and Oasis HLB for estuarine water and wastewater treatment plant effluent, and (iv) molecular imprinted polymers for biofluids. The methods afforded satisfactory apparent recoveries (80-126%) and repeatability (RSD < 15%), except for sparfloxacin, which showed a lack of correction with the available isotopically labeled surrogates ([ 2 H 8 ]-ciprofloxacin and [ 2 H 5 ]-enrofloxacin). Ciprofloxacin, norfloxacin, and ofloxacin were detected in both water and fish liver samples from the Biscay Coast at concentrations up to 278 ng/L and 4 ng/g, respectively. To the best of our knowledge, this work is one of the few analyzing up to ten FQs and in so many fish tissues and biofluids. Graphical abstract Determination of fluoroquinolones in different environmental matrices, such as water (estuarine, seawater, and wastewater treatment plant effluent), fish tissues (muscle and liver), and fish biofluids (plasma and bile).

Interest of fluorine-19 nuclear magnetic resonance spectroscopy in the detection, identification and quantification of metabolites of anticancer and antifungal fluoropyrimidine drugs in human biofluids.

PubMed

Martino, Robert; Gilard, Véronique; Desmoulin, Franck; Malet-Martino, Myriam

2006-01-01

The metabolism of fluorouracil and fluorocytosine, two 5-fluoropyrimidine drugs in clinical use, was investigated. (19)F nuclear magnetic resonance (NMR) spectroscopy was used as an analytical technique for the detection, identification and quantification of fluorinated metabolites of these drugs in intact human biofluids as well as fluorinated degradation compounds of fluorouracil in commercial vials. (19)F NMR provides a highly specific tool for the detection and absolute quantification, in a single run, of all the fluorinated species, including unexpected substances, present in biofluids of patients treated with fluorouracil or fluorocytosine. Besides the parent drug and the already known fluorinated metabolites, nine new metabolites were identified for the first time with (19)F NMR in human biofluids. Six of them can only be observed with this technique: fluoride ion, N-carboxy-alpha-fluoro-beta-alanine, alpha-fluoro-beta-alanine conjugate with deoxycholic acid, 2-fluoro-3-hydroxypropanoic acid, fluoroacetic acid, O(2)-beta-glucuronide of fluorocytosine. (19)F NMR studies of biological fluids of patients treated with anticancer fluorouracil or antifungal fluorocytosine have furthered the understanding of their catabolic pathways.

Competitive adsorption of heavy metal ions on carbon nanotubes and the desorption in simulated biofluids.

PubMed

Ma, Xin; Yang, Sheng-Tao; Tang, Huan; Liu, Yuanfang; Wang, Haifang

2015-06-15

Carbon nanotubes (CNTs) had meaningful adsorption capacities for Pb(2+), Cu(2+), Zn(2+) and Cd(2+), while Pb(2+) showed the highest adsorption in the competitive adsorption evaluations. The desorption behaviors of heavy metal ions were completely different in various biofluids, where the desorption was significantly influenced by pH and the presence of proteins/other cations. The desorption was most effective in simulated stomach juice, and much less effective in other simulated biofluids. More Pb(2+) stuck to CNTs than others, resulting in less desorption. Interestingly, the competitive desorption behaviors of four ions were largely changed comparing to the individual desorption behaviors. The implications to the biosafety evaluations and synergistic effects of CNT are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis.

PubMed

Emwas, Abdul-Hamid; Roy, Raja; McKay, Ryan T; Ryan, Danielle; Brennan, Lorraine; Tenori, Leonardo; Luchinat, Claudio; Gao, Xin; Zeri, Ana Carolina; Gowda, G A Nagana; Raftery, Daniel; Steinbeck, Christoph; Salek, Reza M; Wishart, David S

2016-02-05

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.

Salivary DNA Methylation Profiling: Aspects to Consider for Biomarker Identification.

PubMed

Langie, Sabine A S; Moisse, Matthieu; Declerck, Ken; Koppen, Gudrun; Godderis, Lode; Vanden Berghe, Wim; Drury, Stacy; De Boever, Patrick

2017-09-01

Is it not more comfortable to spit saliva in a tube than to be pricked with a needle to draw blood to analyse your health and disease risk? Many patients, study participants and (parents of) young children undoubtedly prefer non-invasive and convenient procedures. Such procedures increase compliance rates especially for longitudinal prospective studies. Saliva is an attractive biofluid providing good quality DNA to study epigenetic mechanisms underlying disease across development. In this MiniReview, we will describe the different applications of saliva in the field of epigenetics, focusing on genomewide methylation analysis. Advantages of the use of saliva and its comparability with blood will be discussed, as will the challenges in data processing and interpretation. Knowledge gaps will be identified and suggestions given on how to improve the analysis, making saliva 'the' biofluid of choice for future biomarker initiatives in many different epidemiological and public health studies. © 2016 The Authors. Basic & Clinical Pharmacology & Toxicology published by John Wiley & Sons Ltd on behalf of Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).

Method development in high-performance liquid chromatography for high-throughput profiling and metabonomic studies of biofluid samples.

PubMed

Pham-Tuan, Hai; Kaskavelis, Lefteris; Daykin, Clare A; Janssen, Hans-Gerd

2003-06-15

"Metabonomics" has in the past decade demonstrated enormous potential in furthering the understanding of, for example, disease processes, toxicological mechanisms, and biomarker discovery. The same principles can also provide a systematic and comprehensive approach to the study of food ingredient impact on consumer health. However, "metabonomic" methodology requires the development of rapid, advanced analytical tools to comprehensively profile biofluid metabolites within consumers. Until now, NMR spectroscopy has been used for this purpose almost exclusively. Chromatographic techniques and in particular HPLC, have not been exploited accordingly. The main drawbacks of chromatography are the long analysis time, instabilities in the sample fingerprint and the rigorous sample preparation required. This contribution addresses these problems in the quest to develop generic methods for high-throughput profiling using HPLC. After a careful optimization process, stable fingerprints of biofluid samples can be obtained using standard HPLC equipment. A method using a short monolithic column and a rapid gradient with a high flow-rate has been developed that allowed rapid and detailed profiling of larger numbers of urine samples. The method can be easily translated into a slow, shallow-gradient high-resolution method for identification of interesting peaks by LC-MS/NMR. A similar approach has been applied for cell culture media samples. Due to the much higher protein content of such samples non-porous polymer-based small particle columns yielded the best results. The study clearly shows that HPLC can be used in metabonomic fingerprinting studies.

Introducing Discrete Frequency Infrared Technology for High-Throughput Biofluid Screening

NASA Astrophysics Data System (ADS)

Hughes, Caryn; Clemens, Graeme; Bird, Benjamin; Dawson, Timothy; Ashton, Katherine M.; Jenkinson, Michael D.; Brodbelt, Andrew; Weida, Miles; Fotheringham, Edeline; Barre, Matthew; Rowlette, Jeremy; Baker, Matthew J.

2016-02-01

Accurate early diagnosis is critical to patient survival, management and quality of life. Biofluids are key to early diagnosis due to their ease of collection and intimate involvement in human function. Large-scale mid-IR imaging of dried fluid deposits offers a high-throughput molecular analysis paradigm for the biomedical laboratory. The exciting advent of tuneable quantum cascade lasers allows for the collection of discrete frequency infrared data enabling clinically relevant timescales. By scanning targeted frequencies spectral quality, reproducibility and diagnostic potential can be maintained while significantly reducing acquisition time and processing requirements, sampling 16 serum spots with 0.6, 5.1 and 15% relative standard deviation (RSD) for 199, 14 and 9 discrete frequencies respectively. We use this reproducible methodology to show proof of concept rapid diagnostics; 40 unique dried liquid biopsies from brain, breast, lung and skin cancer patients were classified in 2.4 cumulative seconds against 10 non-cancer controls with accuracies of up to 90%.

MicroRNA Biomarkers of Toxicity in Biological Matrices ...

EPA Pesticide Factsheets

Biomarker measurements that reliably correlate with tissue injury and can be measured from sampling accessible biofluids offer enormous benefits in terms of cost, time, and convenience when assessing environmental and drug-induced toxicity in model systems or human cohorts. MicroRNAs (miRNAs) have emerged in recent years as a promising new type of biomarker for monitoring toxicity. Recent enthusiasm for miRNA biomarker research has been fueled by discoveries that certain miRNA species are cell-type specific and released during injury, thus raising the possibility of using biofluid-based miRNAs as a “liquid biopsy” that may be obtained by sampling extracellular fluids. As biomarkers, miRNAs demonstrate improved stability as compared to many protein markers and sequences are largely conserved across species, simplifying analytical techniques. Recent efforts have sought to identify miRNAs that are released into accessible biofluids following xenobiotic exposure, using compounds that target specific organs. While still early in the discovery phase, miRNA biomarkers will have an increasingly important role in the assessment of adverse effects of both environmental chemicals and pharmaceutical drugs. Here, we review the current findings of biofluid-based miRNAs, as well as highlight technical challenges in assessing toxicologic pathology using these biomarkers. MicroRNAs (miRNAs) are small, non-coding RNA species that selectively bind mRNA molecules and alter thei

Development of a Pipeline for Exploratory Metabolic Profiling of Infant Urine

PubMed Central

Jackson, Frances; Georgakopoulou, Nancy; Kaluarachchi, Manuja; Kyriakides, Michael; Andreas, Nicholas; Przysiezna, Natalia; Hyde, Matthew J.; Modi, Neena; Nicholson, Jeremy K.; Wijeyesekera, Anisha; Holmes, Elaine

2017-01-01

Numerous metabolic profiling pipelines have been developed to characterize the composition of human biofluids and tissues, the vast majority of these being for studies in adults. To accommodate limited sample volume and to take into account the compositional differences between adult and infant biofluids, we developed and optimized sample handling and analytical procedures for studying urine from newborns. A robust pipeline for metabolic profiling using NMR spectroscopy was established, encompassing sample collection, preparation, spectroscopic measurement, and computational analysis. Longitudinal samples were collected from five infants from birth until 14 months of age. Methods of extraction and effects of freezing and sample dilution were assessed, and urinary contaminants from breakdown of polymers in a range of diapers and cotton wool balls were identified and compared, including propylene glycol, acrylic acid, and tert-butanol. Finally, assessment of urinary profiles obtained over the first few weeks of life revealed a dramatic change in composition, with concentrations of phenols, amino acids, and betaine altering systematically over the first few months of life. Therefore, neonatal samples require more stringent standardization of experimental design, sample handling, and analysis compared to that of adult samples to accommodate the variability and limited sample volume. PMID:27476583

Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis

PubMed Central

2016-01-01

NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many “unwanted” or “undesirable” compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment. PMID:26745651

Bioaccessibility and Risk of Exposure to Metals and SVOCs in Artificial Turf Field Fill Materials and Fibers.

PubMed

Pavilonis, Brian T; Weisel, Clifford P; Buckley, Brian; Lioy, Paul J

2014-01-01

To reduce maintenance costs, municipalities and schools are starting to replace natural grass fields with a new generation synthetic turf. Unlike Astro-Turf, which was first introduced in the 1960s, synthetic field turf provides more cushioning to athletes. Part of this cushioning comes from materials like crumb rubber infill, which is manufactured from recycled tires and may contain a variety of chemicals. The goal of this study was to evaluate potential exposures from playing on artificial turf fields and associated risks to trace metals, semi-volatile organic compounds (SVOCs), and polycyclic aromatic hydrocarbons (PAHs) by examining typical artificial turf fibers (n = 8), different types of infill (n = 8), and samples from actual fields (n = 7). Three artificial biofluids were prepared, which included: lung, sweat, and digestive fluids. Artificial biofluids were hypothesized to yield a more representative estimation of dose than the levels obtained from total extraction methods. PAHs were routinely below the limit of detection across all three biofluids, precluding completion of a meaningful risk assessment. No SVOCs were identified at quantifiable levels in any extracts based on a match of their mass spectrum to compounds that are regulated in soil. The metals were measurable but at concentrations for which human health risk was estimated to be low. The study demonstrated that for the products and fields we tested, exposure to infill and artificial turf was generally considered de minimus, with the possible exception of lead for some fields and materials. © 2013 Society for Risk Analysis.

Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review.

PubMed

Emwas, Abdul-Hamid; Luchinat, Claudio; Turano, Paola; Tenori, Leonardo; Roy, Raja; Salek, Reza M; Ryan, Danielle; Merzaban, Jasmeen S; Kaddurah-Daouk, Rima; Zeri, Ana Carolina; Nagana Gowda, G A; Raftery, Daniel; Wang, Yulan; Brennan, Lorraine; Wishart, David S

The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.

Evaluation of U.S. Commercial-Off-the-Shelf Hand-Held Assays to Detect Opiate Pain Reliever Compounds in Multiple Biofluids

DTIC Science & Technology

2016-09-01

EVALUATION OF U.S. COMMERCIAL-OFF-THE-SHELF HAND-HELD ASSAYS TO DETECT OPIATE PAIN RELIEVER COMPOUNDS IN...Commercial-Off-the-Shelf Hand-Held Assays to Detect Opiate Pain Reliever Compounds in Multiple Biofluids 5a. CONTRACT NUMBER 5b. GRANT NUMBER R...study, we evaluated the potential for several U.S. commercial-off-the-shelf (COTS) hand-held assays (HHAs) to detect members of the opiate pain reliever

Evaluation of analytical performance and reliability of direct nanoLC-nanoESI-high resolution mass spectrometry for profiling the (xeno)metabolome.

PubMed

Chetwynd, Andrew J; David, Arthur; Hill, Elizabeth M; Abdul-Sada, Alaa

2014-10-01

Mass spectrometry (MS) profiling techniques are used for analysing metabolites and xenobiotics in biofluids; however, detection of low abundance compounds using conventional MS techniques is poor. To counter this, nanoflow ultra-high-pressure liquid chromatography-nanoelectrospray ionization-time-of-flight MS (nUHPLC-nESI-TOFMS), which has been used primarily for proteomics, offers an innovative prospect for profiling small molecules. Compared to conventional UHPLC-ESI-TOFMS, nUHPLC-nESI-TOFMS enhanced detection limits of a variety of (xeno)metabolites by between 2 and 2000-fold. In addition, this study demonstrates for the first time excellent repeatability and reproducibility for analysis of urine and plasma samples using nUHPLC-nESI-TOFMS, supporting implementation of this platform as a novel approach for high-throughput (xeno)metabolomics. Copyright © 2014 John Wiley & Sons, Ltd.

Comparison of cyanide exposure markers in the biofluids of smokers and non-smokers.

PubMed

Vinnakota, Chakravarthy V; Peetha, Naga S; Perrizo, Mitch G; Ferris, David G; Oda, Robert P; Rockwood, Gary A; Logue, Brian A

2012-11-01

Cyanide is highly toxic and is present in many foods, combustion products (e.g. cigarette smoke), industrial processes, and has been used as a terrorist weapon. In this study, cyanide and its major metabolites, thiocyanate and 2-amino-2-thiazoline-4-carboxylic acid (ATCA), were analyzed from various human biofluids of smokers (low-level chronic cyanide exposure group) and non-smokers to gain insight into the relationship of these biomarkers to cyanide exposure. The concentrations of each biomarker tested were elevated for smokers in each biofluid. Significant differences (p < 0.05) were found for thiocyanate in plasma and urine, and ATCA showed significant differences in plasma and saliva. Additionally, biomarker concentration ratios, correlations between markers of cyanide exposure, and other statistical methods were performed to better understand the relationship between cyanide and its metabolites. Of the markers studied, the results indicate plasma ATCA, in particular, showed excellent promise as a biomarker for chronic low-level cyanide exposure.

Blue and UV fluorescence of biological fluids and carbon nanodots

NASA Astrophysics Data System (ADS)

Kuznetsov, A.; Frorip, A.; Ots-Rosenberg, M.; Sünter, A.

2013-11-01

Comparative optical study of biofluids (serum, urine, hemodialysate) and carbon nanodots (CND) aqueous solutions has been done. Biofluids were collected from chronic kidney diseases patients (CKD Pts) as well as from normal controls (NCs). Sugar derived CND and oxidized graphene solutions were prepared and used. Fluorescence and excitation spectra have mainly been measured and compared for two sets of subjects. For both family of subjects typical fluorescence with parameters λexсmax/ λemmax = 320+/-5/420+/-5 nm is observed and has many analogeous properties. New effective method of additional similarity identification with use of aluminum salts Al2 (SO4)3, Al (N03)3 and AlCl3 is proposed. Aluminum ions induce the fluorescence band at 380 nm in all substances investigated. Plenty of similar features (12) in optical properties create a united platform for further investigation of the topic - the nature of endogenous near UV and visible fluorescence in biofluids and CND.

Metabolomics as a tool to identify biomarkers to predict and improve outcomes in reproductive medicine: a systematic review.

PubMed

Bracewell-Milnes, Timothy; Saso, Srdjan; Abdalla, Hossam; Nikolau, Dimitrios; Norman-Taylor, Julian; Johnson, Mark; Holmes, Elaine; Thum, Meen-Yau

2017-11-01

Infertility is a complex disorder with significant medical, psychological and financial consequences for patients. With live-birth rates per cycle below 30% and a drive from the Human Fertilisation and Embryology Authority (HFEA) to encourage single embryo transfer, there is significant research in different areas aiming to improve success rates of fertility treatments. One such area is investigating the causes of infertility at a molecular level, and metabolomics techniques provide a platform for studying relevant biofluids in the reproductive tract. The aim of this systematic review is to examine the recent findings for the potential application of metabolomics to female reproduction, specifically to the metabolomics of follicular fluid (FF), embryo culture medium (ECM) and endometrial fluid. To our knowledge no other systematic review has investigated this topic. English peer-reviewed journals on PubMed, Science Direct, SciFinder, were systematically searched for studies investigating metabolomics and the female reproductive tract with no time restriction set for publications. Studies were assessed for quality using the risk of bias assessment and ROBIN-I. There were 21 studies that met the inclusion criteria and were included in the systematic review. Metabolomic studies have been employed for the compositional analysis of various biofluids in the female reproductive tract, including FF, ECM, blastocoele fluid and endometrial fluid. There is some weak evidence that metabolomics technologies studying ECM might be able to predict the viability of individual embryos and implantation rate better than standard embryo morphology, However these data were not supported by randomized the controlled trials (RCTs) which showed no evidence that using metabolomics is able to improve the most important reproductive outcomes, such as clinical pregnancy and live-birth rates. This systematic review provides guidance for future metabolomic studies on biofluids of the female reproductive tract, with a summary of the current findings, promise and pitfalls in metabolomic techniques. The approaches discussed can be adapted by other metabolomic studies. A range of sophisticated modern metabolomic techniques are now more widely available and have been applied to the analysis of the female reproductive tract. However, this review has revealed the paucity of metabolomic studies in the field of fertility and the inconsistencies of findings between different studies, as well as a lack of research examining the metabolic effects of various gynecological diseases. By incorporating metabolomic technology into an increased number of well designed studies, a much greater understanding of infertility at a molecular level could be achieved. However, there is currently no evidence for the use of metabolomics in clinical practice to improve fertility outcomes. © The Author 2017. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com

An ultra high performance liquid chromatography with tandem mass spectrometry method for plasma and cerebrospinal fluid pharmacokinetics of rhein in patients with traumatic brain injury after administration of rhubarb decoction.

PubMed

Wang, Yang; Fan, Rong; Luo, Jiekun; Tang, Tao; Xing, Zhihua; Xia, Zian; Peng, Weijun; Wang, Wenzhu; Lv, Huiying; Huang, Wei; Liang, Yizeng; Yi, Lunzhao; Lu, Hongmei; Huang, Xi

2015-04-01

Damage of blood-brain barrier is a common result of traumatic brain injury. This damage can open the blood-brain barrier and allow drug passage. An ultraperformance liquid chromatography with tandem mass spectrometry method was established to determine the concentration of rhein in the biofluids (plasma and cerebrospinal fluid) of patients with a compromised blood-brain barrier following traumatic brain injury after rhubarb administration. Furthermore, the pharmacokinetic profiles were analyzed. A triple-quadruple tandem mass spectrometer with electrospray ionization was used for rhein detection. The mass transition followed was m/z 283.06→239.0. The calibration curve was linear in the concentration range of 10-8000 ng/mL for the biofluids. The intra- and interday precisions were less than 10%. The relative standard deviation of recovery was less than 15% in biological matrices. The pharmacokinetic data showed that rhein was rapidly transported into biofluids, and exhibited a peak concentration 1 h after rhubarb administration. The elimination rate of rhein was slow. The AUCcerebrospinal fluid /AUCplasma (AUC is area under curve) of rhein was approximately 17%, indicating that portions of rhein could pass the impaired blood-brain barrier. The method was successfully applied to quantify rhein in the biofluids of all patients. The data presented can help to guide clinical applications of rhubarb for treating traumatic brain injury. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Controlling Heat Transport and Flow Structures in Thermal Turbulence Using Ratchet Surfaces

NASA Astrophysics Data System (ADS)

Jiang, Hechuan; Zhu, Xiaojue; Mathai, Varghese; Verzicco, Roberto; Lohse, Detlef; Sun, Chao

2018-01-01

In this combined experimental and numerical study on thermally driven turbulence in a rectangular cell, the global heat transport and the coherent flow structures are controlled with an asymmetric ratchetlike roughness on the top and bottom plates. We show that, by means of symmetry breaking due to the presence of the ratchet structures on the conducting plates, the orientation of the large scale circulation roll (LSCR) can be locked to a preferred direction even when the cell is perfectly leveled out. By introducing a small tilt to the system, we show that the LSCR orientation can be tuned and controlled. The two different orientations of LSCR give two quite different heat transport efficiencies, indicating that heat transport is sensitive to the LSCR direction over the asymmetric roughness structure. Through a quantitative analysis of the dynamics of thermal plume emissions and the orientation of the LSCR over the asymmetric structure, we provide a physical explanation for these findings. The current work has important implications for passive and active flow control in engineering, biofluid dynamics, and geophysical flows.

A mixed boundary representation to simulate the displacement of a biofluid by a biomaterial in porous media.

PubMed

Widmer, René P; Ferguson, Stephen J

2011-05-01

Characterization of the biomaterial flow through porous bone is crucial for the success of the bone augmentation process in vertebroplasty. The biofluid, biomaterial, and local morphological bone characteristics determine the final shape of the filling, which is important both for the post-treatment mechanical loading and the risk of intraoperative extraosseous leakage. We have developed a computational model that describes the flow of biomaterials in porous bone structures by considering the material porosity, the region-dependent intrinsic permeability of the porous structure, the rheological properties of the biomaterial, and the boundary conditions of the filling process. To simulate the process of the substitution of a biofluid (bone marrow) by a biomaterial (bone cement), we developed a hybrid formulation to describe the evolution of the fluid boundary and properties and coupled it to a modified version of Darcy's law. The apparent rheological properties are derived from a fluid-fluid interface tracking algorithm and a mixed boundary representation. The region- specific intrinsic permeability of the bone is governed by an empirical relationship resulting from a fitting process of experimental data. In a first step, we verified the model by studying the displacement process in spherical domains, where the spreading pattern is known in advance. The mixed boundary model demonstrated, as expected, that the determinants of the spreading pattern are the local intrinsic permeability of the porous matrix and the ratio of the viscosity of the fluids that are contributing to the displacement process. The simulations also illustrate the sensitivity of the mixed boundary representation to anisotropic permeability, which is related to the directional dependent microstructural properties of the porous medium. Furthermore, we compared the nonlinear finite element model to different published experimental studies and found a moderate to good agreement (R(2)=0.9895 for a one-dimensional bone core infiltration test and a 10.94-16.92% relative error for a three-dimensional spreading pattern study, respectively) between computational and experimental results.

An integrated platform for directly widely-targeted quantitative analysis of feces part I: Platform configuration and method validation.

PubMed

Song, Yuelin; Song, Qingqing; Li, Jun; Zheng, Jiao; Li, Chun; Zhang, Yuan; Zhang, Lingling; Jiang, Yong; Tu, Pengfei

2016-07-08

Direct analysis is of great importance to understand the real chemical profile of a given sample, notably biological materials, because either chemical degradation or diverse errors and uncertainties might be resulted from sophisticated protocols. In comparison with biofluids, it is still challenging for direct analysis of solid biological samples using high performance liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Herein, a new analytical platform was configured by online hyphenating pressurized liquid extraction (PLE), turbulent flow chromatography (TFC), and LC-MS/MS. A facile, but robust PLE module was constructed based on the phenomenon that noticeable back-pressure can be generated during rapid fluid passing through a narrow tube. TFC column that is advantageous at extracting low molecular analytes from rushing fluid was employed to link at the outlet of the PLE module to capture constituents-of-interest. An electronic 6-port/2-position valve was introduced between TFC column and LC-MS/MS to fragment each measurement into extraction and elution phases, whereas LC-MS/MS took the charge of analyte separation and monitoring. As a proof of concept, simultaneous determination of 24 endogenous substances including eighteen steroids, five eicosanoids, and one porphyrin in feces was carried out in this paper. Method validation assays demonstrated the analytical platform to be qualified for directly simultaneous measurement of diverse endogenous analytes in fecal matrices. Application of this integrated platform on homolog-focused profiling of feces is discussed in a companion paper. Copyright © 2016 Elsevier B.V. All rights reserved.

Sweat: a sample with limited present applications and promising future in metabolomics.

PubMed

Mena-Bravo, A; Luque de Castro, M D

2014-03-01

Sweat is a biofluid with present scant use as clinical sample. This review tries to demonstrate the advantages of sweat over other biofluids such as blood or urine for routine clinical analyses and the potential when related to metabolomics. With this aim, critical discussion of sweat samplers and equipment for analysis of target compounds in this sample is made. Well established routine analyses in sweat as is that to diagnose cystic fibrosis, and the advantages and disadvantages of sweat versus urine or blood for doping control have also been discussed. Methods for analytes such as essential metals and xenometals, ethanol and electrolytes in sweat in fact constitute target metabolomics approaches or belong to any metabolomics subdiscipline such as metallomics, ionomics or xenometabolomics. The higher development of biomarkers based on genomics or proteomics as omics older than metabolomics is discussed and also the potential role of metabolomics in systems biology taking into account its emergent implementation. Normalization of the volume of sampled sweat constitutes a present unsolved shortcoming that deserves investigation. Foreseeable trends in this area are outlined. Copyright © 2013 Elsevier B.V. All rights reserved.

Raman spectroscopy of bio fluids: an exploratory study for oral cancer detection

NASA Astrophysics Data System (ADS)

Brindha, Elumalai; Rajasekaran, Ramu; Aruna, Prakasarao; Koteeswaran, Dornadula; Ganesan, Singaravelu

2016-03-01

ion for various disease diagnosis including cancers. Oral cancer is one of the most common cancers in India and it accounts for one third of the global oral cancer burden. Raman spectroscopy of tissues has gained much attention in the diagnostic oncology, as it provides unique spectral signature corresponding to metabolic alterations under different pathological conditions and micro-environment. Based on these, several studies have been reported on the use of Raman spectroscopy in the discrimination of diseased conditions from their normal counterpart at cellular and tissue level but only limited studies were available on bio-fluids. Recently, optical characterization of bio-fluids has also geared up for biomarker identification in the disease diagnosis. In this context, an attempt was made to study the metabolic variations in the blood, urine and saliva of oral cancer patients and normal subjects using Raman spectroscopy. Principal Component based Linear Discriminant Analysis (PC-LDA) followed by Leave-One-Out Cross-Validation (LOOCV) was employed to find the statistical significance of the present technique in discriminating the malignant conditions from normal subjects.

Biofluid-Based Detection of the Migration Switch in Prostate Cancer to Predict Metastatic Disease

DTIC Science & Technology

2016-09-01

developed with a laboratory in oncology studying osteosarcoma using Dr. Lewis’ in house imaging platforms. 15. SUBJECT TERMS Metastasis, motility...that may have a role in breast cancer. Another in-house collaboration was developed with a laboratory in oncology studying osteosarcoma using Dr. Lewis...Lewis. Quantitative Analysis of human Cancer Cell Extravasation Using Intravital Imaging, Department of Oncology , University of Alberta (2016) Vol. 1458

Dynamic metabolic response of mice to acute mequindox exposure.

PubMed

Zhao, Xiu-Ju; Huang, Chongyang; Lei, Hehua; Nie, Xiu; Tang, Huiru; Wang, Yulan

2011-11-04

Mequindox is used as a veterinary antibiotic drug. As part of systematic investigations into mequindox as a veterinary medicine and its subsequent applications in food safety, we conducted the investigation to assess the metabolic response of mice to mequindox using metabonomics, which combines NMR metabolic profiles of biofluids or tissues and pattern recognition data analysis. In this study, we delivered a single dose of mequindox to mice with dosage levels of 15, 75, and 350 mg/kg body weight and collected urine samples over a 7 day period, as well as plasma and liver tissues at 7 days postdose. Principal components analysis (PCA) and orthogonal projection to latent structure discriminant analysis (O-PLS-DA) were performed on (1)H NMR spectra of biofluids and liver, showing that low dose levels of mequindox exposure had no adverse effects, consistent with histological observations of the liver. High and moderate levels of mequindox exposure caused suppression of glycolysis and stimulation of fatty acid oxidation accompanied with increased levels of oxidative stress. Our metabonomic analyses also showed disruption of amino acid metabolism, consistent with liver damage observed from histopathological examinations. Furthermore, mequindox perturbed gut microbial activity manifested in the altered excretion of urinary trimethylamine (TMA), trimethylamine-N-oxide (TMAO), hippurate, phenylacetylglycine (PAG), and phenylacetate. The putative gut microbial function may also contribute to the assembly and secretion of very-low-density lipoproteins from the liver to the plasma. Our work provides important insights on the metabolic responses of mequindox.

NMR and MS Methods for Metabolomics.

PubMed

Amberg, Alexander; Riefke, Björn; Schlotterbeck, Götz; Ross, Alfred; Senn, Hans; Dieterle, Frank; Keck, Matthias

2017-01-01

Metabolomics, also often referred as "metabolic profiling," is the systematic profiling of metabolites in biofluids or tissues of organisms and their temporal changes. In the last decade, metabolomics has become more and more popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabolomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabolomics, i.e., NMR, UPLC-MS, and GC-MS, have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabolomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation to determining the measurement details of all analytical platforms, and finally to discussing the corresponding specific steps of data analysis.

NMR and MS methods for metabonomics.

PubMed

Dieterle, Frank; Riefke, Björn; Schlotterbeck, Götz; Ross, Alfred; Senn, Hans; Amberg, Alexander

2011-01-01

Metabonomics, also often referred to as "metabolomics" or "metabolic profiling," is the systematic profiling of metabolites in bio-fluids or tissues of organisms and their temporal changes. In the last decade, metabonomics has become increasingly popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabonomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabonomics, i.e., NMR, LC-MS, UPLC-MS, and GC-MS have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabonomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation, to determining the measurement details of all analytical platforms, and finally, to discussing the corresponding specific steps of data analysis.

Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

PubMed Central

Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

2017-01-01

We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L−1. PMID:28102316

Electrolyte-Sensing Transistor Decals Enabled by Ultrathin Microbial Nanocellulose

NASA Astrophysics Data System (ADS)

Yuen, Jonathan D.; Walper, Scott A.; Melde, Brian J.; Daniele, Michael A.; Stenger, David A.

2017-01-01

We report an ultra-thin electronic decal that can simultaneously collect, transmit and interrogate a bio-fluid. The described technology effectively integrates a thin-film organic electrochemical transistor (sensing component) with an ultrathin microbial nanocellulose wicking membrane (sample handling component). As far as we are aware, OECTs have not been integrated in thin, permeable membrane substrates for epidermal electronics. The design of the biocompatible decal allows for the physical isolation of the electronics from the human body while enabling efficient bio-fluid delivery to the transistor via vertical wicking. High currents and ON-OFF ratios were achieved, with sensitivity as low as 1 mg·L-1.

Liquid refractive index sensing independent of opacity using an optofluidic diffraction sensor.

PubMed

Xu, Zhida; Han, Kevin; Khan, Ibrahim; Wang, Xinhao; Liu, G Logan

2014-10-15

We have implemented a multifunctional optofluidic sensor that can monitor changes in the refractive index and pressure of biofluid simultaneously and can detect free-solution molecular interaction in situ. In this Letter, we demonstrate two major improvements of this sensor proven by both simulation and experiments. One improvement is the broader measurement range of refractive index by making the diffraction grating with high-index polymer. The other improvement is the separation of refractive index sensing from opacity sensing by using the relative power ratio of diffraction orders. This simple, compact and low-cost multifunctional optofluidic sensor has the potential to be used for in situ biofluid monitoring.

Fluorine nuclear magnetic resonance spectroscopy of human biofluids in the field of metabolic studies of anticancer and antifungal fluoropyrimidine drugs.

PubMed

Malet-Martino, Myriam; Gilard, Véronique; Desmoulin, Franck; Martino, Robert

2006-04-01

Fluorine-19 nuclear magnetic resonance (19F NMR) spectroscopy provides a highly specific tool for the detection, identification and quantification of fluorine-containing drugs and their metabolites in biofluids. The value and difficulties encountered in investigations on drug metabolism are first discussed. Then the metabolism of three fluoropyrimidines in clinical use, 5-fluorouracil, 5-fluorocytosine and capecitabine are reported. Besides the parent drug and the already known fluorinated metabolites, 12 new metabolites were identified for the first time with 19F NMR in human biofluids. Nine of them can only be observed with this technique: fluoride ion, N-carboxy-alpha-fluoro-beta-alanine, alpha-fluoro-beta-alanine conjugate with deoxycholic acid, 2-fluoro-3-hydroxypropanoic acid, fluoroacetic acid, O2-beta-glucuronide of fluorocytosine, fluoroacetaldehyde hydrate and its adduct with urea, fluoromalonic acid semi-aldehyde adducts with urea. This emphasizes the high analytical potential of 19F NMR for the furtherance in the understanding of fluoropyrimidine catabolic pathways. 19F NMR should also play a role in the therapeutic monitoring of FU and its prodrugs in specific groups of patients, e.g. hemodialyzed patients or patients with deficiency in FU catabolic enzymes.

The Human Urine Metabolome

PubMed Central

Bouatra, Souhaila; Aziat, Farid; Mandal, Rupasri; Guo, An Chi; Wilson, Michael R.; Knox, Craig; Bjorndahl, Trent C.; Krishnamurthy, Ramanarayan; Saleem, Fozia; Liu, Philip; Dame, Zerihun T.; Poelzer, Jenna; Huynh, Jessica; Yallou, Faizath S.; Psychogios, Nick; Dong, Edison; Bogumil, Ralf; Roehring, Cornelia; Wishart, David S.

2013-01-01

Urine has long been a “favored” biofluid among metabolomics researchers. It is sterile, easy-to-obtain in large volumes, largely free from interfering proteins or lipids and chemically complex. However, this chemical complexity has also made urine a particularly difficult substrate to fully understand. As a biological waste material, urine typically contains metabolic breakdown products from a wide range of foods, drinks, drugs, environmental contaminants, endogenous waste metabolites and bacterial by-products. Many of these compounds are poorly characterized and poorly understood. In an effort to improve our understanding of this biofluid we have undertaken a comprehensive, quantitative, metabolome-wide characterization of human urine. This involved both computer-aided literature mining and comprehensive, quantitative experimental assessment/validation. The experimental portion employed NMR spectroscopy, gas chromatography mass spectrometry (GC-MS), direct flow injection mass spectrometry (DFI/LC-MS/MS), inductively coupled plasma mass spectrometry (ICP-MS) and high performance liquid chromatography (HPLC) experiments performed on multiple human urine samples. This multi-platform metabolomic analysis allowed us to identify 445 and quantify 378 unique urine metabolites or metabolite species. The different analytical platforms were able to identify (quantify) a total of: 209 (209) by NMR, 179 (85) by GC-MS, 127 (127) by DFI/LC-MS/MS, 40 (40) by ICP-MS and 10 (10) by HPLC. Our use of multiple metabolomics platforms and technologies allowed us to identify several previously unknown urine metabolites and to substantially enhance the level of metabolome coverage. It also allowed us to critically assess the relative strengths and weaknesses of different platforms or technologies. The literature review led to the identification and annotation of another 2206 urinary compounds and was used to help guide the subsequent experimental studies. An online database containing the complete set of 2651 confirmed human urine metabolite species, their structures (3079 in total), concentrations, related literature references and links to their known disease associations are freely available at http://www.urinemetabolome.ca. PMID:24023812

Dissolution chemistry and biocompatibility of single-crystalline silicon nanomembranes and associated materials for transient electronics.

PubMed

Hwang, Suk-Won; Park, Gayoung; Edwards, Chris; Corbin, Elise A; Kang, Seung-Kyun; Cheng, Huanyu; Song, Jun-Kyul; Kim, Jae-Hwan; Yu, Sooyoun; Ng, Joanne; Lee, Jung Eun; Kim, Jiyoung; Yee, Cassian; Bhaduri, Basanta; Su, Yewang; Omennetto, Fiorenzo G; Huang, Yonggang; Bashir, Rashid; Goddard, Lynford; Popescu, Gabriel; Lee, Kyung-Mi; Rogers, John A

2014-06-24

Single-crystalline silicon nanomembranes (Si NMs) represent a critically important class of material for high-performance forms of electronics that are capable of complete, controlled dissolution when immersed in water and/or biofluids, sometimes referred to as a type of "transient" electronics. The results reported here include the kinetics of hydrolysis of Si NMs in biofluids and various aqueous solutions through a range of relevant pH values, ionic concentrations and temperatures, and dependence on dopant types and concentrations. In vitro and in vivo investigations of Si NMs and other transient electronic materials demonstrate biocompatibility and bioresorption, thereby suggesting potential for envisioned applications in active, biodegradable electronic implants.

Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans.

PubMed

Walsh, Marianne C; Brennan, Lorraine; Malthouse, J Paul G; Roche, Helen M; Gibney, Michael J

2006-09-01

Metabolomics in human nutrition research is faced with the challenge that changes in metabolic profiles resulting from diet may be difficult to differentiate from normal physiologic variation. We assessed the extent of intra- and interindividual variation in normal human metabolic profiles and investigated the effect of standardizing diet on reducing variation. Urine, plasma, and saliva were collected from 30 healthy volunteers (23 females, 7 males) on 4 separate mornings. For visits 1 and 2, free food choice was permitted on the day before biofluid collection. Food choice on the day before visit 3 was intended to mimic that for visit 2, and all foods were standardized on the day before visit 4. Samples were analyzed by using 1H nuclear magnetic resonance spectroscopy followed by multivariate data analysis. Intra- and interindividual variations were considerable for each biofluid. Visual inspection of the principal components analysis scores plots indicated a reduction in interindividual variation in urine, but not in plasma or saliva, after the standard diet. Partial least-squares discriminant analysis indicated time-dependent changes in urinary and salivary samples, mainly resulting from creatinine in urine and acetate in saliva. The predictive power of each model to classify the samples as either night or morning was 85% for urine and 75% for saliva. Urine represented a sensitive metabolic profile that reflected acute dietary intake, whereas plasma and saliva did not. Future metabolomics studies should consider recent dietary intake and time of sample collection as a means of reducing normal physiologic variation.

Biofluid mechanics of special organs and the issue of system control. Sixth International Bio-Fluid Mechanics Symposium and Workshop, March 28-30, 2008 Pasadena, California.

PubMed

Zamir, Mair; Moore, James E; Fujioka, Hideki; Gaver, Donald P

2010-03-01

In the field of fluid flow within the human body, focus has been placed on the transportation of blood in the systemic circulation since the discovery of that system; but, other fluids and fluid flow phenomena pervade the body. Some of the most fascinating fluid flow phenomena within the human body involve fluids other than blood and a service other than transport--the lymphatic and pulmonary systems are two striking examples. While transport is still involved in both cases, this is not the only service which they provide and blood is not the only fluid involved. In both systems, filtration, extraction, enrichment, and in general some "treatment" of the fluid itself is the primary function. The study of the systemic circulation has also been conventionally limited to treating the system as if it were an open-loop system governed by the laws of fluid mechanics alone, independent of physiological controls and regulations. This implies that system failures can be explained fully in terms of the laws of fluid mechanics, which of course is not the case. In this paper we examine the clinical implications of these issues and of the special biofluid mechanics issues involved in the lymphatic and pulmonary systems.

Discrimination of premalignant conditions of oral cancer using Raman spectroscopy of urinary metabolites

NASA Astrophysics Data System (ADS)

Elumalai, Brindha; Rajasekaran, Ramu; Aruna, Prakasarao; Koteeswaran, Dornadula; Ganesan, Singaravelu

2015-03-01

Oral cancers are considered to be one of the most commonly occurring malignancy worldwide. Over 70% of the cases report to the doctor only in advanced stages of the disease, resulting in poor survival rates. Hence it is necessary to detect the disease at the earliest which may increase the five year survival rate up to 90%. Among various optical spectroscopic techniques, Raman spectroscopy has been emerged as a tool in identifying several diseased conditions, including oral cancers. Around 30 - 80% of the malignancies of the oral cavity arise from premalignant lesions. Hence, understanding the molecular/spectral differences at the premalignant stage may help in identifying the cancer at the earliest and increase patient's survival rate. Among various bio-fluids such as blood, urine and saliva, urine is considered as one of the diagnostically potential bio-fluids, as it has many metabolites. The distribution and the physiochemical properties of the urinary metabolites may vary due to the changes associated with the pathologic conditions. The present study is aimed to characterize the urine of 70 healthy subjects and 51 pre-malignant patients using Raman spectroscopy under 785nm excitation, to know the molecular/spectral differences between healthy subjects and premalignant conditions of oral malignancy. Principal component analysis based Linear discriminant analysis were also made to find the statistical significance and the present technique yields the sensitivity and specificity of 86.3% and 92.9% with an overall accuracy of 90.9% in the discrimination of premalignant conditions from healthy subjects urine.

Metabolomic applications in radiation biodosimetry: exploring radiation effects through small molecules.

PubMed

Pannkuk, Evan L; Fornace, Albert J; Laiakis, Evagelia C

2017-10-01

Exposure of the general population to ionizing radiation has increased in the past decades, primarily due to long distance travel and medical procedures. On the other hand, accidental exposures, nuclear accidents, and elevated threats of terrorism with the potential detonation of a radiological dispersal device or improvised nuclear device in a major city, all have led to increased needs for rapid biodosimetry and assessment of exposure to different radiation qualities and scenarios. Metabolomics, the qualitative and quantitative assessment of small molecules in a given biological specimen, has emerged as a promising technology to allow for rapid determination of an individual's exposure level and metabolic phenotype. Advancements in mass spectrometry techniques have led to untargeted (discovery phase, global assessment) and targeted (quantitative phase) methods not only to identify biomarkers of radiation exposure, but also to assess general perturbations of metabolism with potential long-term consequences, such as cancer, cardiovascular, and pulmonary disease. Metabolomics of radiation exposure has provided a highly informative snapshot of metabolic dysregulation. Biomarkers in easily accessible biofluids and biospecimens (urine, blood, saliva, sebum, fecal material) from mouse, rat, and minipig models, to non-human primates and humans have provided the basis for determination of a radiation signature to assess the need for medical intervention. Here we provide a comprehensive description of the current status of radiation metabolomic studies for the purpose of rapid high-throughput radiation biodosimetry in easily accessible biofluids and discuss future directions of radiation metabolomics research.

Monitoring Tensile Fatigue of Superelastic NiTi Wire in Liquids by Electrochemical Potential

NASA Astrophysics Data System (ADS)

Racek, Jan; Stora, Marc; Šittner, Petr; Heller, Luděk; Kopeček, Jaromir; Petrenec, Martin

2015-06-01

Fatigue of superelastic NiTi wires was investigated by cyclic tension in simulated biofluid. The state of the surface of the fatigued NiTi wire was monitored by following the evolution of the electrochemical open circuit potential (OCP) together with macroscopic stresses and strains. The ceramic TiO2 oxide layer on the NiTi wire surface cannot withstand the large transformation strain and fractures in the first cycle. Based on the analysis of the results of in situ OCP experiments and SEM observation of cracks, it is claimed that the cycled wire surface develops mechanochemical reactions at the NiTi/liquid interface leading to cumulative generation of hydrogen, uptake of the hydrogen by the NiTi matrix, local loss of the matrix strength, crack transfer into the NiTi matrix, accelerated crack growth, and ultimately to the brittle fracture of the wire. Fatigue degradation is thus claimed to originate from the mechanochemical processes occurring at the excessively deforming surface not from the accumulation of defects due to energy dissipative bulk deformation processes. Ironically, combination of the two exciting properties of NiTi—superelasticity due to martensitic transformation and biocompatibility due to the protective TiO2 surface oxide layer—leads to excessive fatigue damage during cyclic mechanical loading in biofluids.

Systematic analysis of the polyphenol metabolome using the Phenol-Explorer database.

PubMed

Rothwell, Joseph A; Urpi-Sarda, Mireia; Boto-Ordoñez, Maria; Llorach, Rafael; Farran-Codina, Andreu; Barupal, Dinesh Kumar; Neveu, Vanessa; Manach, Claudine; Andres-Lacueva, Cristina; Scalbert, Augustin

2016-01-01

The Phenol-Explorer web database details 383 polyphenol metabolites identified in human and animal biofluids from 221 publications. Here, we exploit these data to characterize and visualize the polyphenol metabolome, the set of all metabolites derived from phenolic food components. Qualitative and quantitative data on 383 polyphenol metabolites as described in 424 human and animal intervention studies were systematically analyzed. Of these metabolites, 301 were identified without prior enzymatic hydrolysis of biofluids, and included glucuronide and sulfate esters, glycosides, aglycones, and O-methyl ethers. Around one-third of these compounds are also known as food constituents and corresponded to polyphenols absorbed without further metabolism. Many ring-cleavage metabolites formed by gut microbiota were noted, mostly derived from hydroxycinnamates, flavanols, and flavonols. Median maximum plasma concentrations (C(max)) of all human metabolites were 0.09 and 0.32 μM when consumed from foods or dietary supplements, respectively. Median time to reach maximum plasma concentration in humans (T(max)) was 2.18 h. These data show the complexity of the polyphenol metabolome and the need to take into account biotransformations to understand in vivo bioactivities and the role of dietary polyphenols in health and disease. © 2015 The Authors. Molecular Nutrition & Food Research published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of Organic Matter - Mineral Interfacial Reactions on Metal(loid) Speciation and Bioaccessibility

NASA Astrophysics Data System (ADS)

Chorover, J.; Kong, S.; Root, R. A.; Thomas, A.

2015-12-01

Bioaccessibility of contaminant metals in geomedia is often measured on the basis of kinetic release to solution during in vitro reaction with biofluid simulants. We postulate that development of a predictive-mechanistic understanding of bioaccessibility requires knowledge of metal(loid) molecular speciation upon sample introduction, as well as its change over the course of the in vitro reaction. Our results - including data from batch, column, mesocosm and field studies pertaining to arsenic, lead, and zinc contaminated materials - indicate the strong influence of organic matter and associated biological activity on metal(loid) speciation in mine tailings and related model systems. Furthermore, presence/absence of organic matter during bioassays affects the kinetics of metal(loid) release into biofluid simulants through multiple mechanisms.

Quantitative analysis of urea in human urine and serum by 1H nuclear magnetic resonance†

PubMed Central

Liu, Lingyan; Mo, Huaping; Wei, Siwei

2016-01-01

A convenient and fast method for quantifying urea in biofluids is demonstrated using NMR analysis and the solvent water signal as a concentration reference. The urea concentration can be accurately determined with errors less than 3% between 1 mM and 50 mM, and less than 2% above 50 mM in urine and serum. The method is promising for various applications with advantages of simplicity, high accuracy, and fast non-destructive detection. With an ability to measure other metabolites simultaneously, this NMR method is also likely to find applications in metabolic profiling and system biology. PMID:22179722

An insight into the metabolic responses of ultra-small superparamagnetic particles of iron oxide using metabonomic analysis of biofluids

NASA Astrophysics Data System (ADS)

Feng, Jianghua; Liu, Huili; Zhang, Limin; Bhakoo, Kishore; Lu, Lehui

2010-10-01

Ultra-small superparamagnetic particles of iron oxides (USPIO) have been developed as intravenous organ/tissue-targeted contrast agents to improve magnetic resonance imaging (MRI) in vivo. However, their potential toxicity and effects on metabolism have attracted particular attention. In the present study, uncoated and dextran-coated USPIO were investigated by analyzing both rat urine and plasma metabonomes using high-resolution NMR-based metabonomic analysis in combination with multivariate statistical analysis. The wealth of information gathered on the metabolic profiles from rat urine and plasma has revealed subtle metabolic changes in response to USPIO administration. The metabolic changes include the elevation of urinary α-hydroxy-n-valerate, o- and p-HPA, PAG, nicotinate and hippurate accompanied by decreases in the levels of urinary α-ketoglutarate, succinate, citrate, N-methylnicotinamide, NAG, DMA, allantoin and acetate following USPIO administration. The changes associated with USPIO administration included a gradual increase in plasma glucose, N-acetyl glycoprotein, saturated fatty acid, citrate, succinate, acetate, GPC, ketone bodies (β-hydroxybutyrate, acetone and acetoacetate) and individual amino acids, such as phenylalanine, lysine, isoleucine, glycine, glutamine and glutamate and a gradual decrease of myo-inositol, unsaturated fatty acid and triacylglycerol. Hence USPIO administration effects are reflected in changes in a number of metabolic pathways including energy, lipid, glucose and amino acid metabolism. The size- and surface chemistry-dependent metabolic responses and possible toxicity were observed using NMR analysis of biofluids. These changes may be attributed to the disturbances of hepatic, renal and cardiac functions following USPIO administrations. The potential biotoxicity can be derived from metabonomic analysis and serum biochemistry analysis. Metabonomic strategy offers a promising approach for the detection of subtle physiological responses on mammalian metabolism, and can be employed to investigate the potential adverse effects of other nanoparticles and nanomaterials on the environment and human health.

Ultrathin, transferred layers of thermally grown silicon dioxide as biofluid barriers for biointegrated flexible electronic systems.

PubMed

Fang, Hui; Zhao, Jianing; Yu, Ki Jun; Song, Enming; Farimani, Amir Barati; Chiang, Chia-Han; Jin, Xin; Xue, Yeguang; Xu, Dong; Du, Wenbo; Seo, Kyung Jin; Zhong, Yiding; Yang, Zijian; Won, Sang Min; Fang, Guanhua; Choi, Seo Woo; Chaudhuri, Santanu; Huang, Yonggang; Alam, Muhammad Ashraful; Viventi, Jonathan; Aluru, N R; Rogers, John A

2016-10-18

Materials that can serve as long-lived barriers to biofluids are essential to the development of any type of chronic electronic implant. Devices such as cardiac pacemakers and cochlear implants use bulk metal or ceramic packages as hermetic enclosures for the electronics. Emerging classes of flexible, biointegrated electronic systems demand similar levels of isolation from biofluids but with thin, compliant films that can simultaneously serve as biointerfaces for sensing and/or actuation while in contact with the soft, curved, and moving surfaces of target organs. This paper introduces a solution to this materials challenge that combines (i) ultrathin, pristine layers of silicon dioxide (SiO 2 ) thermally grown on device-grade silicon wafers, and (ii) processing schemes that allow integration of these materials onto flexible electronic platforms. Accelerated lifetime tests suggest robust barrier characteristics on timescales that approach 70 y, in layers that are sufficiently thin (less than 1 μm) to avoid significant compromises in mechanical flexibility or in electrical interface fidelity. Detailed studies of temperature- and thickness-dependent electrical and physical properties reveal the key characteristics. Molecular simulations highlight essential aspects of the chemistry that governs interactions between the SiO 2 and surrounding water. Examples of use with passive and active components in high-performance flexible electronic devices suggest broad utility in advanced chronic implants.

Ultrathin, transferred layers of thermally grown silicon dioxide as biofluid barriers for biointegrated flexible electronic systems

PubMed Central

Fang, Hui; Yu, Ki Jun; Song, Enming; Farimani, Amir Barati; Chiang, Chia-Han; Jin, Xin; Xu, Dong; Du, Wenbo; Seo, Kyung Jin; Zhong, Yiding; Yang, Zijian; Won, Sang Min; Fang, Guanhua; Choi, Seo Woo; Chaudhuri, Santanu; Huang, Yonggang; Alam, Muhammad Ashraful; Viventi, Jonathan; Aluru, N. R.; Rogers, John A.

2016-01-01

Materials that can serve as long-lived barriers to biofluids are essential to the development of any type of chronic electronic implant. Devices such as cardiac pacemakers and cochlear implants use bulk metal or ceramic packages as hermetic enclosures for the electronics. Emerging classes of flexible, biointegrated electronic systems demand similar levels of isolation from biofluids but with thin, compliant films that can simultaneously serve as biointerfaces for sensing and/or actuation while in contact with the soft, curved, and moving surfaces of target organs. This paper introduces a solution to this materials challenge that combines (i) ultrathin, pristine layers of silicon dioxide (SiO2) thermally grown on device-grade silicon wafers, and (ii) processing schemes that allow integration of these materials onto flexible electronic platforms. Accelerated lifetime tests suggest robust barrier characteristics on timescales that approach 70 y, in layers that are sufficiently thin (less than 1 μm) to avoid significant compromises in mechanical flexibility or in electrical interface fidelity. Detailed studies of temperature- and thickness-dependent electrical and physical properties reveal the key characteristics. Molecular simulations highlight essential aspects of the chemistry that governs interactions between the SiO2 and surrounding water. Examples of use with passive and active components in high-performance flexible electronic devices suggest broad utility in advanced chronic implants. PMID:27791052

DNA hydrogel-based supercapacitors operating in physiological fluids

PubMed Central

Hur, Jaehyun; Im, Kyuhyun; Hwang, Sekyu; Choi, ByoungLyong; Kim, Sungjee; Hwang, Sungwoo; Park, Nokyoung; Kim, Kinam

2013-01-01

DNA nanostructures have been attractive due to their structural properties resulting in many important breakthroughs especially in controlled assemblies and many biological applications. Here, we report a unique energy storage device which is a supercapacitor that uses nanostructured DNA hydrogel (Dgel) as a template and layer-by-layer (LBL)-deposited polyelectrolyte multilayers (PEMs) as conductors. Our device, named as PEM-Dgel supercapacitor, showed excellent performance in direct contact with physiological fluids such as artificial urine and phosphate buffered saline without any need of additional electrolytes, and exhibited almost no cytotoxicity during cycling tests in cell culture medium. Moreover, we demonstrated that the PEM-Dgel supercapacitor has greater charge-discharge cycling stability in physiological fluids than highly concentrated acid electrolyte solution which is normally used for supercapacitor operation. These conceptually new supercapacitors have the potential to be a platform technology for the creation of implantable energy storage devices for packageless applications directly utilizing biofluids. PMID:23412432

Biocorrosion studies of TiO2 nanoparticle-coated Ti-6Al-4V implant in simulated biofluids

NASA Astrophysics Data System (ADS)

Zaveri, Nikita; McEwen, Gerald D.; Karpagavalli, Ramji; Zhou, Anhong

2010-06-01

The corrosion behaviors of the TiO2 nanoparticles coated bioimplant Ti-6Al-4V exposed to three different simulated biofluids (SBF), namely, (1) NaCl solution, (2) Hank's solution, and (3) Cigada solution, were studied by using micro-Raman spectroscopy, electrochemical techniques, and scanning electron microscopy (SEM) with energy dispersive X-ray spectroscopy (EDS). The different electrochemical impedance spectroscopy models were applied to fit the data obtained from the implants before and after the coating of TiO2 nanoparticles (50-100 nm). It was found that the TiO2 nanoparticle coatings increased the thickness of the pre-existing oxide layer on the Ti-6Al-4V surface, serving to improve the bioimplant corrosion resistance.

Metabolomic profiling of urine samples from mice exposed to protons reveals radiation quality and dose specific differences.

PubMed

Laiakis, Evagelia C; Trani, Daniela; Moon, Bo-Hyun; Strawn, Steven J; Fornace, Albert J

2015-04-01

As space travel is expanding to include private tourism and travel beyond low-Earth orbit, so is the risk of exposure to space radiation. Galactic cosmic rays and solar particle events have the potential to expose space travelers to significant doses of radiation that can lead to increased cancer risk and other adverse health consequences. Metabolomics has the potential to assess an individual's risk by exploring the metabolic perturbations in a biofluid or tissue. In this study, C57BL/6 mice were exposed to 0.5 and 2 Gy of 1 GeV/nucleon of protons and the levels of metabolites were evaluated in urine at 4 h after radiation exposure through liquid chromatography coupled to time-of-flight mass spectrometry. Significant differences were identified in metabolites that map to the tricarboxylic acid (TCA) cycle and fatty acid metabolism, suggesting that energy metabolism is severely impacted after exposure to protons. Additionally, various pathways of amino acid metabolism (tryptophan, tyrosine, arginine and proline and phenylalanine) were affected with potential implications for DNA damage repair and cognitive impairment. Finally, presence of products of purine and pyrimidine metabolism points to direct DNA damage or increased apoptosis. Comparison of these metabolomic data to previously published data from our laboratory with gamma radiation strongly suggests a more pronounced effect on metabolism with protons. This is the first metabolomics study with space radiation in an easily accessible biofluid such as urine that further investigates and exemplifies the biological differences at early time points after exposure to different radiation qualities.

Metabolomic Profiling of Urine Samples from Mice Exposed to Protons Reveals Radiation Quality and Dose Specific Differences

PubMed Central

Laiakis, Evagelia C.; Trani, Daniela; Moon, Bo-Hyun; Strawn, Steven J.; Fornace, Albert J.

2015-01-01

As space travel is expanding to include private tourism and travel beyond low-Earth orbit, so is the risk of exposure to space radiation. Galactic cosmic rays and solar particle events have the potential to expose space travelers to significant doses of radiation that can lead to increased cancer risk and other adverse health consequences. Metabolomics has the potential to assess an individual’s risk by exploring the metabolic perturbations in a biofluid or tissue. In this study, C57BL/6 mice were exposed to 0.5 and 2 Gy of 1 GeV/nucleon of protons and the levels of metabolites were evaluated in urine at 4 h after radiation exposure through liquid chromatography coupled to time-of-flight mass spectrometry. Significant differences were identified in metabolites that map to the tricarboxylic acid (TCA) cycle and fatty acid metabolism, suggesting that energy metabolism is severely impacted after exposure to protons. Additionally, various pathways of amino acid metabolism (tryptophan, tyrosine, arginine and proline and phenylalanine) were affected with potential implications for DNA damage repair and cognitive impairment. Finally, presence of products of purine and pyrimidine metabolism points to direct DNA damage or increased apoptosis. Comparison of these metabolomic data to previously published data from our laboratory with gamma radiation strongly suggests a more pronounced effect on metabolism with protons. This is the first metabolomics study with space radiation in an easily accessible biofluid such as urine that further investigates and exemplifies the biological differences at early time points after exposure to different radiation qualities. PMID:25768838

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.

Promising Metabolite Profiles in the Plasma and CSF of Early Clinical Parkinson's Disease

PubMed Central

Stoessel, Daniel; Schulte, Claudia; Teixeira dos Santos, Marcia C.; Scheller, Dieter; Rebollo-Mesa, Irene; Deuschle, Christian; Walther, Dirk; Schauer, Nicolas; Berg, Daniela; Nogueira da Costa, Andre; Maetzler, Walter

2018-01-01

Parkinson's disease (PD) shows high heterogeneity with regard to the underlying molecular pathogenesis involving multiple pathways and mechanisms. Diagnosis is still challenging and rests entirely on clinical features. Thus, there is an urgent need for robust diagnostic biofluid markers. Untargeted metabolomics allows establishing low-molecular compound biomarkers in a wide range of complex diseases by the measurement of various molecular classes in biofluids such as blood plasma, serum, and cerebrospinal fluid (CSF). Here, we applied untargeted high-resolution mass spectrometry to determine plasma and CSF metabolite profiles. We semiquantitatively determined small-molecule levels (≤1.5 kDa) in the plasma and CSF from early PD patients (disease duration 0–4 years; n = 80 and 40, respectively), and sex- and age-matched controls (n = 76 and 38, respectively). We performed statistical analyses utilizing partial least square and random forest analysis with a 70/30 training and testing split approach, leading to the identification of 20 promising plasma and 14 CSF metabolites. These metabolites differentiated the test set with an AUC of 0.8 (plasma) and 0.9 (CSF). Characteristics of the metabolites indicate perturbations in the glycerophospholipid, sphingolipid, and amino acid metabolism in PD, which underscores the high power of metabolomic approaches. Further studies will enable to develop a potential metabolite-based biomarker panel specific for PD. PMID:29556190

Potential oxidative stress biomarkers of mild cognitive impairment due to Alzheimer disease.

PubMed

García-Blanco, Ana; Baquero, Miguel; Vento, Máximo; Gil, Esperanza; Bataller, Luis; Cháfer-Pericás, Consuelo

2017-02-15

The high and increasing incidence of Alzheimer Disease (AD) worldwide is a major global concern. Classical diagnosis is carried out in the dementia phase, often in the moderate stages when treatment efficacy is limited. Nowadays, early diagnosis, even in pre-dementia stages, is possible in selected cases within an appropriate clinical setting, employing cerebral spinal fluid (CSF) sample analysis and neuroimaging procedures. In spite of the accurate diagnosis achieved by novel CSF biomarkers or positron emission tomography beta-amyloid tracers, these tests are invasive and expensive. Therefore, important work is being carried out to discover reliable biomarkers in peripheral biofluids (blood, plasma, urine) to be incorporated in clinical routine for early AD diagnosis. Although the nature of AD pathogenesis is complex, it is known that oxidative stress plays a key role, for which biomarkers are easily determined in peripheral biofluids. This review summarizes recent research on oxidative stress biomarkers in mild cognitive impairment due to AD. Among them, a promising research line is the study of the relationship between lipid peroxidation biomarkers and early AD clinical features. Results show a pronounced imbalance between scientific production and clinical reality due to the lack of clinical validation. We conclude that an important field in oxidative stress biomarkers could be developed with the aim to help clinicians in early disease diagnosis, effective treatment initiation and reliable disease monitoring. Copyright © 2017 Elsevier B.V. All rights reserved.

MicroRNAs as Biomarkers for Diagnosis, Prognosis and Theranostics in Prostate Cancer

PubMed Central

Bertoli, Gloria; Cava, Claudia; Castiglioni, Isabella

2016-01-01

Prostate cancer (PC) includes several phenotypes, from indolent to highly aggressive cancer. Actual diagnostic and prognostic tools have several limitations, and there is a need for new biomarkers to stratify patients and assign them optimal therapies by taking into account potential genetic and epigenetic differences. MicroRNAs (miRNAs) are small sequences of non-coding RNA regulating specific genes involved in the onset and development of PC. Stable miRNAs have been found in biofluids, such as serum and plasma; thus, the measurement of PC-associated miRNAs is emerging as a non-invasive tool for PC detection and monitoring. In this study, we conduct an in-depth literature review focusing on miRNAs that may contribute to the diagnosis and prognosis of PC. The role of miRNAs as a potential theranostic tool in PC is discussed. Using a meta-analysis approach, we found a group of 29 miRNAs with diagnostic properties and a group of seven miRNAs with prognostic properties, which were found already expressed in both biofluids and PC tissues. We tested the two miRNA groups on The Cancer Genome Atlas dataset of PC tissue samples with a machine-learning approach. Our results suggest that these 29 miRNAs should be considered as potential panel of biomarkers for the diagnosis of PC, both as in vivo non-invasive test and ex vivo confirmation test. PMID:27011184

Optimization study for metabolomics analysis of human sweat by liquid chromatography-tandem mass spectrometry in high resolution mode.

PubMed

Calderón-Santiago, M; Priego-Capote, F; Jurado-Gámez, B; Luque de Castro, M D

2014-03-14

Sweat has recently gained popularity as a potential tool for diagnostics and biomarker monitoring as it is a non-invasive biofluid the composition of which could be modified by certain pathologies, as is the case with cystic fibrosis, which increases chloride levels in sweat. The aim of the present study was to develop an analytical method for analysis of human sweat by liquid chromatography-mass spectrometry (LC-Q-TOF MS/MS) in high resolution mode. Thus, different sample preparation strategies and different chromatographic modes (HILIC and C18 reverse modes) were compared to check their effect on the profile of sweat metabolites. Forty-one compounds were identified by the MS/MS information obtained with a mass tolerance window below 4 ppm. Amino acids, dicarboxylic acids and other interesting metabolites such as inosine, choline, uric acid and tyramine were identified. Among the tested protocols, direct analysis after dilution was a suited option to obtain a representative snapshot of sweat metabolome. In addition, sample clean up by C18 SpinColumn SPE cartridges improved the sensitivity of most identified compounds and reduced the number of interferents. As most of the identified metabolites are involved in key biochemical pathways, this study opens new possibilities to the use of sweat as a source of metabolite biomarkers of specific disorders. Copyright © 2014 Elsevier B.V. All rights reserved.

Bio-accessibility and Risk of Exposure to Metals and SVOCs in Artificial Turf Field Fill Materials and Fibers

PubMed Central

Pavilonis, Brian T.; Weisel, Clifford P.; Buckley, Brian; Lioy, Paul J.

2014-01-01

To reduce maintenance costs, municipalities and schools are starting to replace natural grass fields with a new generation synthetic turf. Unlike Astro-Turf, which was first introduced in the 1960’s, synthetic field turf provides more cushioning to athletes. Part of this cushioning comes from materials like crumb rubber infill, which is manufactured from recycled tires and may contain a variety of chemicals. The goal of this study was to evaluate potential exposures from playing on artificial turf fields and associated risks to trace metals, semivolatile organic compounds (SVOCs), and polycyclic aromatic hydrocarbons (PAHs) by examining typical artificial turf fibers (n=8), different types of infill (n=8), and samples from actual fields (n=7). Three artificial biofluids were prepared which included: lung, sweat, and digestive fluids. Artificial biofluids were hypothesized to yield a more representative estimation of dose than the levels obtained from total extraction methods. PAHs were routinely below the limit of detection across all three biofluids precluding completion of a meaningful risk assessment. No SVOCs were identified at quantifiable levels in any extracts based on a match of their mass spectrum to compounds that are regulated in soil. The metals were measurable but at concentrations for which human health risk was estimated to be low. The study demonstrated that for the products and fields we tested, exposure to infill and artificial turf was generally considered de minimus, with the possible exception of lead for some fields and materials. PMID:23758133

Monitoring Healthy Metabolic Trajectories with Nutritional Metabonomics

PubMed Central

Collino, Sebastiano; Martin, François-Pierre J.; Kochhar, Sunil; Rezzi, Serge

2009-01-01

Metabonomics is a well established analytical approach for the analysis of physiological regulatory processes via the metabolic profiling of biofluids and tissues in living organisms. Its potential is fully exploited in the field of “nutrimetabonomics” that aims at assessing the metabolic effects of active ingredients and foods in individuals. Yet, one of the greatest challenges in nutrition research is to decipher the critical interactions between mammalian organisms and environmental factors, including the gut microbiota. “Nutrimetabonomics” is today foreseen as a powerful approach for future nutritional programs tailored at health maintenance and disease prevention. PMID:22253970

Potentials and capabilities of the Extracellular Vesicle (EV) Array.

PubMed

Jørgensen, Malene Møller; Bæk, Rikke; Varming, Kim

2015-01-01

Extracellular vesicles (EVs) and exosomes are difficult to enrich or purify from biofluids, hence quantification and phenotyping of these are tedious and inaccurate. The multiplexed, highly sensitive and high-throughput platform of the EV Array presented by Jørgensen et al., (J Extracell Vesicles, 2013; 2: 10) has been refined regarding the capabilities of the method for characterization and molecular profiling of EV surface markers. Here, we present an extended microarray platform to detect and phenotype plasma-derived EVs (optimized for exosomes) for up to 60 antigens without any enrichment or purification prior to analysis.

Ultrasensitive multiplex optical quantification of bacteria in large samples of biofluids

PubMed Central

Pazos-Perez, Nicolas; Pazos, Elena; Catala, Carme; Mir-Simon, Bernat; Gómez-de Pedro, Sara; Sagales, Juan; Villanueva, Carlos; Vila, Jordi; Soriano, Alex; García de Abajo, F. Javier; Alvarez-Puebla, Ramon A.

2016-01-01

Efficient treatments in bacterial infections require the fast and accurate recognition of pathogens, with concentrations as low as one per milliliter in the case of septicemia. Detecting and quantifying bacteria in such low concentrations is challenging and typically demands cultures of large samples of blood (~1 milliliter) extending over 24–72 hours. This delay seriously compromises the health of patients. Here we demonstrate a fast microorganism optical detection system for the exhaustive identification and quantification of pathogens in volumes of biofluids with clinical relevance (~1 milliliter) in minutes. We drive each type of bacteria to accumulate antibody functionalized SERS-labelled silver nanoparticles. Particle aggregation on the bacteria membranes renders dense arrays of inter-particle gaps in which the Raman signal is exponentially amplified by several orders of magnitude relative to the dispersed particles. This enables a multiplex identification of the microorganisms through the molecule-specific spectral fingerprints. PMID:27364357

Non-perturbative Quantification of Ionic Charge Transfer through Nm-Scale Protein Pores Using Graphene Microelectrodes

NASA Astrophysics Data System (ADS)

Ping, Jinglei; Johnson, A. T. Charlie; A. T. Charlie Johnson Team

Conventional electrical methods for detecting charge transfer through protein pores perturb the electrostatic condition of the solution and chemical reactivity of the pore, and are not suitable to be used for complex biofluids. We developed a non-perturbative methodology ( fW input power) for quantifying trans-pore electrical current and detecting the pore status (i.e., open vs. closes) via graphene microelectrodes. Ferritin was used as a model protein featuring a large interior compartment, well-separated from the exterior solution with discrete pores as charge commuting channels. The charge flowing through the ferritin pores transfers into the graphene microelectrode and is recorded by an electrometer. In this example, our methodology enables the quantification of an inorganic nanoparticle-protein nanopore interaction in complex biofluids. The authors acknowledge the support from the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under Grant Number W911NF1010093.

Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing.

PubMed

Li, Feng; Kaczor-Urbanowicz, Karolina Elżbieta; Sun, Jie; Majem, Blanca; Lo, Hsien-Chun; Kim, Yong; Koyano, Kikuye; Liu Rao, Shannon; Young Kang, So; Mi Kim, Su; Kim, Kyoung-Mee; Kim, Sung; Chia, David; Elashoff, David; Grogan, Tristan R; Xiao, Xinshu; Wong, David T W

2018-04-23

It was recently discovered that abundant and stable extracellular RNA (exRNA) species exist in bodily fluids. Saliva is an emerging biofluid for biomarker development for noninvasive detection and screening of local and systemic diseases. Use of RNA-Sequencing (RNA-Seq) to profile exRNA is rapidly growing; however, no single preparation and analysis protocol can be used for all biofluids. Specifically, RNA-Seq of saliva is particularly challenging owing to high abundance of bacterial contents and low abundance of salivary exRNA. Given the laborious procedures needed for RNA-Seq library construction, sequencing, data storage, and data analysis, saliva-specific and optimized protocols are essential. We compared different RNA isolation methods and library construction kits for long and small RNA sequencing. The role of ribosomal RNA (rRNA) depletion also was evaluated. The miRNeasy Micro Kit (Qiagen) showed the highest total RNA yield (70.8 ng/mL cell-free saliva) and best small RNA recovery, and the NEBNext library preparation kits resulted in the highest number of detected human genes [5649-6813 at 1 reads per kilobase RNA per million mapped (RPKM)] and small RNAs [482-696 microRNAs (miRNAs) and 190-214 other small RNAs]. The proportion of human RNA-Seq reads was much higher in rRNA-depleted saliva samples (41%) than in samples without rRNA depletion (14%). In addition, the transfer RNA (tRNA)-derived RNA fragments (tRFs), a novel class of small RNAs, were highly abundant in human saliva, specifically tRF-4 (4%) and tRF-5 (15.25%). Our results may help in selection of the best adapted methods of RNA isolation and small and long RNA library constructions for salivary exRNA studies. © 2018 American Association for Clinical Chemistry.

Semiconductor Microcavity Flow Spectroscopy of Intracellular Protein in Human Cells

NASA Astrophysics Data System (ADS)

Gourley, Paul; Cox, Jim; Hendricks, Judy; McDonald, Anthony; Copeland, Guild; Sasaki, Darryl; Skirboll, Steve; Curry, Mark

2001-03-01

The speed of light through a biofluid or biological cell is inversely related to the biomolecular concentration of proteins and other complex molecules that modify the refractive index at wavelengths accessible to semiconductor lasers. By placing a fluid or cell into a semiconductor microcavity laser, these decreases in light speed can be sensitively recorded in picoseconds as frequency red-shifts in the laser output spectrum. This biocavity laser equipped with microfluidics for transporting cells at high speed through the laser microcavity has shown potential for rapid analysis of biomolecular mass of normal and malignant human cells in their physiologic condition without time-consuming fixing, staining, or tagging. We have used biocavity laser spectroscopy to measure the optical properties of solutions of standard biomolecules (sugars, proteins, DNA, and ions) and human cells. The technique determines the frequency shift, relative to that of water, of spontaneous or stimulated emission from cavity filled with a biomolecular solution. The shift was also measured in human glioblastoma cells that had been sorted by conventional fluorescence-activated cell sorting according to protein content. The results show a direct correlation between protein measured by fluorescence and the frequency shift observed in the microcavity laser.

Bio-Fluid Dynamics in a Centimeter-Scale Diagnostics Incubator with Integrated Perfusion

NASA Astrophysics Data System (ADS)

Vukasinovic, J.; Cullen, D. K.; Glezer, A.; Laplaca, M. C.

2006-11-01

Growing demands for long-term incubation of biologically faithful, three-dimensional neuronal and other cultures during extended physiological studies require efficient perfusion platforms with functional vasculatures that mimic the in vivo condition in a thermally regulated environment. While thermostatically controlled incubation baths with capillary action perfusion are available, their use is confined to specific experimental conditions. The interstitial nutrient and gas delivery remains diffusion limited over the long term and cultures decay metabolically. To overcome these problems, we describe simple fabrication and experimental characterization of a compact, diagnostics incubator that allows in situ monitoring of culture activity with a superior control of critical biological functions using convectively enhanced heat and mass transport. To overcome intercellular diffusion barriers culture is exposed to a direct flow of media issuing from an array of micro-nozzles that are directed normal to the substrate upholding the culture, and further improved by 3-D convection induced by jet interactions and biased, peripheral perfusate extraction through an array of microchannels as demonstrated by microPIV measurements.

Plasma and serum from nonfasting men and women differ in their lipidomic profiles.

PubMed

Ishikawa, Masaki; Tajima, Yoko; Murayama, Mayumi; Senoo, Yuya; Maekawa, Keiko; Saito, Yoshiro

2013-01-01

Biomarkers will play important roles in disease diagnosis, drug development, and the proper use of drugs. Blood is considered the best biofluid for biomarker research because it is easy to access and a wealth of data are available. However, previous studies revealed that several ionic metabolites showed different levels (including presence or absence) in plasma and serum. Thus, attention should be paid to selecting the best biofluid for biomarker exploration. Many lipid molecules have biological significance and thus would be candidate biomarkers. However, no comprehensive study revealing differences in lipid metabolite levels between plasma and serum has been undertaken. Furthermore, gender differences have not been reported. To clarify the difference in the levels of lipid metabolites between human plasma and serum from both genders, we performed lipid metabolomic analysis using liquid chromatography-mass spectrometry-based systems for phospholipids (PLs), lysoPLs, sphingomyelins, ceramides and oxidative fatty acids. Our results revealed that most of the lipid metabolites were present at similar levels in plasma and serum and in males and females. However, several oxidative fatty acid metabolites showed differences. Of the metabolites related to clotting processes, three showed higher levels in serum than in plasma, and three were detected only in serum. Furthermore, four metabolites were present at different levels between males and females, and two were detected only in males. Thus, attention should be paid to the selection of plasma or serum when utilizing these lipid metabolites as biomarkers.

Principal component directed partial least squares analysis for combining nuclear magnetic resonance and mass spectrometry data in metabolomics: application to the detection of breast cancer.

PubMed

Gu, Haiwei; Pan, Zhengzheng; Xi, Bowei; Asiago, Vincent; Musselman, Brian; Raftery, Daniel

2011-02-07

Nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) are the two most commonly used analytical tools in metabolomics, and their complementary nature makes the combination particularly attractive. A combined analytical approach can improve the potential for providing reliable methods to detect metabolic profile alterations in biofluids or tissues caused by disease, toxicity, etc. In this paper, (1)H NMR spectroscopy and direct analysis in real time (DART)-MS were used for the metabolomics analysis of serum samples from breast cancer patients and healthy controls. Principal component analysis (PCA) of the NMR data showed that the first principal component (PC1) scores could be used to separate cancer from normal samples. However, no such obvious clustering could be observed in the PCA score plot of DART-MS data, even though DART-MS can provide a rich and informative metabolic profile. Using a modified multivariate statistical approach, the DART-MS data were then reevaluated by orthogonal signal correction (OSC) pretreated partial least squares (PLS), in which the Y matrix in the regression was set to the PC1 score values from the NMR data analysis. This approach, and a similar one using the first latent variable from PLS-DA of the NMR data resulted in a significant improvement of the separation between the disease samples and normals, and a metabolic profile related to breast cancer could be extracted from DART-MS. The new approach allows the disease classification to be expressed on a continuum as opposed to a binary scale and thus better represents the disease and healthy classifications. An improved metabolic profile obtained by combining MS and NMR by this approach may be useful to achieve more accurate disease detection and gain more insight regarding disease mechanisms and biology. Copyright © 2010 Elsevier B.V. All rights reserved.

MicroRNA Biomarkers of Toxicity in Biological Matrices

EPA Science Inventory

Biomarker measurements that reliably correlate with tissue injury and can be measured from sampling accessible biofluids offer enormous benefits in terms of cost, time, and convenience when assessing environmental and drug-induced toxicity in model systems or human cohorts. Micro...

METABOLOMICS FOR DEVELOPING MARKERS OF CHEMICAL EXPOSURE AND DISTINGUISHING TOXICITY PATHWAYS

EPA Science Inventory

Metabolomics involves the application of advanced analytical and statistical tools to profile changes in levels of endogenous metabolites in tissues and biofluids resulting from disease onset, stress, or chemical exposure. Nuclear Magnetic Resonance (NMR) spectroscopy-based meta...

METABOLOMICS AS A DIAGNOSTIC TOOL FOR SMALL FISH TOXICOLOGY RESEARCH

EPA Science Inventory

Metabolomics involves the application of advanced analytical and statistical tools to profile changes in levels of endogenous metabolites in tissues and biofluids resulting from disease onset or stress. While certain metabolites are being specifically targeted in these studies, w...

Microfluidic Sample Preparation for Diagnostic Cytopathology

PubMed Central

Mach, Albert J.; Adeyiga, Oladunni B.; Di Carlo, Dino

2014-01-01

The cellular components of body fluids are routinely analyzed to identify disease and treatment approaches. While significant focus has been placed on developing cell analysis technologies, tools to automate the preparation of cellular specimens have been more limited, especially for body fluids beyond blood. Preparation steps include separating, concentrating, and exposing cells to reagents. Sample preparation continues to be routinely performed off-chip by technicians, preventing cell-based point-of-care diagnostics, increasing the cost of tests, and reducing the consistency of the final analysis following multiple manually-performed steps. Here, we review the assortment of biofluids for which suspended cells are analyzed, along with their characteristics and diagnostic value. We present an overview of the conventional sample preparation processes for cytological diagnosis. We finally discuss the challenges and opportunities in developing microfluidic devices for the purpose of automating or miniaturizing these processes, with particular emphases on preparing large or small volume samples, working with samples of high cellularity, automating multi-step processes, and obtaining high purity subpopulations of cells. We hope to convey the importance of and help identify new research directions addressing the vast biological and clinical applications in preparing and analyzing the array of available biological fluids. Successfully addressing the challenges described in this review can lead to inexpensive systems to improve diagnostic accuracy while simultaneously reducing overall systemic healthcare costs. PMID:23380972

Metabolomics: Insulin Resistance and Type 2 Diabetes Mellitus

USDA-ARS?s Scientific Manuscript database

Type 2 diabetes mellitus (T2DM) develops over many years, providing an opportunity to consider early prognostic tools that guide interventions to thwart disease. Advancements in analytical chemistry enable quantitation of hundreds of metabolites in biofluids and tissues (metabolomics), providing in...

CHARACTERIZATION OF METABOLITES IN SMALL FISH BIOFLUIDS AND TISSUES BY NMR SPECTROSCOPY

EPA Science Inventory

Nuclear magnetic resonance (NMR) spectroscopy has been utilized for assessing ecotoxicity in small fish models by means of metabolomics. Two fundamental challenges of NMR-based metabolomics are the detection limit and characterization of metabolites (or NMR resonance assignments...

High-Throughput Quantitative Lipidomics Analysis of Nonesterified Fatty Acids in Plasma by LC-MS.

PubMed

Christinat, Nicolas; Morin-Rivron, Delphine; Masoodi, Mojgan

2017-01-01

Nonesterified fatty acids are important biological molecules which have multiple functions such as energy storage, gene regulation, or cell signaling. Comprehensive profiling of nonesterified fatty acids in biofluids can facilitate studying and understanding their roles in biological systems. For these reasons, we have developed and validated a high-throughput, nontargeted lipidomics method coupling liquid chromatography to high-resolution mass spectrometry for quantitative analysis of nonesterified fatty acids. Sufficient chromatographic separation is achieved to separate positional isomers such as polyunsaturated and branched-chain species and quantify a wide range of nonesterified fatty acids in human plasma samples. However, this method is not limited only to these fatty acid species and offers the possibility to perform untargeted screening of additional nonesterified fatty acid species.

Structural analysis of two different stent configurations.

PubMed

Simão, M; Ferreira, J M; Mora-Rodriguez, J; Ramos, H M

2017-06-01

Two different stent configurations (i.e. the well known Palmaz-Schatz (PS) and a new stent configuration) are mechanically investigated. A finite element model was used to study the two geometries under combining loads and a computational fluid dynamic model based on fluid structure interaction was developed investigating the plaque and the artery wall reactions in a stented arterial segment. These models determine the stress and displacement fields of the two stents under internal pressure conditions. Results suggested that stent designs cause alterations in vascular anatomy that adversely affect arterial stress distributions within the wall, which have impact in the vessel responses such as the restenosis. The hemodynamic analysis shows the use of new stent geometry suggests better biofluid mechanical response such as the deformation and the progressive amount of plaque growth.

Two-step activation of paper batteries for high power generation: design and fabrication of biofluid- and water-activated paper batteries

NASA Astrophysics Data System (ADS)

Lee, Ki Bang

2006-11-01

Two-step activation of paper batteries has been successfully demonstrated to provide quick activation and to supply high power to credit card-sized biosystems on a plastic chip. A stack of a magnesium layer (an anode), a fluid guide (absorbent paper), a highly doped filter paper with copper chloride (a cathode) and a copper layer as a current collector is laminated between two transparent plastic films into a high power biofluid- and water-activated battery. The battery is activated by two-step activation: (1) after placing a drop of biofluid/water-based solution on the fluid inlet, the surface tension first drives the fluid to soak the fluid guide; (2) the fluid in the fluid guide then penetrates into the heavily doped filter paper with copper chloride to start the battery reaction. The fabricated half credit card-sized battery was activated by saliva, urine and tap water and delivered a maximum voltage of 1.56 V within 10 s after activation and a maximum power of 15.6 mW. When 10 kΩ and 1 KΩ loads are used, the service time with water, urine and saliva is measured as more than 2 h. An in-series battery of 3 V has been successfully tested to power two LEDs (light emitting diodes) and an electric driving circuit. As such, this high power paper battery could be integrated with on-demand credit card-sized biosystems such as healthcare test kits, biochips, lab-on-a-chip, DNA chips, protein chips or even test chips for water quality checking or chemical checking.

Raman spectroscopy for medical diagnostics--From in-vitro biofluid assays to in-vivo cancer detection.

PubMed

Kong, Kenny; Kendall, Catherine; Stone, Nicholas; Notingher, Ioan

2015-07-15

Raman spectroscopy is an optical technique based on inelastic scattering of light by vibrating molecules and can provide chemical fingerprints of cells, tissues or biofluids. The high chemical specificity, minimal or lack of sample preparation and the ability to use advanced optical technologies in the visible or near-infrared spectral range (lasers, microscopes, fibre-optics) have recently led to an increase in medical diagnostic applications of Raman spectroscopy. The key hypothesis underpinning this field is that molecular changes in cells, tissues or biofluids, that are either the cause or the effect of diseases, can be detected and quantified by Raman spectroscopy. Furthermore, multivariate calibration and classification models based on Raman spectra can be developed on large "training" datasets and used subsequently on samples from new patients to obtain quantitative and objective diagnosis. Historically, spontaneous Raman spectroscopy has been known as a low signal technique requiring relatively long acquisition times. Nevertheless, new strategies have been developed recently to overcome these issues: non-linear optical effects and metallic nanoparticles can be used to enhance the Raman signals, optimised fibre-optic Raman probes can be used for real-time in-vivo single-point measurements, while multimodal integration with other optical techniques can guide the Raman measurements to increase the acquisition speed and spatial accuracy of diagnosis. These recent efforts have advanced Raman spectroscopy to the point where the diagnostic accuracy and speed are compatible with clinical use. This paper reviews the main Raman spectroscopy techniques used in medical diagnostics and provides an overview of various applications. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Single-Use Poly(etheretherketone) Solid-Phase Microextraction-Transmission Mode Devices for Rapid Screening and Quantitation of Drugs of Abuse in Oral Fluid and Urine via Direct Analysis in Real-Time Tandem Mass Spectrometry.

PubMed

Vasiljevic, Tijana; Gómez-Ríos, Germán Augusto; Pawliszyn, Janusz

2018-01-02

The analysis of oral fluid (OF) and urine samples to detect drug consumption has garnered considerable attention as alternative biomatrices. Efficient implementation of microextraction and ambient ionization technologies for rapid detection of target compounds in such biomatrices creates a need for biocompatible devices which can be implemented for in vivo sampling and easily interfaced with mass spectrometry (MS) analyzers. This study introduces a novel solid-phase microextraction-transmission mode (SPME-TM) device made of poly(etheretherketone) (PEEK) mesh that can rapidly detect prohibited substances in biofluids via direct analysis in real-time tandem MS (DART-MS/MS). PEEK mesh was selected due to its biocompatibility, excellent resistance to various organic solvents, and its ability to withstand relatively high temperatures (≤350 °C). The meshes were coated with hydrophilic-lipophilic-balance particle-poly(acrylonitrile) (HLB-PAN) slurry. The robustness of the coated meshes was tested by performing rapid vortex agitation (≥3200 rpm) in LC/MS-grade solvents and by exposing them to the DART source jet stream at typical operational temperatures (∼250-350 °C). PEEK SPME-TM devices proved to be robust and were therefore used to perform ex vivo analysis of drugs of abuse spiked in urine and OF samples. Excellent results were obtained for all analytes under study; furthermore, the tests yielded satisfactory limits of quantitation (median, ∼0.5 ng mL -1 ), linearity (≥0.99), and accuracy (80-120%) over the evaluated range (0.5-200 ng mL -1 ). This research highlights plastic SPME-TM's potential usefulness as a method for rapidly screening for prohibited substances in on-site/in vivo scenarios, such as roadside or workplace drug testing, antidoping controls, and pain management programs.

Detection of Radiation-Exposure Biomarkers by Differential Mobility Prefiltered Mass Spectrometry (DMS-MS)

PubMed Central

Coy, Stephen L.; Krylov, Evgeny V.; Schneider, Bradley B.; Covey, Thomas R.; Brenner, David J.; Tyburski, John B.; Patterson, Andrew D.; Krausz, Kris W.; Fornace, Albert J.; Nazarov, Erkinjon G.

2010-01-01

Technology to enable rapid screening for radiation exposure has been identified as an important need, and, as a part of a NIH / NIAD effort in this direction, metabolomic biomarkers for radiation exposure have been identified in a recent series of papers. To reduce the time necessary to detect and measure these biomarkers, differential mobility spectrometry – mass spectrometry (DMS-MS) systems have been developed and tested. Differential mobility ion filters preselect specific ions and also suppress chemical noise created in typical atmospheric-pressure ionization sources (ESI, MALDI, and others). Differential-mobility-based ion selection is based on the field dependence of ion mobility, which, in turn, depends on ion characteristics that include conformation, charge distribution, molecular polarizability, and other properties, and on the transport gas composition which can be modified to enhance resolution. DMS-MS is able to resolve small-molecule biomarkers from nearly-isobaric interferences, and suppresses chemical noise generated in the ion source and in the mass spectrometer, improving selectivity and quantitative accuracy. Our planar DMS design is rapid, operating in a few milliseconds, and analyzes ions before fragmentation. Depending on MS inlet conditions, DMS-selected ions can be dissociated in the MS inlet expansion, before mass analysis, providing a capability similar to MS/MS with simpler instrumentation. This report presents selected DMS-MS experimental results, including resolution of complex test mixtures of isobaric compounds, separation of charge states, separation of isobaric biomarkers (citrate and isocitrate), and separation of nearly-isobaric biomarker anions in direct analysis of a bio-fluid sample from the radiation-treated group of a mouse-model study. These uses of DMS combined with moderate resolution MS instrumentation indicate the feasibility of field-deployable instrumentation for biomarker evaluation. PMID:20305793

Plasmonic nanoparticles-decorated diatomite biosilica: extending the horizon of on-chip chromatography and label-free biosensing.

PubMed

Kong, Xianming; Li, Erwen; Squire, Kenny; Liu, Ye; Wu, Bo; Cheng, Li-Jing; Wang, Alan X

2017-11-01

Diatomite consists of fossilized remains of ancient diatoms and is a type of naturally abundant photonic crystal biosilica with multiple unique physical and chemical functionalities. In this paper, we explored the fluidic properties of diatomite as the matrix for on-chip chromatography and, simultaneously, the photonic crystal effects to enhance the plasmonic resonances of metallic nanoparticles for surface-enhanced Raman scattering (SERS) biosensing. The plasmonic nanoparticle-decorated diatomite biosilica provides a lab-on-a-chip capability to separate and detect small molecules from mixture samples with ultra-high detection sensitivity down to 1 ppm. We demonstrate the significant potential for biomedical applications by screening toxins in real biofluid, achieving simultaneous label-free biosensing of phenethylamine and miR21cDNA in human plasma with unprecedented sensitivity and specificity. To the best of our knowledge, this is the first time demonstration to detect target molecules from real biofluids by on-chip chromatography-SERS techniques. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sizing nanomaterials in bio-fluids by cFRAP enables protein aggregation measurements and diagnosis of bio-barrier permeability

NASA Astrophysics Data System (ADS)

Xiong, Ranhua; Vandenbroucke, Roosmarijn E.; Broos, Katleen; Brans, Toon; van Wonterghem, Elien; Libert, Claude; Demeester, Jo; de Smedt, Stefaan C.; Braeckmans, Kevin

2016-09-01

Sizing nanomaterials in complex biological fluids, such as blood, remains a great challenge in spite of its importance for a wide range of biomedical applications. In drug delivery, for instance, it is essential that aggregation of protein-based drugs is avoided as it may alter their efficacy or elicit immune responses. Similarly it is of interest to determine which size of molecules can pass through biological barriers in vivo to diagnose pathologies, such as sepsis. Here, we report on continuous fluorescence recovery after photobleaching (cFRAP) as a analytical method enabling size distribution measurements of nanomaterials (1-100 nm) in undiluted biological fluids. We demonstrate that cFRAP allows to measure protein aggregation in human serum and to determine the permeability of intestinal and vascular barriers in vivo. cFRAP is a new analytical technique that paves the way towards exciting new applications that benefit from nanomaterial sizing in bio-fluids.

Chiral metabonomics: 1H NMR-based enantiospecific differentiation of metabolites in human urine via direct cosolvation with β-cyclodextrin.

PubMed

Pérez-Trujillo, Míriam; Lindon, John C; Parella, Teodor; Keun, Hector C; Nicholson, Jeremy K; Athersuch, Toby J

2012-03-20

Differences in molecular chirality remain an important issue in drug metabolism and pharmacokinetics for the pharmaceutical industry and regulatory authorities, and chirality is an important feature of many endogenous metabolites. We present a method for the rapid, direct differentiation and identification of chiral drug enantiomers in human urine without pretreatment of any kind. Using the well-known anti-inflammatory chemical ibuprofen as one example, we demonstrate that the enantiomers of ibuprofen and the diastereoisomers of one of its main metabolites, the glucuronidated carboxylate derivative, can be resolved by (1)H NMR spectroscopy as a consequence of direct addition of the chiral cosolvating agent (CSA) β-cyclodextrin (βCD). This approach is simple, rapid, and robust, involves minimal sample manipulation, and does not require derivatization or purification of the sample. In addition, the method should allow the enantiodifferentiation of endogenous chiral metabolites, and this has potential value for differentiating metabolites from mammalian and microbial sources in biofluids. From these initial findings, we propose that more extensive and detailed enantiospecific metabolic profiling could be possible using CSA-NMR spectroscopy than has been previously reported.

Salivary hormone measurement using LC/MS/MS: specific and patient-friendly tool for assessment of endocrine function.

PubMed

Higashi, Tatsuya

2012-01-01

Saliva has recently been attracting attention as a patient-friendly available bio-fluid and an alternative to serum/plasma for hormone tests. LC coupled with atmospheric pressure ionization-MS/MS, especially electrospray ionization (ESI)-MS/MS, has been recently valued as a highly specific method in the analysis of salivary hormones. In this article, LC/ESI-MS/MS assays for salivary hormones are overviewed according to the papers that have been published during the last 5 years. Practical derivatization to enhance the detectabilities of hormones in ESI-MS/MS is also discussed, because a major disadvantage of using saliva is low hormone concentrations.

Blood-borne biomarkers and bioindicators for linking exposure to health effects in environmental health science.

PubMed

Wallace, M Ariel Geer; Kormos, Tzipporah M; Pleil, Joachim D

2016-01-01

Environmental health science aims to link environmental pollution sources to adverse health outcomes to develop effective exposure intervention strategies that reduce long-term disease risks. Over the past few decades, the public health community recognized that health risk is driven by interaction between the human genome and external environment. Now that the human genetic code has been sequenced, establishing this "G × E" (gene-environment) interaction requires a similar effort to decode the human exposome, which is the accumulation of an individual's environmental exposures and metabolic responses throughout the person's lifetime. The exposome is composed of endogenous and exogenous chemicals, many of which are measurable as biomarkers in blood, breath, and urine. Exposure to pollutants is assessed by analyzing biofluids for the pollutant itself or its metabolic products. New methods are being developed to use a subset of biomarkers, termed bioindicators, to demonstrate biological changes indicative of future adverse health effects. Typically, environmental biomarkers are assessed using noninvasive (excreted) media, such as breath and urine. Blood is often avoided for biomonitoring due to practical reasons such as medical personnel, infectious waste, or clinical setting, despite the fact that blood represents the central compartment that interacts with every living cell and is the most relevant biofluid for certain applications and analyses. The aims of this study were to (1) review the current use of blood samples in environmental health research, (2) briefly contrast blood with other biological media, and (3) propose additional applications for blood analysis in human exposure research.

Comprehensive Analysis of LC/MS Data Using Pseudocolor Plots

NASA Astrophysics Data System (ADS)

Crutchfield, Christopher A.; Olson, Matthew T.; Gourgari, Evgenia; Nesterova, Maria; Stratakis, Constantine A.; Yergey, Alfred L.

2013-02-01

We have developed new applications of the pseudocolor plot for the analysis of LC/MS data. These applications include spectral averaging, analysis of variance, differential comparison of spectra, and qualitative filtering by compound class. These applications have been motivated by the need to better understand LC/MS data generated from analysis of human biofluids. The examples presented use data generated to profile steroid hormones in urine extracts from a Cushing's disease patient relative to a healthy control, but are general to any discovery-based scanning mass spectrometry technique. In addition to new visualization techniques, we introduce a new metric of variance: the relative maximum difference from the mean. We also introduce the concept of substructure-dependent analysis of steroid hormones using precursor ion scans. These new analytical techniques provide an alternative approach to traditional untargeted metabolomics workflow. We present an approach to discovery using MS that essentially eliminates alignment or preprocessing of spectra. Moreover, we demonstrate the concept that untargeted metabolomics can be achieved using low mass resolution instrumentation.

CFD - Mature Technology?

NASA Technical Reports Server (NTRS)

Kwak, Dochan

2005-01-01

Over the past 30 years, numerical methods and simulation tools for fluid dynamic problems have advanced as a new discipline, namely, computational fluid dynamics (CFD). Although a wide spectrum of flow regimes are encountered in many areas of science and engineering, simulation of compressible flow has been the major driver for developing computational algorithms and tools. This is probably due to a large demand for predicting the aerodynamic performance characteristics of flight vehicles, such as commercial, military, and space vehicles. As flow analysis is required to be more accurate and computationally efficient for both commercial and mission-oriented applications (such as those encountered in meteorology, aerospace vehicle development, general fluid engineering and biofluid analysis) CFD tools for engineering become increasingly important for predicting safety, performance and cost. This paper presents the author's perspective on the maturity of CFD, especially from an aerospace engineering point of view.

Analysis of the extreme diversity of salivary alpha-amylase isoforms generated by physiological proteolysis using liquid chromatography-tandem mass spectrometry.

PubMed

Bailey, Ulla-Maja; Punyadeera, Chamindie; Cooper-White, Justin J; Schulz, Benjamin L

2012-12-12

Saliva is a crucial biofluid for oral health and is also of increasing importance as a non-invasive source of disease biomarkers. Salivary alpha-amylase is an abundant protein in saliva, and changes in amylase expression have been previously associated with a variety of diseases and conditions. Salivary alpha-amylase is subject to a high diversity of post-translational modifications, including physiological proteolysis in the oral cavity. Here we developed methodology for rapid sample preparation and non-targeted LC-ESI-MS/MS analysis of saliva from healthy subjects and observed an extreme diversity of alpha-amylase proteolytic isoforms. Our results emphasize the importance of consideration of post-translational events such as proteolysis in proteomic studies, biomarker discovery and validation, particularly in saliva. Copyright © 2012 Elsevier B.V. All rights reserved.

Thrombus Formation at High Shear Rates.

PubMed

Casa, Lauren D C; Ku, David N

2017-06-21

The final common pathway in myocardial infarction and ischemic stroke is occlusion of blood flow from a thrombus forming under high shear rates in arteries. A high-shear thrombus forms rapidly and is distinct from the slow formation of coagulation that occurs in stagnant blood. Thrombosis at high shear rates depends primarily on the long protein von Willebrand factor (vWF) and platelets, with hemodynamics playing an important role in each stage of thrombus formation, including vWF binding, platelet adhesion, platelet activation, and rapid thrombus growth. The prediction of high-shear thrombosis is a major area of biofluid mechanics in which point-of-care testing and computational modeling are promising future directions for clinically relevant research. Further research in this area will enable identification of patients at high risk for arterial thrombosis, improve prevention and treatment based on shear-dependent biological mechanisms, and improve blood-contacting device design to reduce thrombosis risk.

Development of rheological characterization and twin-screw extrusion/spiral winding processing methods for functionally-graded tissue engineering scaffolds and characterization of cell/biomaterial interactions

NASA Astrophysics Data System (ADS)

Ozkan, Seher

Tissue engineering involves the fabrication of biodegradable scaffolds, on which various types of cells are grown, to provide tissue constructs for tissue repair/regeneration. Native tissues have complex structures, with functions and properties changing spatially and temporally, and require special tailoring of tissue engineering scaffolds to allow mimicking of their complex elegance. The understanding of the rheological behavior of the biodegradable polymer and the thermo-mechanical history that the polymer experiences during processing is critical in fabricating scaffolds with appropriate microstructural distributions. This study has first focused on the rheological material functions of various gel-like fluids including biofluids and hydrogels, which can emulate the viscoelastic behavior of biofluids. Viscoplasticity and wall slip were recognized as key attributes of such systems. Furthermore, a new technology base involving twin-screw extrusion/spiral winding (TSESW) process was developed for the shaping of functionally-graded scaffolds. This novel scaffold fabrication technology was applied to the development of polycaprolactone (PCL) scaffolds, incorporated with tricalcium phosphate nanoparticles and various porogens in graded fashion. The protein encapsulation and controlled release capabilities of the TSESW process was also demonstrated by dispersing bovine serum albumin (BSA) protein into the PCL matrix. Effects of processing conditions and porosity distributions on compressive properties, surface topography, encapsulation efficiency, release profiles and the secondary structure of BSA were investigated. The PCL scaffolds were determined to be biocompatible, with the proliferation rates of human fetal osteoblast cells (hFOB) increasing with increasing porosity and decreasing concentration of TCP. BSA proteins were determined to be denatured to a greater extent with melt extrusion in the 80-100°C range (in comparison to wet extrusion using organic solvents). Finally, the surface topographies of melt processed poly(L-lactic acid) (ranging from nanoindentations to spherulitic protrusions) were determined to affect the orientation directions of fibroblast and osteoblast-like cells and the spherulitic surfaces giving rise to reduced proliferation rates of fibroblasts.

Combining random forest and 2D correlation analysis to identify serum spectral signatures for neuro-oncology.

PubMed

Smith, Benjamin R; Ashton, Katherine M; Brodbelt, Andrew; Dawson, Timothy; Jenkinson, Michael D; Hunt, Neil T; Palmer, David S; Baker, Matthew J

2016-06-07

Fourier transform infrared (FTIR) spectroscopy has long been established as an analytical technique for the measurement of vibrational modes of molecular systems. More recently, FTIR has been used for the analysis of biofluids with the aim of becoming a tool to aid diagnosis. For the clinician, this represents a convenient, fast, non-subjective option for the study of biofluids and the diagnosis of disease states. The patient also benefits from this method, as the procedure for the collection of serum is much less invasive and stressful than traditional biopsy. This is especially true of patients in whom brain cancer is suspected. A brain biopsy is very unpleasant for the patient, potentially dangerous and can occasionally be inconclusive. We therefore present a method for the diagnosis of brain cancer from serum samples using FTIR and machine learning techniques. The scope of the study involved 433 patients from whom were collected 9 spectra each in the range 600-4000 cm(-1). To begin the development of the novel method, various pre-processing steps were investigated and ranked in terms of final accuracy of the diagnosis. Random forest machine learning was utilised as a classifier to separate patients into cancer or non-cancer categories based upon the intensities of wavenumbers present in their spectra. Generalised 2D correlational analysis was then employed to further augment the machine learning, and also to establish spectral features important for the distinction between cancer and non-cancer serum samples. Using these methods, sensitivities of up to 92.8% and specificities of up to 91.5% were possible. Furthermore, ratiometrics were also investigated in order to establish any correlations present in the dataset. We show a rapid, computationally light, accurate, statistically robust methodology for the identification of spectral features present in differing disease states. With current advances in IR technology, such as the development of rapid discrete frequency collection, this approach is of importance to enable future clinical translation and enables IR to achieve its potential.

Urine-based Metabolomics with Fish: Use of Repeat Sampling (of an individual) to Non-lethally Assess Temporal Effects of Contaminants

EPA Science Inventory

Environmental metabolomics is a rapidly developing field for assessing the global metabolite profiles of tissues and/or biofluids from ecologically relevant organisms to identify biomarkers of exposure to various stressors, elucidate a chemical’s mode(s)-of-action, and decipher t...

Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications.

PubMed

Jimenez, Connie R; Verheul, Henk M W

2014-01-01

Proteomics is optimally suited to bridge the gap between genomic information on the one hand and biologic functions and disease phenotypes at the other, since it studies the expression and/or post-translational modification (especially phosphorylation) of proteins--the major cellular players bringing about cellular functions--at a global level in biologic specimens. Mass spectrometry technology and (bio)informatic tools have matured to the extent that they can provide high-throughput, comprehensive, and quantitative protein inventories of cells, tissues, and biofluids in clinical samples at low level. In this article, we focus on next-generation proteomics employing nanoliquid chromatography coupled to high-resolution tandem mass spectrometry for in-depth (phospho)protein profiling of tumor tissues and (proximal) biofluids, with a focus on studies employing clinical material. In addition, we highlight emerging proteogenomic approaches for the identification of tumor-specific protein variants, and targeted multiplex mass spectrometry strategies for large-scale biomarker validation. Below we provide a discussion of recent progress, some research highlights, and challenges that remain for clinical translation of proteomic discoveries.

Development of an enrichment method for endogenous phosphopeptide characterization in human serum.

PubMed

La Barbera, Giorgia; Capriotti, Anna Laura; Cavaliere, Chiara; Ferraris, Francesca; Laus, Michele; Piovesana, Susy; Sparnacci, Katia; Laganà, Aldo

2018-01-01

The work describes the development of an enrichment method for the analysis of endogenous phosphopeptides in serum. Endogenous peptides can play significant biological roles, and some of them could be exploited as future biomarkers. In this context, blood is one of the most useful biofluids for screening, but a systematic investigation of the endogenous peptides, especially phosphorylated ones, is still lacking, mainly due to the lack of suitable analytical methods. Thus, in this paper, different phosphopeptide enrichment strategies were pursued, based either on metal oxide affinity chromatography (MOAC, in the form of commercial TiO 2 spin columns or magnetic graphitized carbon black-TiO 2 composite), or on immobilized metal ion affinity chromatography (IMAC, in the form of Ti 4+ -IMAC magnetic material or commercial Fe 3+ -IMAC spin columns). While MOAC strategies proved completely unsuccessful, probably due to interfering phospholipids displacing phosphopeptides, the IMAC materials performed very well. Different sample preparation strategies were tested, comprising direct dilution with the loading buffer, organic solvent precipitation, and lipid removal from the matrix, as well as the addition of phosphatase inhibitors during sample handling for maximized endogenous phosphopeptide enrichment. All data were acquired by a shotgun peptidomics approach, in which peptide samples were separated by reversed-phase nanoHPLC hyphenated with high-resolution tandem mass spectrometry. The devised method allowed the identification of 176 endogenous phosphopeptides in fresh serum added with inhibitors by the direct dilution protocol and the Ti 4+ -IMAC magnetic material enrichment, but good results could also be obtained from the commercial Fe 3+ -IMAC spin column adapted to the batch enrichment protocol.

Nano-plasmonic exosome diagnostics

PubMed Central

Im, Hyungsoon; Shao, Huilin; Weissleder, Ralph; Castro, Cesar M.; Lee, Hakho

2015-01-01

Exosomes have emerged as a promising biomarker. These vesicles abound in biofluids and harbor molecular constituents from their parent cells, thereby offering a minimally-invasive avenue for molecular analyses. Despite such clinical potential, routine exosomal analysis, particularly the protein assay, remains challenging, due to requirements for large sample volumes and extensive processing. We have been developing miniaturized systems to facilitate clinical exosome studies. These systems can be categorized into two components: microfluidics for sample preparation and analytical tools for protein analyses. In this report, we review a new assay platform, nano-plasmonic exosome (nPLEX), in which sensing is based on surface plasmon resonance to achieve label-free exosome detection. Looking forward, we also discuss some potential challenges and improvements in exosome studies. PMID:25936957

Feasibility study of mid-infrared absorption spectroscopy using electrospray ionization

NASA Astrophysics Data System (ADS)

Ahmed, Tahsin; Foster, Erick; Bohn, Paul; Howard, Scott

2016-09-01

Precise detection of trace amount of molecules, such as the disease biomarkers present in biofluids or explosive residues, requires high sensitivity detection. electrospray ionization-mass spectrometry (ESI-MS) is a common and effective technique for sensitive trace molecular detection in small-volume liquid samples. In ESI-MS, nano-liter volume samples are ionized and aerosolized by ESI, and fed into MS for mass analysis. ESI-MS has proven to be a reliable ionization technique for coupling liquid phase separations like liquid chromatography (LC) and capillary zone electrophoresis (CE) with the highly specific resolving power of MS. While CE and ESI can be performed on a microfluidic chip having a footprint of a few cm2, MS is typically at least 100 times bigger in size than a micro-chip. A reduced size, weight, and power profile would enable semi-portable applications in forensics, environmental monitoring, defense, and biological/pharmaceutical applications. To achieve this goal, we present an initial study evaluating the use of mid-infrared absorption spectroscopy (MIRAS) in place of MS to create a ESI-MIRAS system. To establish feasibility, we perform ESI-MIRAS on phospholipid samples, which have been previously demonstrated to be separable by CE. Phospholipids are biomarkers of degenerative neurological, kidney, and bone diseases and can be found in biofluids such as blood, urine and cerebrospinal fluid. To establish sensitivity limits, calibration samples of 100 μM concentration are electrospray deposited on to a grounded Si wafer for different times (1 minutes to 4 minutes with a 1 minute step). The minimum detectable concentration-time product, where a FTIR globar is used as the MIR source, is found 200 μM·s.

Maternal and fetal metabonomic alterations in prenatal nicotine exposure-induced rat intrauterine growth retardation.

PubMed

Feng, Jiang-hua; Yan, You-e; Liang, Gai; Liu, Yan-song; Li, Xiao-jun; Zhang, Ben-jian; Chen, Liao-bin; Yu, Hong; He, Xiao-hua; Wang, Hui

2014-08-25

Prenatal nicotine exposure causes adverse birth outcome. However, the corresponding metabonomic alterations and underlying mechanisms of nicotine-induced developmental toxicity remain unclear. The aims of this study were to characterize the metabolic alterations in biofluids in nicotine-induced intrauterine growth retardation (IUGR) rat model. In the present study, pregnant Wistar rats were intragastrically administered with different doses of nicotine (0.5, 1.0 and 2.0 mg/kg d) from gestational day (GD) 11-20. The metabolic profiles of the biofluids, including maternal plasma, fetal plasma and amniotic fluid, were analyzed using (1)H nuclear magnetic resonance (NMR)-based metabonomic techniques. Prenatal nicotine exposure caused noticeably lower body weights, higher IUGR rates of fetal rats, and elevated maternal and fetal corticosterone (CORT) levels compared to the controls. The correlation analysis among maternal, fetal serum CORT levels and fetal bodyweight suggested that the levels of maternal and fetal serum CORT presented a positive correlation (r=0.356, n=32, P<0.05), while there was a negative correlation between fetal (r=-0.639, n=32, P<0.01) and maternal (r=-0.530, n=32, P<0.01) serum CORT level and fetal bodyweight. The fetal metabonome alterations included the stimulation of lipogenesis and the decreased levels of glucose and amino acids. The maternal metabonome alterations involved the enhanced blood glucose levels, fatty acid oxygenolysis, proteolysis and amino acid accumulation. These results suggested that prenatal nicotine exposure is associated with an altered maternal and fetal metabonome, which may be related to maternal increased glucocorticoid level induced by nicotine. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid.

PubMed

Hyung, Seok-Won; Piehowski, Paul D; Moore, Ronald J; Orton, Daniel J; Schepmoes, Athena A; Clauss, Therese R; Chu, Rosalie K; Fillmore, Thomas L; Brewer, Heather; Liu, Tao; Zhao, Rui; Smith, Richard D

2014-11-01

Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 μL) due to low yields stemming from losses caused by nonspecific binding to the column matrix and concentration of large eluent volumes. Additionally, the cost of the depletion media can be prohibitive for larger-scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large-scale studies. We characterized the performance of a 346 μL column volume microscale depletion system, using four different flow rates to determine the most effective depletion conditions for ∼6-μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10-mL depletion column served as the control. Results showed depletion efficiency of the microscale column increased as flow rate decreased, and that our microdepletion was reproducible. In an initial application, a 600-μL sample of human cerebrospinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.

Rapid analysis of bile acids in different biological matrices using LC-ESI-MS/MS for the investigation of bile acid transformation by mammalian gut bacteria.

PubMed

Wegner, Katrin; Just, Sarah; Gau, Laura; Mueller, Henrike; Gérard, Philippe; Lepage, Patricia; Clavel, Thomas; Rohn, Sascha

2017-02-01

Bile acids are important signaling molecules that regulate cholesterol, glucose, and energy homoeostasis and have thus been implicated in the development of metabolic disorders. Their bioavailability is strongly modulated by the gut microbiota, which contributes to generation of complex individual-specific bile acid profiles. Hence, it is important to have accurate methods at hand for precise measurement of these important metabolites. Here, a rapid and sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous identification and quantitation of primary and secondary bile acids as well as their taurine and glycine conjugates was developed and validated. Applicability of the method was demonstrated for mammalian tissues, biofluids, and cell culture media. The analytical approach mainly consists of a simple and rapid liquid-liquid extraction procedure in presence of deuterium-labeled internal standards. Baseline separation of all isobaric bile acid species was achieved and a linear correlation over a broad concentration range was observed. The method showed acceptable accuracy and precision on intra-day (1.42-11.07 %) and inter-day (2.11-12.71 %) analyses and achieved good recovery rates for representative analytes (83.7-107.1 %). As a proof of concept, the analytical method was applied to mouse tissues and biofluids, but especially to samples from in vitro fermentations with gut bacteria of the family Coriobacteriaceae. The developed method revealed that the species Eggerthella lenta and Collinsella aerofaciens possess bile salt hydrolase activity, and for the first time that the species Enterorhabdus mucosicola is able to deconjugate and dehydrogenate primary bile acids in vitro.

Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: Analysis of human plasma and cerebrospinal fluid

DOE PAGES

Hyung, Seok Won; Piehowski, Paul D.; Moore, Ronald J.; ...

2014-09-06

Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 µL) due to low yields stemming from losses caused by nonspecific binding to the column matrix. Additionally, the cost of the depletion media can be prohibitive for larger scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizingmore » sample recovery when samples are limited, as well as for reducing the expense of large scale studies. We characterized the performance of a 346 µL column volume micro-scale depletion system, using four different flow rates to determine the most effective depletion conditions for ~6 μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10 mL depletion column served as the control. Results showed depletion efficiency of the micro-scale column increased as flow rate decreased, and that our micro-depletion was reproducible. We found, in an initial application, a 600 µL sample of human cerebral spinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.« less

Rapid, Automated, and Specific Immunoassay to Directly Measure Matrix Metalloproteinase-9–Tissue Inhibitor of Metalloproteinase-1 Interactions in Human Plasma Using AlphaLISA Technology: A New Alternative to Classical ELISA

PubMed Central

Pulido-Olmo, Helena; Rodríguez-Sánchez, Elena; Navarro-García, José Alberto; Barderas, María G.; Álvarez-Llamas, Gloria; Segura, Julián; Fernández-Alfonso, Marisol; Ruilope, Luis M.; Ruiz-Hurtado, Gema

2017-01-01

The protocol describes a novel, rapid, and no-wash one-step immunoassay for highly sensitive and direct detection of the complexes between matrix metalloproteinases (MMPs) and their tissue inhibitor of metalloproteinases (TIMPs) based on AlphaLISA® technology. We describe two procedures: (i) one approach is used to analyze MMP-9–TIMP-1 interactions using recombinant human MMP-9 with its corresponding recombinant human TIMP-1 inhibitor and (ii) the second approach is used to analyze native or endogenous MMP-9–TIMP-1 protein interactions in samples of human plasma. Evaluating native MMP-9–TIMP-1 complexes using this approach avoids the use of indirect calculations of the MMP-9/TIMP-1 ratio for which independent MMP-9 and TIMP-1 quantifications by two conventional ELISAs are needed. The MMP-9–TIMP-1 AlphaLISA® assay is quick, highly simplified, and cost-effective and can be completed in less than 3 h. Moreover, the assay has great potential for use in basic and preclinical research as it allows direct determination of native MMP-9–TIMP-1 complexes in circulating blood as biofluid. PMID:28791014

Plasma metabolic profiling analysis of nephrotoxicity induced by acyclovir using metabonomics coupled with multivariate data analysis.

PubMed

Zhang, Xiuxiu; Li, Yubo; Zhou, Huifang; Fan, Simiao; Zhang, Zhenzhu; Wang, Lei; Zhang, Yanjun

2014-08-01

Acyclovir (ACV) is an antiviral agent. However, its use is limited by adverse side effect, particularly by its nephrotoxicity. Metabonomics technology can provide essential information on the metabolic profiles of biofluids and organs upon drug administration. Therefore, in this study, mass spectrometry-based metabonomics coupled with multivariate data analysis was used to identify the plasma metabolites and metabolic pathways related to nephrotoxicity caused by intraperitoneal injection of low (50mg/kg) and high (100mg/kg) doses of acyclovir. Sixteen biomarkers were identified by metabonomics and nephrotoxicity results revealed the dose-dependent effect of acyclovir on kidney tissues. The present study showed that the top four metabolic pathways interrupted by acyclovir included the metabolisms of arachidonic acid, tryptophan, arginine and proline, and glycerophospholipid. This research proves the established metabonomic approach can provide information on changes in metabolites and metabolic pathways, which can be applied to in-depth research on the mechanism of acyclovir-induced kidney injury. Copyright © 2014 Elsevier B.V. All rights reserved.

Tracking fetal development through molecular analysis of maternal biofluids☆

PubMed Central

Edlow, Andrea G.; Bianchi, Diana W.

2015-01-01

Current monitoring of fetal development includes fetal ultrasonography, chorionic villus sampling or amniocentesis for chromosome analysis, and maternal serum biochemical screening for analytes associated with aneuploidy and open neural tube defects. Over the last 15 years, significant advances in noninvasive prenatal diagnosis (NIPD) via cell-free fetal (cff) nucleic acids in maternal plasma have resulted in the ability to determine fetal sex, RhD genotype, and aneuploidy. Cff nucleic acids in the maternal circulation originate primarily from the placenta. This contrasts with cff nucleic acids in amniotic fluid, which derive from the fetus, and are present in significantly higher concentrations than in maternal blood. The fetal origin of cff nucleic acids in the amniotic fluid permits the acquisition of real-time information about fetal development and gene expression. This review seeks to provide a comprehensive summary of the molecular analysis of cff nucleic acids in maternal biofluids to elucidate mechanisms of fetal development, physiology, and pathology. This article is part of a Special Issue entitled: Molecular Genetics of Human Reproductive Failure. PMID:22542507

Modelling short time series in metabolomics: a functional data analysis approach.

PubMed

Montana, Giovanni; Berk, Maurice; Ebbels, Tim

2011-01-01

Metabolomics is the study of the complement of small molecule metabolites in cells, biofluids and tissues. Many metabolomic experiments are designed to compare changes observed over time under two or more experimental conditions (e.g. a control and drug-treated group), thus producing time course data. Models from traditional time series analysis are often unsuitable because, by design, only very few time points are available and there are a high number of missing values. We propose a functional data analysis approach for modelling short time series arising in metabolomic studies which overcomes these obstacles. Our model assumes that each observed time series is a smooth random curve, and we propose a statistical approach for inferring this curve from repeated measurements taken on the experimental units. A test statistic for detecting differences between temporal profiles associated with two experimental conditions is then presented. The methodology has been applied to NMR spectroscopy data collected in a pre-clinical toxicology study.

High wavenumber Raman spectroscopic characterization of normal and oral cancer using blood plasma

NASA Astrophysics Data System (ADS)

Pachaiappan, Rekha; Prakasarao, Aruna; Suresh Kumar, Murugesan; Singaravelu, Ganesan

2017-02-01

Blood plasma possesses the biomolecules released from cells/tissues after metabolism and reflects the pathological conditions of the subjects. The analysis of biofluids for disease diagnosis becomes very attractive in the diagnosis of cancers due to the ease in the collection of samples, easy to transport, multiple sampling for regular screening of the disease and being less invasive to the patients. Hence, the intention of this study was to apply near-infrared (NIR) Raman spectroscopy in the high wavenumber (HW) region (2500-3400 cm-1) for the diagnosis of oral malignancy using blood plasma. From the Raman spectra it is observed that the biomolecules protein and lipid played a major role in the discrimination between groups. The diagnostic algorithms based on principal components analysis coupled with linear discriminant analysis (PCA-LDA) with the leave-one-patient-out cross-validation method on HW Raman spectra yielded a promising results in the identification of oral malignancy. The details of results will be discussed.

The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification

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

Wang, Hui; Shi, Tujin; Qian, Wei-Jun

2015-12-04

Mass spectrometry-based proteomics has become an indispensable tool in biomedical research with broad applications ranging from fundamental biology, systems biology, and biomarker discovery. Recent advances in LC-MS have made it become a major technology in clinical applications, especially in cancer biomarker discovery and verification. To overcome the challenges associated with the analysis of clinical samples, such as extremely wide dynamic range of protein concentrations in biofluids and the need to perform high throughput and accurate quantification, significant efforts have been devoted to improve the overall performance of LC-MS bases clinical proteomics. In this review, we summarize the recent advances inmore » LC-MS in the aspect of cancer biomarker discovery and quantification, and discuss its potentials, limitations, and future perspectives.« less

A Metabolomic Perspective on Coeliac Disease

PubMed Central

Calabrò, Antonio

2014-01-01

Metabolomics is an “omic” science that is now emerging with the purpose of elaborating a comprehensive analysis of the metabolome, which is the complete set of metabolites (i.e., small molecules intermediates) in an organism, tissue, cell, or biofluid. In the past decade, metabolomics has already proved to be useful for the characterization of several pathological conditions and offers promises as a clinical tool. A metabolomics investigation of coeliac disease (CD) revealed that a metabolic fingerprint for CD can be defined, which accounts for three different but complementary components: malabsorption, energy metabolism, and alterations in gut microflora and/or intestinal permeability. In this review, we will discuss the major advancements in metabolomics of CD, in particular with respect to the role of gut microbiome and energy metabolism. PMID:24665364

Transport of magneto-nanoparticles during electro-osmotic flow in a micro-tube in the presence of magnetic field for drug delivery application

NASA Astrophysics Data System (ADS)

Mondal, A.; Shit, G. C.

2017-11-01

In this paper, we have examined the motion of magnetic-nanoparticles and the flow characteristics of biofluid in a micro-tube in the presence of externally applied magnetic field and electrokinetic effects. In the drug delivery system, the motion of the magnetic nanoparticles as carriers is important for therapeutic procedure in the treatment of tumor cells, infections and removing blood clots. The unidirectional electro-osmotic flow of biofluid is driven by the combined effects of pulsatile pressure gradient and electrokinetic force. The governing equation for unsteady electromagnetohydrodynamic flow subject to the no-slip boundary condition has been solved numerically by using Crank-Nicolson implicit finite difference scheme. We have analyzed the variation of axial velocity, velocity distribution of magnetic nanoparticles, volumetric flow rate and wall shear stress for various values of the non-dimensional parameters. The study reveals that blood flow velocity, carriers velocity and flow rate are strongly influenced by the electro-osmotic parameter as well as the Hartmann number. The particle mass parameter as well as the particle concentration parameter have efficient capturing effect on magnetic nanoparticles during blood flow through a micro-tube for drug delivery.

Drug-conjugated polymers as gene carriers for synergistic therapeutic effect.

PubMed

Pofali, P A; Singh, B; Dandekar, P; Jain, R D; Maharjan, S; Choi, Y J; Arote, R B; Cho, C S

2016-05-01

The ability to safely and effectively transfer gene into cells is the fundamental goal of gene delivery. In spite of the best efforts of researchers around the world, gene therapy has limited success. This may be because of several limitations of delivering gene which is one of the greatest technical challenges in the modern medicine. To address these issues, many efforts have been made to bind drugs and genes together by polymers for co-delivery to achieve synergistic effect. Usually, binding interaction of drugs with polymers is either physical or chemical. In case of drug-polymer physical interaction, the efficiency of drugs generally decreases because of separation of drugs from polymers in vivo whenever it comes in contact with charged biofluid/s or cells. While chemical interaction of drug-polymer overcomes the aforementioned obstacle, several problems such as steric hindrance, solubility, and biodegradability hinder it to develop as gene carrier. Considering these benefits and pitfalls, the objective of this review is to discuss the possible extent of drug-conjugated polymers as safe and efficient gene delivery carriers for achieving synergistic effect to combat various genetic disorders. © 2015 Wiley Periodicals, Inc.

Gold nanoparticle flow sensors designed for dynamic X-ray imaging in biofluids.

PubMed

Ahn, Sungsook; Jung, Sung Yong; Lee, Jin Pyung; Kim, Hae Koo; Lee, Sang Joon

2010-07-27

X-ray-based imaging is one of the most powerful and convenient methods in terms of versatility in applicable energy and high performance in use. Different from conventional nuclear medicine imaging, contrast agents are required in X-ray imaging especially for effectively targeted and molecularly specific functions. Here, in contrast to much reported static accumulation of the contrast agents in targeted organs, dynamic visualization in a living organism is successfully accomplished by the particle-traced X-ray imaging for the first time. Flow phenomena across perforated end walls of xylem vessels in rice are monitored by a gold nanoparticle (AuNP) (approximately 20 nm in diameter) as a flow tracing sensor working in nontransparent biofluids. AuNPs are surface-modified to control the hydrodynamic properties such as hydrodynamic size (DH), zeta-potential, and surface plasmonic properties in aqueous conditions. Transmission electron microscopy (TEM), scanning electron microscopy (SEM), X-ray nanoscopy (XN), and X-ray microscopy (XM) are used to correlate the interparticle interactions with X-ray absorption ability. Cluster formation and X-ray contrast ability of the AuNPs are successfully modulated by controlling the interparticle interactions evaluated as flow-tracing sensors.

Liquid Biopsies in the Screening of Oncogenic Mutations in NSCLC and its Application in Targeted Therapy.

PubMed

Tang, Jason H; Chia, David

2015-01-01

Non-small cell lung cancer (NSCLC) still dominates cancer-related deaths in America. Despite this, new discoveries and advancements in technology are helping with the detection and treatment of NSCLC. The discovery of circulating tumor DNA in blood and other biofluids is essential for the creation of a DNA biomarker. Limitations in technology and sequencing have stunted assay development, but with recent advancements in the next-generation sequencing, droplet digital PCR, and EFIRM, the detection of mutations in biofluids has become possible with reasonable sensitivity and specificity. These methods have been applied to the detection of mutations in NSCLC by measuring the levels of circulating tumor DNA. ALK fusion genes along with mutations in EGFR and KRAS have been shown to correlate to tumor size and metastasis. These methods allow for noninvasive, affordable, and efficient diagnoses of oncogenic mutations that overcome the issues of traditional biopsies. These issues include tumor heterogeneity and early detection of cancers with asymptomatic early stages. Early detection and treatment remain the best way to ensure survival. This review aims to describe these new technologies along with their application in mutation detection in NSCLC in order to proactively utilize targeted anticancer therapy.

Liquid biopsy for detection of actionable oncogenic mutations in human cancers and electric field induced release and measurement liquid biopsy (eLB).

PubMed

Tu, Michael; Chia, David; Wei, Fang; Wong, David

2016-01-21

Oncogenic activations by mutations in key cancer genes such as EGFR and KRAS are frequently associated with human cancers. Molecular targeting of specific oncogenic mutations in human cancer is a major therapeutic inroad for anti-cancer drug therapy. In addition, progressive developments of oncogene mutations lead to drug resistance. Therefore, the ability to detect and continuously monitor key actionable oncogenic mutations is important to guide the use of targeted molecular therapies to improve long-term clinical outcomes in cancer patients. Current oncogenic mutation detection is based on direct sampling of cancer tissue by surgical resection or biopsy. Oncogenic mutations were recently shown to be detectable in circulating bodily fluids of cancer patients. This field of investigation, termed liquid biopsy, permits a less invasive means of assessing the oncogenic mutation profile of a patient. This paper will review the analytical strategies used to assess oncogenic mutations from biofluid samples. Clinical applications will also be discussed.

Liquid Biopsy for Detection of Actionable Oncogenic Mutations in Human Cancers and Electric Field Induced Release and Measurement Liquid Biopsy (eLB)

PubMed Central

Tu, Michael; Chia, David; Wei, Fang; Wong, David

2015-01-01

Oncogenic activations by mutations in key cancer genes such as EGFR and KRAS are frequently associated with human cancers. Molecular targeting of specific oncogenic mutations in human cancer is a major therapeutic inroad for anti-cancer drug therapy. In addition, progressive developments of oncogene mutations lead to drug resistance. Therefore, the ability to detect and continuously monitor key actionable oncogenic mutations is important to guide the use of targeted molecular therapies to improve long-term clinical outcomes in cancer patients. Current oncogenic mutation detection is based on direct sampling of cancer tissue by surgical resection or biopsy. Oncogenic mutations were recently shown to be detectable in circulating bodily fluids of cancer patients. This field of investigation, termed liquid biopsy, permits a less invasive means of assessing the oncogenic mutation profile of a patient. This paper will review the analytical strategies used to assess oncogenic mutations from biofluid samples. Clinical applications will also be discussed. PMID:26645892

Biofluidic Transport and Molecular Recognition in Polymer Microdevices

DTIC Science & Technology

2005-04-29

flexible membrane separating the particles and reservoir. B. Using photopolymerizable wires, an electrolysis pump was fabricated on a microdevice. It...Antigen detection was accomplished by grafting the approximate antibody or sensing compound via acrylation and polymerization to the surface. Figure 14...were detected with assay times of approximately 10 minutes. Figure 15 shows detection data for a compound (glucagon) that is impossible to detect by

Discrimination of serum Raman spectroscopy between normal and colorectal cancer

NASA Astrophysics Data System (ADS)

Li, Xiaozhou; Yang, Tianyue; Yu, Ting; Li, Siqi

2011-07-01

Raman spectroscopy of tissues has been widely studied for the diagnosis of various cancers, but biofluids were seldom used as the analyte because of the low concentration. Herein, serum of 30 normal people, 46 colon cancer, and 44 rectum cancer patients were measured Raman spectra and analyzed. The information of Raman peaks (intensity and width) and that of the fluorescence background (baseline function coefficients) were selected as parameters for statistical analysis. Principal component regression (PCR) and partial least square regression (PLSR) were used on the selected parameters separately to see the performance of the parameters. PCR performed better than PLSR in our spectral data. Then linear discriminant analysis (LDA) was used on the principal components (PCs) of the two regression method on the selected parameters, and a diagnostic accuracy of 88% and 83% were obtained. The conclusion is that the selected features can maintain the information of original spectra well and Raman spectroscopy of serum has the potential for the diagnosis of colorectal cancer.

Saliva diagnostics – Current views and directions

PubMed Central

Kaczor-Urbanowicz, Karolina Elżbieta; Martin Carreras-Presas, Carmen; Aro, Katri; Tu, Michael; Wong, David TW

2016-01-01

In this review, we provide an update on the current and future applications of saliva for diagnostic purposes. There are many advantages of using saliva as a biofluid. Its collection is fast, easy, inexpensive, and non-invasive. In addition, saliva, as a “mirror of the body,” can reflect the physiological and pathological state of the body. Therefore, it serves as a diagnostic and monitoring tool in many fields of science such as medicine, dentistry, and pharmacotherapy. Introduced in 2008, the term “Salivaomics” aimed to highlight the rapid development of knowledge about various “omics” constituents of saliva, including: proteome, transcriptome, micro-RNA, metabolome, and microbiome. In the last few years, researchers have developed new technologies and validated a wide range of salivary biomarkers that will soon make the use of saliva a clinical reality. However, a great need still exists for convenient and accurate point-of-care devices that can serve as a non-invasive diagnostic tool. In addition, there is an urgent need to decipher the scientific rationale and mechanisms that convey systemic diseases to saliva. Another promising technology called liquid biopsy enables detection of circulating tumor cells (CTCs) and fragments of tumor DNA in saliva, thus enabling non-invasive early detection of various cancers. The newly developed technology—electric field-induced release and measurement (EFIRM) provides near perfect detection of actionable mutations in lung cancer patients. These recent advances widened the salivary diagnostic approach from the oral cavity to the whole physiological system, and thus point towards a promising future of salivary diagnostics for personalized individual medicine applications including clinical decisions and post-treatment outcome predictions. Impact statement The purpose of this mini-review is to make an update about the present and future applications of saliva as a diagnostic biofluid in many fields of science such as dentistry, medicine and pharmacotherapy. Using saliva as a fluid for diagnostic purposes would be a huge breakthrough for both patients and healthcare providers since saliva collection is easy, non-invasive and inexpensive. We will go through the current main diagnostic applications of saliva, and provide a highlight on the emerging, newly developing technologies and tools for cancer screening, detection and monitoring. PMID:27903834

Enrichment of low-molecular-weight proteins from biofluids for biomarker discovery.

PubMed

Chertov, Oleg; Simpson, John T; Biragyn, Arya; Conrads, Thomas P; Veenstra, Timothy D; Fisher, Robert J

2005-01-01

The dramatic progress in mass spectrometry-based methods of protein identification has triggered a new quest for disease-associated biomarkers. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and its variant surface-enhanced laser desorption/ionization mass spectrometry, provide effective means to explore the less studied information slice of the human serum proteome -- low-molecular-weight proteins and peptides. These low-molecular-weight proteins and peptides are promising for the detection of important biomarkers. Due to the significant experimental problems imposed by high-abundance and high-molecular-weight proteins, it is important to effectively remove these species prior to mass spectrometry analysis of the low-molecular-weight serum and plasma proteomes. In this review, the advantages afforded by recently introduced methods for prefractionation of serum, as they pertain to the detection and identification of biomarkers, will be discussed.

The Role of Mass Spectrometry-Based Metabolomics in Medical Countermeasures Against Radiation

PubMed Central

Patterson, Andrew D.; Lanz, Christian; Gonzalez, Frank J.; Idle, Jeffrey R.

2013-01-01

Radiation metabolomics can be defined as the global profiling of biological fluids to uncover latent, endogenous small molecules whose concentrations change in a dose-response manner following exposure to ionizing radiation. In response to the potential threat of nuclear or radiological terrorism, the Center for High-Throughput Minimally Invasive Radiation Biodosimetry (CMCR) was established to develop field-deployable biodosimeters based, in principle, on rapid analysis by mass spectrometry of readily and easily obtainable biofluids. In this review, we briefly summarize radiation biology and key events related to actual and potential nuclear disasters, discuss the important contributions the field of mass spectrometry has made to the field of radiation metabolomics, and summarize current discovery efforts to use mass spectrometry-based metabolomics to identify dose-responsive urinary constituents, and ultimately to build and deploy a noninvasive high-throughput biodosimeter. PMID:19890938

Nanoengineered capsules for selective SERS analysis of biological samples

NASA Astrophysics Data System (ADS)

You, Yil-Hwan; Schechinger, Monika; Locke, Andrea; Coté, Gerard; McShane, Mike

2018-02-01

Metal nanoparticles conjugated with DNA oligomers have been intensively studied for a variety of applications, including optical diagnostics. Assays based on aggregation of DNA-coated particles in proportion to the concentration of target analyte have not been widely adopted for clinical analysis, however, largely due to the nonspecific responses observed in complex biofluids. While sample pre-preparation such as dialysis is helpful to enable selective sensing, here we sought to prove that assay encapsulation in hollow microcapsules could remove this requirement and thereby facilitate more rapid analysis on complex samples. Gold nanoparticle-based assays were incorporated into capsules comprising polyelectrolyte multilayer (PEMs), and the response to small molecule targets and larger proteins were compared. Gold nanoparticles were able to selectively sense small Raman dyes (Rhodamine 6G) in the presence of large protein molecules (BSA) when encapsulated. A ratiometric based microRNA-17 sensing assay exhibited drastic reduction in response after encapsulation, with statistically-significant relative Raman intensity changes only at a microRNA-17 concentration of 10 nM compared to a range of 0-500 nM for the corresponding solution-phase response.

Global metabolic profiling procedures for urine using UPLC-MS.

PubMed

Want, Elizabeth J; Wilson, Ian D; Gika, Helen; Theodoridis, Georgios; Plumb, Robert S; Shockcor, John; Holmes, Elaine; Nicholson, Jeremy K

2010-06-01

The production of 'global' metabolite profiles involves measuring low molecular-weight metabolites (<1 kDa) in complex biofluids/tissues to study perturbations in response to physiological challenges, toxic insults or disease processes. Information-rich analytical platforms, such as mass spectrometry (MS), are needed. Here we describe the application of ultra-performance liquid chromatography-MS (UPLC-MS) to urinary metabolite profiling, including sample preparation, stability/storage and the selection of chromatographic conditions that balance metabolome coverage, chromatographic resolution and throughput. We discuss quality control and metabolite identification, as well as provide details of multivariate data analysis approaches for analyzing such MS data. Using this protocol, the analysis of a sample set in 96-well plate format, would take ca. 30 h, including 1 h for system setup, 1-2 h for sample preparation, 24 h for UPLC-MS analysis and 1-2 h for initial data processing. The use of UPLC-MS for metabolic profiling in this way is not faster than the conventional HPLC-based methods but, because of improved chromatographic performance, provides superior metabolome coverage.

Screening and analysis of aconitum alkaloids and their metabolites in rat urine after oral administration of aconite roots extract using LC-TOFMS-based metabolomics.

PubMed

Tan, Guangguo; Lou, Ziyang; Jing, Jing; Li, Wuhong; Zhu, Zhenyu; Zhao, Liang; Zhang, Guoqing; Chai, Yifeng

2011-12-01

Aconite roots are popularly used in herbal medicines in China. Many cases of accidental and intentional intoxication with this plant have been reported; some of these are fatal because the toxicity of aconitum is very high. It is thus important to detect and identify aconitum alkaloids in biofluids. In this work, an improved method employing LC-TOFMS with multivariate data analysis was developed for screening and analysis of major aconitum alkaloids and their metabolites in rat urine following oral administration of aconite roots extract. Thirty-four signals highlighted by multivariate statistical analyses including 24 parent components and 10 metabolites were screened out and further identified by adjustment of the fragmentor voltage to produce structure-relevant fragment ions. It is helpful for studying aconite roots in toxicology, pharmacology and forensic medicine. This work also confirmed that the metabolomic approach provides effective tools for screening multiple absorbed and metabolic components of Chinese herbal medicines in vivo. Copyright © 2011 John Wiley & Sons, Ltd.

Superfast Near-Infrared Light-Driven Polymer Multilayer Rockets.

PubMed

Wu, Zhiguang; Si, Tieyan; Gao, Wei; Lin, Xiankun; Wang, Joseph; He, Qiang

2016-02-03

A gold nanoshell-functionalized polymer multilayer nanorocket performs self-propulsion upon the irradiation with NIR light in the absence of chemical fuel. Theoretical simulations reveal that the NIR light-triggered self-thermophoresis drives the propulsion of the nanorocket. The nanorocket also displays -efficient NIR light-triggered propulsion in -biofluids and thus holds considerable promise for various potential biomedical applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biofluidic Intelligent Processors for Preparative Manipulations of Biological Warfare Agents at the Attomole Level

DTIC Science & Technology

2005-11-01

micromixing and microreactor concept. OPA by itself is non- fluorescent, but it reacts with primary amine groups in the presence of β-mercaptoethanol to form...hybrid microchannel/nanopore-membrane devices can serve as efficient micromixers and microreactors, and (2) microscopic kinetics can be obtained from...single image measurements. An immediate application which extended from the micromixing and microreactor concept was microsensing. Calcium ions

Bio-Fluid Transport Models Through Nano and Micro-Fluidic Components

DTIC Science & Technology

2005-08-01

nm of the wall in steady electroosmotic flow with good accuracy. The nPIV data were in excellent agreement with the model predictions for monovalent...first experimental probe inside the electric double layer in electroosmotic flow of an aqueous electrolyte solution. 15. NUMBER OF PAGES 225 14...SUBJECT TERMS Micro And Nanofluidics, Electroosmotic Flow, Nano Particle Image Velocimetry 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT

Accelerated Biofluid Filling in Complex Microfluidic Networks by Vacuum-Pressure Accelerated Movement (V-PAM).

PubMed

Yu, Zeta Tak For; Cheung, Mei Ki; Liu, Shirley Xiaosu; Fu, Jianping

2016-09-01

Rapid fluid transport and exchange are critical operations involved in many microfluidic applications. However, conventional mechanisms used for driving fluid transport in microfluidics, such as micropumping and high pressure, can be inaccurate and difficult for implementation for integrated microfluidics containing control components and closed compartments. Here, a technology has been developed termed Vacuum-Pressure Accelerated Movement (V-PAM) capable of significantly enhancing biofluid transport in complex microfluidic environments containing dead-end channels and closed chambers. Operation of the V-PAM entails a pressurized fluid loading into microfluidic channels where gas confined inside can rapidly be dissipated through permeation through a thin, gas-permeable membrane sandwiched between microfluidic channels and a network of vacuum channels. Effects of different structural and operational parameters of the V-PAM for promoting fluid filling in microfluidic environments have been studied systematically. This work further demonstrates the applicability of V-PAM for rapid filling of temperature-sensitive hydrogels and unprocessed whole blood into complex irregular microfluidic networks such as microfluidic leaf venation patterns and blood circulatory systems. Together, the V-PAM technology provides a promising generic microfluidic tool for advanced fluid control and transport in integrated microfluidics for different microfluidic diagnosis, organs-on-chips, and biomimetic studies. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Study of bioconcentration of oxybenzone in gilt-head bream and characterization of its by-products.

PubMed

Ziarrusta, Haizea; Mijangos, Leire; Montes, Rosa; Rodil, Rosario; Anakabe, Eneritz; Izagirre, Urtzi; Prieto, Ailette; Etxebarria, Nestor; Olivares, Maitane; Zuloaga, Olatz

2018-05-25

The widespread occurrence of UV filters such as oxybenzone (OXY) in the aquatic ecosystems has raised social and scientific concern due to their high bioaccumulation potential and possible adverse effects in organisms. Within this context, the aim of the present work was to study the uptake, distribution, metabolization and elimination of OXY in different tissues (liver, gill and muscle) and biofluids (bile and plasma) of gilt-head bream (Sparus aurata) in a controlled seawater ecosystem (50 ng/mL OXY) within a 14-day exposure. The highest OXY concentrations in all the tissue/biofluids were found at the end of the experiment. The highest OXY levels were found in bile (1.8-17 μg/mL). In the case of liver, the concentrations found (9-160 ng/g) were lower than those expected for a lipidic matrix, which could be explained by a high OXY metabolization. Up to 20 Phase I and Phase II by-products of OXY were annotated by means of liquid chromatography-high resolution mass spectrometry, of which 12 were reported for the first time. In addition to OXY, its by-products might also cause adverse effects and their biomonitoring is advisable in order to fully characterize OXY exposure. Copyright © 2018 Elsevier Ltd. All rights reserved.

Application of miRNAs as Biomarkers of Exposure and Effects ...

EPA Pesticide Factsheets

Of the known epigenetic mechanisms, non-coding RNA and more specifically, microRNA (miRNA), offer the most immediate promise for risk assessment applications because these molecules can serve as excellent biomarkers of toxicity. The advantages of miRNA versus more classical protein toxicity biomarkers include: greater stability and earlier appearance in biofluids that can be obtained by relatively non-invasive approaches; tissue- and/or cell-specific expression patterns; evolutionary conservation in both sequence and function across species; and novel technologies for sensitive and accurate quantification. Further, information on individual miRNA is readily available through databases such as miRBase and others. Thus miRNA biomarkers offer substantial benefits in terms of cost, time, convenience, sensitivity, and specificity when assessing environmental-induced toxicity in model systems or human cohorts. Although this field is rapidly expanding, documented examples include associations of miR-155 with lymphocytic leukemia, miR-122 with liver toxicity; miR-206 with skeletal muscle disease; and miR-208a-3p with cardiac toxicity. Despite their promise, some challenges in using miRNAs as toxicity biomarkers remain, including the need for improved methods for normalizing miRNA measurements, translating findings of biofluid-based miRNA biomarker alterations in experimental models to human health and specific cell/tissue injury, and finally, the need to better defi

Determination of the Nicotine Metabolites Cotinine and Trans-3′-Hydroxycotinine in Biologic fluids of Smokers and Non-Smokers using Liquid Chromatography - Tandem Mass Spectrometry: Biomarkers for Tobacco Smoke Exposure and for Phenotyping Cytochrome P450 2A6 Activity

PubMed Central

Jacob, Peyton; Yu, Lisa; Duan, Minjiang; Ramos, Lita; Yturralde, Olivia; Benowitz, Neal L.

2011-01-01

The nicotine metabolite cotinine is widely used to assess the extent of tobacco use in smokers, and secondhand smoke exposure in non-smokers. The ratio of another nicotine metabolite, trans-3′-hydroxycotinine, to cotinine in biofluids is highly correlated with the rate of nicotine metabolism, which is catalyzed mainly by Cytochrome P450 2A6 (CYP2A6). Consequently, this nicotine metabolite ratio is being used to phenotype individuals for CYP2A6 activity and to individualize pharmacotherapies for tobacco addiction. In this paper we describe a highly sensitive liquid chromatography – tandem mass spectrometry method for determination of the nicotine metabolites cotinine and trans-3′-hydroxycotinine in human plasma, urine, and saliva. Lower limits of quantitation range from 0.02 to 0.1 ng/ mL. The extraction procedure is straightforward and suitable for large-scale studies. The method has been applied to several thousand biofluid samples for pharmacogenetic studies and for studies of exposure to low levels of secondhand smoke. Concentrations of both metabolites in urine of non-smokers with different levels of secondhand smoke exposure are presented. PMID:21208832

Looking into aqueous humor through metabolomics spectacles - exploring its metabolic characteristics in relation to myopia.

PubMed

Barbas-Bernardos, Cecilia; Armitage, Emily G; García, Antonia; Mérida, Salvador; Navea, Amparo; Bosch-Morell, Francisco; Barbas, Coral

2016-08-05

Aqueous humor is the transparent fluid found in the anterior chamber of the eye that provides the metabolic requirements to the avascular tissues surrounding it. Despite the fact that metabolomics could be a powerful tool in the characterization of this biofluid and in revealing metabolic signatures of common ocular diseases such as myopia, it has never to our knowledge previously been applied in humans. In this research a novel method for the analysis of aqueous humor is presented to show its application in the characterization of this biofluid using CE-MS. The method was extended to a dual platform method (CE-MS and LC-MS) in order to compare samples from patients with different severities of myopia in order to explore the disease from the metabolic phenotype point of view. With this method, a profound knowledge of the metabolites present in human aqueous humor has been obtained: over 40 metabolites were reproducibly and simultaneously identified from a low volume of sample by CE-MS, including among others, a vast number of amino acids and derivatives. When this method was extended to study groups of patients with high or low myopia in both CE-MS and LC-MS, it has been possible to identify over 20 significantly different metabolite and lipid signatures that distinguish patients based on the severity of myopia. Among these, the most notable higher abundant metabolites in high myopia were aminooctanoic acid, arginine, citrulline and sphinganine while features of low myopia were aminoundecanoic acid, dihydro-retinoic acid and cysteinylglycine disulfide. This dual platform approach offered complementarity such that different metabolites were detected in each technique. Together the experiments presented provide a whelm of valuable information about human aqueous humor and myopia, proving the utility of non-targeted metabolomics for the first time in analyzing this type of sample and the metabolic phenotype of this disease. Copyright © 2016 Elsevier B.V. All rights reserved.

Fibrosis biomarkers in workers exposed to MWCNTs

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

Fatkhutdinova, Liliya M., E-mail: liliya.fatkhutdi

Multi-walled carbon nanotubes (MWCNT) with their unique physico-chemical properties offer numerous technological advantages and are projected to drive the next generation of manufacturing growth. As MWCNT have already found utility in different industries including construction, engineering, energy production, space exploration and biomedicine, large quantities of MWCNT may reach the environment and inadvertently lead to human exposure. This necessitates the urgent assessment of their potential health effects in humans. The current study was carried out at NanotechCenter Ltd. Enterprise (Tambov, Russia) where large-scale manufacturing of MWCNT along with relatively high occupational exposure levels was reported. The goal of this small cross-sectionalmore » study was to evaluate potential biomarkers during occupational exposure to MWCNT. All air samples were collected at the workplaces from both specific areas and personal breathing zones using filter-based devices to quantitate elemental carbon and perform particle analysis by TEM. Biological fluids of nasal lavage, induced sputum and blood serum were obtained from MWCNT-exposed and non-exposed workers for assessment of inflammatory and fibrotic markers. It was found that exposure to MWCNTs caused significant increase in IL-1β, IL6, TNF-α, inflammatory cytokines and KL-6, a serological biomarker for interstitial lung disease in collected sputum samples. Moreover, the level of TGF-β1 was increased in serum obtained from young exposed workers. Overall, the results from this study revealed accumulation of inflammatory and fibrotic biomarkers in biofluids of workers manufacturing MWCNTs. Therefore, the biomarkers analyzed should be considered for the assessment of health effects of occupational exposure to MWCNT in cross-sectional epidemiological studies. - Highlights: • The effects of MWCNT exposure in humans remain unclear. • We found increased KL-6/TGF-β levels in the biofluids of MWCNT-exposed workers. • Inflammatory cytokines content was also increased in these workers. • The identified markers could be useful for potential health surveillance in exposed populations.« less

Method and platform standardization in MRM-based quantitative plasma proteomics.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Jackson, Angela M; Domanski, Dominik; Burkhart, Julia; Sickmann, Albert; Borchers, Christoph H

2013-12-16

There exists a growing demand in the proteomics community to standardize experimental methods and liquid chromatography-mass spectrometry (LC/MS) platforms in order to enable the acquisition of more precise and accurate quantitative data. This necessity is heightened by the evolving trend of verifying and validating candidate disease biomarkers in complex biofluids, such as blood plasma, through targeted multiple reaction monitoring (MRM)-based approaches with stable isotope-labeled standards (SIS). Considering the lack of performance standards for quantitative plasma proteomics, we previously developed two reference kits to evaluate the MRM with SIS peptide approach using undepleted and non-enriched human plasma. The first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). Here, these kits have been refined for practical use and then evaluated through intra- and inter-laboratory testing on 6 common LC/MS platforms. For an identical panel of 22 plasma proteins, similar concentrations were determined, regardless of the kit, instrument platform, and laboratory of analysis. These results demonstrate the value of the kit and reinforce the utility of standardized methods and protocols. The proteomics community needs standardized experimental protocols and quality control methods in order to improve the reproducibility of MS-based quantitative data. This need is heightened by the evolving trend for MRM-based validation of proposed disease biomarkers in complex biofluids such as blood plasma. We have developed two kits to assist in the inter- and intra-laboratory quality control of MRM experiments: the first kit tests the effectiveness of the LC/MRM-MS platform (kit #1), while the second evaluates the performance of an entire analytical workflow (kit #2). In this paper, we report the use of these kits in intra- and inter-laboratory testing on 6 common LC/MS platforms. This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics. © 2013.

Metabolome analysis for discovering biomarkers of gastroenterological cancer.

PubMed

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

2014-09-01

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

SimExTargId: A comprehensive package for real-time LC-MS data acquisition and analysis.

PubMed

Edmands, William M B; Hayes, Josie; Rappaport, Stephen M

2018-05-22

Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis. Users are notified of detrimental instrument drift or errors by email. Also included are two shiny applications, targetId for real-time MS2 target identification, and peakMonitor to monitor targeted metabolites. SimExTargId is publicly available under GNU LGPL v3.0 license at https://github.com/JosieLHayes/simExTargId, which includes a vignette with example data. SimExTargId should be installed on a dedicated data-processing workstation or server that is networked to the LC-MS platform to facilitate MS1 profiling of metabolomic data. josie.hayes@berkeley.edu. Supplementary data are available at Bioinformatics online.

PharmaSat: drug dose response in microgravity from a free-flying integrated biofluidic/optical culture-and-analysis satellite

NASA Astrophysics Data System (ADS)

Ricco, Antonio J.; Parra, Macarena; Niesel, David; Piccini, Matthew; Ly, Diana; McGinnis, Michael; Kudlicki, Andrzej; Hines, John W.; Timucin, Linda; Beasley, Chris; Ricks, Robert; McIntyre, Michael; Friedericks, Charlie; Henschke, Michael; Leung, Ricky; Diaz-Aguado, Millan; Kitts, Christopher; Mas, Ignacio; Rasay, Mike; Agasid, Elwood; Luzzi, Ed; Ronzano, Karolyn; Squires, David; Yost, Bruce

2011-02-01

We designed, built, tested, space-qualified, launched, and collected telemetered data from low Earth orbit from Pharma- Sat, a 5.1-kg free flying "nanosatellite" that supported microbial growth in 48 microfluidic wells, dosed microbes with multiple concentrations of a pharmaceutical agent, and monitored microbial growth and metabolic activity using a dedicated 3-color optical absorbance system at each microwell. The PharmaSat nanosatellite comprised a structure approximately 10 x 10 x 35 cm, including triple-junction solar cells, bidirectional communications, power-generation and energy- storage system, and a sealed payload 1.2-L containment vessel that housed the biological organisms along with the fluidic, optical, thermal, sensor, and electronic subsystems. Growth curves for S. cerevisiae (Brewer's yeast) were obtained for multiple concentrations of the antifungal drug voriconazole in the microgravity conditions of low Earth orbit. Corresponding terrestrial control experiments were conducted for comparison.

Breast Milk Oligosaccharides: Structure-Function Relationships in the Neonate

PubMed Central

Smilowitz, Jennifer T.; Lebrilla, Carlito B.; Mills, David A.; German, J. Bruce; Freeman, Samara L.

2015-01-01

In addition to providing complete postnatal nutrition, breast milk is a complex biofluid that delivers bioactive components for the growth and development of the intestinal and immune systems. Lactation is a unique opportunity to understand the role of diet in shaping the intestinal environment including the infant microbiome. Of considerable interest is the diversity and abundance of milk glycans that are energetically costly for the mammary gland to produce yet indigestible by infants. Milk glycans comprise free oligosaccharides, glycoproteins, glycopeptides, and glycolipids. Emerging technological advances are enabling more comprehensive, sensitive, and rapid analyses of these different classes of milk glycans. Understanding the impact of inter- and intraindividual glycan diversity on function is an important step toward interventions aimed at improving health and preventing disease. This review discusses the state of technology for glycan analysis and how specific structure-function knowledge is enhancing our understanding of early nutrition in the neonate. PMID:24850388

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

Baker, Erin Shammel; Burnum-Johnson, Kristin E.; Jacobs, Jon M.

Rapid diagnosis of disease states using less invasive, safer, and more clinically acceptable approaches than presently employed is an imperative goal for the field of medicine. While mass spectrometry (MS)-based proteomics approaches have attempted to meet these objectives, challenges such as the enormous dynamic range of protein concentrations in clinically relevant biofluid samples coupled with the need to address human biodiversity have slowed their employment. Herein, we report on the use of a new platform that addresses these challenges by coupling technical advances in rapid gas phase multiplexed ion mobility spectrometry (IMS) separations [1, 2] with liquid chromatography (LC) andmore » MS to dramatically increase measurement sensitivity and throughput, further enabling future MS-based clinical applications. An initial application of the LC-IMS-MS platform for the analysis of blood serum samples from stratified post-liver transplant patients with recurrent fibrosis progression illustrates its potential utility for disease characterization and use in personalized medicine [3, 4].« less

Molecular Mechanisms Underlying the Role of MicroRNAs in the Chemoresistance of Pancreatic Cancer

PubMed Central

Garajová, Ingrid; Le Large, Tessa Y.; Frampton, Adam E.; Voortman, Johannes

2014-01-01

Pancreatic ductal adenocarcinoma (PDAC) is an extremely severe disease where the mortality and incidence rates are almost identical. This is mainly due to late diagnosis and limited response to current treatments. The tumor macroenvironment/microenvironment have been frequently reported as the major contributors to chemoresistance in PDAC, preventing the drugs from reaching their intended site of action (i.e., the malignant duct cells). However, the recent discovery of microRNAs (miRNAs) has provided new directions for research on mechanisms underlying response to chemotherapy. Due to their tissue-/disease-specific expression and high stability in tissues and biofluids, miRNAs represent new promising diagnostic and prognostic/predictive biomarkers and therapeutic targets. Furthermore, several studies have documented that selected miRNAs, such as miR-21 and miR-34a, may influence response to chemotherapy in several tumor types, including PDAC. In this review, we summarize the current knowledge on the role of miRNAs in PDAC and recent advances in understanding their role in chemoresistance through multiple molecular mechanisms. PMID:25250326

Molecular mechanisms underlying the role of microRNAs in the chemoresistance of pancreatic cancer.

PubMed

Garajová, Ingrid; Le Large, Tessa Y; Frampton, Adam E; Rolfo, Christian; Voortman, Johannes; Giovannetti, Elisa

2014-01-01

Pancreatic ductal adenocarcinoma (PDAC) is an extremely severe disease where the mortality and incidence rates are almost identical. This is mainly due to late diagnosis and limited response to current treatments. The tumor macroenvironment/microenvironment have been frequently reported as the major contributors to chemoresistance in PDAC, preventing the drugs from reaching their intended site of action (i.e., the malignant duct cells). However, the recent discovery of microRNAs (miRNAs) has provided new directions for research on mechanisms underlying response to chemotherapy. Due to their tissue-/disease-specific expression and high stability in tissues and biofluids, miRNAs represent new promising diagnostic and prognostic/predictive biomarkers and therapeutic targets. Furthermore, several studies have documented that selected miRNAs, such as miR-21 and miR-34a, may influence response to chemotherapy in several tumor types, including PDAC. In this review, we summarize the current knowledge on the role of miRNAs in PDAC and recent advances in understanding their role in chemoresistance through multiple molecular mechanisms.

Experimental and Study Design Considerations for Uncovering Oncometabolites.

PubMed

Haznadar, Majda; Mathé, Ewy A

2017-01-01

Metabolomics as a field has gained attention due to its potential for biomarker discovery, namely because it directly reflects disease phenotype and is the downstream effect of posttranslational modifications. The field provides a "top-down," integrated view of biochemistry in complex organisms, as opposed to the traditional "bottom-up" approach that aims to analyze networks of interactions between genes, proteins and metabolites. It also allows for the detection of thousands of endogenous metabolites in various clinical biospecimens in a high-throughput manner, including tissue and biofluids such as blood and urine. Of note, because biological fluid samples can be collected relatively easily, the time-dependent fluctuations of metabolites can be readily studied in detail.In this chapter, we aim to provide an overview of (1) analytical methods that are currently employed in the field, and (2) study design concepts that should be considered prior to conducting high-throughput metabolomics studies. While widely applicable, the concepts presented here are namely applicable to high-throughput untargeted studies that aim to search for metabolite biomarkers that are associated with a particular human disease.

Heparin affinity purification of extracellular vesicles

PubMed Central

Balaj, Leonora; Atai, Nadia A.; Chen, Weilin; Mu, Dakai; Tannous, Bakhos A.; Breakefield, Xandra O.; Skog, Johan; Maguire, Casey A.

2015-01-01

Extracellular vesicles (EVs) are lipid membrane vesicles released by cells. They carry active biomolecules including DNA, RNA, and protein which can be transferred to recipient cells. Isolation and purification of EVs from culture cell media and biofluids is still a major challenge. The most widely used isolation method is ultracentrifugation (UC) which requires expensive equipment and only partially purifies EVs. Previously we have shown that heparin blocks EV uptake in cells, supporting a direct EV-heparin interaction. Here we show that EVs can be purified from cell culture media and human plasma using ultrafiltration (UF) followed by heparin-affinity beads. UF/heparin-purified EVs from cell culture displayed the EV marker Alix, contained a diverse RNA profile, had lower levels of protein contamination, and were functional at binding to and uptake into cells. RNA yield was similar for EVs isolated by UC. We were able to detect mRNAs in plasma samples with comparable levels to UC samples. In conclusion, we have discovered a simple, scalable, and effective method to purify EVs taking advantage of their heparin affinity. PMID:25988257

Comparison of Methods for miRNA Extraction from Plasma and Quantitative Recovery of RNA from Cerebrospinal Fluid

PubMed Central

McAlexander, Melissa A.; Phillips, Maggie J.; Witwer, Kenneth W.

2013-01-01

Interest in extracellular RNA (exRNA) has intensified as evidence accumulates that these molecules may be useful as indicators of a wide variety of biological conditions. To establish specific exRNA molecules as clinically relevant biomarkers, reproducible recovery from biological samples and reliable measurements of the isolated RNA are paramount. Toward these ends, careful and rigorous comparisons of technical procedures are needed at all steps from sample handling to RNA isolation to RNA measurement protocols. In the investigations described in this methods paper, RT-qPCR was used to examine the apparent recovery of specific endogenous miRNAs and a spiked-in synthetic RNA from blood plasma samples. RNA was isolated using several widely used RNA isolation kits, with or without the addition of glycogen as a carrier. Kits examined included total RNA isolation systems that have been commercially available for several years and commonly adapted for extraction of biofluid RNA, as well as more recently introduced biofluids-specific RNA methods. Our conclusions include the following: some RNA isolation methods appear to be superior to others for the recovery of RNA from biological fluids; addition of a carrier molecule seems to be beneficial for some but not all isolation methods; and quantitative recovery of RNA is observed from increasing volumes of cerebrospinal fluid. PMID:23720669

Proteomic profiling of eccrine sweat reveals its potential as a diagnostic biofluid for active tuberculosis.

PubMed

Adewole, Olanisun Olufemi; Erhabor, Greg Efosa; Adewole, Temitayo Oluwatoyin; Ojo, Abiodun Oluwasesan; Oshokoya, Harriet; Wolfe, Lisa M; Prenni, Jessica E

2016-05-01

Excessive sweating is a common symptom of the disease and an unexplored biofluid for TB diagnosis; we conducted a proof-of-concept study to identify potential diagnostic biomarkers of active TB in eccrine sweat. We performed a global proteomic profile of eccrine sweat sampled from patients with active pulmonary TB, other lung diseases (non-TB disease), and healthy controls. A comparison of proteomics between Active-TB, Non-TB, and Healthy Controls was done in search for potential biomarkers of active TB. Sweat specimens were pooled from 32 active TB patients, 27 patients with non-TB diseases, and 24 apparently healthy controls, all were negative for HIV. Over 100 unique proteins were identified in the eccrine sweat of all three groups. Twenty-six proteins were exclusively detected in the sweat of patients with active TB while the remaining detected proteins overlapped between three groups. Gene ontology evaluation indicated that the proteins detected uniquely in sweat of active TB patients were involved in immune response and auxiliary protein transport. Gene products for cellular components (e.g. ribosomes) were detected only in active TB patients. Data are available via ProteomeXchange with identifier PXD003224. Proteomics of sweat from active TB patients is a viable approach for biomarker identification, which could be used to develop a nonsputum-based test for detection of active TB. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nuclear magnetic resonance (NMR)-based metabolomics for cancer research.

PubMed

Ranjan, Renuka; Sinha, Neeraj

2018-05-07

Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research. Copyright © 2018 John Wiley & Sons, Ltd.

Bioinformatics tools for the analysis of NMR metabolomics studies focused on the identification of clinically relevant biomarkers.

PubMed

Puchades-Carrasco, Leonor; Palomino-Schätzlein, Martina; Pérez-Rambla, Clara; Pineda-Lucena, Antonio

2016-05-01

Metabolomics, a systems biology approach focused on the global study of the metabolome, offers a tremendous potential in the analysis of clinical samples. Among other applications, metabolomics enables mapping of biochemical alterations involved in the pathogenesis of diseases, and offers the opportunity to noninvasively identify diagnostic, prognostic and predictive biomarkers that could translate into early therapeutic interventions. Particularly, metabolomics by Nuclear Magnetic Resonance (NMR) has the ability to simultaneously detect and structurally characterize an abundance of metabolic components, even when their identities are unknown. Analysis of the data generated using this experimental approach requires the application of statistical and bioinformatics tools for the correct interpretation of the results. This review focuses on the different steps involved in the metabolomics characterization of biofluids for clinical applications, ranging from the design of the study to the biological interpretation of the results. Particular emphasis is devoted to the specific procedures required for the processing and interpretation of NMR data with a focus on the identification of clinically relevant biomarkers. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Study of the Pressure and Velocity Across the Aortic Valve

NASA Astrophysics Data System (ADS)

Kyung, Seo Young; Chung, Erica Soyun; Lee, Joo Hee; Kyung, Hayoung; Choi, Si Young

Biomechanics of the heart, requiring an extensive understanding of the complexity of the heart, have become the interests of many biomedical engineers in cardiology today. In order to study aortic valve disease, engineers have focused on the data obtained through bio-fluid flow analysis. To further this study, physical and computational analysis on the biomechanical determinants of blood flow in the stenosed aortic valve have been examined. These observations, along with the principles of cardiovascular physiology, confirm that when blood flows through the valve opening, pressure gradient across the valve is produced as a result of stenosis of the aortic valve. The aortic valve gradient is used to interpret the increase and decrease on each side of the defective valve. To compute different pressure gradients across the aortic valve, this paper analyzes Aortic Valve Areas (AVA) using simulations based on the continuity equation and Gorlin equation. The data obtained from such analysis consist of patients in the AS category that display mild Aortic Valve Velocity (AVV) and pressure gradient. Such correlation results in the construction of a dependent relationship between severe AS causing LV systolic dysfunction and the transaortic velocity.

Application of Fourier transform infrared spectroscopy with chemometrics on postmortem interval estimation based on pericardial fluids.

PubMed

Zhang, Ji; Li, Bing; Wang, Qi; Wei, Xin; Feng, Weibo; Chen, Yijiu; Huang, Ping; Wang, Zhenyuan

2017-12-21

Postmortem interval (PMI) evaluation remains a challenge in the forensic community due to the lack of efficient methods. Studies have focused on chemical analysis of biofluids for PMI estimation; however, no reports using spectroscopic methods in pericardial fluid (PF) are available. In this study, Fourier transform infrared (FTIR) spectroscopy with attenuated total reflectance (ATR) accessory was applied to collect comprehensive biochemical information from rabbit PF at different PMIs. The PMI-dependent spectral signature was determined by two-dimensional (2D) correlation analysis. The partial least square (PLS) and nu-support vector machine (nu-SVM) models were then established based on the acquired spectral dataset. Spectral variables associated with amide I, amide II, COO - , C-H bending, and C-O or C-OH vibrations arising from proteins, polypeptides, amino acids and carbohydrates, respectively, were susceptible to PMI in 2D correlation analysis. Moreover, the nu-SVM model appeared to achieve a more satisfactory prediction than the PLS model in calibration; the reliability of both models was determined in an external validation set. The study shows the possibility of application of ATR-FTIR methods in postmortem interval estimation using PF samples.

Metabolomics: beyond biomarkers and towards mechanisms

PubMed Central

Johnson, Caroline H.; Ivanisevic, Julijana; Siuzdak, Gary

2017-01-01

Metabolomics, which is the profiling of metabolites in biofluids, cells and tissues, is routinely applied as a tool for biomarker discovery. Owing to innovative developments in informatics and analytical technologies, and the integration of orthogonal biological approaches, it is now possible to expand metabolomic analyses to understand the systems-level effects of metabolites. Moreover, because of the inherent sensitivity of metabolomics, subtle alterations in biological pathways can be detected to provide insight into the mechanisms that underlie various physiological conditions and aberrant processes, including diseases. PMID:26979502

Transient, biocompatible electronics and energy harvesters based on ZnO.

PubMed

Dagdeviren, Canan; Hwang, Suk-Won; Su, Yewang; Kim, Stanley; Cheng, Huanyu; Gur, Onur; Haney, Ryan; Omenetto, Fiorenzo G; Huang, Yonggang; Rogers, John A

2013-10-25

The combined use of ZnO, Mg, MgO, and silk provides routes to classes of thin-film transistors and mechanical energy harvesters that are soluble in water and biofluids. Experimental and theoretical studies of the operational aspects and dissolution properties of this type of transient electronics technology illustrate its various capabilities. Application opportunities range from resorbable biomedical implants, to environmentally dissolvable sensors, and degradable consumer electronics. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Materials for bioresorbable radio frequency electronics.

PubMed

Hwang, Suk-Won; Huang, Xian; Seo, Jung-Hun; Song, Jun-Kyul; Kim, Stanley; Hage-Ali, Sami; Chung, Hyun-Joong; Tao, Hu; Omenetto, Fiorenzo G; Ma, Zhenqiang; Rogers, John A

2013-07-12

Materials, device designs and manufacturing approaches are presented for classes of RF electronic components that are capable of complete dissolution in water or biofluids. All individual passive/active components as well as system-level examples such as wireless RF energy harvesting circuits exploit active materials that are biocompatible. The results provide diverse building blocks for physically transient forms of electronics, of particular potential value in bioresorbable medical implants with wireless power transmission and communication capabilities. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bronchoalveolar lavage fluid of lung cancer patients: mapping the uncharted waters using proteomics technology.

PubMed

Oumeraci, Tonio; Schmidt, Bernd; Wolf, Thomas; Zapatka, Marc; Pich, Andreas; Brors, Benedikt; Eils, Roland; Fleischhacker, Michael; Schlegelberger, Brigitte; von Neuhoff, Nils

2011-04-01

The search for proteome-level markers of non-small cell lung cancer (NSCLC) has been mainly limited to serum or cell line screening approaches up to this point. We would like to demonstrate by this proof-of-principle study investigating bronchoalveolar lavage fluid samples from a cohort of NSCLC and control patients, that this readily available biofluid might be a more suitable source for discovering clinically usable NSCLC biomarkers. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Ubiquitin C-Terminal Hydrolase-L1 as a Biomarker for Ischemic and Traumatic Brain Injury in Rats

DTIC Science & Technology

2010-01-01

specific enolase increases in plasma during and immediately after extracorporeal circulation . Ann. Thorac. Surg., 69, 750– 754. Johnston, S.C., Riddle, S.M...and eventually into circulating blood. Materials and methods Materials Sodium bicarbonate was from Sigma (St Louis, MO, USA) (catalog no. C-3041...ischemia is responsible for its release into circulating blood. In this study, the potential of UCH-L1 as a biofluid-based protein biomarker for two

A novel approach using metabolomics coupled with hematological and biochemical parameters to explain the enriching-blood effect and mechanism of unprocessed Angelica sinensis and its 4 kinds of processed products.

PubMed

Ji, Peng; Wei, Yanming; Hua, Yongli; Zhang, Xiaosong; Yao, Wanling; Ma, Qi; Yuan, Ziwen; Wen, Yanqiao; Yang, Chaoxue

2018-01-30

Angelica sinensis (AS), root of Angelica sinensis (Oliv.) Diels, an important kind of Chinese traditional herbal medicine, has been used for women to enrich the blood for thousands of years. It is mainly distributed in Gansu province of China. According to Traditional Chinese medicine usage, unprocessed AS (UAS) and its 4 kinds of processed products (ASs) are all used to treat different diseases or syndromes. The difference among the enriching-blood effects of ASs is unclear. And their exact mechanisms of enriching the blood are not fully understood. In this study, our aim is to compare the enriching-blood effect and explain the related mechanism of ASs, to lay the foundation for the blood deficiency diagnosis and the rational use of ASs in the clinic. ASs were used to intervene the blood deficiency syndrome model mice induced by acetyl phenylhydrazine (APH) and cyclophosphamide (CTX). A novel approach using metabolomics coupled with hematological and biochemical parameters to explain the enriching-blood effect and mechanism of ASs was established. The blood routine examination, ATPase, glucose-6-phosphate dehydrogenase, methemoglobin, glutathion peroxidase, glutathione reductase, and erythropoietin were measured. Two biofluids (plasma and urine) obtained from mice were analyzed with GC-MS. Distinct changes in metabolite patterns of the two biofluids after mice were induced by APH and CTX, and mice were intervened with ASs were analyzed using partial least squares-discriminant analysis. Potential biomarkers were found using a novel method including variable importance in the projection (VIP) >1.0, volcano plot analysis, and significance analysis of microarray. The results of hematological, biochemical parameters and the integrated metabolomics all showed the blood deficiency syndrome model was built successfully, ASs exhibited different degree of enriching-blood effect, and AS pached with alcohol (AAS) exhibited the best enriching-blood effect. 16 metabolites in the plasma and 8 metabolites in the urine were considered as the potential biomarkers. These metabolites were involved in 7 metabolic pathways which were concerned with the different enriching-blood effect mechanisms of ASs. The correlation analysis results confirmed L-Valine (plasma), Linoleic acid (urine), L-Aspartic acid (urine) and Cholesterol (urine) were strong positive or negative associated with biochemical indicators. The enriching-blood effects of ASs are different. The pathological mechanisms of blood deficiency syndrome and the enriching-blood effect mechanism of ASs are involved in 7 metabolic pathways. L-Valine (plasma), Linoleic acid (urine), L-Aspartic acid (urine), Cholesterol (urine) are four important biomarkers being related to the enriching-blood effect of ASs. The combination of VIP, volcano plot analysis and significance analysis of microarray is suitable for screening biomarkers in metabolomics study. They can lay the foundation for clinical practice. Copyright © 2017 Elsevier B.V. All rights reserved.

Lipoaspirate fluid proteome: A preliminary investigation by LC-MS top-down/bottom-up integrated platform of a high potential biofluid in regenerative medicine.

PubMed

Inserra, Ilaria; Martelli, Claudia; Cipollina, Mara; Cicione, Claudia; Iavarone, Federica; Taranto, Giuseppe Di; Barba, Marta; Castagnola, Massimo; Desiderio, Claudia; Lattanzi, Wanda

2016-04-01

The lipoaspirate fluid (LAF) is emerging as a potentially valuable source in regenerative medicine. In particular, our group recently demonstrated that it is able to exert osteoinductive properties in vitro. This original observation stimulated the investigation of the proteomic component of LAF, by means of LC-ESI-LTQ-Orbitrap-MS top-down/bottom-up integrated approach, which represents the object of the present study. Top-down analyses required the optimization of sample pretreatment procedures to enable the correct investigation of the intact proteome. Bottom-up analyses have been directly applied to untreated samples after monodimensional SDS-PAGE separation. The analysis of the acid-soluble fraction of LAF by top-down approach allowed demonstrating the presence of albumin and hemoglobin fragments (i.e. VV- and LVV-hemorphin-7), thymosins β4 and β10 peptides, ubiquitin and acyl-CoA binding protein; adipogenesis regulatory factor, perilipin-1 fragments, and S100A6, along with their PTMs. Part of the bottom-up proteomic profile was reproducibly found in both tested samples. The bottom-up approach allowed demonstrating the presence of proteins, listed among the components of adipose tissue and/or comprised within the ASCs intracellular content and secreted proteome. Our data provide a first glance on the LAF molecular profile, which is consistent with its tissue environment. LAF appeared to contain bioactive proteins, peptides and paracrine factors, suggesting its potential translational exploitation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Applications of tapered flat silver halide fiber elements for infrared biospectroscopy with aspects of optical stability and biocompatibility

NASA Astrophysics Data System (ADS)

Delbeck, Sven; Küpper, Lukas; Heise, Herbert M.

2018-02-01

Spectroscopic analysis of different biofluids and bodyfluid-like media has been realized by using tapered flat silver halide fiber elements as infrared biosensors. Optical stability and biocompatibility testing of the sensor elements have been performed with in-vitro samples under representative physiological conditions. After improving the reproducibility of manufacturing the sensor elements, the incoupling of radiation and the general handling including their chemical composition characterization, the fiber sensors were further optimized for the experiments. Stability tests in physiological solutions as well as porcine blood have shown that best results for biospectroscopic applications are available for the mid-IR fingerprint region, with the most stable behaviour as analyzed by the single-beam spectra. Despite several contrary reports, the silver halide material tested is toxic to cell lines chosen from the DIN standard specification for biocompatibility testing. Spectral changes as well as the results based on the DIN standard showed that pretreatment of the fibers is unavoidable to prevent direct contact of cells or human tissue and the silver halide material. Further applications of tapered flat silver halide fibers for the quantification of analytes in bodyfluids have also been tested by ensheathing the fiber-optic sensor element with a dialysis membrane. With the successfully produced prototype, results of diffusion rates and performance of a membrane-ensheathed fiber probe have been obtained. An invitro monitoring fiber sensor was developed aiming at the implantation of a microdialysis system for the analytical quantification of biomolecules such as glucose, lactate and others.

The ROSAS Cohort: A Prospective, Longitudinal Study of Biomarkers for Alzheimer's Disease. Strategy, Methods and Initial Results.

PubMed

de Mauléon, A; Soto, M; Kiyasova, V; Delrieu, J; Guignot, I; Galtier, S; Lilamand, M; Cantet, C; Lala, F; Sastre, N; Andrieu, S; Pueyo, M; Ousset, P J; Vellas, B

2017-01-01

The aims of the Research Of biomarkers in Alzheimer's diseaSe (ROSAS) study were to determine the biofluid and imaging biomarkers permitting an early diagnosis of Alzheimer's disease and better characterisation of cognitive and behavioural course of the pathology. This paper outlines the overall strategy, methodology of the study, baseline characteristics of the population and first longitudinal results from the ROSAS cohort. Longitudinal prospective monocentric observational study performed at the Alzheimer's disease Research centre in Toulouse. A total of 387 patients were studied and analyzed in 3 groups: 184 patients with dementia of Alzheimer's type, 96 patients with memory disorders without dementia (Mild Cognitive Impairment) and 107 patients without abnormal memory tests (control group), and were followed up during 4 years. Patient's sociodemographic characteristics, risk factors, medical conditions, previous and current medications, neuropsychological assessment and overall cognitive status were recorded. Blood and urine samples were collected at every year, Magnetic Resonance Imaging were performed at inclusion, after one year of follow-up and at the end of the study. At baseline, three different groups of the cohort differed interestingly in age, level of education, and in percentage of ApoEε4 carriers whereas the history of cardiovascular and endocrine pathologies were similar among the groups. During the follow-up period (3-4 years) 42 mild cognitive impairment patients (43.8%) progressed to dementia, 7 controls progressed into mild cognitive impairment and 1 patient in the control group converted from mild cognitive impairment group to dementia of Alzheimer's type group. During the first year of follow up, the incidence of progression from mild cognitive impairment to dementia of Alzheimer's type was 12.7 per 100, during the second year 33.9 per 100 and 46.7 per 100 for the third year. This paper presents the baseline characteristics of the unique French prospective monocenter study in which the natural course of dementia of Alzheimer's type was evaluated. Future analysis of blood and urine samples collection from the ROSAS study will permit to identify possible biofluid biomarkers predicting the early stages of the dementia of Alzheimer's type and risk of progression from Mild Cognitive Impairment to Alzheimer's disease.

Human plasma and serum extracellular small RNA reference profiles and their clinical utility.

PubMed

Max, Klaas E A; Bertram, Karl; Akat, Kemal Marc; Bogardus, Kimberly A; Li, Jenny; Morozov, Pavel; Ben-Dov, Iddo Z; Li, Xin; Weiss, Zachary R; Azizian, Azadeh; Sopeyin, Anuoluwapo; Diacovo, Thomas G; Adamidi, Catherine; Williams, Zev; Tuschl, Thomas

2018-06-05

Circulating extracellular RNAs (exRNAs) have the potential to serve as biomarkers for a wide range of medical conditions. However, limitations in existing exRNA isolation methods and a lack of knowledge on parameters affecting exRNA variability in human samples may hinder their successful discovery and clinical implementation. Using combinations of denaturants, reducing agents, proteolysis, and revised organic extraction, we developed an automated, high-throughput approach for recovery of exRNAs and exDNA from the same biofluid sample. We applied this method to characterize exRNAs from 312 plasma and serum samples collected from 13 healthy volunteers at 12 time points over a 2-month period. Small RNA cDNA library sequencing identified nearly twofold increased epithelial-, muscle-, and neuroendocrine-cell-specific miRNAs in females, while fasting and hormonal cycle showed little effect. External standardization helped to detect quantitative differences in erythrocyte and platelet-specific miRNA contributions and in miRNA concentrations between biofluids. It also helped to identify a study participant with a unique exRNA phenotype featuring a miRNA signature of up to 20-fold elevated endocrine-cell-specific miRNAs and twofold elevated total miRNA concentrations stable for over 1 year. Collectively, these results demonstrate an efficient and quantitative method to discern exRNA phenotypes and suggest that plasma and serum RNA profiles are stable over months and can be routinely monitored in long-term clinical studies. Copyright © 2018 the Author(s). Published by PNAS.

miRNAs as Circulating Biomarkers for Alzheimer's Disease and Parkinson's Disease.

PubMed

Mushtaq, Gohar; Greig, Nigel H; Anwar, Firoz; Zamzami, Mazin A; Choudhry, Hani; Shaik, Munvar M; Tamargo, Ian A; Kamal, Mohammad A

2016-01-01

Detection of biomarkers for neurodegenerative disorders (NDDs) within brain tissues of Alzheimer's disease (AD) and Parkinson's disease (PD) patients has always been hampered by our inability to access and biopsy tissue of key brain regions implicated in disease occurrence and progression. Currently, diagnosis of NDDs is principally based on clinical observations of symptoms that present at later stages of disease progression, followed by neuroimaging and, possibly, CSF evaluation. One way to potentially detect and diagnose NDDs at a far earlier stage is to screen for abnormal levels of specific disease markers within the peripheral circulation of patients with NDDs. Increasing evidence suggests that there is dysregulation of microRNAs (miRNAs) in NDDs. Peripheral blood mononuclear cells, as well as biofluids, such as plasma, serum, urine and cerebrospinal fluid, contain miRNAs that can be identified and quantified. Circulating miRNAs within blood and other biofluids may thus be characterized and used as non-invasive, diagnostic biomarkers that facilitate the early detection of disease and potentially the continual monitoring of disease progression for NDDs such as AD and PD. Plainly, such a screen is only possible with a clear understanding of which miRNAs change with disease, and when these changes occur during the progression of AD and PD. Such information is becoming increasingly available and, in the near future, may not only support disease diagnosis, but provide the opportunity to evaluate therapeutic interventions earlier in the disease process.

Electro-osmotic flow of power-law fluid and heat transfer in a micro-channel with effects of Joule heating and thermal radiation

NASA Astrophysics Data System (ADS)

Shit, G. C.; Mondal, A.; Sinha, A.; Kundu, P. K.

2016-11-01

A mathematical model has been developed for studying the electro-osmotic flow and heat transfer of bio-fluids in a micro-channel in the presence of Joule heating effects. The flow of bio-fluid is governed by the non-Newtonian power-law fluid model. The effects of thermal radiation and velocity slip condition have been examined in the case of hydrophobic channel. The Poisson-Boltzmann equation governing the electrical double layer field and a body force generated by the applied electric potential field are taken into consideration. The results presented here pertain to the case where the height of the channel is much greater than the thickness of electrical double layer comprising the Stern and diffuse layers. The expressions for flow characteristics such as velocity, temperature, shear stress and Nusselt number have been derived analytically under the purview of the present model. The results estimated on the basis of the data available in the existing scientific literatures are presented graphically. The effects of thermal radiation have an important bearing on the therapeutic procedure of hyperthermia, particularly in understanding the heat transfer in micro-channel in the presence of electric potential. The dimensionless Joule heating parameter has a reducing impact on Nusselt number for both pseudo-plastic and dilatant fluids, nevertheless its impact on Nusselt number is more pronounced for dilatant fluid. Furthermore, the effect of viscous dissipation has a significant role in controlling heat transfer and should not be neglected.

Electro-osmotic mobility of non-Newtonian fluids

PubMed Central

Zhao, Cunlu; Yang, Chun

2011-01-01

Electrokinetically driven microfluidic devices are usually used to analyze and process biofluids which can be classified as non-Newtonian fluids. Conventional electrokinetic theories resulting from Newtonian hydrodynamics then fail to describe the behaviors of these fluids. In this study, a theoretical analysis of electro-osmotic mobility of non-Newtonian fluids is reported. The general Cauchy momentum equation is simplified by incorporation of the Gouy–Chapman solution to the Poisson–Boltzmann equation and the Carreau fluid constitutive model. Then a nonlinear ordinary differential equation governing the electro-osmotic velocity of Carreau fluids is obtained and solved numerically. The effects of the Weissenberg number (Wi), the surface zeta potential (ψ¯s), the power-law exponent(n), and the transitional parameter (β) on electro-osmotic mobility are examined. It is shown that the results presented in this study for the electro-osmotic mobility of Carreau fluids are quite general so that the electro-osmotic mobility for the Newtonian fluids and the power-law fluids can be obtained as two limiting cases. PMID:21503161

[Bio-Resources and Database for Preemptive Medicine.

PubMed

Saito, Kuniaki

2016-05-01

Establishing a primary defense for the improvement of individual quality of life by epidemiology and various clinical studies applying bio-resources/database analysis is very important. Furthermore, recent studies on understanding the epigenetic regulatory mechanisms of developmental origins of health and diseases are attracting increasing interest. Therefore, the storing of not only bio-fluid (i.e., blood, urine) but also certain tissues (i.e., placenta, cord) is very important for research. The Resource Center for Health Science (RECHS) and Bio-databases Institute of Reproductive and Developmental Medicine (BIRD) have estab- lished Bio-bank and initiated a project based on the development and utilization of bio-resources/database, comprising personal health records (PHR), such as health/medical records including individual records of daily diet and exercise, physically consolidated with bio-resources, taken from the same individuals. These Bio-Resources/Database projects are very important for the establishment of preemptive medicine and un- derstanding the mechanisms of the developmental origins of health and diseases.

Ion-size dependent electroosmosis of viscoelastic fluids in microfluidic channels with interfacial slip

NASA Astrophysics Data System (ADS)

Mukherjee, Siddhartha; Goswami, Prakash; Dhar, Jayabrata; Dasgupta, Sunando; Chakraborty, Suman

2017-07-01

We report a study on the ion-size dependent electroosmosis of viscoelastic fluids in microfluidic channels with interfacial slip. Here, we derive an analytical solution for the potential distribution in a parallel plate microchannel, where the effects of finite sized ionic species are taken into account by invoking the free energy formalism. Following this, a purely electroosmotic flow of a simplified Phan-Thien-Tanner (sPTT) fluid is considered. For the sPTT model, linear, quadratic, and exponential kernels are chosen for the stress coefficient function describing its viscoelastic nature across various ranges of Deborah number. The theoretical framework presented in our analysis has been successfully compared with experimental results available in the literature. We believe that the implications of the considered effects on the net volumetric throughput will not only provide a deeper theoretical insight to interpret the electrokinetic data in the presence of ionic species but also serve as a fundamental design tool for novel electrokinetically driven lab-on-a-chip biofluidic devices.

Zinc oxide nanorods functionalized paper for protein preconcentration in biodiagnostics

NASA Astrophysics Data System (ADS)

Tiwari, Sadhana; Vinchurkar, Madhuri; Rao, V. Ramgopal; Garnier, Gil

2017-03-01

Distinguishing a specific biomarker from a biofluid sample containing a large variety of proteins often requires the selective preconcentration of that particular biomarker to a detectable level for analysis. Low-cost, paper-based device is an emerging opportunity in diagnostics. In the present study, we report a novel Zinc oxide nanorods functionalized paper platform for the preconcentration of Myoglobin, a cardiac biomarker. Zinc oxide nanorods were grown on a Whatman filter paper no. 1 via the standard hydrothermal route. The growth of Zinc oxide nanorods on paper was confirmed by a combination of techniques consisting of X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS,) scanning electron microscopy (SEM), and energy dispersive spectroscopy (EDX) analysis. The Zinc oxide nanorods modified Whatman filter paper (ZnO-NRs/WFP) was further tested for use as a protein preconcentrator. Paper-based ELISA was performed for determination of pre-concentration of cardiac marker protein Myoglobin using the new ZnO-NRs/WFP platform. The ZnO-NRs/WFP could efficiently capture the biomarker even from a very dilute solution (Myoglobin < 50 nM). Our ELISA results show a threefold enhancement in protein capture with ZnO-NRs/WFP compared to unmodified Whatman filter paper, allowing accurate protein analysis and showing the diagnostic concept.

Identification of Pulmonary Edema in Forensic Autopsy Cases of Sudden Cardiac Death Using Fourier Transform Infrared Microspectroscopy: A Pilot Study.

PubMed

Lin, Hancheng; Luo, Yiwen; Sun, Qiran; Zhang, Ji; Tuo, Ya; Zhang, Zhong; Wang, Lei; Deng, Kaifei; Chen, Yijiu; Huang, Ping; Wang, Zhenyuan

2018-02-20

Many studies have proven the usefulness of biofluid-based infrared spectroscopy in the clinical domain for diagnosis and monitoring the progression of diseases. Here we present a state-of-the-art study in the forensic field that employed Fourier transform infrared microspectroscopy for postmortem diagnosis of sudden cardiac death (SCD) by in situ biochemical investigation of alveolar edema fluid in lung tissue sections. The results of amide-related spectral absorbance analysis demonstrated that the pulmonary edema fluid of the SCD group was richer in protein components than that of the neurologic catastrophe (NC) and lethal multiple injuries (LMI) groups. The complementary results of unsupervised principle component analysis (PCA) and genetic algorithm-guided partial least-squares discriminant analysis (GA-PLS-DA) further indicated different global spectral band patterns of pulmonary edema fluids between these three groups. Ultimately, a random forest (RF) classification model for postmortem diagnosis of SCD was built and achieved good sensitivity and specificity scores of 97.3% and 95.5%, respectively. Classification predictions of unknown pulmonary edema fluid collected from 16 cases were also performed by the model, resulting in 100% correct discrimination. This pilot study demonstrates that FTIR microspectroscopy in combination with chemometrics has the potential to be an effective aid for postmortem diagnosis of SCD.

Silicon microneedle array for minimally invasive human health monitoring

NASA Astrophysics Data System (ADS)

Smith, Rosemary L.; Collins, Scott D.; Duy, Janice; Minogue, Timothy D.

2018-02-01

A silicon microneedle array with integrated microfluidic channels is presented, which is designed to extract dermal interstitial fluid (ISF) for biochemical analysis. ISF is a cell-free biofluid that is known to contain many of the same constituents as blood plasma, but the scope and dynamics of biomarker similarities are known for only a few components, most notably glucose. Dermal ISF is accessible just below the outer skin layer (epidermis), which can be reached and extracted with minimal sensation and tissue trauma by using a microneedle array. The microneedle arrays presented here are being developed to extract dermal ISF for off-chip profiling of nucleic acid constituents in order to identify potential biomarkers of disease. In order to assess sample volume requirements, preliminary RNA profiling was performed with suction blister ISF. The microneedles are batch fabricated using established silicon technology (low cost), are small in size, and can be integrated with sensors for on-chip analysis. This approach portends a more rapid, less expensive, self-administered assessment of human health than is currently achievable with blood sampling, especially in non-clinical and austere settings. Ultimately, a wearable device for monitoring a person's health in any setting is envisioned.

Acoustic Enrichment of Extracellular Vesicles from Biological Fluids.

PubMed

Ku, Anson; Lim, Hooi Ching; Evander, Mikael; Lilja, Hans; Laurell, Thomas; Scheding, Stefan; Ceder, Yvonne

2018-06-11

Extracellular vesicles (EVs) have emerged as a rich source of biomarkers providing diagnostic and prognostic information in diseases such as cancer. Large-scale investigations into the contents of EVs in clinical cohorts are warranted, but a major obstacle is the lack of a rapid, reproducible, efficient, and low-cost methodology to enrich EVs. Here, we demonstrate the applicability of an automated acoustic-based technique to enrich EVs, termed acoustic trapping. Using this technology, we have successfully enriched EVs from cell culture conditioned media and urine and blood plasma from healthy volunteers. The acoustically trapped samples contained EVs ranging from exosomes to microvesicles in size and contained detectable levels of intravesicular microRNAs. Importantly, this method showed high reproducibility and yielded sufficient quantities of vesicles for downstream analysis. The enrichment could be obtained from a sample volume of 300 μL or less, an equivalent to 30 min of enrichment time, depending on the sensitivity of downstream analysis. Taken together, acoustic trapping provides a rapid, automated, low-volume compatible, and robust method to enrich EVs from biofluids. Thus, it may serve as a novel tool for EV enrichment from large number of samples in a clinical setting with minimum sample preparation.

Molecularly imprinted polymer-sol-gel tablet toward micro-solid phase extraction: II. Determination of amphetamine in human urine samples by liquid chromatography-tandem mass spectrometry.

PubMed

El-Beqqali, Aziza; Andersson, Lars I; Jeppsson, Amin Dadoun; Abdel-Rehim, Mohamed

2017-09-15

Amphetamine selective molecularly imprinted sol-gel polymer tablets, MIP-tablets, for solid-phase microextraction of biofluid samples were prepared. An acetonitrile solution of deuterated amphetamine template and silane precursor, 3-(propylmethacrylate) trimethoxysilane, was soaked into the pores of polyethylene tablet substrates and polymerized by an acid-catalysed sol-gel process. Application of the resultant MIP-tablets to extract amphetamine from human urine samples followed by LC-MS/MS analysis was investigated. The extraction protocol was optimised with respect to pH of sample, addition of sodium chloride, extraction time, desorption solvent and desorption time. The final analysis method determined amphetamine in human urine with a limit of detection (LOD) of 1.0ng/mL and a lower limit of quantification (LLOQ) of 5ng/mL. Validation demonstrated accuracy of the method was 91.0-104.0% and inter-assay precision was 4.8-8.5% (RSD). Extraction recovery was 80%. The MIP-tablets could be re-used and the same tablet could be employed for more than twenty extractions. Copyright © 2017 Elsevier B.V. All rights reserved.

Mass spectrometric based approaches in urine metabolomics and biomarker discovery.

PubMed

Khamis, Mona M; Adamko, Darryl J; El-Aneed, Anas

2017-03-01

Urine metabolomics has recently emerged as a prominent field for the discovery of non-invasive biomarkers that can detect subtle metabolic discrepancies in response to a specific disease or therapeutic intervention. Urine, compared to other biofluids, is characterized by its ease of collection, richness in metabolites and its ability to reflect imbalances of all biochemical pathways within the body. Following urine collection for metabolomic analysis, samples must be immediately frozen to quench any biogenic and/or non-biogenic chemical reactions. According to the aim of the experiment; sample preparation can vary from simple procedures such as filtration to more specific extraction protocols such as liquid-liquid extraction. Due to the lack of comprehensive studies on urine metabolome stability, higher storage temperatures (i.e. 4°C) and repetitive freeze-thaw cycles should be avoided. To date, among all analytical techniques, mass spectrometry (MS) provides the best sensitivity, selectivity and identification capabilities to analyze the majority of the metabolite composition in the urine. Combined with the qualitative and quantitative capabilities of MS, and due to the continuous improvements in its related technologies (i.e. ultra high-performance liquid chromatography [UPLC] and hydrophilic interaction liquid chromatography [HILIC]), liquid chromatography (LC)-MS is unequivocally the most utilized and the most informative analytical tool employed in urine metabolomics. Furthermore, differential isotope tagging techniques has provided a solution to ion suppression from urine matrix thus allowing for quantitative analysis. In addition to LC-MS, other MS-based technologies have been utilized in urine metabolomics. These include direct injection (infusion)-MS, capillary electrophoresis-MS and gas chromatography-MS. In this article, the current progresses of different MS-based techniques in exploring the urine metabolome as well as the recent findings in providing potentially diagnostic urinary biomarkers are discussed. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:115-134, 2017. © 2015 Wiley Periodicals, Inc.

Bio-analytical applications of mid-infrared spectroscopy using silver halide fiber-optic probes1

NASA Astrophysics Data System (ADS)

Heise, H. M.; Küpper, L.; Butvina, L. N.

2002-10-01

Infrared-spectroscopy has proved to be a powerful method for the study of various biomedical samples, in particular for in-vitro analysis in the clinical laboratory and for non-invasive diagnostics. In general, the analysis of biofluids such as whole blood, urine, microdialysates and bioreactor broth media takes advantage of the fact that a multitude of analytes can be quantified simultaneously and rapidly without the need for reagents. Progress in the quality of infrared silver halide fibers enabled us to construct several flexible fiber-optic probes of different geometries, which are particularly suitable for the measurement of small biosamples. Recent trends show that dry film measurements by mid-infrared spectroscopy could revolutionize analytical tools in the clinical chemistry laboratory, and an example is given. Infrared diagnostic tools show a promising potential for patients, and minimal-invasive blood glucose assays or skin tissue pathology in particular cannot be left out using mid-infrared fiber-based probes. Other applications include the measurement of skin samples including penetration studies of vitamins and constituents of cosmetic cream formulations. A further field is the micro-domain analysis of biopsy samples from bog mummified corpses, and recent results on the chemistry of dermis and hair samples are reported. Another field of application, for which results are reported, is food analysis and bio-reactor monitoring.

Laboratory diagnosis of creatine deficiency syndromes: a technical standard and guideline of the American College of Medical Genetics and Genomics.

PubMed

Sharer, J Daniel; Bodamer, Olaf; Longo, Nicola; Tortorelli, Silvia; Wamelink, Mirjam M C; Young, Sarah

2017-02-01

Disclaimer: These ACMG Standards and Guidelines are intended as an educational resource for clinical laboratory geneticists to help them provide quality clinical laboratory genetic services. Adherence to these standards and guidelines is voluntary and does not necessarily assure a successful medical outcome. These Standards and Guidelines should not be considered inclusive of all proper procedures and tests or exclusive of others that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, clinical laboratory geneticists should apply their professional judgment to the specific circumstances presented by the patient or specimen. Clinical laboratory geneticists are encouraged to document in the patient's record the rationale for the use of a particular procedure or test, whether or not it is in conformance with these Standards and Guidelines. They also are advised to take notice of the date any particular guideline was adopted, and to consider other relevant medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures.Cerebral creatine deficiency syndromes are neurometabolic conditions characterized by intellectual disability, seizures, speech delay, and behavioral abnormalities. Several laboratory methods are available for preliminary and confirmatory diagnosis of these conditions, including measurement of creatine and related metabolites in biofluids using liquid chromatography-tandem mass spectrometry or gas chromatography-mass spectrometry, enzyme activity assays in cultured cells, and DNA sequence analysis. These guidelines are intended to standardize these procedures to help optimize the diagnosis of creatine deficiency syndromes. While biochemical methods are emphasized, considerations for confirmatory molecular testing are also discussed, along with variables that influence test results and interpretation.Genet Med 19 2, 256-263.

Usage of CO2 microbubbles as flow-tracing contrast media in X-ray dynamic imaging of blood flows.

PubMed

Lee, Sang Joon; Park, Han Wook; Jung, Sung Yong

2014-09-01

X-ray imaging techniques have been employed to visualize various biofluid flow phenomena in a non-destructive manner. X-ray particle image velocimetry (PIV) was developed to measure velocity fields of blood flows to obtain hemodynamic information. A time-resolved X-ray PIV technique that is capable of measuring the velocity fields of blood flows under real physiological conditions was recently developed. However, technical limitations still remained in the measurement of blood flows with high image contrast and sufficient biocapability. In this study, CO2 microbubbles as flow-tracing contrast media for X-ray PIV measurements of biofluid flows was developed. Human serum albumin and CO2 gas were mechanically agitated to fabricate CO2 microbubbles. The optimal fabricating conditions of CO2 microbubbles were found by comparing the size and amount of microbubbles fabricated under various operating conditions. The average size and quantity of CO2 microbubbles were measured by using a synchrotron X-ray imaging technique with a high spatial resolution. The quantity and size of the fabricated microbubbles decrease with increasing speed and operation time of the mechanical agitation. The feasibility of CO2 microbubbles as a flow-tracing contrast media was checked for a 40% hematocrit blood flow. Particle images of the blood flow were consecutively captured by the time-resolved X-ray PIV system to obtain velocity field information of the flow. The experimental results were compared with a theoretically amassed velocity profile. Results show that the CO2 microbubbles can be used as effective flow-tracing contrast media in X-ray PIV experiments.

Immunoaffinity based methods are superior to kits for purification of prostate derived extracellular vesicles from plasma samples.

PubMed

Brett, Sabine I; Lucien, Fabrice; Guo, Charles; Williams, Karla C; Kim, Yohan; Durfee, Paul N; Brinker, C J; Chin, Joseph I; Yang, Jun; Leong, Hon S

2017-05-01

The ability to isolate extracellular vesicles (EVs) such as exosomes or microparticles is an important method that is currently not standardized. While commercially available kits offer purification of EVs from biofluids, such purified EV samples will also contain non-EV entities such as soluble protein and nucleic acids that could confound subsequent experimentation. Ideally, only EVs would be isolated and no soluble protein would be present in the final EV preparation. We compared commercially available EV isolation kits with immunoaffinity purification techniques and evaluated our final EV preparations using atomic force microscopy (AFM) and nanoscale flow cytometry (NFC). AFM is the only modality capable of detecting distinguishing soluble protein from EVs which is important for downstream proteomics approaches. NFC is the only technique capable of quantitating the proportion of target EVs to non-target EVs in the final EV preparation. To determine enrichment of prostate derived EVs relative to non-target MPs, anti-PSMA (Prostate Specific Membrane Antigen) antibodies were used in NFC. Antibody-based immunoaffinity purification generated the highest quality of prostate derived EV preparations due to the lack of protein and RNA present in the samples. All kits produced poor purity EV preparations that failed to deplete the sample of plasma protein. While attractive due to their ease of use, EV purification kits do not provide substantial improvements in isolation of EVs from biofluids such as plasma. Immunoaffinity approaches are more efficient and economical and will also eliminate a significant portion of plasma proteins which is necessary for downstream approaches. © 2017 Wiley Periodicals, Inc.

[Utilisation of salivary markers in nephrology].

PubMed

Podracká, Ľudmila; Celec, Peter; Šebeková, Katarína

2016-01-01

Saliva has a broad diagnostic potential which can be used for detection many pathological conditions including renal dysfunction. In saliva can be measured concentration of urea and creatinine as well as the other uremic markers. Saliva urea nitrogen and creatinine and blood urea and creatinine highly correlated therefore might be used for screening in patients with CKD. Saliva collection is truly non-invasive and is especially suitable for small children and elderly patients. Recently, semiquantitative saliva urea test strip is available. Saliva might become promising dia-gnostic biofluid in nephrological practice.Key words: chronic kidney disease - renal failure - salivary dipstick - salivary markers.

Real-Time, Single-Step Bioassay Using Nanoplasmonic Resonator With Ultra-High Sensitivity

NASA Technical Reports Server (NTRS)

Zhang, Xiang (Inventor); Chen, Fanqing Frank (Inventor); Su, Kai-Hang (Inventor); Wei, Qi-Huo (Inventor); Ellman, Jonathan A. (Inventor); Sun, Cheng (Inventor)

2014-01-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

DOEpatents

Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng

2014-04-01

A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

Oral Biofluid Biomarker Research: Current Status and Emerging Frontiers

PubMed Central

Wang, Austin; Wang, Chris P.; Tu, Michael; Wong, David T.W.

2016-01-01

Salivary diagnostics is a rapidly advancing field that offers clinicians and patients the potential of rapid, noninvasive diagnostics with excellent accuracy. In order for the complete realization of the potential of saliva, however, extensive profiling of constituents must be conducted and diagnostic biomarkers must be thoroughly validated. This article briefly overviews the process of conducting a study of salivary biomarkers in a patient cohort and highlights the studies that have been conducted on different classes of molecules in the saliva. Emerging frontiers in salivary diagnostics research that may significantly advance the field will also be highlighted. PMID:27999326

Working Up a Good Sweat – The Challenges of Standardising Sweat Collection for Metabolomics Analysis

PubMed Central

Hussain, Joy N; Mantri, Nitin; Cohen, Marc M

2017-01-01

Introduction Human sweat is a complex biofluid of interest to diverse scientific fields. Metabolomics analysis of sweat promises to improve screening, diagnosis and self-monitoring of numerous conditions through new applications and greater personalisation of medical interventions. Before these applications can be fully developed, existing methods for the collection, handling, processing and storage of human sweat need to be revised. This review presents a cross-disciplinary overview of the origins, composition, physical characteristics and functional roles of human sweat, and explores the factors involved in standardising sweat collection for metabolomics analysis. Methods A literature review of human sweat analysis over the past 10 years (2006–2016) was performed to identify studies with metabolomics or similarly applicable ‘omics’ analysis. These studies were reviewed with attention to sweat induction and sampling techniques, timing of sweat collection, sweat storage conditions, laboratory derivation, processing and analytical platforms. Results Comparative analysis of 20 studies revealed numerous factors that can significantly impact the validity, reliability and reproducibility of sweat analysis including: anatomical site of sweat sampling, skin integrity and preparation; temperature and humidity at the sweat collection sites; timing and nature of sweat collection; metabolic quenching; transport and storage; qualitative and quantitative measurements of the skin microbiota at sweat collection sites; and individual variables such as diet, emotional state, metabolic conditions, pharmaceutical, recreational drug and supplement use. Conclusion Further development of standard operating protocols for human sweat collection can open the way for sweat metabolomics to significantly add to our understanding of human physiology in health and disease. PMID:28798503

Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS

NASA Astrophysics Data System (ADS)

Sitnikov, Dmitri G.; Monnin, Cian S.; Vuckovic, Dajana

2016-12-01

The comparison of extraction methods for global metabolomics is usually executed in biofluids only and focuses on metabolite coverage and method repeatability. This limits our detailed understanding of extraction parameters such as recovery and matrix effects and prevents side-by-side comparison of different sample preparation strategies. To address this gap in knowledge, seven solvent-based and solid-phase extraction methods were systematically evaluated using standard analytes spiked into both buffer and human plasma. We compared recovery, coverage, repeatability, matrix effects, selectivity and orthogonality of all methods tested for non-lipid metabolome in combination with reversed-phased and mixed-mode liquid chromatography mass spectrometry analysis (LC-MS). Our results confirmed wide selectivity and excellent precision of solvent precipitations, but revealed their high susceptibility to matrix effects. The use of all seven methods showed high overlap and redundancy which resulted in metabolite coverage increases of 34-80% depending on LC-MS method employed as compared to the best single extraction protocol (methanol/ethanol precipitation) despite 7x increase in MS analysis time and sample consumption. The most orthogonal methods to methanol-based precipitation were ion-exchange solid-phase extraction and liquid-liquid extraction using methyl-tertbutyl ether. Our results help facilitate rational design and selection of sample preparation methods and internal standards for global metabolomics.

Development of a method for enhancing metabolomics coverage of human sweat by gas chromatography-mass spectrometry in high resolution mode.

PubMed

Delgado-Povedano, M M; Calderón-Santiago, M; Priego-Capote, F; Luque de Castro, M D

2016-01-28

Sweat has recently gained popularity as clinical sample in metabolomics analysis as it is a non-invasive biofluid the composition of which could be modified by certain pathologies, as is the case with cystic fibrosis that increases chloride levels in sweat. However, the whole composition of sweat is still unknown and there is a lack of analytical strategies for sweat analysis. The aim of the present study was to develop and validate a method for metabolomic analysis of human sweat by gas chromatography-time of flight/mass spectrometry (GC-TOF/MS) in high resolution mode. Thus, different sample preparation strategies were compared to check their effect on the profile of sweat metabolites. Sixty-six compounds were tentatively identified by the obtained MS information. Amino acids, dicarboxylic acids and other interesting metabolites such as myo-inositol and urocanic acid were identified. Among the tested protocols, methyoxiamination plus silylation after deproteinization was the most suited option to obtain a representative snapshot of sweat metabolome. The intra-day repeatability of the method ranged from 0.60 to 16.99% and the inter-day repeatability from 2.75 to 31.25%. As most of the identified metabolites are involved in key biochemical pathways, this study opens new possibilities to the use of sweat as a source of metabolite biomarkers of specific disorders. Copyright © 2015 Elsevier B.V. All rights reserved.

Systematic Assessment of Seven Solvent and Solid-Phase Extraction Methods for Metabolomics Analysis of Human Plasma by LC-MS

PubMed Central

Sitnikov, Dmitri G.; Monnin, Cian S.; Vuckovic, Dajana

2016-01-01

The comparison of extraction methods for global metabolomics is usually executed in biofluids only and focuses on metabolite coverage and method repeatability. This limits our detailed understanding of extraction parameters such as recovery and matrix effects and prevents side-by-side comparison of different sample preparation strategies. To address this gap in knowledge, seven solvent-based and solid-phase extraction methods were systematically evaluated using standard analytes spiked into both buffer and human plasma. We compared recovery, coverage, repeatability, matrix effects, selectivity and orthogonality of all methods tested for non-lipid metabolome in combination with reversed-phased and mixed-mode liquid chromatography mass spectrometry analysis (LC-MS). Our results confirmed wide selectivity and excellent precision of solvent precipitations, but revealed their high susceptibility to matrix effects. The use of all seven methods showed high overlap and redundancy which resulted in metabolite coverage increases of 34–80% depending on LC-MS method employed as compared to the best single extraction protocol (methanol/ethanol precipitation) despite 7x increase in MS analysis time and sample consumption. The most orthogonal methods to methanol-based precipitation were ion-exchange solid-phase extraction and liquid-liquid extraction using methyl-tertbutyl ether. Our results help facilitate rational design and selection of sample preparation methods and internal standards for global metabolomics. PMID:28000704

Not All Biofluids Are Created Equal: Chewing Over Salivary Diagnostics and the Epigenome

PubMed Central

Wren, M.E.; Shirtcliff, E.A.; Drury, Stacy S.

2015-01-01

Purpose This article describes progress to date in the characterization of the salivary epigenome and considers the importance of previous work in the salivary microbiome, proteome, endocrine analytes, genome, and transcriptome. Methods PubMed and Web of Science were used to extensively search the existing literature (original research and reviews) related to salivary diagnostics and bio-marker development, of which 125 studies were examined. This article was derived from the most relevant 73 sources highlighting the recent state of the evolving field of salivary epigenomics and contributing significantly to the foundational work in saliva-based research. Findings Validation of any new saliva-based diagnostic or analyte will require comparison to previously accepted standards established in blood. Careful attention to the collection, processing, and analysis of salivary analytes is critical for the development and implementation of newer applications that include genomic, transcriptomic, and epigenomic markers. All these factors must be integrated into initial study design. Implications This commentary highlights the appeal of the salivary epigenome for translational applications and its utility in future studies of development and the interface among environment, disease, and health. PMID:25778408

Subnanogram determination of aniracetam in pharmaceutical preparations and biofluids by flow injection analysis with chemiluminescence detection based on its enhancement of the myoglobin-luminol reaction.

PubMed

Shao, Xiaodong; Li, Ying; Li, Fagen; Liu, Yangqin; Song, Zhenghua

2011-01-01

A novel flow injection chemiluminescence method with a myoglobin-luminol system is described for determining aniracetam. Myoglobin-bound aniracetam produced a complex that catalyzed the chemiluminescence reaction between luminol and myoglobin, leading to fast chemiluminescence. The chemiluminescence intensity in the presence of aniracetam was remarkably enhanced compared with that in the absence of aniracetam. Under the optimum reaction conditions the chemiluminescence increment produced was proportional to the concentration of aniracetam in the range of 0.1-1000.0 ng/mL (R2 = 0.9992), with a detection limit of 0.03 ng/mL (3delta). At a flow rate of 2.0 mL/min, the whole process, including sampling and washing, could be completed in 0.5 min, offering a sampling efficiency of 120/h; the RSD was less than 3.0% (n = 5). The method was satisfactory for determination of aniracetam in pharmaceutical preparations and human urine and serum samples. A possible mechanism of the reaction is also discussed.

Differential Attenuation of NMR Signals by Complementary Ion-Exchange Resin Beads for De Novo Analysis of Complex Metabolomics Mixtures.

PubMed

Zhang, Bo; Yuan, Jiaqi; Brüschweiler, Rafael

2017-07-12

A primary goal of metabolomics is the characterization of a potentially very large number of metabolites that are part of complex mixtures. Application to biofluids and tissue samples offers insights into biochemical metabolic pathways and their role in health and disease. 1D 1 H and 2D 13 C- 1 H HSQC NMR spectra are most commonly used for this purpose. They yield quantitative information about each proton of the mixture, but do not tell which protons belong to the same molecule. Interpretation requires the use of NMR spectral databases, which naturally limits these investigations to known metabolites. Here, a new method is presented that uses complementary ion exchange resin beads to differentially attenuate 2D NMR cross-peaks that belong to different metabolites. Based on their characteristic attenuation patterns, cross-peaks could be clustered and assigned to individual molecules, including unknown metabolites with multiple spin systems, as demonstrated for a metabolite model mixture and E. coli cell lysate. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Precise quantitation of 136 urinary proteins by LC/MRM-MS using stable isotope labeled peptides as internal standards for biomarker discovery and/or verification studies.

PubMed

Percy, Andrew J; Yang, Juncong; Hardie, Darryl B; Chambers, Andrew G; Tamura-Wells, Jessica; Borchers, Christoph H

2015-06-15

Spurred on by the growing demand for panels of validated disease biomarkers, increasing efforts have focused on advancing qualitative and quantitative tools for more highly multiplexed and sensitive analyses of a multitude of analytes in various human biofluids. In quantitative proteomics, evolving strategies involve the use of the targeted multiple reaction monitoring (MRM) mode of mass spectrometry (MS) with stable isotope-labeled standards (SIS) used for internal normalization. Using that preferred approach with non-invasive urine samples, we have systematically advanced and rigorously assessed the methodology toward the precise quantitation of the largest, multiplexed panel of candidate protein biomarkers in human urine to date. The concentrations of the 136 proteins span >5 orders of magnitude (from 8.6 μg/mL to 25 pg/mL), with average CVs of 8.6% over process triplicate. Detailed here is our quantitative method, the analysis strategy, a feasibility application to prostate cancer samples, and a discussion of the utility of this method in translational studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Characterization of an RNA aptamer against HPV-16 L1 virus-like particles.

PubMed

Leija-Montoya, Ana Gabriela; Benítez-Hess, María Luisa; Toscano-Garibay, Julia Dolores; Alvarez-Salas, Luis Marat

2014-10-01

The human papillomavirus (HPV) capsid is mainly composed of the L1 protein that can self-assemble into virus-like particles (VLPs) that are structurally and immunologically similar to the infectious virions. We report here the characterization of RNA aptamers that recognize baculovirus-produced HPV-16 L1 VLPs. Interaction and slot-blot binding assays showed that all isolated aptamers efficiently bound HPV-16 VLPs, although the Sc5-c3 aptamer showed the highest specificity and affinity (Kd=0.05 pM). Sc5-c3 secondary structure consisted of a hairpin with a symmetric bubble and an unstructured 3'end. Biochemical and genetic analyses showed that the Sc5-c3 main loop is directly involved on VLPs binding. In particular, binding specificity appeared mediated by five non-consecutive nucleotide positions. Experiments using bacterial-produced HPV-16 L1 resulted in low Sc5-c3 binding, suggesting that recognition of HPV-16 L1 VLPs relies on quaternary structure features not present in bacteria-produced L1 protein. Sc5-c3 produced specific and stable binding to HPV-16 L1 VLPs even in biofluid protein mixes and thus it may provide a potential diagnostic tool for active HPV infection.

Characterization of an RNA Aptamer Against HPV-16 L1 Virus-Like Particles

PubMed Central

Leija-Montoya, Ana Gabriela; Benítez-Hess, María Luisa; Toscano-Garibay, Julia Dolores

2014-01-01

The human papillomavirus (HPV) capsid is mainly composed of the L1 protein that can self-assemble into virus-like particles (VLPs) that are structurally and immunologically similar to the infectious virions. We report here the characterization of RNA aptamers that recognize baculovirus-produced HPV-16 L1 VLPs. Interaction and slot-blot binding assays showed that all isolated aptamers efficiently bound HPV-16 VLPs, although the Sc5-c3 aptamer showed the highest specificity and affinity (Kd=0.05 pM). Sc5-c3 secondary structure consisted of a hairpin with a symmetric bubble and an unstructured 3′end. Biochemical and genetic analyses showed that the Sc5-c3 main loop is directly involved on VLPs binding. In particular, binding specificity appeared mediated by five non-consecutive nucleotide positions. Experiments using bacterial-produced HPV-16 L1 resulted in low Sc5-c3 binding, suggesting that recognition of HPV-16 L1 VLPs relies on quaternary structure features not present in bacteria-produced L1 protein. Sc5-c3 produced specific and stable binding to HPV-16 L1 VLPs even in biofluid protein mixes and thus it may provide a potential diagnostic tool for active HPV infection. PMID:25111024

A Comprehensive Metabolomic Investigation in Urine of Mice Exposed to Strontium-90

PubMed Central

Goudarzi, Maryam; Weber, Waylon M.; Mak, Tytus D.; Chung, Juijung; Doyle-Eisele, Melanie; Melo, Dunstana R.; Strawn, Steven J.; Brenner, David J.; Guilmette, Raymond A.; Fornace, Albert J.

2017-01-01

Internal emitters such as Strontium-90 (90Sr) pose a substantial health risk during and immediately after a nuclear disaster or detonation of an improvised device. The environmental persistency and potency of 90Sr calls for urgent development of high-throughput tests to establish levels of exposure and to help triage potentially exposed individuals who were in the immediate area of the disaster. In response to these concerns, our team focused on developing a robust metabolomic profile for 90Sr exposure in urine using a mouse model. The sensitivity of modern time-of-flight mass spectrometry (TOFMS) combined with the separation power of ultra performance liquid chromatography (UPLC) was used to determine perturbations in the urinary metabolome of mice exposed to 90Sr. The recently developed statistical suite, MetaboLyzer, was used to explore the mass spectrometry data. The results indicated a significant change in the urinary abundances of metabolites pertaining to butanoate metabolism, vitamin B metabolism, glutamate and fatty acid oxidation. All of these pathways are either directly or indirectly connected to the central energy production pathway, the tricarboxylic acid (TCA) cycle. To our knowledge, this is the first in vivo metabolomics to evaluate the effects of exposure to 90Sr using the easily accessible biofluid, urine. PMID:26010713

A Comprehensive Metabolomic Investigation in Urine of Mice Exposed to Strontium-90.

PubMed

Goudarzi, Maryam; Weber, Waylon M; Mak, Tytus D; Chung, Juijung; Doyle-Eisele, Melanie; Melo, Dunstana R; Strawn, Steven J; Brenner, David J; Guilmette, Raymond A; Fornace, Albert J

2015-06-01

Internal emitters such as Strontium-90 ((90)Sr) pose a substantial health risk during and immediately after a nuclear disaster or detonation of an improvised device. The environmental persistency and potency of (90)Sr calls for urgent development of high-throughput tests to establish levels of exposure and to help triage potentially exposed individuals who were in the immediate area of the disaster. In response to these concerns, our team focused on developing a robust metabolomic profile for (90)Sr exposure in urine using a mouse model. The sensitivity of modern time-of-flight mass spectrometry (TOFMS) combined with the separation power of ultra performance liquid chromatography (UPLC) was used to determine perturbations in the urinary metabolome of mice exposed to (90)Sr. The recently developed statistical suite, MetaboLyzer, was used to explore the mass spectrometry data. The results indicated a significant change in the urinary abundances of metabolites pertaining to butanoate metabolism, vitamin B metabolism, glutamate and fatty acid oxidation. All of these pathways are either directly or indirectly connected to the central energy production pathway, the tricarboxylic acid (TCA) cycle. To our knowledge, this is the first in vivo metabolomics to evaluate the effects of exposure to (90)Sr using the easily accessible biofluid, urine.

Organic solvent-free air-assisted liquid-liquid microextraction for optimized extraction of illegal azo-based dyes and their main metabolite from spices, cosmetics and human bio-fluid samples in one step.

PubMed

Barfi, Behruz; Asghari, Alireza; Rajabi, Maryam; Sabzalian, Sedigheh

2015-08-15

Air-assisted liquid-liquid microextraction (AALLME) has unique capabilities to develop as an organic solvent-free and one-step microextraction method, applying ionic-liquids as extraction solvent and avoiding centrifugation step. Herein, a novel and simple eco-friendly method, termed one-step air-assisted liquid-liquid microextraction (OS-AALLME), was developed to extract some illegal azo-based dyes (including Sudan I to IV, and Orange G) from food and cosmetic products. A series of experiments were investigated to achieve the most favorable conditions (including extraction solvent: 77μL of 1-Hexyl-3-methylimidazolium hexafluorophosphate; sample pH 6.3, without salt addition; and extraction cycles: 25 during 100s of sonication) using a central composite design strategy. Under these conditions, limits of detection, linear dynamic ranges, enrichment factors and consumptive indices were in the range of 3.9-84.8ngmL(-1), 0.013-3.1μgmL(-1), 33-39, and 0.13-0.15, respectively. The results showed that -as well as its simplicity, fastness, and use of no hazardous disperser and extraction solvents- OS-AALLME is an enough sensitive and efficient method for the extraction of these dyes from complex matrices. After optimization and validation, OS-AALLME was applied to estimate the concentration of 1-amino-2-naphthol in human bio-fluids as a main reductive metabolite of selected dyes. Levels of 1-amino-2-naphthol in plasma and urinary excretion suggested that this compound may be used as a new potential biomarker of these dyes in human body. Copyright © 2015 Elsevier B.V. All rights reserved.

Complex and biofluids: From Maxwell to nowadays

NASA Astrophysics Data System (ADS)

Misbah, Chaouqi

2009-11-01

Complex fluids are the rule in biology and in many industrial applications. Typical examples are blood, cartilage, and polymer solutions. Unlike water (as well as domestic oils, soft clear drinks, and so on), the law(s) describing the behavior of complex fluids are not yet fully established. The complexity arises from strong coupling between microscopic scales (like the motion of a red blood cell in the case of blood, or a polymer molecule for a polymer solution) and the global scale of the flow (say at the scale of a blood artery, or a channel in laboratory experiments). In this issue entitled Complex and Biofluids a large panel of experimental and theoretical problems of complex fluids is exposed. The topics range from dilute polymer solutions, food products, to biology (blood flow, cell and tissue mechanics). One of the earliest model put forward as an attempt to describe a complex fluid was suggested a long time ago by James Clerk Maxwell (in 1867). Other famous scientists, like Einstein (in 1906), and Taylor (in 1932) have made important contributions to the field, but the topic of complex fluids still continues to pose a formidable challenge to science. This field has known during the past decade an unbelievable upsurge of interest in many branches of science (physics, mechanics, chemistry, biology, medical science, mathematics, and so on). Understanding complex fluids is viewed as one of the biggest challenge of the present century. This synthesis will provide a simple introduction to the topic, summarize the main contribution of this issue, and list major open questions in this field. To cite this article: C. Misbah, C. R. Physique 10 (2009).

Urine Metabolomics Analysis for Biomarker Discovery and Detection of Jaundice Syndrome in Patients With Liver Disease*

PubMed Central

Wang, Xijun; Zhang, Aihua; Han, Ying; Wang, Ping; Sun, Hui; Song, Gaochen; Dong, Tianwei; Yuan, Ye; Yuan, Xiaoxia; Zhang, Miao; Xie, Ning; Zhang, He; Dong, Hui; Dong, Wei

2012-01-01

Metabolomics is a powerful new technology that allows for the assessment of global metabolic profiles in easily accessible biofluids and biomarker discovery in order to distinguish between diseased and nondiseased status information. Deciphering the molecular networks that distinguish diseases may lead to the identification of critical biomarkers for disease aggressiveness. However, current diagnostic methods cannot predict typical Jaundice syndrome (JS) in patients with liver disease and little is known about the global metabolomic alterations that characterize JS progression. Emerging metabolomics provides a powerful platform for discovering novel biomarkers and biochemical pathways to improve diagnostic, prognostication, and therapy. Therefore, the aim of this study is to find the potential biomarkers from JS disease by using a nontarget metabolomics method, and test their usefulness in human JS diagnosis. Multivariate data analysis methods were utilized to identify the potential biomarkers. Interestingly, 44 marker metabolites contributing to the complete separation of JS from matched healthy controls were identified. Metabolic pathways (Impact-value≥0.10) including alanine, aspartate, and glutamate metabolism and synthesis and degradation of ketone bodies were found to be disturbed in JS patients. This study demonstrates the possibilities of metabolomics as a diagnostic tool in diseases and provides new insight into pathophysiologic mechanisms. PMID:22505723

Stretchable, wireless sensors and functional substrates for epidermal characterization of sweat.

PubMed

Huang, Xian; Liu, Yuhao; Chen, Kaile; Shin, Woo-Jung; Lu, Ching-Jui; Kong, Gil-Woo; Patnaik, Dwipayan; Lee, Sang-Heon; Cortes, Jonathan Fajardo; Rogers, John A

2014-08-13

This paper introduces materials and architectures for ultrathin, stretchable wireless sensors that mount on functional elastomeric substrates for epidermal analysis of biofluids. Measurement of the volume and chemical properties of sweat via dielectric detection and colorimetry demonstrates some capabilities. Here, inductively coupled sensors consisting of LC resonators with capacitive electrodes show systematic responses to sweat collected in microporous substrates. Interrogation occurs through external coils placed in physical proximity to the devices. The substrates allow spontaneous sweat collection through capillary forces, without the need for complex microfluidic handling systems. Furthermore, colorimetric measurement modes are possible in the same system by introducing indicator compounds into the depths of the substrates, for sensing specific components (OH(-) , H(+) , Cu(+) , and Fe(2+) ) in the sweat. The complete devices offer Young's moduli that are similar to skin, thus allowing highly effective and reliable skin integration without external fixtures. Experimental results demonstrate volumetric measurement of sweat with an accuracy of 0.06 μL/mm(2) with good stability and low drift. Colorimetric responses to pH and concentrations of various ions provide capabilities relevant to analysis of sweat. Similar materials and device designs can be used in monitoring other body fluids. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests

PubMed Central

Liu, Tao; Hossain, Mahmud; Schepmoes, Athena A.; Fillmore, Thomas L.; Sokoll, Lori J.; Kronewitter, Scott R.; Izmirlian, Grant; Shi, Tujin; Qian, Wei-Jun; Leach, Robin J.; Thompson, Ian M.; Chan, Daniel W.; Smith, Richard D.; Kagan, Jacob; Srivastava, Sudhir; Rodland, Karin D.; Camp, David G.

2012-01-01

Recently, selected reaction monitoring mass spectrometry (SRM-MS) has been more frequently applied to measure low abundance biomarker candidates in tissues and biofluids, owing to its high sensitivity and specificity, simplicity of assay configuration, and exceptional multiplexing capability. In this study, we report for the first time the development of immunoaffinity depletion-based workflows and SRM-MS assays that enable sensitive and accurate quantification of total and free prostate-specific antigen (PSA) in serum without the requirement for specific PSA antibodies. Low ng/mL level detection of both total and free PSA was consistently achieved in both PSA-spiked female serum samples and actual patient serum samples. Moreover, comparison of the results obtained when SRM PSA assays and conventional immunoassays were applied to the same samples showed good correlation in several independent clinical serum sample sets. These results demonstrate that the workflows and SRM assays developed here provide an attractive alternative for reliably measuring candidate biomarkers in human blood, without the need to develop affinity reagents. Furthermore, the simultaneous measurement of multiple biomarkers, including the free and bound forms of PSA, can be performed in a single multiplexed analysis using high-resolution liquid chromatographic separation coupled with SRM-MS. PMID:22846433

Analytical resolution of the reactive diffusion equation for transient electronics including materials whose porosity value changes in terms of their thickness

NASA Astrophysics Data System (ADS)

Vargas Toro, Agustín.

2014-05-01

Transient electronic devices are a new technology development whose main characteristic is that its components can disappear in a programmed and controlled way, which means such devices have a pre-engineered service life. Nowadays, transient electronics have a large application field, involving from the reduction of e-waste in the planet until the development of medical instruments and implants that can be discarded when the patients do not need it anymore, avoiding the trouble of having an extra procedure for them. These devices must be made from biocompatible materials avoiding long-term adverse effects in the environment and patients. It is fundamental to develop an analytical model that allows describing the behavior of these materials considering cases which its porosity may be constant or not, in presence of water or any other biofluid. In order to accomplish this analysis was solve the reactive diffusion equation based on Bromwich's integral and the Residue theorem for two material cases, those whose porosity is constant, and those whose porosity increases linearly in terms of its thickness, where was found a general expression. This allows to the analysis of the relation of the electric resistance (per unit length) and the rate of dissolution of the material.

The MetabolomeExpress Project: enabling web-based processing, analysis and transparent dissemination of GC/MS metabolomics datasets.

PubMed

Carroll, Adam J; Badger, Murray R; Harvey Millar, A

2010-07-14

Standardization of analytical approaches and reporting methods via community-wide collaboration can work synergistically with web-tool development to result in rapid community-driven expansion of online data repositories suitable for data mining and meta-analysis. In metabolomics, the inter-laboratory reproducibility of gas-chromatography/mass-spectrometry (GC/MS) makes it an obvious target for such development. While a number of web-tools offer access to datasets and/or tools for raw data processing and statistical analysis, none of these systems are currently set up to act as a public repository by easily accepting, processing and presenting publicly submitted GC/MS metabolomics datasets for public re-analysis. Here, we present MetabolomeExpress, a new File Transfer Protocol (FTP) server and web-tool for the online storage, processing, visualisation and statistical re-analysis of publicly submitted GC/MS metabolomics datasets. Users may search a quality-controlled database of metabolite response statistics from publicly submitted datasets by a number of parameters (eg. metabolite, species, organ/biofluid etc.). Users may also perform meta-analysis comparisons of multiple independent experiments or re-analyse public primary datasets via user-friendly tools for t-test, principal components analysis, hierarchical cluster analysis and correlation analysis. They may interact with chromatograms, mass spectra and peak detection results via an integrated raw data viewer. Researchers who register for a free account may upload (via FTP) their own data to the server for online processing via a novel raw data processing pipeline. MetabolomeExpress https://www.metabolome-express.org provides a new opportunity for the general metabolomics community to transparently present online the raw and processed GC/MS data underlying their metabolomics publications. Transparent sharing of these data will allow researchers to assess data quality and draw their own insights from published metabolomics datasets.

Extracellular vesicles: roles in gamete maturation, fertilization and embryo implantation

PubMed Central

Machtinger, Ronit; Laurent, Louise C.; Baccarelli, Andrea A.

2016-01-01

BACKGROUND Extracellular vesicles (EVs) are membrane-bound vesicles, found in biofluids, that carry and transfer regulatory molecules, such as microRNAs (miRNAs) and proteins, and may mediate intercellular communication between cells and tissues. EVs have been isolated from a wide variety of biofluids, including plasma, urine, and, relevant to this review, seminal, follicular and uterine luminal fluid. We conducted a systematic search of the literature to review and present the currently available evidence on the possible roles of EVs in follicular growth, resumption of oocyte development and maturation (meiosis), sperm maturation, fertilization and embryo implantation. METHODS MEDLINE, Embase and Web of Science databases were searched using keywords pertaining to EVs, including ‘extracellular vesicles’, ‘microvesicles’, ‘microparticles’ and ‘exosomes’, combined with a range of terms associated with the period of development between fertilization and implantation, including ‘oocyte’, 'sperm’, 'semen’, 'fertilization’, ‘implantation’, ‘embryo’, ‘follicular fluid’, ‘epididymal fluid’ and ‘seminal fluid’. Relevant research articles published in English (both animal and human studies) were reviewed with no restrictions on publication date (i.e. from earliest database dates to July 2015). References from these articles were used to obtain additional articles. RESULTS A total of 1556 records were retrieved from the three databases. After removing duplicates and irrelevant titles, we reviewed the abstracts of 201 articles, which included 92 relevant articles. Both animal and human studies unequivocally identified various types of EVs in seminal, follicular and ULFs. Several studies provided evidence for the roles of EVs in these biofluids. In men, EVs in seminal fluid were linked with post-testicular sperm maturation, including sperm motility acquisition and reduction of oxidative stress. In women, EVs in follicular fluid were shown to contain miRNAs with potential roles in follicular growth, resumption of oocyte meiosis, steroidogenesis and prevention of polyspermy after fertilization. EVs were also detected in the media of cultured embryos, suggesting that EVs released from embryos and the uterus may mediate embryo-endometrium cross-talk during implantation. It is important to note that many of the biologically plausible functions of EVs in reproduction discussed in the current literature have not yet been substantiated by conclusive experimental evidence. CONCLUSIONS A detailed understanding of the contributions of EVs in the series of events from gametogenesis to fertilization and then on to implantation, in both normal and pathological cases, may enable the development of valuable tools to advance reproductive health. Because of the early stage of the field, it is unsurprising that the current literature includes not only growing experimental evidence, but also as-yet unproven hypotheses pertaining to the roles of EVs in key reproductive processes. In this review, we present a comprehensive survey of the rapidly expanding literature on this subject, highlighting both relevant findings and gaps in knowledge. PMID:26663221

Sources, behaviour, and environmental and human health risks of high-technology rare earth elements as emerging contaminants.

PubMed

Gwenzi, Willis; Mangori, Lynda; Danha, Concilia; Chaukura, Nhamo; Dunjana, Nothando; Sanganyado, Edmond

2018-04-26

Recent studies show that high-technology rare earth elements (REEs) of anthropogenic origin occur in the environment including in aquatic systems, suggesting REEs are contaminants of emerging concern. However, compared to organic contaminants, there is a lack of comprehensive reviews on the anthropogenic sources, environmental behaviour, and public and ecological health risks of REEs. The current review aims to: (1) identify anthropogenic sources, transfer mechanisms, and environmental behaviour of REEs; (2) highlight the human and ecological health risks of REEs and propose mitigation measures; and (3) identify knowledge gaps and future research directions. Out of the 17 REEs, La, Gd, Ce and Eu are the most studied. The main sources of anthropogenic REE include; medical facilities, petroleum refining, mining and technology industries, fertilizers, livestock feeds, and electronic wastes and recycling plants. REEs are mobilized and transported in the environment by hydrological and wind-driven processes. Ecotoxicological effects include reduced plant growth, function and nutritional quality, genotoxicity and neurotoxicity in animals, trophic bioaccumulation, chronic and acute toxicities in soil organisms. Human exposure to REEs occurs via ingestion of contaminated water and food, inhalation, and direct intake during medical administration. REEs have been detected in human hair, nails, and biofluids. In humans, REEs cause nephrogenic systemic fibrosis and severe damage to nephrological systems associated with Gd-based contrast agents, dysfunctional neurological disorder, fibrotic tissue injury, oxidative stress, pneumoconiosis, cytotoxicity, anti-testicular effects, and male sterility. Barring REEs in medical devices, epidemiological evidence directly linking REEs in the environment to human health conditions remains weak. To minimize health risks, a conceptual framework and possible mitigation measures are highlighted. Future research is needed to better understand sources, environmental behaviour, ecotoxicology, and human epidemiology. Moreover, research on REEs in developing regions, including Africa, is needed given prevailing conditions predisposing humans to health risks (e.g., untreated drinking water). Copyright © 2018 Elsevier B.V. All rights reserved.

Proteomic analysis of bronchoalveolar lavage fluid (BALF) from lung cancer patients using label-free mass spectrometry.

PubMed

Hmmier, Abduladim; O'Brien, Michael Emmet; Lynch, Vincent; Clynes, Martin; Morgan, Ross; Dowling, Paul

2017-06-01

Lung cancer is the leading cause of cancer-related mortality in both men and women throughout the world. The need to detect lung cancer at an early, potentially curable stage, is essential and may reduce mortality by 20%. The aim of this study was to identify distinct proteomic profiles in bronchoalveolar fluid (BALF) and plasma that are able to discriminate individuals with benign disease from those with non-small cell lung cancer (NSCLC). Using label-free mass spectrometry analysis of BALF during discovery-phase analysis, a significant number of proteins were found to have different abundance levels when comparing control to adenocarcinoma (AD) or squamous cell lung carcinoma (SqCC). Validation of candidate biomarkers identified in BALF was performed in a larger cohort of plasma samples by detection with enzyme-linked immunoassay. Four proteins (Cystatin-C, TIMP-1, Lipocalin-2 and HSP70/HSPA1A) were selected as a representative group from discovery phase mass spectrometry BALF analysis. Plasma levels of TIMP-1, Lipocalin-2 and Cystatin-C were found to be significantly elevated in AD and SqCC compared to control. The results presented in this study indicate that BALF is an important proximal biofluid for the discovery and identification of candidate lung cancer biomarkers. There is good correlation between the trend of protein abundance levels in BALF and that of plasma which validates this approach to develop a blood biomarker to aid lung cancer diagnosis, particularly in the era of lung cancer screening. The protein signatures identified also provide insight into the molecular mechanisms associated with lung malignancy.

Determination of sulfates and glucuronides of endogenic steroids in biofluids by high-performance liquid chromatography/orbitrap mass spectrometry

NASA Astrophysics Data System (ADS)

Semenistaya, E. N.; Virus, E. D.; Rodchenkov, G. M.

2009-04-01

the possibility of selective determination of testosterone and epitestosterone glucuronides in urine by high-performance liquid chromatography/high-resolution mass spectrometry using solid phase microextraction on a meps cartridge was studied. the effect of the biological matrix on the spectra of conjugated steroids can be taken into account by using the spectra of conjugates recorded for urine samples after hydrolysis as reference spectra. the conditions of fragmentation in the ion source were optimized for separate analytes. this method was used for analyzing real samples with different testosterone/epitestosterone ratios. variations in conjugate contents and qualitative changes in the steroid profile of endogenic compounds were observed.

Dissolution chemistry and biocompatibility of silicon- and germanium-based semiconductors for transient electronics.

PubMed

Kang, Seung-Kyun; Park, Gayoung; Kim, Kyungmin; Hwang, Suk-Won; Cheng, Huanyu; Shin, Jiho; Chung, Sangjin; Kim, Minjin; Yin, Lan; Lee, Jeong Chul; Lee, Kyung-Mi; Rogers, John A

2015-05-06

Semiconducting materials are central to the development of high-performance electronics that are capable of dissolving completely when immersed in aqueous solutions, groundwater, or biofluids, for applications in temporary biomedical implants, environmentally degradable sensors, and other systems. The results reported here include comprehensive studies of the dissolution by hydrolysis of polycrystalline silicon, amorphous silicon, silicon-germanium, and germanium in aqueous solutions of various pH values and temperatures. In vitro cellular toxicity evaluations demonstrate the biocompatibility of the materials and end products of dissolution, thereby supporting their potential for use in biodegradable electronics. A fully dissolvable thin-film solar cell illustrates the ability to integrate these semiconductors into functional systems.

Coherence-domain imaging with harmonic holography

NASA Astrophysics Data System (ADS)

Pu, Ye; Psaltis, Demetri

2017-08-01

Observing the fast dynamics of specific molecules or targets in three-dimensional (3D) space and time inside a crowded and complex environment, such as living cells or tissues, remain one of the grand open challenges in modern science. Harmonic holography tackle this challenge by combining the 3D imaging capability of holography with the ultrafast, coherent optical contrast offered by second-harmonic radiating imaging probes (SHRIMPs). Similar to fluorescence, the second-harmonic signal emitted from SHRIMPs provides a color contrast against the uninterested background scattering, which can be efficiently suppressed by an optical filter. We review the latest developments in SHRIMPs and harmonic holography and discuss their further applications in fluidics and biofluidics.

Bio resorbability of the modified hydroxyapatite in Tris-HCL buffer

NASA Astrophysics Data System (ADS)

Golovanova, O. A.; Izmailov, R. R.; Ghyngazov, S. A.

2016-02-01

The solubility of carbonated hydroxyapatite powders and granulated carbonated hydroxyapatite produced from the synovial biofluid model solution has been studied. The kinetic characteristics of dissolution were determined. It was found that the solubility of carbonated hydroxyapatite is higher as compared to that of hydroxyapatite. The impact of the organic matrix on the rate of sample dissolution was revealed. For HA-gelatin composites, as the gelatin concentration grows, the dissolution rate becomes greater, and a sample of 6.0 g / L concentration has higher resorbability. The results of the research can be used to study the kinetics of dissolution and the biocompatibility of ceramic materials for medicine, namely for reconstructive surgery, dentistry, and development of drug delivery systems.

Particle-based methods for multiscale modeling of blood flow in the circulation and in devices: challenges and future directions. Sixth International Bio-Fluid Mechanics Symposium and Workshop March 28-30, 2008 Pasadena, California.

PubMed

Yamaguchi, Takami; Ishikawa, Takuji; Imai, Y; Matsuki, N; Xenos, Mikhail; Deng, Yuefan; Bluestein, Danny

2010-03-01

A major computational challenge for a multiscale modeling is the coupling of disparate length and timescales between molecular mechanics and macroscopic transport, spanning the spatial and temporal scales characterizing the complex processes taking place in flow-induced blood clotting. Flow and pressure effects on a cell-like platelet can be well represented by a continuum mechanics model down to the order of the micrometer level. However, the molecular effects of adhesion/aggregation bonds are on the order of nanometer. A successful multiscale model of platelet response to flow stresses in devices and the ensuing clotting responses should be able to characterize the clotting reactions and their interactions with the flow. This paper attempts to describe a few of the computational methods that were developed in recent years and became available to researchers in the field. They differ from traditional approaches that dominate the field by expanding on prevailing continuum-based approaches, or by completely departing from them, yielding an expanding toolkit that may facilitate further elucidation of the underlying mechanisms of blood flow and the cellular response to it. We offer a paradigm shift by adopting a multidisciplinary approach with fluid dynamics simulations coupled to biophysical and biochemical transport.

Metabonomics identifies serum metabolite markers of colorectal cancer.

PubMed

Tan, Binbin; Qiu, Yunping; Zou, Xia; Chen, Tianlu; Xie, Guoxiang; Cheng, Yu; Dong, Taotao; Zhao, Linjing; Feng, Bo; Hu, Xiaofang; Xu, Lisa X; Zhao, Aihua; Zhang, Menghui; Cai, Guoxiang; Cai, Sanjun; Zhou, Zhanxiang; Zheng, Minhua; Zhang, Yan; Jia, Wei

2013-06-07

Recent studies suggest that biofluid-based metabonomics may identify metabolite markers promising for colorectal cancer (CRC) diagnosis. We report here a follow-up replication study, after a previous CRC metabonomics study, aiming to identify a distinct serum metabolic signature of CRC with diagnostic potential. Serum metabolites from newly diagnosed CRC patients (N = 101) and healthy subjects (N = 102) were profiled using gas chromatography time-of-flight mass spectrometry (GC-TOFMS) and ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QTOFMS). Differential metabolites were identified with statistical tests of orthogonal partial least-squares-discriminant analysis (VIP > 1) and the Mann-Whitney U test (p < 0.05). With a total of 249 annotated serum metabolites, we were able to differentiate CRC patients from the healthy controls using an orthogonal partial least-squares-discriminant analysis (OPLS-DA) in a learning sample set of 62 CRC patients and 62 matched healthy controls. This established model was able to correctly assign the rest of the samples to the CRC or control groups in a validation set of 39 CRC patients and 40 healthy controls. Consistent with our findings from the previous study, we observed a distinct metabolic signature in CRC patients including tricarboxylic acid (TCA) cycle, urea cycle, glutamine, fatty acids, and gut flora metabolism. Our results demonstrated that a panel of serum metabolite markers is of great potential as a noninvasive diagnostic method for the detection of CRC.

Quality assurance in the pre-analytical phase of human urine samples by (1)H NMR spectroscopy.

PubMed

Budde, Kathrin; Gök, Ömer-Necmi; Pietzner, Maik; Meisinger, Christine; Leitzmann, Michael; Nauck, Matthias; Köttgen, Anna; Friedrich, Nele

2016-01-01

Metabolomic approaches investigate changes in metabolite profiles, which may reflect changes in metabolic pathways and provide information correlated with a specific biological process or pathophysiology. High-resolution (1)H NMR spectroscopy is used to identify metabolites in biofluids and tissue samples qualitatively and quantitatively. This pre-analytical study evaluated the effects of storage time and temperature on (1)H NMR spectra from human urine in two settings. Firstly, to evaluate short time effects probably due to acute delay in sample handling and secondly, the effect of prolonged storage up to one month to find markers of sample miss-handling. A number of statistical procedures were used to assess the differences between samples stored under different conditions, including Projection to Latent Structure Discriminant Analysis (PLS-DA), non-parametric testing as well as mixed effect linear regression analysis. The results indicate that human urine samples can be stored at 10 °C for 24 h or at -80 °C for 1 month, as no relevant changes in (1)H NMR fingerprints were observed during these time periods and temperature conditions. However, some metabolites most likely of microbial origin showed alterations during prolonged storage but without facilitating classification. In conclusion, the presented protocol for urine sample handling and semi-automatic metabolite quantification is suitable for large-scale epidemiological studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Metabolomic phenotyping of a cloned pig model

PubMed Central

2011-01-01

Background Pigs are widely used as models for human physiological changes in intervention studies, because of the close resemblance between human and porcine physiology and the high degree of experimental control when using an animal model. Cloned animals have, in principle, identical genotypes and possibly also phenotypes and this offer an extra level of experimental control which could possibly make them a desirable tool for intervention studies. Therefore, in the present study, we address how phenotype and phenotypic variation is affected by cloning, through comparison of cloned pigs and normal outbred pigs. Results The metabolic phenotype of cloned pigs (n = 5) was for the first time elucidated by nuclear magnetic resonance (NMR)-based metabolomic analysis of multiple bio-fluids including plasma, bile and urine. The metabolic phenotype of the cloned pigs was compared with normal outbred pigs (n = 6) by multivariate data analysis, which revealed differences in the metabolic phenotypes. Plasma lactate was higher for cloned vs control pigs, while multiple metabolites were altered in the bile. However a lower inter-individual variability for cloned pigs compared with control pigs could not be established. Conclusions From the present study we conclude that cloned and normal outbred pigs are phenotypically different. However, it cannot be concluded that the use of cloned animals will reduce the inter-individual variation in intervention studies, though this is based on a limited number of animals. PMID:21859467

Simultaneous Speciation of Arsenic, Selenium, and Chromium by HPLC-ICP-MS

USGS Publications Warehouse

Wolf, Ruth E.; Morman, Suzette A.; Morrison, Jean M.; Lamothe, Paul J.

2008-01-01

An adaptation of an analytical method developed for chromium speciation has been utilized for the simultaneous determination of As(III), As(V), Se(IV), Se(VI), Cr(III), and Cr(VI) species using high performance liquid chromatography (HPLC) separation with ICP-MS detection. Reduction of interferences for the determination of As, Se, and Cr by ICP-MS is a major consideration for this method. Toward this end, a Dynamic Reaction Cell (DRC) ICP-MS system was used to detect the species eluted from the chromatographic column. A variety of reaction cell gases and conditions may be utilized, and the advantages and limitations of the gases tested to date will be presented and discussed. The separation and detection of the As, Se, and Cr species of interest can be achieved using the same chromatographic conditions in less than 2 minutes by complexing the Cr(III) with EDTA prior to injection on the HPLC column. Practical aspects of simultaneous speciation analysis will be presented and discussed, including issues with HPLC sample vial contamination, standard and sample contamination, species stability, and considerations regarding sample collection and preservation methods. The results of testing to determine the method's robustness to common concomitant element and anion effects will also be discussed. Finally, results will be presented using the method for the analysis of a variety of environmental and geological samples including waters, soil leachates and simulated bio-fluid leachates.

Automatic alignment of individual peaks in large high-resolution spectral data sets

NASA Astrophysics Data System (ADS)

Stoyanova, Radka; Nicholls, Andrew W.; Nicholson, Jeremy K.; Lindon, John C.; Brown, Truman R.

2004-10-01

Pattern recognition techniques are effective tools for reducing the information contained in large spectral data sets to a much smaller number of significant features which can then be used to make interpretations about the chemical or biochemical system under study. Often the effectiveness of such approaches is impeded by experimental and instrument induced variations in the position, phase, and line width of the spectral peaks. Although characterizing the cause and magnitude of these fluctuations could be important in its own right (pH-induced NMR chemical shift changes, for example) in general they obscure the process of pattern discovery. One major area of application is the use of large databases of 1H NMR spectra of biofluids such as urine for investigating perturbations in metabolic profiles caused by drugs or disease, a process now termed metabonomics. Frequency shifts of individual peaks are the dominant source of such unwanted variations in this type of data. In this paper, an automatic procedure for aligning the individual peaks in the data set is described and evaluated. The proposed method will be vital for the efficient and automatic analysis of large metabonomic data sets and should also be applicable to other types of data.

Lack of Association between Human Plasma Oxytocin and Interpersonal Trust in a Prisoner’s Dilemma Paradigm

PubMed Central

Christensen, James C.; Shiyanov, Pavel A.; Estepp, Justin R.; Schlager, John J.

2014-01-01

Expanding interest in oxytocin, particularly the role of endogenous oxytocin in human social behavior, has created a pressing need for replication of results and verification of assay methods. In this study, we sought to replicate and extend previous results correlating plasma oxytocin with trust and trustworthy behavior. As a necessary first step, the two most commonly used commercial assays were compared in human plasma via the addition of a known quantity of exogenous oxytocin, with and without sample extraction. Plasma sample extraction was found to be critical in obtaining repeatable concentrations of oxytocin. In the subsequent trust experiment, twelve samples in duplicate, from each of 82 participants, were collected over approximately six hours during the performance of a Prisoner’s Dilemma task paradigm that stressed human interpersonal trust. We found no significant relationship between plasma oxytocin concentrations and trusting or trustworthy behavior. In light of these findings, previous published work that used oxytocin immunoassays without sample extraction should be reexamined and future research exploring links between endogenous human oxytocin and trust or social behavior should proceed with careful consideration of methods and appropriate biofluids for analysis. PMID:25549255

Learning Probabilistic Logic Models from Probabilistic Examples

PubMed Central

Chen, Jianzhong; Muggleton, Stephen; Santos, José

2009-01-01

Abstract We revisit an application developed originally using abductive Inductive Logic Programming (ILP) for modeling inhibition in metabolic networks. The example data was derived from studies of the effects of toxins on rats using Nuclear Magnetic Resonance (NMR) time-trace analysis of their biofluids together with background knowledge representing a subset of the Kyoto Encyclopedia of Genes and Genomes (KEGG). We now apply two Probabilistic ILP (PILP) approaches - abductive Stochastic Logic Programs (SLPs) and PRogramming In Statistical modeling (PRISM) to the application. Both approaches support abductive learning and probability predictions. Abductive SLPs are a PILP framework that provides possible worlds semantics to SLPs through abduction. Instead of learning logic models from non-probabilistic examples as done in ILP, the PILP approach applied in this paper is based on a general technique for introducing probability labels within a standard scientific experimental setting involving control and treated data. Our results demonstrate that the PILP approach provides a way of learning probabilistic logic models from probabilistic examples, and the PILP models learned from probabilistic examples lead to a significant decrease in error accompanied by improved insight from the learned results compared with the PILP models learned from non-probabilistic examples. PMID:19888348

Learning Probabilistic Logic Models from Probabilistic Examples.

PubMed

Chen, Jianzhong; Muggleton, Stephen; Santos, José

2008-10-01

We revisit an application developed originally using abductive Inductive Logic Programming (ILP) for modeling inhibition in metabolic networks. The example data was derived from studies of the effects of toxins on rats using Nuclear Magnetic Resonance (NMR) time-trace analysis of their biofluids together with background knowledge representing a subset of the Kyoto Encyclopedia of Genes and Genomes (KEGG). We now apply two Probabilistic ILP (PILP) approaches - abductive Stochastic Logic Programs (SLPs) and PRogramming In Statistical modeling (PRISM) to the application. Both approaches support abductive learning and probability predictions. Abductive SLPs are a PILP framework that provides possible worlds semantics to SLPs through abduction. Instead of learning logic models from non-probabilistic examples as done in ILP, the PILP approach applied in this paper is based on a general technique for introducing probability labels within a standard scientific experimental setting involving control and treated data. Our results demonstrate that the PILP approach provides a way of learning probabilistic logic models from probabilistic examples, and the PILP models learned from probabilistic examples lead to a significant decrease in error accompanied by improved insight from the learned results compared with the PILP models learned from non-probabilistic examples.

Urinary Metabolomic Approach Provides New Insights into Distinct Metabolic Profiles of Glutamine and N-Carbamylglutamate Supplementation in Rats.

PubMed

Liu, Guangmang; Cao, Wei; Fang, Tingting; Jia, Gang; Zhao, Hua; Chen, Xiaoling; Wu, Caimei; Wang, Jing

2016-08-04

Glutamine and N-carbamylglutamate can enhance growth performance and health in animals, but the underlying mechanisms are not yet elucidated. This study aimed to investigate the effect of glutamine and N-carbamylglutamate supplementation in rat metabolism. Thirty rats were fed a control, glutamine, or N-carbamylglutamate diet for four weeks. Urine samples were analyzed by nuclear magnetic resonance (NMR)-based metabolomics, specifically high-resolution ¹H NMR metabolic profiling combined with multivariate data analysis. Glutamine significantly increased the urine levels of acetamide, acetate, citrulline, creatinine, and methymalonate, and decreased the urine levels of ethanol and formate (p < 0.05). Moreover, N-carbamylglutamate significantly increased the urine levels of creatinine, ethanol, indoxyl sulfate, lactate, methymalonate, acetoacetate, m-hydroxyphenylacetate, and sarcosine, and decreased the urine levels of acetamide, acetate, citrulline, creatine, glycine, hippurate, homogentisate, N-acetylglutamate, phenylacetyglycine, acetone, and p-hydroxyphenylacetate (p < 0.05). Results suggested that glutamine and N-carbamylglutamate could modify urinary metabolome related to nitrogen metabolism and gut microbiota metabolism. Moreover, N-carbamylglutamate could alter energy and lipid metabolism. These findings indicate that different arginine precursors may lead to differences in the biofluid profile in rats.

Urinary Metabolomic Approach Provides New Insights into Distinct Metabolic Profiles of Glutamine and N-Carbamylglutamate Supplementation in Rats

PubMed Central

Liu, Guangmang; Cao, Wei; Fang, Tingting; Jia, Gang; Zhao, Hua; Chen, Xiaoling; Wu, Caimei; Wang, Jing

2016-01-01

Glutamine and N-carbamylglutamate can enhance growth performance and health in animals, but the underlying mechanisms are not yet elucidated. This study aimed to investigate the effect of glutamine and N-carbamylglutamate supplementation in rat metabolism. Thirty rats were fed a control, glutamine, or N-carbamylglutamate diet for four weeks. Urine samples were analyzed by nuclear magnetic resonance (NMR)-based metabolomics, specifically high-resolution 1H NMR metabolic profiling combined with multivariate data analysis. Glutamine significantly increased the urine levels of acetamide, acetate, citrulline, creatinine, and methymalonate, and decreased the urine levels of ethanol and formate (p < 0.05). Moreover, N-carbamylglutamate significantly increased the urine levels of creatinine, ethanol, indoxyl sulfate, lactate, methymalonate, acetoacetate, m-hydroxyphenylacetate, and sarcosine, and decreased the urine levels of acetamide, acetate, citrulline, creatine, glycine, hippurate, homogentisate, N-acetylglutamate, phenylacetyglycine, acetone, and p-hydroxyphenylacetate (p < 0.05). Results suggested that glutamine and N-carbamylglutamate could modify urinary metabolome related to nitrogen metabolism and gut microbiota metabolism. Moreover, N-carbamylglutamate could alter energy and lipid metabolism. These findings indicate that different arginine precursors may lead to differences in the biofluid profile in rats. PMID:27527211

Determination of Bile Acids in Piglet Bile by Solid Phase Extraction and Liquid Chromatography-Electrospray Tandem Mass Spectrometry.

PubMed

Mi, Si; Lim, David W; Turner, Justine M; Wales, Paul W; Curtis, Jonathan M

2016-03-01

An LC/MS/MS-based method was developed for the determination of individual bile acids (BA) and their conjugates in porcine bile samples. The C18-based solid-phase extraction (SPE) procedure was optimized so that all 19 target BA and their glycine and taurine conjugates were collected with high recoveries for standards (89.1-100.2%). Following this, all 19 compounds were separated and quantified in a single 12 min chromatographic run. The method was validated in terms of linearity, sensitivity, accuracy, precision, and recovery. An LOD in the low ppb range with measured precisions in the range of 0.5-9.3% was achieved. The recoveries for all of the 19 analytes in bile samples were all >80%. The validated method was successfully applied to the profiling of BA and their conjugates in the bile from piglets treated with exogenous glucagon-like peptide-2 (GLP-2) in a preclinical model of neonatal parenteral nutrition-associated liver disease (PNALD). The method developed is rapid and could be easily implemented for routine analysis of BA and their conjugates in other biofluids or tissues.

Mathematical methods in medicine: neuroscience, cardiology and pathology

PubMed Central

Amigó, José M.

2017-01-01

The application of mathematics, natural sciences and engineering to medicine is gaining momentum as the mutual benefits of this collaboration become increasingly obvious. This theme issue is intended to highlight the trend in the case of mathematics. Specifically, the scope of this theme issue is to give a general view of the current research in the application of mathematical methods to medicine, as well as to show how mathematics can help in such important aspects as understanding, prediction, treatment and data processing. To this end, three representative specialties have been selected: neuroscience, cardiology and pathology. Concerning the topics, the 12 research papers and one review included in this issue cover biofluids, cardiac and virus dynamics, computational neuroscience, functional magnetic resonance imaging data processing, neural networks, optimization of treatment strategies, time-series analysis and tumour growth. In conclusion, this theme issue contains a collection of fine contributions at the intersection of mathematics and medicine, not as an exercise in applied mathematics but as a multidisciplinary research effort that interests both communities and our society in general. This article is part of the themed issue ‘Mathematical methods in medicine: neuroscience, cardiology and pathology’. PMID:28507240

Mathematical methods in medicine: neuroscience, cardiology and pathology.

PubMed

Amigó, José M; Small, Michael

2017-06-28

The application of mathematics, natural sciences and engineering to medicine is gaining momentum as the mutual benefits of this collaboration become increasingly obvious. This theme issue is intended to highlight the trend in the case of mathematics. Specifically, the scope of this theme issue is to give a general view of the current research in the application of mathematical methods to medicine, as well as to show how mathematics can help in such important aspects as understanding, prediction, treatment and data processing. To this end, three representative specialties have been selected: neuroscience, cardiology and pathology. Concerning the topics, the 12 research papers and one review included in this issue cover biofluids, cardiac and virus dynamics, computational neuroscience, functional magnetic resonance imaging data processing, neural networks, optimization of treatment strategies, time-series analysis and tumour growth. In conclusion, this theme issue contains a collection of fine contributions at the intersection of mathematics and medicine, not as an exercise in applied mathematics but as a multidisciplinary research effort that interests both communities and our society in general.This article is part of the themed issue 'Mathematical methods in medicine: neuroscience, cardiology and pathology'. © 2017 The Author(s).

NMR-based metabolomics approach to study the chronic toxicity of crude ricin from castor bean kernels on rats.

PubMed

Guo, Pingping; Wang, Junsong; Dong, Ge; Wei, Dandan; Li, Minghui; Yang, Minghua; Kong, Lingyi

2014-07-29

Ricin, a large, water soluble toxic glycoprotein, is distributed majorly in the kernels of castor beans (the seeds of Ricinus communis L.) and has been used in traditional Chinese medicine (TCM) or other folk remedies throughout the world. The toxicity of crude ricin (CR) from castor bean kernels was investigated for the first time using an NMR-based metabolomic approach complemented with histopathological inspection and clinical chemistry. The chronic administration of CR could cause kidney and lung impairment, spleen and thymus dysfunction and diminished nutrient intake in rats. An orthogonal signal correction partial least-squares discriminant analysis (OSC-PLSDA) of metabolomic profiles of rat biofluids highlighted a number of metabolic disturbances induced by CR. Long-term CR treatment produced perturbations on energy metabolism, nitrogen metabolism, amino acid metabolism and kynurenine pathway, and evoked oxidative stress. These findings could explain well the CR induced nephrotoxicity and pulmonary toxicity, and provided several potential biomarkers for diagnostics of these toxicities. Such a (1)H NMR based metabolomics approach showed its ability to give a systematic and holistic view of the response of an organism to drugs and is suitable for dynamic studies on the toxicological effects of TCM.

Not all biofluids are created equal: chewing over salivary diagnostics and the epigenome.

PubMed

Wren, Michael E; Shirtcliff, Elizabeth A; Drury, Stacy S

2015-03-01

This article describes progress to date in the characterization of the salivary epigenome and considers the importance of previous work in the salivary microbiome, proteome, endocrine analytes, genome, and transcriptome. PubMed and Web of Science were used to extensively search the existing literature (original research and reviews) related to salivary diagnostics and biomarker development, of which 125 studies were examined. This article was derived from the most relevant 74 sources highlighting the recent state of the evolving field of salivary epigenomics and contributing significantly to the foundational work in saliva-based research. Validation of any new saliva-based diagnostic or analyte will require comparison to previously accepted standards established in blood. Careful attention to the collection, processing, and analysis of salivary analytes is critical for the development and implementation of newer applications that include genomic, transcriptomic, and epigenomic markers. All these factors must be integrated into initial study design. This commentary highlights the appeal of the salivary epigenome for translational applications and its utility in future studies of development and the interface among environment, disease, and health. Copyright © 2015 Elsevier HS Journals, Inc. All rights reserved.

Derivatized graphitic nanofibres (GNF) as a new support material for mass spectrometric analysis of peptides and proteins.

PubMed

Greiderer, Andreas; Rainer, Matthias; Najam-ul-Haq, Muhammad; Vallant, Rainer M; Huck, Christian W; Bonn, Günther K

2009-07-01

Graphitic nanofibres (GNFs), 100-200 nm in diameter and 5-20 microm in length have been modified in order to yield different affinities (Cu2+ and Fe3+ loaded immobilized metal affinity chromatography (IMAC) as well as cation and anion exchange materials) for the extraction of a range of biomolecules by their inherited hydrophobicity and the hydrophilic chemical functionalities, obtained by derivatization. Modified GNFs have for the first time been employed as carrier materials for protein profiling in material-enhanced laser desorption/ionization (MELDI) for the enrichment and screening of biofluids. For that purpose, the derivatized GNF materials have comprehensively been characterized regarding surface area, structural changes during derivatization, IMAC, as well as ion exchange and protein-loading capacity and recovery. GNF derivatives revealed high protein-binding capacity (2,000 microg ml(-1) for insulin) and ideal sensitivities, resulting in a detection limit of 50 fmol microl(-1) (for insulin), which is crucial for the detection of low abundant species in biological samples. Compared to other MELDI carrier materials, sensitivity was enhanced on GNF derivatives, which might be ascribed to the fact that GNFs support desorption and ionization mechanisms and by absorbing laser energy in addition to matrix.

Clinical application of metabolomics in neonatology.

PubMed

Fanos, Vassilios; Antonucci, Roberto; Barberini, Luigi; Noto, Antonio; Atzori, Luigi

2012-04-01

The youngest and more rapidly increasing "omic" discipline, called metabolomics, is the process of describing the phenotype of a cell, tissue or organism through the full complement of metabolites present. Metabolomics measure global sets of low molecular weight metabolites (including amino acids, organic acids, sugars, fatty acids, lipids, steroids, small peptides, vitamins, etc.), thus providing a "snapshot" of the metabolic status of a cell, tissue or organism in relation to genetic variations or external stimuli. The use of metabolomics appears to be a promising tool in neonatology. The management of sick newborns might improve if more information on perinatal/neonatal maturational processes and their metabolic background were available. Urine ("a window on the organism") is a biofluid particularly suitable for metabolomic analysis in neonatology because it may be collected by using simple, noninvasive techniques and because it may provide valuable diagnostic information. In this review, the authors report the few literature data on neonatal metabolomics, including their personal experience, in the following fields: intrauterine growth restriction, perinatal transition, asphyxia, brain injury and hypothermia, maternal milk evaluation, postnatal maturation, bronchiolitis, sepsis, patent ductus arteriosus, respiratory distress syndrome, nephrouropathies, metabolic diseases, antibiotic treatment, perinatal programming and long-term outcome in extremely low birth-weight infants.

Validation of a highly sensitive ICP-MS method for the determination of platinum in biofluids: application to clinical pharmacokinetic studies with oxaliplatin.

PubMed

Morrison, J G; White, P; McDougall, S; Firth, J W; Woolfrey, S G; Graham, M A; Greenslade, D

2000-12-01

ELOXATIN (Oxaliplatin) is a novel platinum containing anti-cancer agent with a diaminocyclohexane carrier ligand which has been approved in several major European countries. Clinical studies have demonstrated that the compound exhibits marked activity against colorectal cancers in combination with 5-fluorouracil (5-FU). The aim of this work was to develop and validate a highly sensitive inductively coupled plasma mass spectrometry assay for the determination of oxaliplatin-derived platinum in plasma ultrafiltrate, plasma and whole blood and to apply this technique to clinical pharmacokinetic studies with oxaliplatin. Ultratrace detection of platinum in plasma ultrafiltrate was achieved using ultrasonic nebulisation combined with ICP-MS. This technique allows detection of platinum at the 0.001 microg Pt/ml level in only 100 microl of matrix. Assays in blood and plasma utilised a standard Meinhardt nebuliser and spray chamber, achieving detection limits of 0.1 microg Pt/ml in 100 and 200 microl of matrix, respectively. The assays were validated (accuracy and precision within +/- 15%) over the concentration ranges: 0.001-0.250 microg Pt/ml in plasma ultrafiltrate and 0.1-10 microg Pt/ml for plasma and whole blood. The effect of sample digestion. dilution, long term frozen storage and quantitation in the presence of 5-FU were also investigated and validated. The method was used to monitor platinum exposure following oxaliplatin administration (130 mg/m2) to cancer patients. Following a 2 h i.v. infusion, peak platinum levels declined in a triphasic manner in all blood compartments. Free platinum was detected in plasma ultrafiltrate at low levels (0.001 0.010 microg Pt/ml) for up to 3 weeks. In conclusion, a highly sensitive and specific assay has been developed for the determination of platinum in biofluids. This method enabled characterisation of the long term exposure to platinum in patients following oxaliplatin treatment.

Comparison of the bioavailability of elemental waste laden soils using in vivo and in vitro analytical methodology and refinement of exposure/dose models. 1998 annual progress report

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

Lioy, P.J.; Gallo, M.; Georgopoulos, P.

1998-06-01

'The authors hypotheses are: (1) the more closely the synthetic, in vitro, extractant mimics the extraction properties of the human digestive bio-fluids, the more accurate will be the estimate of an internal dose; (2) performance can be evaluated by in vivo studies with a rat model and quantitative examination of a mass balance, calculation and dose estimates from model simulations for the in vitro and in vivo system; and (3) the concentration of the elements Pb, Cd, Cr and selected Radionuclides present in the bioavailable fraction obtained with a synthetic extraction system will be a better indicator of contaminant ingestionmore » from a contaminated soil because it represents the portion of the mass which can yield exposure, uptake and then the internal dose to an individual. As of April 15, 1998, they have made significant progress in the development of a unified approach to the examination of bioavailability and bioaccessibility of elemental contamination of soils for the ingestion route of exposure. This includes the initial characterization of the soil, in vitro measurements of bioaccessibility, and in vivo measurements of bioavailability. They have identified the basic chemical and microbiological characteristics of waste laden soils. These have been used to prioritize the soils for potential mobility of the trace elements present in the soil. Subsequently they have employed a mass balance technique, which for the first time tracked the movement and distribution of elements through an in vitro or in vivo experimental protocol to define the bioaccessible and the bioavailable fractions of digested soil. The basic mass balance equation for the in vitro system is: MT = MSGJ + MIJ + MR. where MT is the total mass extractable by a specific method, MSGJ, is the mass extracted by the saliva and the gastric juices, MIJ is the mass extracted by the intestinal fluid, and MR is the unextractable portion of the initial mass. The above is based upon the use of a synthetic digestive bio-fluids model that includes the saliva, gastric juices, and intestinal fluids. The system has been devised to sequentially extract elements from soil by starting with an extraction by the saliva and carrying the entire mixture to the subsequent bio-fluids for further extraction. The residence time of the soil in each extractant and the liquid to mass ratio in the gastric juices are based upon typical values known for the human digestive system. Experiments were conducted to examine the sensitivity of the extractions to changes in these major variables. The results indicated the lack of significant extraction after 2 h of residence in gastric fluid. The range of variation of the liquid to mass ratio was element dependent over the interval 100:1 and 5,000:1. The final values used for the extraction protocol were: 2 h residence time , and a ratio of 1,000:1. Details of the chemical composition of the extraction protocol are found in Hamel, 1998.'« less

Convergence of excitatory and inhibitory hair cell transmitters shapes vestibular afferent responses.

PubMed

Holstein, Gay R; Rabbitt, Richard D; Martinelli, Giorgio P; Friedrich, Victor L; Boyle, Richard D; Highstein, Stephen M

2004-11-02

The vestibular semicircular canals respond to angular acceleration that is integrated to angular velocity by the biofluid mechanics of the canals and is the primary origin of afferent responses encoding velocity. Surprisingly, some afferents actually report angular acceleration. Our data indicate that hair-cell/afferent synapses introduce a mathematical derivative in these afferents that partially cancels the biomechanical integration and results in discharge rates encoding angular acceleration. We examined the role of convergent synaptic inputs from hair cells to this mathematical differentiation. A significant reduction in the order of the differentiation was observed for low-frequency stimuli after gamma-aminobutyric acid type B receptor antagonist administration. Results demonstrate that gamma-aminobutyric acid participates in shaping the temporal dynamics of afferent responses.

Diagnosis of coinfection by schistosomiasis and viral hepatitis B or C using 1H NMR-based metabonomics.

PubMed

Gouveia, Liana Ribeiro; Santos, Joelma Carvalho; Silva, Ronaldo Dionísio; Batista, Andrea Dória; Domingues, Ana Lúcia Coutinho; Lopes, Edmundo Pessoa de Almeida; Silva, Ricardo Oliveira

2017-01-01

Diagnosis of liver involvement due to schistosomiasis in asymptomatic patients from endemic areas previously diagnosed with chronic hepatitis B (HBV) or C (HCV) and periportal fibrosis is challenging. H-1 Nuclear Magnetic Resonance (NMR)-based metabonomics strategy is a powerful tool for providing a profile of endogenous metabolites of low molecular weight in biofluids in a non-invasive way. The aim of this study was to diagnose periportal fibrosis due to schistosomiasis mansoni in patients with chronic HBV or HCV infection through NMR-based metabonomics models. The study included 40 patients divided into two groups: (i) 18 coinfected patients with schistosomiasis mansoni and HBV or HCV; and (ii) 22 HBV or HCV monoinfected patients. The serum samples were analyzed through H-1 NMR spectroscopy and the models were based on Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA). Ultrasonography examination was used to ascertain the diagnosis of periportal fibrosis. Exploratory analysis showed a clear separation between coinfected and monoinfected samples. The supervised model built from PLS-DA showed accuracy, R2 and Q2 values equal to 100%, 98.1% and 97.5%, respectively. According to the variable importance in the projection plot, lactate serum levels were higher in the coinfected group, while the signals attributed to HDL serum cholesterol were more intense in the monoinfected group. The metabonomics models constructed in this study are promising as an alternative tool for diagnosis of periportal fibrosis by schistosomiasis in patients with chronic HBV or HCV infection from endemic areas for Schistosoma mansoni.

Laser Capture Microdissection of Pancreatic Acinar Cells to Identify Proteomic Alterations in a Murine Model of Caerulein-Induced Pancreatitis

PubMed Central

Shapiro, John P; Komar, Hannah M; Hancioglu, Baris; Yu, Lianbo; Jin, Ming; Ogata, Yuko; Hart, Phil A; Cruz-Monserrate, Zobeida; Lesinski, Gregory B; Conwell, Darwin L

2017-01-01

Objectives: Chronic pancreatitis (CP) is characterized by inflammation and fibrosis of the pancreas, leading to pain, parenchymal damage, and loss of exocrine and endocrine function. There are currently no curative therapies; diagnosis remains difficult and aspects of pathogenesis remain unclear. Thus, there is a need to identify novel biomarkers to improve diagnosis and understand pathophysiology. We hypothesize that pancreatic acinar regions contain proteomic signatures relevant to disease processes, including secreted proteins that could be detected in biofluids. Methods: Acini from pancreata of mice injected with or without caerulein were collected using laser capture microdissection followed by mass spectrometry analysis. This protocol enabled high-throughput analysis that captured altered protein expression throughout the stages of CP. Results: Over 2,900 proteins were identified, whereas 331 were significantly changed ≥2-fold by mass spectrometry spectral count analysis. Consistent with pathogenesis, we observed increases in proteins related to fibrosis (e.g., collagen, P<0.001), several proteases (e.g., trypsin 1, P<0.001), and altered expression of proteins associated with diminished pancreas function (e.g., lipase, amylase, P<0.05). In comparison with proteomic data from a public data set of CP patients, a significant correlation was observed between proteomic changes in tissue from both the caerulein model and CP patients (r=0.725, P<0.001). CONCLUSIONS: This study illustrates the ability to characterize proteome changes of acinar cells isolated from pancreata of caerulein-treated mice and demonstrates a relationship between signatures from murine and human CP. PMID:28406494

Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach.

PubMed

Percy, Andrew J; Yang, Juncong; Chambers, Andrew G; Mohammed, Yassene; Miliotis, Tasso; Borchers, Christoph H

2016-01-01

Quantitative mass spectrometry (MS)-based approaches are emerging as a core technology for addressing health-related queries in systems biology and in the biomedical and clinical fields. In several 'omics disciplines (proteomics included), an approach centered on selected or multiple reaction monitoring (SRM or MRM)-MS with stable isotope-labeled standards (SIS), at the protein or peptide level, has emerged as the most precise technique for quantifying and screening putative analytes in biological samples. To enable the widespread use of MRM-based protein quantitation for disease biomarker assessment studies and its ultimate acceptance for clinical analysis, the technique must be standardized to facilitate precise and accurate protein quantitation. To that end, we have developed a number of kits for assessing method/platform performance, as well as for screening proposed candidate protein biomarkers in various human biofluids. Collectively, these kits utilize a bottom-up LC-MS methodology with SIS peptides as internal standards and quantify proteins using regression analysis of standard curves. This chapter details the methodology used to quantify 192 plasma proteins of high-to-moderate abundance (covers a 6 order of magnitude range from 31 mg/mL for albumin to 18 ng/mL for peroxidredoxin-2), and a 21-protein subset thereof. We also describe the application of this method to patient samples for biomarker discovery and verification studies. Additionally, we introduce our recently developed Qualis-SIS software, which is used to expedite the analysis and assessment of protein quantitation data in control and patient samples.

Computational Flow Analysis of a Left Ventricular Assist Device

NASA Technical Reports Server (NTRS)

Kiris, Cetin; Kwak, Dochan; Benkowski, Robert

1995-01-01

Computational fluid dynamics has been developed to a level where it has become an Indispensable part of aerospace research and design. Technology developed foe aerospace applications am also be utilized for the benefit of human health. For example, a flange-to-flange rocket engine fuel-pump simulation includes the rotating and non-rotating components: the flow straighteners, the impeller, and diffusers A Ventricular Assist Device developed by NASA Johnson Space Center and Baylor College of Medicine has a design similar to a rocket engine fuel pump in that it also consists of a flow straightener, an impeller, and a diffuser. Accurate and detailed knowledge of the flowfield obtained by incompressible flow calculations can be greatly beneficial to designers in their effort to reduce the cost and improve the reliability of these devices. In addition to the geometric complexities, a variety of flow phenomena are encountered in biofluids Then include turbulent boundary layer separation, wakes, transition, tip vortex resolution, three-dimensional effects, and Reynolds number effects. In order to increase the role of Computational Fluid Dynamics (CFD) in the design process the CFD analysis tools must be evaluated and validated so that designers gain Confidence in their use. The incompressible flow solver, INS3D, has been applied to flow inside of a liquid rocket engine turbopump components and extensively validated. This paper details how the computational flow simulation capability developed for liquid rocket engine pump component analysis has bean applied to the Left Ventricular Assist Device being developed jointly by NASA JSC and Baylor College of Medicine.

Fast and automated characterization of major constituents in rat biofluid after oral administration of Abelmoschus manihot extract using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry and MetaboLynx.

PubMed

Guo, Jianming; Shang, Er-Xin; Duan, Jin-Ao; Tang, Yuping; Qian, Dawei; Su, Shulan

2010-02-01

In drug metabolism research, the setting up of a complex series of mass spectrometry experiments and the subsequent analysis of the large amounts of data produced are often time-consuming. In this paper, we describe a strategy using ultra-performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UPLC/QTOFMS) with automated data analysis software (MetaboLynx) for fast analysis of the metabolic profile of flavonoids in Abelmoschus manihot. Rat plasma and urine samples collected 1 h and 0-12 h after oral administration of Abelmoschus manihot were analyzed by UPLC/QTOFMS within 15 min. The post-acquisition data were processed using MetaboLynx. With key parameters carefully set, MetaboLynx is able to show the presence of a wide range of metabolites with only a limited requirement for manual intervention and data interpretation time. A total of 16 and 38 metabolites were identified in plasma and urine compared with blank samples. The results indicated that methylation and glucuronidation after deglycosylation were the major metabolic pathways of flavonoid glycosides in Abelmoschus manihot. The present study provided important information about the metabolism of flavonoid glycosides in Abelmoschus manihot which will be helpful for fully understanding the mechanism of action of this herb. Furthermore, this work demonstrated the potential of the UPLC/QTOFMS approach using MetaboLynx for fast and automated identification of metabolites from Chinese herbal medicines. Copyright (c) 2010 John Wiley & Sons, Ltd.

The influence of a sports drink on the postexercise metabolism of elite athletes as investigated by NMR-based metabolomics.

PubMed

Miccheli, Alfredo; Marini, Federico; Capuani, Giorgio; Miccheli, Alberta Tomassini; Delfini, Maurizio; Di Cocco, Maria Enrica; Puccetti, Caterina; Paci, Maurizio; Rizzo, Marta; Spataro, Antonio

2009-10-01

The aim of this study is to evaluate the systemic effects of an isotonic sports drink on the metabolic status of athletes of the Italian Olympic rowing team during recovery after strenuous and prolonged physical exercise by means of nuclear magnetic resonance (NMR)-based metabolomics analysis on plasma and urine. Forty-four male athletes of the Italian Olympic rowing team were enrolled in a double-blind crossover study. All subjects underwent 2 evaluations at 1-week intervals. The evaluation was performed on a rowing ergometer after strenuous physical exercise to produce a state of dehydration. Afterward, the athletes were rehydrated either with a green tea-based carbohydrate-hydroelectrolyte drink or with oligomineral water. Three blood samples were drawn for each subject: at rest, after the exercise, and following rehydratation, while 2 urine samples were collected: at rest and after the rehydratation period. Biofluid samples were analyzed by high-resolution (1)H NMR metabolic profiling combined with multilevel simultaneous data-analysis (MSCA) and partial-least squares-discriminant analysis (PLS-DA). The between-subject variations, as evaluated by MSCA, reflected the variations of lactate levels induced by the physical exercise. Analysis of the within-individual variance using multilevel PLS-DA models of plasma and urine metabolic profiles showed an effect of the green tea-based sports drink on glucose, citrate, and lactate levels in plasma and on acetone, 3-OH-butyrate, and lactate levels in urine. The increase of caffeine and hippuric acid levels in urine indicated the absorption of green tea extract components. NMR-based metabolomics allowed the complex effects of a green tea extract-based carbohydrate/hydroelectrolyte beverage on the energy metabolism of athletes during recovery by postexercise rehydration to be evaluated.

The Emerging Field of Quantitative Blood Metabolomics for Biomarker Discovery in Critical Illnesses

PubMed Central

Serkova, Natalie J.; Standiford, Theodore J.

2011-01-01

Metabolomics, a science of systems biology, is the global assessment of endogenous metabolites within a biologic system and represents a “snapshot” reading of gene function, enzyme activity, and the physiological landscape. Metabolite detection, either individual or grouped as a metabolomic profile, is usually performed in cells, tissues, or biofluids by either nuclear magnetic resonance spectroscopy or mass spectrometry followed by sophisticated multivariate data analysis. Because loss of metabolic homeostasis is common in critical illness, the metabolome could have many applications, including biomarker and drug target identification. Metabolomics could also significantly advance our understanding of the complex pathophysiology of acute illnesses, such as sepsis and acute lung injury/acute respiratory distress syndrome. Despite this potential, the clinical community is largely unfamiliar with the field of metabolomics, including the methodologies involved, technical challenges, and, most importantly, clinical uses. Although there is evidence of successful preclinical applications, the clinical usefulness and application of metabolomics in critical illness is just beginning to emerge, the advancement of which hinges on linking metabolite data to known and validated clinically relevant indices. In addition, other important aspects, such as patient selection, sample collection, and processing, as well as the needed multivariate data analysis, have to be taken into consideration before this innovative approach to biomarker discovery can become a reliable tool in the intensive care unit. The purpose of this review is to begin to familiarize clinicians with the field of metabolomics and its application for biomarker discovery in critical illnesses such as sepsis. PMID:21680948

Evaluation of 1H NMR metabolic profiling using biofluid mixture design.

PubMed

Athersuch, Toby J; Malik, Shahid; Weljie, Aalim; Newton, Jack; Keun, Hector C

2013-07-16

A strategy for evaluating the performance of quantitative spectral analysis tools in conditions that better approximate background variation in a metabonomics experiment is presented. Three different urine samples were mixed in known proportions according to a {3, 3} simplex lattice experimental design and analyzed in triplicate by 1D (1)H NMR spectroscopy. Fifty-four urinary metabolites were subsequently quantified from the sample spectra using two methods common in metabolic profiling studies: (1) targeted spectral fitting and (2) targeted spectral integration. Multivariate analysis using partial least-squares (PLS) regression showed the latent structure of the spectral set recapitulated the experimental mixture design. The goodness-of-prediction statistic (Q(2)) of each metabolite variable in a PLS model was calculated as a metric for the reliability of measurement, across the sample compositional space. Several metabolites were observed to have low Q(2) values, largely as a consequence of their spectral resonances having low s/n or strong overlap with other sample components. This strategy has the potential to allow evaluation of spectral features obtained from metabolic profiling platforms in the context of the compositional background found in real biological sample sets, which may be subject to considerable variation. We suggest that it be incorporated into metabolic profiling studies to improve the estimation of matrix effects that confound accurate metabolite measurement. This novel method provides a rational basis for exploiting information from several samples in an efficient manner and avoids the use of multiple spike-in authentic standards, which may be difficult to obtain.

Real-time bilinear rotation decoupling in absorptive mode J-spectroscopy: Detecting low-intensity metabolite peak close to high-intensity metabolite peak with convenience.

PubMed

Verma, Ajay; Baishya, Bikash

2016-05-01

"Pure shift" NMR spectra display singlet peak per chemical site. Thus, high resolution is offered at the cost of valuable J-coupling information. In the present work, real-time BIRD (BIlinear Rotation Decoupling) is applied to the absorptive-mode 2D J-spectroscopy to provide pure shift spectrum in the direct dimension and J-coupling information in the indirect dimension. Quite often in metabolomics, proton NMR spectra from complex bio-fluids display tremendous signal overlap. Although conventional J-spectroscopy in principle overcomes this problem by separating the multiplet information from chemical shift information, however, only magnitude mode of the experiment is practical, sacrificing much of the potential high resolution that could be achieved. Few J-spectroscopy methods have been reported so far that produce high-resolution pure shift spectrum along with J-coupling information for crowded spectral regions. In the present work, high-quality J-resolved spectrum from important metabolomic mixture such as tissue extract from rat cortex is demonstrated. Many low-intensity metabolite peaks which are obscured by the broad dispersive tails from high-intensity metabolite peaks in regular magnitude mode J-spectrum can be clearly identified in real-time BIRD J-resolved spectrum. The general practice of removing such spectral overlap is tedious and time-consuming as it involves repeated sample preparation to change the pH of the tissue extract sample and subsequent spectra recording. Copyright © 2016 Elsevier Inc. All rights reserved.

Real-time bilinear rotation decoupling in absorptive mode J-spectroscopy: Detecting low-intensity metabolite peak close to high-intensity metabolite peak with convenience

NASA Astrophysics Data System (ADS)

Verma, Ajay; Baishya, Bikash

2016-05-01

;Pure shift; NMR spectra display singlet peak per chemical site. Thus, high resolution is offered at the cost of valuable J-coupling information. In the present work, real-time BIRD (BIlinear Rotation Decoupling) is applied to the absorptive-mode 2D J-spectroscopy to provide pure shift spectrum in the direct dimension and J-coupling information in the indirect dimension. Quite often in metabolomics, proton NMR spectra from complex bio-fluids display tremendous signal overlap. Although conventional J-spectroscopy in principle overcomes this problem by separating the multiplet information from chemical shift information, however, only magnitude mode of the experiment is practical, sacrificing much of the potential high resolution that could be achieved. Few J-spectroscopy methods have been reported so far that produce high-resolution pure shift spectrum along with J-coupling information for crowded spectral regions. In the present work, high-quality J-resolved spectrum from important metabolomic mixture such as tissue extract from rat cortex is demonstrated. Many low-intensity metabolite peaks which are obscured by the broad dispersive tails from high-intensity metabolite peaks in regular magnitude mode J-spectrum can be clearly identified in real-time BIRD J-resolved spectrum. The general practice of removing such spectral overlap is tedious and time-consuming as it involves repeated sample preparation to change the pH of the tissue extract sample and subsequent spectra recording.

Role of Raman spectroscopy and surface enhanced Raman spectroscopy in colorectal cancer

PubMed Central

Jenkins, Cerys A; Lewis, Paul D; Dunstan, Peter R; Harris, Dean A

2016-01-01

Colorectal cancer (CRC) is the fourth most common cancer in the United Kingdom and is the second largest cause of cancer related death in the United Kingdom after lung cancer. Currently in the United Kingdom there is not a diagnostic test that has sufficient differentiation between patients with cancer and those without cancer so the current referral system relies on symptomatic presentation in a primary care setting. Raman spectroscopy and surface enhanced Raman spectroscopy (SERS) are forms of vibrational spectroscopy that offer a non-destructive method to gain molecular information about biological samples. The techniques offer a wide range of applications from in vivo or in vitro diagnostics using endoscopic probes, to the use of micro-spectrometers for analysis of biofluids. The techniques have the potential to detect molecular changes prior to any morphological changes occurring in the tissue and therefore could offer many possibilities to aid the detection of CRC. The purpose of this review is to look at the current state of diagnostic technology in the United Kingdom. The development of Raman spectroscopy and SERS in clinical applications relation for CRC will then be discussed. Finally, future areas of research of Raman/SERS as a clinical tool for the diagnosis of CRC are also discussed. PMID:27190582

Proteomic Analysis of Saliva in HIV-positive Heroin Addicts Reveals Proteins Correlated with Cognition

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

Dominy, Stephen; Brown, Joseph N.; Ryder, Mark I.

The prevalence of HIV-associated neurocognitive disorders (HAND) remains high despite effective antiretroviral therapies. Multiple etiologies have been proposed over the last few years to account for this phenomenon, including the neurotoxic effects of antiretrovirals and co-morbid substance abuse. However, no underlying molecular mechanism has been identified. Emerging evidence in several fields has linked the gut to brain diseases, but the effect of the gut on the brain during HIV infection has not been explored. Saliva is the most accessible gut biofluid, and is therefore of great scientific interest for diagnostic and prognostic purposes. This study presents a longitudinal, liquid chromatography-massmore » spectrometry-based quantitative proteomics study investigating saliva samples taken from 8 HIV-positive (HIV+) and 11 -negative (HIV-) heroin addicts. In the HIV+ group, 58 proteins were identified that show significant correlations with cognitive scores and that implicate disruption of protein quality control pathways by HIV. Notably, no proteins from the HIV- heroin addict cohort showed significant correlations with cognitive scores. In addition, the majority of correlated proteins have been shown to be associated with exosomes, allowing us to propose that the salivary glands and/or oral epithelium may modulate brain function during HIV infection through the release of discrete packets of proteins in the form of exosomes.« less

In vivo bone remodeling rates determination and compressive stiffness variations before, during 60 days bed rest and two years follow up: A micro-FE-analysis from HR-pQCT measurements of the berlin Bed Rest Study-2

NASA Astrophysics Data System (ADS)

Ritter, Zully; Belavy, Daniel; Baumann, Wolfgang W.; Felsenberg, Dieter

2017-03-01

Bed rest studies are used for simulation and study of physiological changes as observed in unloading/non-gravity environments. Amongst others, bone mass reduction, similar as occurring due to aging osteoporosis, combined with bio-fluids redistribution and muscle atrophy have been observed and analyzed. Advanced radiological methods of high resolution such as HR-pQCT (XtremeCT) allow 3D-visualizing in vivo bone remodeling processes occurring during absence/reduction of mechanical stimuli (0 to <1 g) as simulated by bed rest. Induced bone micro-structure (e.g. trabecular number, cortical thickness, porosity) and density variations can be quantified. However, these parameters are average values of each sample and important information regarding bone mass distribution and within bone mechanical behaviour is lost. Finite element models with hexa-elements of identical size as the HR-pQCT measurements (0.082 mm×0.082 mm×0.082 mm, ca. 7E6 elements/sample) can be used for subject-specific in vivo stiffness calculation. This technique also allows quantifying if bone microstructural changes represent a risk of mechanical bone collapse (fracture).

A Review of Selected Studies That Determine the Physical and Chemical Properties of Saliva in the Field of Dental Treatment

PubMed Central

Kubala, Elżbieta; Strzelecka, Paulina; Grzegocka, Marta; Lietz-Kijak, Danuta; Gronwald, Helena; Skomro, Piotr

2018-01-01

Physiological whole saliva is a unique body fluid constantly washing the mucous membranes of the mouth, throat, and larynx. Saliva is a clear, slightly acidic mucinous-serous secretion, composed of various electrolytes, small organic substances, proteins, peptides, and polynucleotides. There are many ways to use saliva as a biological fluid (biofluid). The significant advantages of saliva as a unique diagnostic material are its availability and the noninvasive method of collection. The aim of this review is to emphasize the diagnostic value of saliva as a research material in the configuration of its structure and secretion disorders. The data were obtained using the MEDLINE (PubMed) search engine, as well as an additional manual search. The analysis covered 77 articles selected from a group of 1986 publications and initially qualified for devising. The results were evaluated and checked for the correctness of qualifying in accordance with inclusion and exclusion criteria. The diagnostic use of saliva has attracted the attention of many researchers due to its noninvasive nature and relative simplicity of collection. In addition, it should be noted that the determination of chemical and physical saliva parameters can be effectively performed in the patient's presence in the dental office. PMID:29854777

Lithography-free nanofluidic concentrator based on droplets-on-demand system

NASA Astrophysics Data System (ADS)

Yu, Miao; Zhou, Hongbo; Yao, Shuhuai

2013-11-01

Biomarkers are usually low-abundance proteins in biofluids and below detection limit of conventional biosensors. Nanofluidic concentration devices allow efficient biomolecules trapping by utilizing ion concentration polarization near nanochannels. However, once the electric field is turned off, the electrokinetic concentration plug cannot maintain its concentration status and starts to diffuse. In order to maintain the high concentration and extract the concentrated sample for further analysis, a good approach is to encapsulate these plugs into water-in-oil droplets. Here we developed a nanofluidic concentrator based on droplet-on-demand generator to encapsulate concentrated sample in nL droplets. The lithography-free nanochannels were patterned by thermal cracking on the surface of PS Petri-dish. The resulting nanochannel arrays were 30 nm in depth. In combination with microchannels on PDMS, the micro-nano hybrid chip was developed. We used FITC solution to demonstrate that the chip significantly increased the sample concentration for more than 100 folds within 5 minutes. By tuning the pulsed pressure imposed by the solenoid valve connected to the concentration channel, the system can generate a desired volume of droplet with a target sample concentration at a prescribed time. This work was supported by the Research Grants Council of Hong Kong under General Research Fund (Grant No. 621110).

NMR metabolomic analysis of dairy cows reveals milk glycerophosphocholine to phosphocholine ratio as prognostic biomarker for risk of ketosis.

PubMed

Klein, Matthias S; Buttchereit, Nina; Miemczyk, Sebastian P; Immervoll, Ann-Kathrin; Louis, Caridad; Wiedemann, Steffi; Junge, Wolfgang; Thaller, Georg; Oefner, Peter J; Gronwald, Wolfram

2012-02-03

Ketosis is a common metabolic disease in dairy cows. Diagnostic markers for ketosis such as acetone and beta-hydroxybutyric acid (BHBA) are known, but disease prediction remains an unsolved challenge. Milk is a steadily available biofluid and routinely collected on a daily basis. This high availability makes milk superior to blood or urine samples for diagnostic purposes. In this contribution, we show that high milk glycerophosphocholine (GPC) levels and high ratios of GPC to phosphocholine (PC) allow for the reliable selection of healthy and metabolically stable cows for breeding purposes. Throughout lactation, high GPC values are connected with a low ketosis incidence. During the first month of lactation, molar GPC/PC ratios equal or greater than 2.5 indicate a very low risk for developing ketosis. This threshold was validated for different breeds (Holstein-Friesian, Brown Swiss, and Simmental Fleckvieh) and for animals in different lactations, with observed odds ratios between 1.5 and 2.38. In contrast to acetone and BHBA, these measures are independent of the acute disease status. A possible explanation for the predictive effect is that GPC and PC are measures for the ability to break down phospholipids as a fatty acid source to meet the enhanced energy requirements of early lactation.

Volatile metabolomic signature of human breast cancer cell lines

PubMed Central

Silva, Catarina L.; Perestrelo, Rosa; Silva, Pedro; Tomás, Helena; Câmara, José S.

2017-01-01

Breast cancer (BC) remains the most prevalent oncologic pathology in women, causing huge psychological, economic and social impacts on our society. Currently, the available diagnostic tools have limited sensitivity and specificity. Metabolome analysis has emerged as a powerful tool for obtaining information about the biological processes that occur in organisms, and is a useful platform for discovering new biomarkers or make disease diagnosis using different biofluids. Volatile organic compounds (VOCs) from the headspace of cultured BC cells and normal human mammary epithelial cells, were collected by headspace solid-phase microextraction (HS-SPME) and analyzed by gas chromatography combined with mass spectrometry (GC–MS), thus defining a volatile metabolomic signature. 2-Pentanone, 2-heptanone, 3-methyl-3-buten-1-ol, ethyl acetate, ethyl propanoate and 2-methyl butanoate were detected only in cultured BC cell lines. Multivariate statistical methods were used to verify the volatomic differences between BC cell lines and normal cells in order to find a set of specific VOCs that could be associated with BC, providing comprehensive insight into VOCs as potential cancer biomarkers. The establishment of the volatile fingerprint of BC cell lines presents a powerful approach to find endogenous VOCs that could be used to improve the BC diagnostic tools and explore the associated metabolomic pathways. PMID:28256598

Optical fiber-based fluorescent viscosity sensor

NASA Astrophysics Data System (ADS)

Haidekker, Mark A.; Akers, Walter J.; Fischer, Derek; Theodorakis, Emmanuel A.

2006-09-01

Molecular rotors are a unique group of viscosity-sensitive fluorescent probes. Several recent studies have shown their applicability as nonmechanical fluid viscosity sensors, particularly in biofluids containing proteins. To date, molecular rotors have had to be dissolved in the fluid for the measurement to be taken. We now show that molecular rotors may be covalently bound to a fiber-optic tip without loss of viscosity sensitivity. The optical fiber itself may be used as a light guide for emission light (external illumination of the tip) as well as for both emission and excitation light. Covalently bound molecular rotors exhibit a viscosity-dependent intensity increase similar to molecular rotors in solution. An optical fiber-based fluorescent viscosity sensor may be used in real-time measurement applications ranging from biomedical applications to the food industry.

Hybrid nanogenerator for concurrently harvesting biomechanical and biochemical energy.

PubMed

Hansen, Benjamin J; Liu, Ying; Yang, Rusen; Wang, Zhong Lin

2010-07-27

Harvesting energy from multiple sources available in our personal and daily environments is highly desirable, not only for powering personal electronics, but also for future implantable sensor-transmitter devices for biomedical and healthcare applications. Here we present a hybrid energy scavenging device for potential in vivo applications. The hybrid device consists of a piezoelectric poly(vinylidene fluoride) nanofiber nanogenerator for harvesting mechanical energy, such as from breathing or from the beat of a heart, and a flexible enzymatic biofuel cell for harvesting the biochemical (glucose/O2) energy in biofluid, which are two types of energy available in vivo. The two energy harvesting approaches can work simultaneously or individually, thereby boosting output and lifetime. Using the hybrid device, we demonstrate a "self-powered" nanosystem by powering a ZnO nanowire UV light sensor.

Effect of Aluminum Coating on the Surface Properties of Ti-(~49 at. pct) Ni Alloy

NASA Astrophysics Data System (ADS)

Sinha, Arijit; Khan, Gobinda Gopal; Mondal, Bholanath; Majumdar, Jyotsna Dutta; Chattopadhyay, Partha Protim

2015-08-01

Stable porous layer of mixed Al2O3 and TiO2 has been formed on the Ti-(~49 at. pct) Ni alloy surface with an aim to suppress leaching of Ni from the alloy surface in contact with bio-fluid and to enhance the process of osseointegration. Aluminum coating on the Ni-Ti alloy surface prior to the anodization treatment has resulted in enhancement of depth and uniformity of pores. Thermal oxidation of the anodized aluminum-coated Ni-Ti samples has exhibited the formation of Al2O3 and TiO2 phases with dense porous structure. The nanoindentation and nanoscratch measurements have indicated a remarkable improvement in the hardness, wear resistance, and adhesiveness of the porous aluminum-coated Ni-Ti sample after thermal oxidation.

Optical fiber-based fluorescent viscosity sensor.

PubMed

Haidekker, Mark A; Akers, Walter J; Fischer, Derek; Theodorakis, Emmanuel A

2006-09-01

Molecular rotors are a unique group of viscosity-sensitive fluorescent probes. Several recent studies have shown their applicability as nonmechanical fluid viscosity sensors, particularly in biofluids containing proteins. To date, molecular rotors have had to be dissolved in the fluid for the measurement to be taken. We now show that molecular rotors may be covalently bound to a fiber-optic tip without loss of viscosity sensitivity. The optical fiber itself may be used as a light guide for emission light (external illumination of the tip) as well as for both emission and excitation light. Covalently bound molecular rotors exhibit a viscosity-dependent intensity increase similar to molecular rotors in solution. An optical fiber-based fluorescent viscosity sensor may be used in real-time measurement applications ranging from biomedical applications to the food industry.

Quantification of cortisol in human eccrine sweat by liquid chromatography - tandem mass spectrometry.

PubMed

Jia, Min; Chew, Wade M; Feinstein, Yelena; Skeath, Perry; Sternberg, Esther M

2016-03-21

Cortisol has long been recognized as the "stress biomarker" in evaluating stress related disorders. Plasma, urine or saliva are the current source for cortisol analysis. The sampling of these biofluids is either invasive or has reliability problems that could lead to inaccurate results. Sweat has drawn increasing attention as a promising source for non-invasive stress analysis. A sensitive HPLC-MS/MS method was developed for the quantitation of cortisol ((11β)-11,17,21-trihydroxypregn-4-ene-3,20-dione) in human eccrine sweat. At least one unknown isomer that has previously not been reported and could potentially interfere with quantification was separated from cortisol with mixed mode RP HPLC. Detection of cortisol was carried out using atmospheric pressure chemical ionization (APCI) and selected reaction monitoring (SRM) in positive ion mode, using cortisol-9,11,12,12-D4 as internal standard. LOD and LOQ were estimated to be 0.04 ng ml(-1) and 0.1 ng ml(-1), respectively. Linear range of 0.10-25.00 ng ml(-1) was obtained. Intraday precision (2.5%-9.7%) and accuracy (0.5%-2.1%), interday precision (12.3%-18.7%) and accuracy (7.1%-15.1%) were achieved. This method has been successfully applied to the cortisol analysis of human eccrine sweat samples. This is the first demonstration that HPLC-MS/MS can be used for the sensitive and highly specific determination of cortisol in human eccrine sweat in the presence of at least one isomer that has similar hydrophobicity as cortisol. This study demonstrated that human eccrine sweat could be used as a promising source for non-invasive assessment of stress biomarkers such as cortisol and other steroid hormones.

Metabolomic analysis of urine with Nuclear Magnetic Resonance spectroscopy in patients with idiopathic sudden sensorineural hearing loss: A preliminary study.

PubMed

Carta, Filippo; Lussu, Milena; Bandino, Fabrizio; Noto, Antonio; Peppi, Marcello; Chuchueva, Natalia; Atzori, Luigi; Fanos, Vassilios; Puxeddu, Roberto

2017-08-01

Idiopathic sudden sensorineural hearing loss is a frequent emergency, with unknown aetiology and usually treated with empiric therapy. Steroids represent the only validated treatment but prognosis is unpredictable and the possibility to select the patients who will not respond to steroids could avoid unnecessary treatments. Metabolomic profiling of the biofluids target the analysis of the final product of genic expression and enzymatic activity, defining the biochemical phenotype of a whole biologic system. We studied the metabolomics of the urine of a cohort of patients with idiopathic sudden sensorineural hearing loss, correlating the metabolic profiles with the clinical outcomes. Metabolomic profiling of urine samples was performed by 1 H Nuclear Magnetic Resonance spectroscopy in combination with multivariate statistical approaches. 26 patients were included in the study: 5 healthy controls, 13 patients who did not recover after treatment at 6 months while the remaining 8 patients recovered from the hearing loss. The orthogonal partial least square-discriminant analysis score plot showed a significant separation between the two groups, responders and non-responders after steroid therapy, R 2 Y of 0.83, Q 2 of 0.38 and p value <0.05. The resulting metabolic profiles were characterized by higher levels of urinary B-Alanine, 3-hydroxybutyrate and Trimethylamine N-oxide, and lower levels of Citrate and Creatinine in patients with worst outcome. Idiopathic sudden sensorineural hearing loss is a specific disease with unclear systemic changes, but our data suggest that there are different types of this disorder or patients predisposed to effective action of steroids allowing the recover after treatment. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

1H NMR spectroscopy analysis of metabolites in the kidneys provides new insight into pathophysiological mechanisms: applications for treatment with Cordyceps sinensis.

PubMed

Zhong, Fang; Liu, Xia; Zhou, Qiao; Hao, Xu; Lu, Ying; Guo, Shanmai; Wang, Weiming; Lin, Donghai; Chen, Nan

2012-02-01

The number of patients with chronic kidney disease (CKD) is continuously growing worldwide. Treatment with traditional Chinese medicine might slow the progression of CKD. In this study, we evaluated the renal protective effects of the Chinese herb Cordyceps sinensis in rats with 5/6 nephrectomy. Male Sprague-Dawley mice (weighing 150-200 g) were subjected to 5/6 nephrectomy. The rats were divided into three groups: (i) untreated nephrectomized group (OP group, n = 16), (ii) oral administration of C. sinensis-treated (4 mg/kg/day) nephrectomized group (CS group, n = 16) and (iii) sham-operated group (SO group, n = 16). The rats were sacrificed at 4 and 8 weeks after 5/6 nephrectomy, and the kidneys, serum and urine were collected for (1)H nuclear magnetic resonance spectral analysis. Multivariate statistical techniques and statistical metabolic correlation comparison analysis were performed to identify metabolic changes in aqueous kidney extracts between these groups. Significant differences between these groups were discovered in the metabolic profiles of the biofluids and kidney extracts. Pathways including the citrate cycle, branched-chain amino acid metabolism and the metabolites that regulate permeate pressure were disturbed in the OP group compared to the SO group; in addition, these pathways were reversed by C. sinensis treatment. Biochemistry and electron microscopic images verified that C. sinensis has curative effects on chronic renal failure. These results were confirmed by metabonomics results. Our study demonstrates that C. sinensis has potential curative effects on CKD, and our metabonomics results provided new insight into the mechanism of treatment of this traditional Chinese medicine.

Serum proteome profiling in canine idiopathic dilated cardiomyopathy using TMT-based quantitative proteomics approach.

PubMed

Bilić, Petra; Guillemin, Nicolas; Kovačević, Alan; Beer Ljubić, Blanka; Jović, Ines; Galan, Asier; Eckersall, Peter David; Burchmore, Richard; Mrljak, Vladimir

2018-05-15

Idiopathic dilated cardiomyopathy (iDCM) is a primary myocardial disorder with an unknown aetiology, characterized by reduced contractility and ventricular dilation of the left or both ventricles. Naturally occurring canine iDCM was used herein to identify serum proteomic signature of the disease compared to the healthy state, providing an insight into underlying mechanisms and revealing proteins with biomarker potential. To achieve this, we used high-throughput label-based quantitative LC-MS/MS proteomics approach and bioinformatics analysis of the in silico inferred interactome protein network created from the initial list of differential proteins. To complement the proteomic analysis, serum biochemical parameters and levels of know biomarkers of cardiac function were measured. Several proteins with biomarker potential were identified, such as inter-alpha-trypsin inhibitor heavy chain H4, microfibril-associated glycoprotein 4 and apolipoprotein A-IV, which were validated using an independent method (Western blotting) and showed high specificity and sensitivity according to the receiver operating characteristic curve analysis. Bioinformatics analysis revealed involvement of different pathways in iDCM, such as complement cascade activation, lipoprotein particles dynamics, elastic fibre formation, GPCR signalling and respiratory electron transport chain. Idiopathic dilated cardiomyopathy is a severe primary myocardial disease of unknown cause, affecting both humans and dogs. This study is a contribution to the canine heart disease research by means of proteomic and bioinformatic state of the art analyses, following similar approach in human iDCM research. Importantly, we used serum as non-invasive and easily accessible biological source of information and contributed to the scarce data on biofluid proteome research on this topic. Bioinformatics analysis revealed biological pathways modulated in canine iDCM with potential of further targeted research. Also, several proteins with biomarker potential have been identified and successfully validated. Copyright © 2018 Elsevier B.V. All rights reserved.

Prescriptive Oriented Drug Analysis of Multiple Sclerosis Disease by LC-UV in Whole Human Blood.

PubMed

Suneetha, A; Rajeswari, Raja K

2016-02-01

As a polytherapy treatment, multiple sclerosis disease demands prescriptions with more than one drug. Polytherapy is sometimes rational for drug combinations chosen to minimize adverse effects. Estimation of drugs that are concomitantly administered in polytherapy is acceptable as it shortens the analytical timepoints and also the usage of biological matrices. In clinical phase trials, the withdrawal of biofluids is a critical issue for each analysis. Estimating all the coadminsitered drugs in a single shot will be more effective and economical for pharmaceuticals. A single, simple, rapid and sensitive high-performance liquid chromatography assay method has been developed with UV detection and fully validated for the quantification of 14 drugs (at random combinations) used in the treatment of multiple sclerosis disease. The set of combinations was based on prescriptions to patients. Separations were achieved on an X-Terra MS C18 (100 × 3.9 mm, 5 µm) column. The analytes were extracted from 50 µL aliquots of whole human blood with protein precipitation using acetonitrile. All the drugs were sufficiently stable during storage for 24 h at room temperature and for 23 days at 2-8°C. The percentage recoveries of all drugs were between 90 and 115%, with RSD values <10.6%. This method has been shown to be reproducible and sensitive and can be applied to clinical samples from pharmacokinetic studies and also a useful tool in studying the drug interaction studies. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

The metabolomic approach identifies a biological signature of low-dose chronic exposure to cesium 137.

PubMed

Grison, Stéphane; Martin, Jean-Charles; Grandcolas, Line; Banzet, Nathalie; Blanchardon, Eric; Tourlonias, Elie; Defoort, Catherine; Favé, Gaëlle; Bott, Romain; Dublineau, Isabelle; Gourmelon, Patrick; Souidi, Maâmar

2012-01-01

Reports have described apparent biological effects of (137)Cs (the most persistent dispersed radionuclide) irradiation in people living in Chernobyl-contaminated territory. The sensitive analytical technology described here should now help assess the relation of this contamination to the observed effects. A rat model chronically exposed to (137)Cs through drinking water was developed to identify biomarkers of radiation-induced metabolic disorders, and the biological impact was evaluated by a metabolomic approach that allowed us to detect several hundred metabolites in biofluids and assess their association with disease states. After collection of plasma and urine from contaminated and non-contaminated rats at the end of the 9-months contamination period, analysis with a LC-MS system detected 742 features in urine and 1309 in plasma. Biostatistical discriminant analysis extracted a subset of 26 metabolite signals (2 urinary, 4 plasma non-polar, and 19 plasma polar metabolites) that in combination were able to predict from 68 up to 94% of the contaminated rats, depending on the prediction method used, with a misclassification rate as low as 5.3%. The difference in this metabolic score between the contaminated and non-contaminated rats was highly significant (P = 0.019 after ANOVA cross-validation). In conclusion, our proof-of-principle study demonstrated for the first time the usefulness of a metabolomic approach for addressing biological effects of chronic low-dose contamination. We can conclude that a metabolomic signature discriminated (137)Cs-contaminated from control animals in our model. Further validation is nevertheless required together with full annotation of the metabolic indicators.

Quantitative Metabolomic Analysis of Urinary Citrulline and Calcitroic Acid in Mice after Exposure to Various Types of Ionizing Radiation.

PubMed

Goudarzi, Maryam; Chauthe, Siddheshwar; Strawn, Steven J; Weber, Waylon M; Brenner, David J; Fornace, Albert J

2016-05-20

With the safety of existing nuclear power plants being brought into question after the Fukushima disaster and the increased level of concern over terrorism-sponsored use of improvised nuclear devices, it is more crucial to develop well-defined radiation injury markers in easily accessible biofluids to help emergency-responders with injury assessment during patient triage. Here, we focused on utilizing ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to identify and quantitate the unique changes in the urinary excretion of two metabolite markers, calcitroic acid and citrulline, in mice induced by different forms of irradiation; external γ irradiation at a low dose rate (LDR) of 3.0 mGy/min and a high dose rate (HDR) of 1.1 Gy/min, and internal exposure to Cesium-137 ((137)Cs) and Strontium-90 ((90)Sr). The multiple reaction monitoring analysis showed that, while exposure to (137)Cs and (90)Sr induced a statistically significant and persistent decrease, similar doses of external γ beam at the HDR had the opposite effect, and the LDR had no effect on the urinary levels of these two metabolites. This suggests that the source of exposure and the dose rate strongly modulate the in vivo metabolomic injury responses, which may have utility in clinical biodosimetry assays for the assessment of exposure in an affected population. This study complements our previous investigations into the metabolomic profile of urine from mice internally exposed to (90)Sr and (137)Cs and to external γ beam radiation.

Comparison of Total RNA Isolation Methods for Analysis of Immune-Related microRNAs in Market Milks

PubMed Central

2015-01-01

Bovine milk provides essential nutrients, including immunologically important molecules, as the primary source of nutrition to newborns. Recent studies showed that RNAs from bovine milk contain immune-related microRNAs (miRNA) that regulate various immune systems. To evaluate the biological and immunological activity of miRNAs from milk products, isolation methods need to be established. Six methods for extracting total RNAs from bovine colostrums were adopted to evaluate the isolating efficiency and expression of miRNAs. Total RNA from milk was presented in formulation of small RNAs, rather than ribosomal RNAs. Column-combined phenol isolating methods showed high recovery of total RNAs, especially the commercial columns for biofluid samples, which demonstrated outstanding efficiency for recovering miRNAs. We also evaluated the quantity of five immune-related miRNAs (miR-93, miR-106a, miR-155, miR-181a, miR-451) in milk processed by temperature treatments including low temperature for long time (LTLT, 63℃ for 30 min)-, high temperature for short time (HTST, 75℃ for 15 s)-, and ultra heat treatment (UHT, 120-130℃ for 0.5-4 s). All targeted miRNAs had significantly reduced levels in processed milks compared to colostrum and raw mature milk. Interestingly, the amount of immune-related miRNAs from HTST milk was more resistant than those of LTLT and UHT milks. Our present study examined defined methods of RNA isolation and quantification of immune-specific miRNAs from small volumes of milk for use in further analysis. PMID:26761866

Comparison of Total RNA Isolation Methods for Analysis of Immune-Related microRNAs in Market Milks.

PubMed

Oh, Sangnam; Park, Mi Ri; Son, Seok Jun; Kim, Younghoon

2015-01-01

Bovine milk provides essential nutrients, including immunologically important molecules, as the primary source of nutrition to newborns. Recent studies showed that RNAs from bovine milk contain immune-related microRNAs (miRNA) that regulate various immune systems. To evaluate the biological and immunological activity of miRNAs from milk products, isolation methods need to be established. Six methods for extracting total RNAs from bovine colostrums were adopted to evaluate the isolating efficiency and expression of miRNAs. Total RNA from milk was presented in formulation of small RNAs, rather than ribosomal RNAs. Column-combined phenol isolating methods showed high recovery of total RNAs, especially the commercial columns for biofluid samples, which demonstrated outstanding efficiency for recovering miRNAs. We also evaluated the quantity of five immune-related miRNAs (miR-93, miR-106a, miR-155, miR-181a, miR-451) in milk processed by temperature treatments including low temperature for long time (LTLT, 63℃ for 30 min)-, high temperature for short time (HTST, 75℃ for 15 s)-, and ultra heat treatment (UHT, 120-130℃ for 0.5-4 s). All targeted miRNAs had significantly reduced levels in processed milks compared to colostrum and raw mature milk. Interestingly, the amount of immune-related miRNAs from HTST milk was more resistant than those of LTLT and UHT milks. Our present study examined defined methods of RNA isolation and quantification of immune-specific miRNAs from small volumes of milk for use in further analysis.

Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers.

PubMed

Skotland, Tore; Ekroos, Kim; Kauhanen, Dimple; Simolin, Helena; Seierstad, Therese; Berge, Viktor; Sandvig, Kirsten; Llorente, Alicia

2017-01-01

Exosomes have recently appeared as a novel source of noninvasive cancer biomarkers, since these nanovesicles contain molecules from cancer cells and can be detected in biofluids. We have here investigated the potential use of lipids in urinary exosomes as prostate cancer biomarkers. A high-throughput mass spectrometry quantitative lipidomic analysis was performed to reveal the lipid composition of urinary exosomes in prostate cancer patients and healthy controls. Control samples were first analysed to characterise the lipidome of urinary exosomes and test the reproducibility of the method. In total, 107 lipid species were quantified in urinary exosomes. Several differences, for example, in cholesterol and phosphatidylcholine, were found between urinary exosomes and exosomes derived from cell lines, thus showing the importance of in vivo studies for biomarker analysis. The 36 most abundant lipid species in urinary exosomes were then quantified in 15 prostate cancer patients and 13 healthy controls. Interestingly, the levels of nine lipids species were found to be significantly different when the two groups were compared. The highest significance was shown for phosphatidylserine (PS) 18:1/18:1 and lactosylceramide (d18:1/16:0), the latter also showed the highest patient-to-control ratio. Furthermore, combinations of these lipid species and PS 18:0-18:2 distinguished the two groups with 93% sensitivity and 100% specificity. Finally, in agreement with the reported dysregulation of sphingolipid metabolism in cancer cells, alteration in specific sphingolipid lipid classes were observed. This study shows for the first time the potential use of exosomal lipid species in urine as prostate cancer biomarkers. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantitative Metabolomic Analysis of Urinary Citrulline and Calcitroic Acid in Mice after Exposure to Various Types of Ionizing Radiation

PubMed Central

Goudarzi, Maryam; Chauthe, Siddheshwar; Strawn, Steven J.; Weber, Waylon M.; Brenner, David J.; Fornace, Albert J.

2016-01-01

With the safety of existing nuclear power plants being brought into question after the Fukushima disaster and the increased level of concern over terrorism-sponsored use of improvised nuclear devices, it is more crucial to develop well-defined radiation injury markers in easily accessible biofluids to help emergency-responders with injury assessment during patient triage. Here, we focused on utilizing ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to identify and quantitate the unique changes in the urinary excretion of two metabolite markers, calcitroic acid and citrulline, in mice induced by different forms of irradiation; X-ray irradiation at a low dose rate (LDR) of 3.0 mGy/min and a high dose rate (HDR) of 1.1 Gy/min, and internal exposure to Cesium-137 (137Cs) and Strontium-90 (90Sr). The multiple reaction monitoring analysis showed that, while exposure to 137Cs and 90Sr induced a statistically significant and persistent decrease, similar doses of X-ray beam at the HDR had the opposite effect, and the LDR had no effect on the urinary levels of these two metabolites. This suggests that the source of exposure and the dose rate strongly modulate the in vivo metabolomic injury responses, which may have utility in clinical biodosimetry assays for the assessment of exposure in an affected population. This study complements our previous investigations into the metabolomic profile of urine from mice internally exposed to 90Sr and 137Cs and to X-ray beam radiation. PMID:27213362

Designing deoxidation inhibiting encapsulation of metal oxide nanostructures for fluidic and biological applications

NASA Astrophysics Data System (ADS)

Ghosh, Moumita; Ghosh, Siddharth; Seibt, Michael; Schaap, Iwan A. T.; Schmidt, Christoph F.; Mohan Rao, G.

2016-12-01

Due to their photoluminescence, metal oxide nanostructures such as ZnO nanostructures are promising candidates in biomedical imaging, drug delivery and bio-sensing. To apply them as label for bio-imaging, it is important to study their structural stability in a bio-fluidic environment. We have explored the effect of water, the main constituent of biological solutions, on ZnO nanostructures with scanning electron microscopy (SEM) and photoluminescence (PL) studies which show ZnO nanorod degeneration in water. In addition, we propose and investigate a robust and inexpensive method to encapsulate these nanostructures (without structural degradation) using bio-compatible non-ionic surfactant in non-aqueous medium, which was not reported earlier. This new finding is an immediate interest to the broad audience of researchers working in biophysics, sensing and actuation, drug delivery, food and cosmetics technology, etc.

Biodegradable elastomers and silicon nanomembranes/nanoribbons for stretchable, transient electronics, and biosensors.

PubMed

Hwang, Suk-Won; Lee, Chi Hwan; Cheng, Huanyu; Jeong, Jae-Woong; Kang, Seung-Kyun; Kim, Jae-Hwan; Shin, Jiho; Yang, Jian; Liu, Zhuangjian; Ameer, Guillermo A; Huang, Yonggang; Rogers, John A

2015-05-13

Transient electronics represents an emerging class of technology that exploits materials and/or device constructs that are capable of physically disappearing or disintegrating in a controlled manner at programmed rates or times. Inorganic semiconductor nanomaterials such as silicon nanomembranes/nanoribbons provide attractive choices for active elements in transistors, diodes and other essential components of overall systems that dissolve completely by hydrolysis in biofluids or groundwater. We describe here materials, mechanics, and design layouts to achieve this type of technology in stretchable configurations with biodegradable elastomers for substrate/encapsulation layers. Experimental and theoretical results illuminate the mechanical properties under large strain deformation. Circuit characterization of complementary metal-oxide-semiconductor inverters and individual transistors under various levels of applied loads validates the design strategies. Examples of biosensors demonstrate possibilities for stretchable, transient devices in biomedical applications.

Localized viscoelasticity measurements with untethered intravitreal microrobots.

PubMed

Pokki, Juho; Ergeneman, Olgaç; Bergeles, Christos; Torun, Hamdi; Nelson, Bradley J

2012-01-01

Microrobots are a promising tool for medical interventions and micromanipulation. In this paper, we explore the concept of using microrobots for microrheology. Untethered magnetically actuated microrobots were used to characterize one of the most complex biofluids, the vitreous humor. In this work we began by experimentally characterizing the viscoelastic properties of an artificial vitreous humor. For comparison, its properties were also measured using special microcantilevers in an atomic force microscope (AFM) setup. Subsequently, an untethered device was used to study the vitreous humor of a porcine eye, which is a valid ex-vivo model of a human eye. Its viscoelasticity model was extracted, which was in agreement with the model of the artificial vitreous. The existing characterization methodology requires eye and vitreous humor dissection for the microrheology measurements. We envision that the method proposed here can be used in in vivo.

Bioaccessibility, release kinetics, and molecular speciation of arsenic and lead in geo-dusts from the Iron King Mine Federal Superfund site in Humboldt, Arizona.

PubMed

Menka, Nazune; Root, Rob; Chorover, Jon

2014-01-01

Mine tailings contain multiple toxic metal(loid)s that pose a threat to human health via inhalation and ingestion. The goals of this research include understanding the speciation and molecular environment of these toxic metal(loid)s (arsenic and lead) as well as the impacts particle size and residence time have on their bioaccessibilty in simulated gastric and lung fluid. Additionally, future work will include smaller size fractions (PM10 and PM2.5) of surface mine tailings, with the goal of increasing our understanding of multi-metal release from contaminated geo-dusts in simulated bio-fluids. This research is important to environmental human health risk assessment as it increases the accuracy of exposure estimations to toxic metal(loid)s.

Phosphoproteins in extracellular vesicles as candidate markers for breast cancer

PubMed Central

Chen, I-Hsuan; Xue, Liang; Hsu, Chuan-Chih; Paez, Juan Sebastian Paez; Pan, Li; Andaluz, Hillary; Wendt, Michael K.; Iliuk, Anton B.; Tao, W. Andy

2017-01-01

The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring. PMID:28270605

Phosphoproteins in extracellular vesicles as candidate markers for breast cancer.

PubMed

Chen, I-Hsuan; Xue, Liang; Hsu, Chuan-Chih; Paez, Juan Sebastian Paez; Pan, Li; Andaluz, Hillary; Wendt, Michael K; Iliuk, Anton B; Zhu, Jian-Kang; Tao, W Andy

2017-03-21

The state of protein phosphorylation can be a key determinant of cellular physiology such as early-stage cancer, but the development of phosphoproteins in biofluids for disease diagnosis remains elusive. Here we demonstrate a strategy to isolate and identify phosphoproteins in extracellular vesicles (EVs) from human plasma as potential markers to differentiate disease from healthy states. We identified close to 10,000 unique phosphopeptides in EVs isolated from small volumes of plasma samples. Using label-free quantitative phosphoproteomics, we identified 144 phosphoproteins in plasma EVs that are significantly higher in patients diagnosed with breast cancer compared with healthy controls. Several biomarkers were validated in individual patients using paralleled reaction monitoring for targeted quantitation. This study demonstrates that the development of phosphoproteins in plasma EV as disease biomarkers is highly feasible and may transform cancer screening and monitoring.

Direct detection of circulating free DNA extracted from serum samples of breast cancer using locked nucleic acid molecular beacon.

PubMed

Gui, Zhen; Wang, Quanbo; Li, Jinchang; Zhu, Mingchen; Yu, Lili; Xun, Tang; Yan, Feng; Ju, Huangxian

2016-07-01

As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB). In order to enhance the stability and detection efficiency of the probe in biofluids, we design a shared-stem molecular beacon containing a 27-mer loop and a 4-mer stem with DNA/LNA alternating bases. The fluorescence is released in the presence of target. The detection procedure is simple and can be completed within 1h. This method shows a sensitive response to UHRF1 DNA with a dynamic range of 3 orders of magnitude. The limit of detection is 11nM (S/N=3) with excellent selectivity. It can discriminate UHRF1 DNA from three-base mismatched DNA with a high specificity. More importantly, this method can distinguish the expression of serum UHRF1 DNA among 5 breast cancer patients and 5 healthy controls. The mentioned superiority may suggest that this assay can be served as a promising noninvasive detection tool for early BC diagnosis and monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

Selenium Levels in Serum, Red Blood Cells, and Cerebrospinal Fluid of Alzheimer's Disease Patients: A Report from the Australian Imaging, Biomarker & Lifestyle Flagship Study of Ageing (AIBL).

PubMed

Cardoso, Bárbara R; Hare, Dominic J; Bush, Ashley I; Li, Qiao-Xin; Fowler, Christopher J; Masters, Colin L; Martins, Ralph N; Ganio, Katherine; Lothian, Amber; Mukherjee, Soumya; Kapp, Eugene A; Roberts, Blaine R

2017-01-01

Selenium (Se) protects cells against oxidative stress damage through a range of bioactive selenoproteins. Increased oxidative stress is a prominent feature of Alzheimer's disease (AD), and previous studies have shown that Se deficiency is associated with age-related cognitive decline. In this study, we assessed Se status in different biofluids from a subgroup of participants in the Australian Imaging, Biomarkers and Lifestyle Flagship Study of Ageing. As Se in humans can either be an active component of selenoproteins or inactive via non-specific incorporation into other proteins, we used both size exclusion chromatography-inductively coupled plasma-mass spectrometry (SEC-ICP-MS) and tandem mass spectrometry to characterize selenoproteins in serum. We observed no differences in total Se concentration in serum or cerebrospinal fluid of AD subjects compared to mildly cognitively impairment patients and healthy controls. However, Se levels in erythrocytes were decreased in AD compared to controls. SEC-ICP-MS analysis revealed a dominant Se-containing fraction. This fraction was subjected to standard protein purification and a bottom-up proteomics approach to confirm that the abundant Se in the fraction was due, in part, to selenoprotein P. The lack of change in the Se level is at odds with our previous observations in a Brazilian population deficient in Se, and we attribute this to the Australian cohort being Se-replete.

Metabolomic analysis of urine samples by UHPLC-QTOF-MS: Impact of normalization strategies.

PubMed

Gagnebin, Yoric; Tonoli, David; Lescuyer, Pierre; Ponte, Belen; de Seigneux, Sophie; Martin, Pierre-Yves; Schappler, Julie; Boccard, Julien; Rudaz, Serge

2017-02-22

Among the various biological matrices used in metabolomics, urine is a biofluid of major interest because of its non-invasive collection and its availability in large quantities. However, significant sources of variability in urine metabolomics based on UHPLC-MS are related to the analytical drift and variation of the sample concentration, thus requiring normalization. A sequential normalization strategy was developed to remove these detrimental effects, including: (i) pre-acquisition sample normalization by individual dilution factors to narrow the concentration range and to standardize the analytical conditions, (ii) post-acquisition data normalization by quality control-based robust LOESS signal correction (QC-RLSC) to correct for potential analytical drift, and (iii) post-acquisition data normalization by MS total useful signal (MSTUS) or probabilistic quotient normalization (PQN) to prevent the impact of concentration variability. This generic strategy was performed with urine samples from healthy individuals and was further implemented in the context of a clinical study to detect alterations in urine metabolomic profiles due to kidney failure. In the case of kidney failure, the relation between creatinine/osmolality and the sample concentration is modified, and relying only on these measurements for normalization could be highly detrimental. The sequential normalization strategy was demonstrated to significantly improve patient stratification by decreasing the unwanted variability and thus enhancing data quality. Copyright © 2016 Elsevier B.V. All rights reserved.

DMS-prefiltered mass spectrometry for the detection of biomarkers

NASA Astrophysics Data System (ADS)

Coy, Stephen L.; Krylov, Evgeny V.; Nazarov, Erkinjon G.

2008-04-01

Technologies based on Differential Mobility Spectrometry (DMS) are ideally matched to rapid, sensitive, and selective detection of chemicals like biomarkers. Biomarkers linked to exposure to radiation, exposure to CWA's, exposure to toxic materials (TICs and TIMs) and to specific diseases are being examined in a number of laboratories. Screening for these types of exposure can be improved in accuracy and greatly speeded up by using DMS-MS instead of slower techniques like LC-MS and GC-MS. We have performed an extensive series of tests with nanospray-DMS-mass spectroscopy and standalone nanospray-DMS obtaining extensive information on chemistry and detectivity. DMS-MS systems implemented with low-resolution, low-cost, portable mass-spectrometry systems are very promising. Lowresolution mass spectrometry alone would be inadequate for the task, but with DMS pre-filtration to suppress interferences, can be quite effective, even for quantitative measurement. Bio-fluids and digests are well suited to ionization by electrospray and detection by mass-spectrometry, but signals from critical markers are overwhelmed by chemical noise from unrelated species, making essential quantitative analysis impossible. Sionex and collaborators have presented data using DMS to suppress chemical noise, allowing detection of cancer biomarkers in 10,000-fold excess of normal products 1,2. In addition, a linear dynamic range of approximately 2,000 has been demonstrated with accurate quantitation 3. We will review the range of possible applications and present new data on DMS-MS biomarker detection.

Flow interactions with cells and tissues: cardiovascular flows and fluid-structure interactions. Sixth International Bio-Fluid Mechanics Symposium and Workshop, March 28-30, 2008, Pasadena, California.

PubMed

Friedman, Morton H; Krams, Rob; Chandran, Krishnan B

2010-03-01

Interactions between flow and biological cells and tissues are intrinsic to the circulatory, respiratory, digestive and genitourinary systems. In the circulatory system, an understanding of the complex interaction between the arterial wall (a living multi-component organ with anisotropic, nonlinear material properties) and blood (a shear-thinning fluid with 45% by volume consisting of red blood cells, platelets, and white blood cells) is vital to our understanding of the physiology of the human circulation and the etiology and development of arterial diseases, and to the design and development of prosthetic implants and tissue-engineered substitutes. Similarly, an understanding of the complex dynamics of flow past native human heart valves and the effect of that flow on the valvular tissue is necessary to elucidate the etiology of valvular diseases and in the design and development of valve replacements. In this paper we address the influence of biomechanical factors on the arterial circulation. The first part presents our current understanding of the impact of blood flow on the arterial wall at the cellular level and the relationship between flow-induced stresses and the etiology of atherosclerosis. The second part describes recent advances in the application of fluid-structure interaction analysis to arterial flows and the dynamics of heart valves.

Lung cancer screening beyond low-dose computed tomography: the role of novel biomarkers.

PubMed

Hasan, Naveed; Kumar, Rohit; Kavuru, Mani S

2014-10-01

Lung cancer is the most common and lethal malignancy in the world. The landmark National lung screening trial (NLST) showed a 20% relative reduction in mortality in high-risk individuals with screening low-dose computed tomography. However, the poor specificity and low prevalence of lung cancer in the NLST provide major limitations to its widespread use. Furthermore, a lung nodule on CT scan requires a nuanced and individualized approach towards management. In this regard, advances in high through-put technology (molecular diagnostics, multi-gene chips, proteomics, and bronchoscopic techniques) have led to discovery of lung cancer biomarkers that have shown potential to complement the current screening standards. Early detection of lung cancer can be achieved by analysis of biomarkers from tissue samples within the respiratory tract such as sputum, saliva, nasal/bronchial airway epithelial cells and exhaled breath condensate or through peripheral biofluids such as blood, serum and urine. Autofluorescence bronchoscopy has been employed in research setting to identify pre-invasive lesions not identified on CT scan. Although these modalities are not yet commercially available in clinic setting, they will be available in the near future and clinicians who care for patients with lung cancer should be aware. In this review, we present up-to-date state of biomarker development, discuss their clinical relevance and predict their future role in lung cancer management.

Comparative assessment of Graves' disease and main extrathyroidal manifestation, Graves' ophthalmopathy, by non-targeted metabolite profiling of blood and orbital tissue.

PubMed

Ji, Dong Yoon; Park, Se Hee; Park, Soo Jin; Kim, Kyoung Heon; Ku, Cheol Ryong; Shin, Dong Yeob; Yoon, Jin Sook; Lee, Do Yup; Lee, Eun Jig

2018-06-18

Graves' disease (GD) is an autoimmune disorder that causes the overproduction of thyroid hormones and consequent cascade of systemic metabolism dysfunction. Moreover, Graves' ophthalmopathy (GO) is the main extrathyroidal manifestation of Graves' disease (GD). The goal of the study was to identify metabolic signatures in association with diagnostic biomarkers of GD without GO and GO, respectively. Ninety metabolites were profiled and analyzed based on a non-targeted primary metabolite profiling from plasma samples of 21 GD patients without GO, 26 subjects with GO, and 32 healthy subjects. Multivariate statistics showed a clear discrimination between healthy controls and disease group (R2Y = 0.518, Q2 = 0.478) and suggested a biomarker panel consisting of 10 metabolites. Among them, most of metabolites showed the positive association with the levels of thyrotropin receptor antibodies. With combination of proline and 1,5-anhydroglucitol, which were identified as GO-specific modulators, the re-constructed biomarker model greatly improved the statistical power and also facilitated simultaneous discrimination among healthy control, GO, and GD without GO groups (AUC = 0.845-0.935). Finally, the comparative analysis of tissue metabolite profiles from GO patients proposed putative metabolic linkage between orbital adipose/connective tissues and the biofluidic consequences, in which fumarate, proline, phenylalanine, and glycerol were coordinately altered with the blood metabolites.

Mechanistic Peptidomics: Factors That Dictate Specificity in the Formation of Endogenous Peptides in Human Milk*

PubMed Central

Guerrero, Andres; Dallas, David C.; Contreras, Stephanie; Chee, Sabrina; Parker, Evan A.; Sun, Xin; Dimapasoc, Lauren; Barile, Daniela; German, J. Bruce; Lebrilla, Carlito B.

2014-01-01

An extensive mass spectrometry analysis of the human milk peptidome has revealed almost 700 endogenous peptides from 30 different proteins. Two in-house computational tools were created and used to visualize and interpret the data through both alignment of the peptide quasi-molecular ion intensities and estimation of the differential enzyme participation. These results reveal that the endogenous proteolytic activity in the mammary gland is remarkably specific and well conserved. Certain proteins—not necessarily the most abundant ones—are digested by the proteases present in milk, yielding endogenous peptides from selected regions. Our results strongly suggest that factors such as the presence of specific proteases, the position and concentration of cleavage sites, and, more important, the intrinsic disorder of segments of the protein drive this proteolytic specificity in the mammary gland. As a consequence of this selective hydrolysis, proteins that typically need to be cleaved at specific positions in order to exert their activity are properly digested, and bioactive peptides encoded in certain protein sequences are released. Proteins that must remain intact in order to maintain their activity in the mammary gland or in the neonatal gastrointestinal tract are unaffected by the hydrolytic environment present in milk. These results provide insight into the intrinsic structural mechanisms that facilitate the selectivity of the endogenous milk protease activity and might be useful to those studying the peptidomes of other biofluids. PMID:25172956

More Analytical Tools for Fluids Management in Space

NASA Astrophysics Data System (ADS)

Weislogel, Mark

Continued advances during the 2000-2010 decade in the analysis of a class of capillary-driven flows relevant to materials processing and fluids management aboard spacecraft have been made. The class of flows addressed concern combined forced and spontaneous capillary flows in complex containers with interior edges. Such flows are commonplace in space-based fluid systems and arise from the particular container geometry and wetting properties of the system. Important applications for this work include low-g liquid fill and/or purge operations and passive fluid phase separation operations, where the container (i.e. fuel tank, water processer, etc.) geometry possesses interior edges, and where quantitative information of fluid location, transients, flow rates, and stability is critical. Examples include the storage and handling of liquid propellants and cryogens, water conditioning for life support, fluid phase-change thermal systems, materials processing in the liquid state, on-orbit biofluids processing, among others. For a growing number of important problems, closed-form expressions to transient three-dimensional flows are possible that, as design tools, replace difficult, time-consuming, and rarely performed numerical calculations. An overview of a selection of solutions in-hand is presented with example problems solved. NASA drop tower, low-g aircraft, and ISS flight ex-periment results are employed where practical to buttress the theoretical findings. The current review builds on a similar review presented at COSPAR, 2002, for the approximate decade 1990-2000.

A Thermally Powered ISFET Array for On-Body pH Measurement.

PubMed

Douthwaite, Matthew; Koutsos, Ermis; Yates, David C; Mitcheson, Paul D; Georgiou, Pantelis

2017-12-01

Recent advances in electronics and electrochemical sensors have led to an emerging class of next generation wearables, detecting analytes in biofluids such as perspiration. Most of these devices utilize ion-selective electrodes (ISEs) as a detection method; however, ion-sensitive field-effect transistors (ISFETs) offer a solution with improved integration and a low power consumption. This work presents a wearable, thermoelectrically powered system composed of an application-specific integrated circuit (ASIC), two commercial power management integrated circuits and a network of commercial thermoelectric generators (TEGs). The ASIC is fabricated in 0.35 m CMOS and contains an ISFET array designed to read pH as a current, a processing module which averages the signal to reduce noise and encodes it into a frequency, and a transmitter. The output frequency has a measured sensitivity of 6 to 8 kHz/pH for a pH range of 7-5. It is shown that the sensing array and processing module has a power consumption 6 W and, therefore, can be entirely powered by body heat using a TEG. Array averaging is shown to reduce noise at these low power levels to 104 V (input referred integrated noise), reducing the minimum detectable limit of the ASIC to 0.008 pH units. The work forms the foundation and proves the feasibility of battery-less, on-body electrochemical for perspiration analysis in sports science and healthcare applications.

Identification and characterization of proliferative retinopathy-related long noncoding RNAs

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

Zhou, Rong-Mei; Wang, Xiao-Qun; Yao, Jin

2015-09-25

Proliferative vitreoretinopathy (PVR) is a serious complication of retinal detachment and vitreoretinal surgery, which can lead to severe vision reduction. Long non-coding RNAs (lncRNAs) play critical roles in many biological processes and disease development. We attempted to determine the role of lncRNAs in the setting of PVR. Microarray analysis revealed that 78 lncRNAs were abnormally expressed in the epiretinal membranes (ERMs) of PVR patients, including 48 up-regulated and 30 down-regulated lncRNA transcripts. We subsequently focus on one lncRNA, MALAT1, and investigated its expression pattern in the biofluid of PVR patients. MALAT1 was significantly up-regulated in the cellular and plasma fractionmore » of peripheral blood in PVR patients. MALAT1 expression was obviously reduced after PVR operation. In vitro experiments revealed the role of MALAT1 in regulating RPE proliferation and migration, which is critical for ERMs formation. This study suggests that lncRNAs are the potential regulators of PVR pathology. MALAT1 is a potential prognostic indicator and a target for the diagnosis and gene therapy for PVR diseases. - Highlights: • 78 lncRNAs are differentially expressed between PVR-ERMs and secondary ERMs. • MALAT1 level is elevated in the ERMs of PVR patients. • Circulating MALAT1 level is up-regulated in PVR patients. • MALAT1 knockdown regulates RPE proliferation and migration.« less

Cerebrospinal Fluid Metabolomics After Natural Product Treatment in an Experimental Model of Cerebral Ischemia.

PubMed

Huan, Tao; Xian, Jia Wen; Leung, Wing Nang; Li, Liang; Chan, Chun Wai

2016-11-01

Cerebrospinal fluid (CSF) is an important biofluid for diagnosis of and research on neurological diseases. However, in-depth metabolomic profiling of CSF remains an analytical challenge due to the small volume of samples, particularly in small animal models. In this work, we report the application of a high-performance chemical isotope labeling (CIL) liquid chromatography-mass spectrometry (LC-MS) workflow for CSF metabolomics in Gastrodia elata and Uncaria rhynchophylla water extract (GUW)-treated experimental cerebral ischemia model of rat. The GUW is a commonly used Traditional Chinese Medicine (TCM) for hypertension and brain disease. This study investigated the amine- and phenol-containing biomarkers in the CSF metabolome. After GUW treatment for 7 days, the neurological deficit score was significantly improved with infarct volume reduction, while the integrity of brain histological structure was preserved. Over 1957 metabolites were quantified in CSF by dansylation LC-MS. The analysis of this comprehensive list of metabolites suggests that metabolites associated with oxidative stress, inflammatory response, and excitotoxicity change during GUW-induced alleviation of ischemic injury. This work is significant in that (1) it shows CIL LC-MS can be used for in-depth profiling of the CSF metabolome in experimental ischemic stroke and (2) identifies several potential molecular targets (that might mediate the central nervous system) and associate with pharmacodynamic effects of some frequently used TCMs.

Black phosphorus-assisted laser desorption ionization mass spectrometry for the determination of low-molecular-weight compounds in biofluids.

PubMed

He, Xiao-Mei; Ding, Jun; Yu, Lei; Hussain, Dilshad; Feng, Yu-Qi

2016-09-01

Quantitative analysis of small molecules by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has been a challenging task due to matrix-derived interferences in low m/z region and poor reproducibility of MS signal response. In this study, we developed an approach by applying black phosphorus (BP) as a matrix-assisted laser desorption ionization (MALDI) matrix for the quantitative analysis of small molecules for the first time. Black phosphorus-assisted laser desorption/ionization mass spectrometry (BP/ALDI-MS) showed clear background and exhibited superior detection sensitivity toward quaternary ammonium compounds compared to carbon-based materials. By combining stable isotope labeling (SIL) strategy with BP/ALDI-MS (SIL-BP/ALDI-MS), a variety of analytes labeled with quaternary ammonium group were sensitively detected. Moreover, the isotope-labeled forms of analytes also served as internal standards, which broadened the analyte coverage of BP/ALDI-MS and improved the reproducibility of MS signals. Based on these advantages, a reliable method for quantitative analysis of aldehydes from complex biological samples (saliva, urine, and serum) was successfully established. Good linearities were obtained for five aldehydes in the range of 0.1-20.0 μM with correlation coefficients (R (2)) larger than 0.9928. The LODs were found to be 20 to 100 nM. Reproducibility of the method was obtained with intra-day and inter-day relative standard deviations (RSDs) less than 10.4 %, and the recoveries in saliva samples ranged from 91.4 to 117.1 %. Taken together, the proposed SIL-BP/ALDI-MS strategy has proved to be a reliable tool for quantitative analysis of aldehydes from complex samples. Graphical Abstract An approach for the determination of small molecules was developed by using black phosphorus (BP) as a matrix-assisted laser desorption ionization (MALDI) matrix.

Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy

PubMed Central

Declerck, Ken; Traen, Sophie; Koppen, Gudrun; Van Camp, Guy; Schoeters, Greet; Vanden Berghe, Wim; De Boever, Patrick

2016-01-01

The etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n = 5) compared to healthy controls (n = 5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437 (P<0.05 and |Δβ|>0.1), respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. The absolute levels of methylation in blood and saliva were confirmed for 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes using pyrosequencing analysis. The differential methylation could only be confirmed for DMS in PM20D1 and STK32C genes in saliva. We show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS when comparing RA cases and healthy controls. The results were replicated in blood cells of the same individuals and confirmed by pyrosequencing analysis. This study provides proof-of-concept for the applicability of saliva-based whole-genome methylation analysis in the field of respiratory allergy. PMID:26999364

Effect of viscoelasticity on the flow pattern and the volumetric flow rate in electroosmotic flows through a microchannel.

PubMed

Park, H M; Lee, W M

2008-07-01

Many lab-on-a-chip based microsystems process biofluids such as blood and DNA solutions. These fluids are viscoelastic and show extraordinary flow behaviors, not existing in Newtonian fluids. Adopting appropriate constitutive equations these exotic flow behaviors can be modeled and predicted reasonably using various numerical methods. In the present paper, we investigate viscoelastic electroosmotic flows through a rectangular straight microchannel with and without pressure gradient. It is shown that the volumetric flow rates of viscoelastic fluids are significantly different from those of Newtonian fluids under the same external electric field and pressure gradient. Moreover, when pressure gradient is imposed on the microchannel there appear appreciable secondary flows in the viscoelastic fluids, which is never possible for Newtonian laminar flows through straight microchannels. The retarded or enhanced volumetric flow rates and secondary flows affect dispersion of solutes in the microchannel nontrivially.

Methylxanthine Drug Monitoring with Wearable Sweat Sensors.

PubMed

Tai, Li-Chia; Gao, Wei; Chao, Minghan; Bariya, Mallika; Ngo, Quynh P; Shahpar, Ziba; Nyein, Hnin Y Y; Park, Hyejin; Sun, Junfeng; Jung, Younsu; Wu, Eric; Fahad, Hossain M; Lien, Der-Hsien; Ota, Hiroki; Cho, Gyoujin; Javey, Ali

2018-06-01

Drug monitoring plays crucial roles in doping control and precision medicine. It helps physicians tailor drug dosage for optimal benefits, track patients' compliance to prescriptions, and understand the complex pharmacokinetics of drugs. Conventional drug tests rely on invasive blood draws. While urine and sweat are attractive alternative biofluids, the state-of-the-art methods require separate sample collection and processing steps and fail to provide real-time information. Here, a wearable platform equipped with an electrochemical differential pulse voltammetry sensing module for drug monitoring is presented. A methylxanthine drug, caffeine, is selected to demonstrate the platform's functionalities. Sweat caffeine levels are monitored under various conditions, such as drug doses and measurement time after drug intake. Elevated sweat caffeine levels upon increasing dosage and confirmable caffeine physiological trends are observed. This work leverages a wearable sweat sensing platform toward noninvasive and continuous point-of-care drug monitoring and management. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Roll-to-Roll Gravure Printed Electrochemical Sensors for Wearable and Medical Devices.

PubMed

Bariya, Mallika; Shahpar, Ziba; Park, Hyejin; Sun, Junfeng; Jung, Younsu; Gao, Wei; Nyein, Hnin Yin Yin; Liaw, Tiffany Sun; Tai, Li-Chia; Ngo, Quynh P; Chao, Minghan; Zhao, Yingbo; Hettick, Mark; Cho, Gyoujin; Javey, Ali

2018-06-25

As recent developments in noninvasive biosensors spearhead the thrust toward personalized health and fitness monitoring, there is a need for high throughput, cost-effective fabrication of flexible sensing components. Toward this goal, we present roll-to-roll (R2R) gravure printed electrodes that are robust under a range of electrochemical sensing applications. We use inks and electrode morphologies designed for electrochemical and mechanical stability, achieving devices with uniform redox kinetics printed on 150 m flexible substrate rolls. We show that these electrodes can be functionalized into consistently high performing sensors for detecting ions, metabolites, heavy metals, and other small molecules in noninvasively accessed biofluids, including sensors for real-time, in situ perspiration monitoring during exercise. This development of robust and versatile R2R gravure printed electrodes represents a key translational step in enabling large-scale, low-cost fabrication of disposable wearable sensors for personalized health monitoring applications.

Insights on diagnosis of oral cavity pathologies by infrared spectroscopy: A review

NASA Astrophysics Data System (ADS)

Giorgini, Elisabetta; Balercia, Paolo; Conti, Carla; Ferraris, Paolo; Sabbatini, Simona; Rubini, Corrado; Tosi, Giorgio

2013-11-01

Fourier-Transform Infrared microspectroscopy, a largely used spectroscopic technique in basic and industrial researches, offers the possibility to analyze the vibrational features of molecular groups within a variety of environments. In the bioclinical field, and, in particular, in the study of cells, tissues and biofluids, it could be considered a supporting objective technique able to characterize the biochemical processes involved in relevant pathologies, such as tumoral diseases, highlighting specific spectral markers associable with the principal biocomponents (proteins, lipids and carbohydrates). In this article, we review the applications of infrared spectroscopy to the study of tumoral diseases of oral cavity compartments with the aim to improve understanding of biological processes involved during the onset of these lesions and to afford to an early diagnosis. Spectral studies on mouth, salivary glands and oral cystic lesions, objectively discriminate normal from dysplastic and cancer states characterizing also the grading.

Parkinson's disease biomarkers: perspective from the NINDS Parkinson's Disease Biomarkers Program

PubMed Central

Gwinn, Katrina; David, Karen K; Swanson-Fischer, Christine; Albin, Roger; Hillaire-Clarke, Coryse St; Sieber, Beth-Anne; Lungu, Codrin; Bowman, F DuBois; Alcalay, Roy N; Babcock, Debra; Dawson, Ted M; Dewey, Richard B; Foroud, Tatiana; German, Dwight; Huang, Xuemei; Petyuk, Vlad; Potashkin, Judith A; Saunders-Pullman, Rachel; Sutherland, Margaret; Walt, David R; West, Andrew B; Zhang, Jing; Chen-Plotkin, Alice; Scherzer, Clemens R; Vaillancourt, David E; Rosenthal, Liana S

2017-01-01

Biomarkers for Parkinson's disease (PD) diagnosis, prognostication and clinical trial cohort selection are an urgent need. While many promising markers have been discovered through the National Institute of Neurological Disorders and Stroke Parkinson's Disease Biomarker Program (PDBP) and other mechanisms, no single PD marker or set of markers are ready for clinical use. Here we discuss the current state of biomarker discovery for platforms relevant to PDBP. We discuss the role of the PDBP in PD biomarker identification and present guidelines to facilitate their development. These guidelines include: harmonizing procedures for biofluid acquisition and clinical assessments, replication of the most promising biomarkers, support and encouragement of publications that report negative findings, longitudinal follow-up of current cohorts including the PDBP, testing of wearable technologies to capture readouts between study visits and development of recently diagnosed (de novo) cohorts to foster identification of the earliest markers of disease onset. PMID:28644039

Surface plasmon polaritons generated by radial polarized laser beam on silver nano-ring

NASA Astrophysics Data System (ADS)

Kozlova, Elena S.; Kotlyar, Victor V.

2017-04-01

In this work the single surface plasmon-polariton was obtained by using frequency-dependent finite difference time domain method for the radial polarized and vortex beams at 532 nm, which were propagating through the silver nanoring on substrate from silica glass, placed in an aqueous medium. The height and width of device were equal to 20 nm and 215 nm respectively. The intensity of surface plasmon-polariton was four times higher and three times higher the intensity of the incident radiation for case of conventional and vortex beams respectively. The full width at half maximum of the nanojet was near 160 nm for each cases. The presented design can be used for manufacturing of highly integrated optical devices and circuits used in high-speed communication applications. The results also can be used to design devices that allow capturing and moving the particles in water or other biofluidics.

Three-Dimensionally Functionalized Reverse Phase Glycoprotein Array for Cancer Biomarker Discovery and Validation.

PubMed

Pan, Li; Aguilar, Hillary Andaluz; Wang, Linna; Iliuk, Anton; Tao, W Andy

2016-11-30

Glycoproteins have vast structural diversity that plays an important role in many biological processes and have great potential as disease biomarkers. Here, we report a novel functionalized reverse phase protein array (RPPA), termed polymer-based reverse phase glycoprotein array (polyGPA), to capture and profile glycoproteomes specifically, and validate glycoproteins. Nitrocellulose membrane functionalized with globular hydroxyaminodendrimers was used to covalently capture preoxidized glycans on glycoproteins from complex protein samples such as biofluids. The captured glycoproteins were subsequently detected using the same validated antibodies as in RPPA. We demonstrated the outstanding specificity, sensitivity, and quantitative capabilities of polyGPA by capturing and detecting purified as well as endogenous α-1-acid glycoprotein (AGP) in human plasma. We further applied quantitative N-glycoproteomics and the strategy to validate a panel of glycoproteins identified as potential biomarkers for bladder cancer by analyzing urine glycoproteins from bladder cancer patients or matched healthy individuals.

Thermo-optical characterization of cadmium selenide/zinc sulfide (CdSe/ZnS) quantum dots embedded in biocompatible materials.

PubMed

Pilla, Viviane; Alves, Leandro P; Iwazaki, Adalberto N; Andrade, Acácio A; Antunes, Andrea; Munin, Egberto

2013-09-01

Cadmium selenide/zinc sulfide (CdSe/ZnS) core-shell quantum dots (QDs) embedded in biocompatible materials were thermally and optically characterized with a thermal lens (TL) technique. Transient TL measurements were performed with a mode-mismatched, dual-beam (excitation and probe) configuration. A thermo-optical study of the CdSe/ZnS QDs was performed for different core diameters (3.5, 4.0, 5.2, and 6.6 nm) in aqueous solution and synthetic saliva, and three different core diameters (2.4, 2.9, and 4.1 nm) embedded in restorative dental resin (0.025% by mass). The thermal diffusivity results are characteristic of the biocompatible matrices. The radiative quantum efficiencies for aqueous solution and biofluid materials are dependent on the core size of the CdSe/ZnS core-shell QDs. The results obtained from the fluorescence spectral measurements for the biocompatible materials support the TL results.

Microfluidic flow spectrometer

NASA Astrophysics Data System (ADS)

Vázquez-Vergara, Pamela; Torres Rojas, Aimee M.; Guevara-Pantoja, Pablo E.; Corvera Poiré, Eugenia; Caballero-Robledo, Gabriel A.

2017-07-01

We present a microfluidic device which allows one to study the dynamics of oscillatory flows for a frequency range between 1 and 300 Hz. The fluid in the microdevice could be Newtonian, viscoelastic, or even a biofluid, since the device is made of PMMA, which makes it biocompatible and free of elastomeric elements. Coupling a piezoelectric to a micropiston allows one to impose periodic movement to the fluid, with zero mean flow and amplitudes of up to 20~μ m, within the microchannels in which the dynamics is studied. The use of a fast camera coupled to a microscope allows one to study the dynamics of 1~μ m tracer particles and interfaces at an image acquisition rate as fast as 5000 frames per second. The fabrication of the device is easy and cost-effective, since it is based on the use of a micromilling machine. The dynamics of a Newtonian fluid is studied as a proof of principle.

Waterproof AlInGaP optoelectronics on stretchable substrates with applications in biomedicine and robotics.

PubMed

Kim, Rak-Hwan; Kim, Dae-Hyeong; Xiao, Jianliang; Kim, Bong Hoon; Park, Sang-Il; Panilaitis, Bruce; Ghaffari, Roozbeh; Yao, Jimin; Li, Ming; Liu, Zhuangjian; Malyarchuk, Viktor; Kim, Dae Gon; Le, An-Phong; Nuzzo, Ralph G; Kaplan, David L; Omenetto, Fiorenzo G; Huang, Yonggang; Kang, Zhan; Rogers, John A

2010-11-01

Inorganic light-emitting diodes and photodetectors represent important, established technologies for solid-state lighting, digital imaging and many other applications. Eliminating mechanical and geometrical design constraints imposed by the supporting semiconductor wafers can enable alternative uses in areas such as biomedicine and robotics. Here we describe systems that consist of arrays of interconnected, ultrathin inorganic light-emitting diodes and photodetectors configured in mechanically optimized layouts on unusual substrates. Light-emitting sutures, implantable sheets and illuminated plasmonic crystals that are compatible with complete immersion in biofluids illustrate the suitability of these technologies for use in biomedicine. Waterproof optical-proximity-sensor tapes capable of conformal integration on curved surfaces of gloves and thin, refractive-index monitors wrapped on tubing for intravenous delivery systems demonstrate possibilities in robotics and clinical medicine. These and related systems may create important, unconventional opportunities for optoelectronic devices.

LC/ESI-MS/MS method for quantification of 28 synthetic cannabinoids in neat oral fluid and its application to preliminary studies on their detection windows.

PubMed

Kneisel, Stefan; Speck, Michael; Moosmann, Bjoern; Corneillie, Todd M; Butlin, Nathaniel G; Auwärter, Volker

2013-05-01

Serum and urine samples are commonly used for the analysis of synthetic cannabinoids in biofluids; however, their utilization as analytical matrices for drug abstinence control features some substantial drawbacks. While for blood collection invasive sampling is inevitable, the urinary analysis of synthetic cannabinoids is limited by the lack of available reference standards of the respective major metabolites. Moreover, the long detectability of synthetic cannabinoids in both matrices hampers the identification of a recent synthetic cannabinoid use. This article describes the development, validation and application of an LC/ESI-MS/MS method for the quantification of 28 synthetic cannabinoids in neat oral fluid (OF) samples. OF samples were prepared by protein precipitation using ice-cold acetonitrile. Chromatographic separation was achieved by gradient elution on a Luna Phenyl Hexyl column (50 × 2 mm, 5 μm), while detection was carried out on a QTrap 4000 instrument in positive ionization mode. The limits of detection ranged from 0.02 to 0.40 ng/mL, whereas the lower limits of quantification ranged from 0.2 to 4.0 ng/mL. The method was applied to authentic samples collected during two preliminary studies in order to obtain insights into the general detectability and detection windows of synthetic cannabinoids in this matrix. The results indicate that synthetic cannabinoids are transferred from the blood stream into OF and vice versa only at a very low rate. Therefore, positive OF samples are due to contamination of the oral cavity during smoking. As these drug-contaminations could be detected up to approximately 2 days, neat oral fluid appears to be well suited for detection of a recent synthetic cannabinoid use.

Analysis of Serum Total and Free PSA Using Immunoaffinity Depletion Coupled to SRM: Correlation with Clinical Immunoassay Tests

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

Liu, Tao; Hossain, Mahmud; Schepmoes, Athena A.

2012-08-03

Sandwich immunoassay is the standard technique used in clinical labs for quantifying protein biomarkers for disease detection, monitoring and therapeutic intervention. Albeit highly sensitive, the development of a specific immunoassay is rather time-consuming and associated with extremely high cost due to the requirement for paired immunoaffinity reagents of high specificity. Recently, mass spectrometry-based methods, specifically selected reaction monitoring mass spectrometry (SRM-MS), have been increasingly applied to measure low abundance biomarker candidates in tissue and biofluids, owing to high sensitivity and specificity, simplicity of assay configuration, and great multiplexing capability. In this study, we report for the first time the developmentmore » of immunoaffinity depletion-based workflows and SRM-MS assays that enable sensitive and accurate quantification of total and free prostate-specific antigen (PSA) in serum without the requirement for specific PSA antibodies. With stable isotope dilution and external calibration, low ng/mL level detection of both total and free PSA was consistently achieved in both PSA-spiked female serum samples and actual patient serum samples. Moreover, comparison of the results obtained when SRM PSA assays and conventional immunoassays were applied to the same samples showed very good correlation (R2 values ranging from 0.90 to 0.99) in several independent clinical serum sample sets, including a set of 33 samples assayed in a blinded test. These results demonstrate that the workflows and SRM assays developed here provide an attractive alternative for reliably measuring total and free PSA in human blood. Furthermore, simultaneous measurement of free and total PSA and many other biomarkers can be performed in a single analysis using high-resolution liquid chromatographic separation coupled with SRM-MS.« less

Simultaneous quantification of PGI2 and TXA2 metabolites in plasma and urine in NO-deficient mice by a novel UHPLC/MS/MS method.

PubMed

Kij, Agnieszka; Mateuszuk, Lukasz; Sitek, Barbara; Przyborowski, Kamil; Zakrzewska, Agnieszka; Wandzel, Krystyna; Walczak, Maria; Chlopicki, Stefan

2016-09-10

The balance between vascular prostacyclin (PGI2) generated mainly via cyclooxygenase-2 (COX-2) and its physiological antagonist platelet-derived thromboxane A2 (TXA2) formed by cyclooxygenase-1 (COX-1) determines cardiovascular homeostasis. In the present work, a novel bioanalytical method for simultaneous quantification of stable plasma and urinary metabolites of PGI2 (6-keto-PGF1α, 2,3-dinor-6-keto-PGF1α) and TXA2 (TXB2, 2,3-dinor-TXB2) using ultra high-performance liquid chromatography coupled with tandem mass spectrometry (UHPLC/MS/MS) was developed. The method was validated using artificial plasma and urine and linearity range, intra- and inter-day precision and accuracy, recovery of analytes, relative and absolute matrix effect and stability of analytes were determined. The use of artificial biofluids improved the method sensitivity as it eliminated the contribution of endogenous metabolites present in mice plasma and urine to validation procedure. The newly developed and validated method allowed to quantify 6-keto-PGF1α and TXB2 in mice plasma as well as 2,3-dinor-6-keto-PGF1α and 2,3-dinor-TXB2 in urine samples with high sensitivity and accuracy. The calibration range was established from 0.1 to 100ng/mL for all analytes using artificial biofluids and the recoveries were greater than 89.9%. All validated parameters met the criteria of acceptance specified in FDA and EMA guidance. This method was successfully employed for profiling of the changes in PGI2 and TXA2 generation in NO-deficient mice. This work demonstrated that NO-deficiency induced by L-NAME, evidenced by a fall in nitrite in plasma and urine, was associated with platelet activation, robust increase in TXB2 and mild increase in 6-keto-PGF1α concentration in plasma. Changes in 2,3-dinor-6-keto-PGF1α and 2,3-dinor-TXB2 concentration in urine were less evident suggesting that the measurements in plasma better reflect modest changes in PGI2/TXA2 homeostasis than measurements in urine. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolomic Analysis in Severe Childhood Pneumonia in The Gambia, West Africa: Findings from a Pilot Study

PubMed Central

Laiakis, Evagelia C.; Morris, Gerard A. J.; Fornace, Albert J.; Howie, Stephen R. C.

2010-01-01

Background Pneumonia remains the leading cause of death in young children globally and improved diagnostics are needed to better identify cases and reduce case fatality. Metabolomics, a rapidly evolving field aimed at characterizing metabolites in biofluids, has the potential to improve diagnostics in a range of diseases. The objective of this pilot study is to apply metabolomic analysis to childhood pneumonia to explore its potential to improve pneumonia diagnosis in a high-burden setting. Methodology/Principal Findings Eleven children with World Health Organization (WHO)-defined severe pneumonia of non-homogeneous aetiology were selected in The Gambia, West Africa, along with community controls. Metabolomic analysis of matched plasma and urine samples was undertaken using Ultra Performance Liquid Chromatography (UPLC) coupled to Time-of-Flight Mass Spectrometry (TOFMS). Biomarker extraction was done using SIMCA-P+ and Random Forests (RF). ‘Unsupervised’ (blinded) data were analyzed by Principal Component Analysis (PCA), while ‘supervised’ (unblinded) analysis was by Partial Least Squares-Discriminant Analysis (PLS-DA) and Orthogonal Projection to Latent Structures (OPLS). Potential markers were extracted from S-plots constructed following analysis with OPLS, and markers were chosen based on their contribution to the variation and correlation within the data set. The dataset was additionally analyzed with the machine-learning algorithm RF in order to address issues of model overfitting and markers were selected based on their variable importance ranking. Unsupervised PCA analysis revealed good separation of pneumonia and control groups, with even clearer separation of the groups with PLS-DA and OPLS analysis. Statistically significant differences (p<0.05) between groups were seen with the following metabolites: uric acid, hypoxanthine and glutamic acid were higher in plasma from cases, while L-tryptophan and adenosine-5′-diphosphate (ADP) were lower; uric acid and L-histidine were lower in urine from cases. The key limitation of this study is its small size. Conclusions/Significance Metabolomic analysis clearly distinguished severe pneumonia patients from community controls. The metabolites identified are important for the host response to infection through antioxidant, inflammatory and antimicrobial pathways, and energy metabolism. Larger studies are needed to determine whether these findings are pneumonia-specific and to distinguish organism-specific responses. Metabolomics has considerable potential to improve diagnostics for childhood pneumonia. PMID:20844590

Metabolomic analysis in severe childhood pneumonia in the Gambia, West Africa: findings from a pilot study.

PubMed

Laiakis, Evagelia C; Morris, Gerard A J; Fornace, Albert J; Howie, Stephen R C

2010-09-09

Pneumonia remains the leading cause of death in young children globally and improved diagnostics are needed to better identify cases and reduce case fatality. Metabolomics, a rapidly evolving field aimed at characterizing metabolites in biofluids, has the potential to improve diagnostics in a range of diseases. The objective of this pilot study is to apply metabolomic analysis to childhood pneumonia to explore its potential to improve pneumonia diagnosis in a high-burden setting. Eleven children with World Health Organization (WHO)-defined severe pneumonia of non-homogeneous aetiology were selected in The Gambia, West Africa, along with community controls. Metabolomic analysis of matched plasma and urine samples was undertaken using Ultra Performance Liquid Chromatography (UPLC) coupled to Time-of-Flight Mass Spectrometry (TOFMS). Biomarker extraction was done using SIMCA-P+ and Random Forests (RF). 'Unsupervised' (blinded) data were analyzed by Principal Component Analysis (PCA), while 'supervised' (unblinded) analysis was by Partial Least Squares-Discriminant Analysis (PLS-DA) and Orthogonal Projection to Latent Structures (OPLS). Potential markers were extracted from S-plots constructed following analysis with OPLS, and markers were chosen based on their contribution to the variation and correlation within the data set. The dataset was additionally analyzed with the machine-learning algorithm RF in order to address issues of model overfitting and markers were selected based on their variable importance ranking. Unsupervised PCA analysis revealed good separation of pneumonia and control groups, with even clearer separation of the groups with PLS-DA and OPLS analysis. Statistically significant differences (p<0.05) between groups were seen with the following metabolites: uric acid, hypoxanthine and glutamic acid were higher in plasma from cases, while L-tryptophan and adenosine-5'-diphosphate (ADP) were lower; uric acid and L-histidine were lower in urine from cases. The key limitation of this study is its small size. Metabolomic analysis clearly distinguished severe pneumonia patients from community controls. The metabolites identified are important for the host response to infection through antioxidant, inflammatory and antimicrobial pathways, and energy metabolism. Larger studies are needed to determine whether these findings are pneumonia-specific and to distinguish organism-specific responses. Metabolomics has considerable potential to improve diagnostics for childhood pneumonia.

Lithotripter shock wave interaction with a bubble near various biomaterials.

PubMed

Ohl, S W; Klaseboer, E; Szeri, A J; Khoo, B C

2016-10-07

Following previous work on the dynamics of an oscillating bubble near a bio-material (Ohl et al 2009 Phys. Med. Biol. 54 6313-36) and the interaction of a bubble with a shockwave (Klaseboer et al 2007 J. Fluid Mech. 593 33-56), the present work concerns the interaction of a gas bubble with a traveling shock wave (such as from a lithotripter) in the vicinity of bio-materials such as fat, skin, muscle, cornea, cartilage, and bone. The bubble is situated in water (to represent a water-like biofluid). The bubble collapses are not spherically symmetric, but tend to feature a high speed jet. A few simulations are performed and compared with available experimental observations from Sankin and Zhong (2006 Phys. Rev. E 74 046304). The collapses of cavitation bubbles (created by laser in the experiment) near an elastic membrane when hit by a lithotripter shock wave are correctly captured by the simulation. This is followed by a more systematic study of the effects involved concerning shockwave bubble biomaterial interactions. If a subsequent rarefaction wave hits the collapsed bubble, it will re-expand to a very large size straining the bio-materials nearby before collapsing once again. It is noted that, for hard bio-material like bone, reflection of the shock wave at the bone-water interface can affect the bubble dynamics. Also the initial size of the bubble has a significant effect. Large bubbles (∼1 mm) will split into smaller bubbles, while small bubbles collapse with a high speed jet in the travel direction of the shock wave. The numerical model offers a computationally efficient way of understanding the complex phenomena involving the interplay of a bubble, a shock wave, and a nearby bio-material.

Lithotripter shock wave interaction with a bubble near various biomaterials

NASA Astrophysics Data System (ADS)

Ohl, S. W.; Klaseboer, E.; Szeri, A. J.; Khoo, B. C.

2016-10-01

Following previous work on the dynamics of an oscillating bubble near a bio-material (Ohl et al 2009 Phys. Med. Biol. 54 6313-36) and the interaction of a bubble with a shockwave (Klaseboer et al 2007 J. Fluid Mech. 593 33-56), the present work concerns the interaction of a gas bubble with a traveling shock wave (such as from a lithotripter) in the vicinity of bio-materials such as fat, skin, muscle, cornea, cartilage, and bone. The bubble is situated in water (to represent a water-like biofluid). The bubble collapses are not spherically symmetric, but tend to feature a high speed jet. A few simulations are performed and compared with available experimental observations from Sankin and Zhong (2006 Phys. Rev. E 74 046304). The collapses of cavitation bubbles (created by laser in the experiment) near an elastic membrane when hit by a lithotripter shock wave are correctly captured by the simulation. This is followed by a more systematic study of the effects involved concerning shockwave bubble biomaterial interactions. If a subsequent rarefaction wave hits the collapsed bubble, it will re-expand to a very large size straining the bio-materials nearby before collapsing once again. It is noted that, for hard bio-material like bone, reflection of the shock wave at the bone—water interface can affect the bubble dynamics. Also the initial size of the bubble has a significant effect. Large bubbles (˜1 mm) will split into smaller bubbles, while small bubbles collapse with a high speed jet in the travel direction of the shock wave. The numerical model offers a computationally efficient way of understanding the complex phenomena involving the interplay of a bubble, a shock wave, and a nearby bio-material.

MicroRNAs associated with small bowel neuroendocrine tumours and their metastases.

PubMed

Miller, Helen C; Frampton, Adam E; Malczewska, Anna; Ottaviani, Silvia; Stronach, Euan A; Flora, Rashpal; Kaemmerer, Daniel; Schwach, Gert; Pfragner, Roswitha; Faiz, Omar; Kos-Kudła, Beata; Hanna, George B; Stebbing, Justin; Castellano, Leandro; Frilling, Andrea

2016-09-01

Novel molecular analytes are needed in small bowel neuroendocrine tumours (SBNETs) to better determine disease aggressiveness and predict treatment response. In this study, we aimed to profile the global miRNome of SBNETs, and identify microRNAs (miRNAs) involved in tumour progression for use as potential biomarkers. Two independent miRNA profiling experiments were performed (n=90), including primary SBNETs (n=28), adjacent normal small bowel (NSB; n=14), matched lymph node (LN) metastases (n=24), normal LNs (n=7), normal liver (n=2) and liver metastases (n=15). We then evaluated potentially targeted genes by performing integrated computational analyses. We discovered 39 miRNAs significantly deregulated in SBNETs compared with adjacent NSB. The most upregulated (miR-204-5p, miR-7-5p and miR-375) were confirmed by qRT-PCR. Two miRNAs (miR-1 and miR-143-3p) were significantly downregulated in LN and liver metastases compared with primary tumours. Furthermore, we identified upregulated gene targets for miR-1 and miR-143-3p in an existing SBNET dataset, which could contribute to disease progression, and show that these miRNAs directly regulate FOSB and NUAK2 oncogenes. Our study represents the largest global miRNA profiling of SBNETs using matched primary tumour and metastatic samples. We revealed novel miRNAs deregulated during SBNET disease progression, and important miRNA-mRNA interactions. These miRNAs have the potential to act as biomarkers for patient stratification and may also be able to guide treatment decisions. Further experiments to define molecular mechanisms and validate these miRNAs in larger tissue cohorts and in biofluids are now warranted. © 2016 Society for Endocrinology.

A review of solid-fluid selection options for optical-based measurements in single-phase liquid, two-phase liquid-liquid and multiphase solid-liquid flows

NASA Astrophysics Data System (ADS)

Wright, Stuart F.; Zadrazil, Ivan; Markides, Christos N.

2017-09-01

Experimental techniques based on optical measurement principles have experienced significant growth in recent decades. They are able to provide detailed information with high-spatiotemporal resolution on important scalar (e.g., temperature, concentration, and phase) and vector (e.g., velocity) fields in single-phase or multiphase flows, as well as interfacial characteristics in the latter, which has been instrumental to step-changes in our fundamental understanding of these flows, and the development and validation of advanced models with ever-improving predictive accuracy and reliability. Relevant techniques rely upon well-established optical methods such as direct photography, laser-induced fluorescence, laser Doppler velocimetry/phase Doppler anemometry, particle image/tracking velocimetry, and variants thereof. The accuracy of the resulting data depends on numerous factors including, importantly, the refractive indices of the solids and liquids used. The best results are obtained when the observational materials have closely matched refractive indices, including test-section walls, liquid phases, and any suspended particles. This paper reviews solid-liquid and solid-liquid-liquid refractive-index-matched systems employed in different fields, e.g., multiphase flows, turbomachinery, bio-fluid flows, with an emphasis on liquid-liquid systems. The refractive indices of various aqueous and organic phases found in the literature span the range 1.330-1.620 and 1.251-1.637, respectively, allowing the identification of appropriate combinations to match selected transparent or translucent plastics/polymers, glasses, or custom materials in single-phase liquid or multiphase liquid-liquid flow systems. In addition, the refractive indices of fluids can be further tuned with the use of additives, which also allows for the matching of important flow similarity parameters such as density and viscosity.

Proteomics as a Quality Control Tool of Pharmaceutical Probiotic Bacterial Lysate Products

PubMed Central

Klein, Günter; Schanstra, Joost P.; Hoffmann, Janosch; Mischak, Harald; Siwy, Justyna; Zimmermann, Kurt

2013-01-01

Probiotic bacteria have a wide range of applications in veterinary and human therapeutics. Inactivated probiotics are complex samples and quality control (QC) should measure as many molecular features as possible. Capillary electrophoresis coupled to mass spectrometry (CE/MS) has been used as a multidimensional and high throughput method for the identification and validation of biomarkers of disease in complex biological samples such as biofluids. In this study we evaluate the suitability of CE/MS to measure the consistency of different lots of the probiotic formulation Pro-Symbioflor which is a bacterial lysate of heat-inactivated Escherichia coli and Enterococcus faecalis. Over 5000 peptides were detected by CE/MS in 5 different lots of the bacterial lysate and in a sample of culture medium. 71 to 75% of the total peptide content was identical in all lots. This percentage increased to 87–89% when allowing the absence of a peptide in one of the 5 samples. These results, based on over 2000 peptides, suggest high similarity of the 5 different lots. Sequence analysis identified peptides of both E. coli and E. faecalis and peptides originating from the culture medium, thus confirming the presence of the strains in the formulation. Ontology analysis suggested that the majority of the peptides identified for E. coli originated from the cell membrane or the fimbrium, while peptides identified for E. faecalis were enriched for peptides originating from the cytoplasm. The bacterial lysate peptides as a whole are recognised as highly conserved molecular patterns by the innate immune system as microbe associated molecular pattern (MAMP). Sequence analysis also identified the presence of soybean, yeast and casein protein fragments that are part of the formulation of the culture medium. In conclusion CE/MS seems an appropriate QC tool to analyze complex biological products such as inactivated probiotic formulations and allows determining the similarity between lots. PMID:23840518

Optimization for Peptide Sample Preparation for Urine Peptidomics

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

Sigdel, Tara K.; Nicora, Carrie D.; Hsieh, Szu-Chuan

2014-02-25

Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput ‘peptidomics’ methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regards to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements that it hampers both the identification of peptides andmore » the depth of the peptidomics read when utilizing LC-MS based peptidome analysis. We report on a novel adaptation of the standard solid phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. Expense and time requirements were comparable for both SPE and mSPE, but more interfering contaminants from the urine matrix were evident in the SPE preparations (e.g., clogging of the LC-MS columns, yellowish background coloration of prepared samples due to retained urobilin, lower peptide yields) when compared to the mSPE method. When we compared data from technical replicates of 4 runs, the mSPE method provided significantly improved efficiencies for the preparation of samples from urine (e.g., mSPE peptide identification 82% versus 18% with SPE; p = 8.92E-05). Additionally, peptide identifications, when applying the mSPE method, highlighted the biology of differential activation of urine peptidases during acute renal transplant rejection with distinct laddering of specific peptides, which was obscured for most proteins when utilizing the conventional SPE method. In conclusion, the mSPE method was found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis due to the optimized sample clean up that provided improved experimental inference from the confidently identified peptides.« less

Personalized liposome-protein corona in the blood of breast, gastric and pancreatic cancer patients.

PubMed

Colapicchioni, Valentina; Tilio, Martina; Digiacomo, Luca; Gambini, Valentina; Palchetti, Sara; Marchini, Cristina; Pozzi, Daniela; Occhipinti, Sergio; Amici, Augusto; Caracciolo, Giulio

2016-06-01

When nanoparticles (NPs) are dispersed in a biofluid, they are covered by a protein corona the composition of which strongly depends on the protein source. Recent studies demonstrated that the type of disease has a crucial role in the protein composition of the NP corona with relevant implications on personalized medicine. Proteomic variations frequently occur in cancer with the consequence that the bio-identity of NPs in the blood of cancer patients may differ from that acquired after administration to healthy volunteers. In this study we investigated the correlation between alterations of plasma proteins in breast, gastric and pancreatic cancer and the biological identity of clinically approved AmBisome-like liposomes as determined by a combination of dynamic light scattering, zeta potential analysis, one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) and semi-quantitative densitometry. While size of liposome-protein complexes was not significantly different between cancer groups, the hard corona from pancreatic cancer patients was significantly less negatively charged. Of note, the hard corona from pancreatic cancer patients was more enriched than those of other cancer types this enrichment being most likely due to IgA and IgG with possible correlations with the autoantibodies productions in cancer. Given the strict relationship between tumor antigen-specific autoantibodies and early cancer detection, our results could be the basis for the development of novel nanoparticle-corona-based screening tests of cancer. Copyright © 2015 Elsevier Ltd. All rights reserved.

Global Metabolomic Identification of Long-Term Dose-Dependent Urinary Biomarkers in Nonhuman Primates Exposed to Ionizing Radiation.

PubMed

Pannkuk, Evan L; Laiakis, Evagelia C; Authier, Simon; Wong, Karen; Fornace, Albert J

2015-08-01

Due to concerns surrounding potential large-scale radiological events, there is a need to determine robust radiation signatures for the rapid identification of exposed individuals, which can then be used to guide the development of compact field deployable instruments to assess individual dose. Metabolomics provides a technology to process easily accessible biofluids and determine rigorous quantitative radiation biomarkers with mass spectrometry (MS) platforms. While multiple studies have utilized murine models to determine radiation biomarkers, limited studies have profiled nonhuman primate (NHP) metabolic radiation signatures. In addition, these studies have concentrated on short-term biomarkers (i.e., <72 h). The current study addresses the need for biomarkers beyond 72 h using a NHP model. Urine samples were collected at 7 days postirradiation (2, 4, 6, 7 and 10 Gy) and processed with ultra-performance liquid chromatography (UPLC) quadrupole time-of-flight (QTOF) MS, acquiring global metabolomic radiation signatures. Multivariate data analysis revealed clear separation between control and irradiated groups. Thirteen biomarkers exhibiting a dose response were validated with tandem MS. There was significantly higher excretion of l-carnitine, l-acetylcarnitine, xanthine and xanthosine in males versus females. Metabolites validated in this study suggest perturbation of several pathways including fatty acid β oxidation, tryptophan metabolism, purine catabolism, taurine metabolism and steroid hormone biosynthesis. In this novel study we detected long-term biomarkers in a NHP model after exposure to radiation and demonstrate differences between sexes using UPLC-QTOF-MS-based metabolomics technology.

Analysis of high gradient magnetic field effects on distribution of nanoparticles injected into pulsatile blood stream

NASA Astrophysics Data System (ADS)

Reza Habibi, Mohammad; Ghassemi, Majid; Hossien Hamedi, Mohammad

2012-04-01

Magnetic nanoparticles are widely used in a wide range of applications including data storage materials, pharmaceutical industries as magnetic separation tools, anti-cancer drug carriers and micro valve applications. The purpose of the current study is to investigate the effect of a non-uniform magnetic field on bio-fluid (blood) with magnetic nanoparticles. The effect of particles as well as mass fraction on flow field and volume concentration is investigated. The governing non-linear differential equations, concentration and Navier-stokes are coupled with the magnetic field. To solve these equations, a finite volume based code is developed and utilized. A real pulsatile velocity is utilized as inlet boundary condition. This velocity is extracted from an actual experimental data. Three percent nanoparticles volume concentration, as drug carrier, is steadily injected in an unsteady, pulsatile and non-Newtonian flow. A power law model is considered for the blood viscosity. The results show that during the systole section of the heartbeat when the blood velocity increases, the magnetic nanoparticles near the magnetic source are washed away. This is due to the sudden increase of the hydrodynamic force, which overcomes the magnetic force. The probability of vein blockage increases when the blood velocity reduces during the diastole time. As nanoparticles velocity injection decreases (longer injection time) the wall shear stress (especially near the injection area) decreases and the retention time of the magnetic nanoparticles in the blood flow increases.

Screening of salivary volatiles for putative breast cancer discrimination: an exploratory study involving geographically distant populations.

PubMed

Cavaco, Carina; Pereira, Jorge A M; Taunk, Khushman; Taware, Ravindra; Rapole, Srikanth; Nagarajaram, Hampapathalu; Câmara, José S

2018-05-07

Saliva is possibly the easiest biofluid to analyse and, despite its simple composition, contains relevant metabolic information. In this work, we explored the potential of the volatile composition of saliva samples as biosignatures for breast cancer (BC) non-invasive diagnosis. To achieve this, 106 saliva samples of BC patients and controls in two distinct geographic regions in Portugal and India were extracted and analysed using optimised headspace solid-phase microextraction gas chromatography mass spectrometry (HS-SPME/GC-MS, 2 mL acidified saliva containing 10% NaCl, stirred (800 rpm) for 45 min at 38 °C and using the CAR/PDMS SPME fibre) followed by multivariate statistical analysis (MVSA). Over 120 volatiles from distinct chemical classes, with significant variations among the groups, were identified. MVSA retrieved a limited number of volatiles, viz. 3-methyl-pentanoic acid, 4-methyl-pentanoic acid, phenol and p-tert-butyl-phenol (Portuguese samples) and acetic, propanoic, benzoic acids, 1,2-decanediol, 2-decanone, and decanal (Indian samples), statistically relevant for the discrimination of BC patients in the populations analysed. This work defines an experimental layout, HS-SPME/GC-MS followed by MVSA, suitable to characterise volatile fingerprints for saliva as putative biosignatures for BC non-invasive diagnosis. Here, it was applied to BC samples from geographically distant populations and good disease separation was obtained. Further studies using larger cohorts are therefore very pertinent to challenge and strengthen this proof-of-concept study. Graphical abstract ᅟ.

Materials, Processes, and Facile Manufacturing for Bioresorbable Electronics: A Review.

PubMed

Yu, Xiaowei; Shou, Wan; Mahajan, Bikram K; Huang, Xian; Pan, Heng

2018-05-07

Bioresorbable electronics refer to a new class of advanced electronics that can completely dissolve or disintegrate with environmentally and biologically benign byproducts in water and biofluids. They have provided a solution to the growing electronic waste problem with applications in temporary usage of electronics such as implantable devices and environmental sensors. Bioresorbable materials such as biodegradable polymers, dissolvable conductors, semiconductors, and dielectrics are extensively studied, enabling massive progress of bioresorbable electronic devices. Processing and patterning of these materials are predominantly relying on vacuum-based fabrication methods so far. However, for the purpose of commercialization, nonvacuum, low-cost, and facile manufacturing/printing approaches are the need of the hour. Bioresorbable electronic materials are generally more chemically reactive than conventional electronic materials, which require particular attention in developing the low-cost manufacturing processes in ambient environment. This review focuses on material reactivity, ink availability, printability, and process compatibility for facile manufacturing of bioresorbable electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Simulation Of The Synovial Fluid In A Deformable Cavity

NASA Astrophysics Data System (ADS)

Martinez-Gutierrez, Nancy; Ibarra-Bracamontes, Laura A.

2016-11-01

The main components of a synovial joint are a cartilage and a biofluid known as the synovial fluid. The results were obtained using the FLUENT software to simulate the behavior of the synovial fluid within a deformable cavity with a simple geometry. The cartilage is represented as a porous region. By reducing the available region for the fluid, a fluid displacement into the cartilage is induced. The total pressure reached in the interface of the deformable cavity and the porous region is presented. The geometry and properties of the system are scaled to values found in a knee joint. The effect of deformation rate, fluid viscosity and properties of the porous medium on the total pressure reached are analyzed. The higher pressures are reached either for high deformation rate or when the fluid viscosity increases. This study was supported by the Mexican Council of Science and Technology (CONACyT) and by the Scientific Research Coordination of the University of Michoacan in Mexico.

Aptamer-based SERRS Sensor for Thrombin Detection

PubMed Central

Cho, Hansang; Baker, Brian R.; Wachsmann-Hogiu, Sebastian; Pagba, Cynthia V.; Laurence, Ted A.; Lane, Stephen M.; Lee, Luke P.; Tok, Jeffrey B.-H.

2012-01-01

We describe an aptamer-based Surface Enhanced Resonance Raman Scattering (SERRS) sensor with high sensitivity, specificity, and stability for the detection of a coagulation protein, human α-thrombin. The sensor achieves high sensitivity and a limit of detection of 100 pM by monitoring the SERRS signal change upon the single step of thrombin binding to immobilized thrombin binding aptamer. The selectivity of the sensor is demonstrated by the specific discrimination of thrombin from other protein analytes. The specific recognition and binding of thrombin by the thrombin binding aptamer is essential to the mechanism of the aptamer-based sensor, as shown through measurements using negative control oligonucleotides. In addition, the sensor can detect 1 nM thrombin in the presence of complex biofluids, such as 10% fetal calf serum, demonstrating that the immobilized, 5'-capped, 3'-capped aptamer is sufficiently robust for clinical diagnostic applications. Furthermore, the proposed sensor may be implemented for multiplexed detection using different aptamer-Raman probe complexes. PMID:19367849

30 s Response Time of K+ Ion-Selective Hydrogels Functionalized with 18-Crown-6 Ether Based on QCM Sensor.

PubMed

Zhang, Zhenxiao; Dou, Qian; Gao, Hongkai; Bai, Bing; Zhang, Yongmei; Hu, Debo; Yetisen, Ali K; Butt, Haider; Yang, Xiaoxia; Li, Congju; Dai, Qing

2018-03-01

Potassium detection is critical in monitoring imbalances in electrolytes and physiological status. The development of rapid and robust potassium sensors is desirable in clinical chemistry and point-of-care applications. In this study, composite supramolecular hydrogels are investigated: polyethylene glycol methacrylate and acrylamide copolymer (P(PEGMA-co-AM)) are functionalized with 18-crown-6 ether by employing surface initiated polymerization. Real-time potassium ion monitoring is realized by combining these compounds with quartz crystal microbalance. The device demonstrates a rapid response time of ≈30 s and a concentration detection range from 0.5 to 7.0 × 10 -3 m. These hydrogels also exhibit high reusability and K + ion selectivity relative to other cations in biofluids such as Na + , NH 4 + , Mg 2+ , and Ca 2+ . These results provide a new approach for sensing alkali metal ions using P(PEGMA-co-AM) hydrogels. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CVD-grown monolayer MoS2 in bioabsorbable electronics and biosensors.

PubMed

Chen, Xiang; Park, Yong Ju; Kang, Minpyo; Kang, Seung-Kyun; Koo, Jahyun; Shinde, Sachin M; Shin, Jiho; Jeon, Seunghyun; Park, Gayoung; Yan, Ying; MacEwan, Matthew R; Ray, Wilson Z; Lee, Kyung-Mi; Rogers, John A; Ahn, Jong-Hyun

2018-04-27

Transient electronics represents an emerging technology whose defining feature is an ability to dissolve, disintegrate or otherwise physically disappear in a controlled manner. Envisioned applications include resorbable/degradable biomedical implants, hardware-secure memory devices, and zero-impact environmental sensors. 2D materials may have essential roles in these systems due to their unique mechanical, thermal, electrical, and optical properties. Here, we study the bioabsorption of CVD-grown monolayer MoS 2 , including long-term cytotoxicity and immunological biocompatibility evaluations in biofluids and tissues of live animal models. The results show that MoS 2 undergoes hydrolysis slowly in aqueous solutions without adverse biological effects. We also present a class of MoS 2 -based bioabsorbable and multi-functional sensor for intracranial monitoring of pressure, temperature, strain, and motion in animal models. Such technology offers specific, clinically relevant roles in diagnostic/therapeutic functions during recovery from traumatic brain injury. Our findings support the broader use of 2D materials in transient electronics and qualitatively expand the design options in other areas.

Emerging Role of MicroRNAs as Liquid Biopsy Biomarkers in Gastrointestinal Cancers

PubMed Central

Shigeyasu, Kunitoshi; Toden, Shusuke; Zumwalt, Timothy J.; Okugawa, Yoshinaga; Goel, Ajay

2017-01-01

Cancer has emerged as a leading cause of mortality worldwide, claiming over 8 million lives annually. Gastrointestinal (GI) cancers account for ~35% of these mortalities. Recent advances in diagnostic and treatment strategies have reduced mortality among GI cancer patients, yet a significant number of patients still develop late-stage cancer, where treatment options are inadequate. Emerging interests in ‘liquid biopsies’ have encouraged investigators to identify and develop clinically-relevant noninvasive genomic and epigenomic signatures that can be exploited as biomarkers capable of detecting premalignant and early-stage cancers. In this context, microRNAs (miRNAs), which are small non-coding RNAs that are frequently dysregulated in cancers, have emerged as promising entities for such diagnostic purposes. Albeit the future looks promising, current approaches for detecting miRNAs in blood and other biofluids remain inadequate. This review summarizes existing efforts to exploit circulating miRNAs as cancer biomarkers, evaluates their potential and challenges as liquid biopsy-based biomarkers for GI cancers. PMID:28143873

ON THE BIOMECHANICS OF HEART VALVE FUNCTION

PubMed Central

Sacks, Michael S.; Merryman, W. David; Schmidt, David E.

2009-01-01

Heart valves (HVs) are fluidic control components of the heart that ensure unidirectional blood flow during the cardiac cycle. However, this description does not adequately describe the biomechanical ramifications of their function in that their mechanics are multi-modal. Moreover, they must replicate their cyclic function over an entire lifetime, with an estimated total functional demand of least 3×109 cycles. The focus of the present review is on the functional biomechanics of heart valves. Thus, the focus of the present review is on functional biomechanics, referring primarily to biosolid as well as several key biofluid mechanical aspects underlying heart valve physiological function. Specifically, we refer to the mechanical behaviors of the extra-cellular matrix structural proteins, underlying cellular function, and their integrated relation to the major aspects of valvular hemodynamic function. While we focus on the work from the author’s laboratories, relevant works of other investigators have been included whenever appropriate. We conclude with a summary of important future trends. PMID:19540499

Evaluation and correction for optical scattering variations in laser speckle rheology of biological fluids.

PubMed

Hajjarian, Zeinab; Nadkarni, Seemantini K

2013-01-01

Biological fluids fulfill key functionalities such as hydrating, protecting, and nourishing cells and tissues in various organ systems. They are capable of these versatile tasks owing to their distinct structural and viscoelastic properties. Characterizing the viscoelastic properties of bio-fluids is of pivotal importance for monitoring the development of certain pathologies as well as engineering synthetic replacements. Laser Speckle Rheology (LSR) is a novel optical technology that enables mechanical evaluation of tissue. In LSR, a coherent laser beam illuminates the tissue and temporal speckle intensity fluctuations are analyzed to evaluate mechanical properties. The rate of temporal speckle fluctuations is, however, influenced by both optical and mechanical properties of tissue. Therefore, in this paper, we develop and validate an approach to estimate and compensate for the contributions of light scattering to speckle dynamics and demonstrate the capability of LSR for the accurate extraction of viscoelastic moduli in phantom samples and biological fluids of varying optical and mechanical properties.

Proceedings of the Fifth Microgravity Fluid Physics and Transport Phenomena Conference

NASA Technical Reports Server (NTRS)

Singh, Bhim S. (Editor)

2000-01-01

The Fifth Microgravity Fluid Physics and Transport Phenomena Conference provided the scientific community the opportunity to view the current scope of the Microgravity Fluid Physics and Transport Phenomena Program and research opportunities and plans for the near future. Consistent with the conference theme "Microgravity Research an Agency-Wide Asset" the conference focused not only on fundamental research but also on applications of this knowledge towards enabling future space exploration missions. The conference included 14 invited plenary talks, 61 technical paper presentations, 61 poster presentations, exhibits and a forum on emerging research themes focusing on nanotechnology and biofluid mechanics. This web-based proceeding includes the presentation and poster charts provided by the presenters of technical papers and posters that were scanned at the conference site. Abstracts of all the papers and posters are included and linked to the presentations charts. The invited and plenary speakers were not required to provide their charts and are generally not available for scanning and hence not posted. The conference program is also included.

Evaluation and Correction for Optical Scattering Variations in Laser Speckle Rheology of Biological Fluids

PubMed Central

Hajjarian, Zeinab; Nadkarni, Seemantini K.

2013-01-01

Biological fluids fulfill key functionalities such as hydrating, protecting, and nourishing cells and tissues in various organ systems. They are capable of these versatile tasks owing to their distinct structural and viscoelastic properties. Characterizing the viscoelastic properties of bio-fluids is of pivotal importance for monitoring the development of certain pathologies as well as engineering synthetic replacements. Laser Speckle Rheology (LSR) is a novel optical technology that enables mechanical evaluation of tissue. In LSR, a coherent laser beam illuminates the tissue and temporal speckle intensity fluctuations are analyzed to evaluate mechanical properties. The rate of temporal speckle fluctuations is, however, influenced by both optical and mechanical properties of tissue. Therefore, in this paper, we develop and validate an approach to estimate and compensate for the contributions of light scattering to speckle dynamics and demonstrate the capability of LSR for the accurate extraction of viscoelastic moduli in phantom samples and biological fluids of varying optical and mechanical properties. PMID:23705028

An efficient and sensitive method for preparing cDNA libraries from scarce biological samples

PubMed Central

Sterling, Catherine H.; Veksler-Lublinsky, Isana; Ambros, Victor

2015-01-01

The preparation and high-throughput sequencing of cDNA libraries from samples of small RNA is a powerful tool to quantify known small RNAs (such as microRNAs) and to discover novel RNA species. Interest in identifying the small RNA repertoire present in tissues and in biofluids has grown substantially with the findings that small RNAs can serve as indicators of biological conditions and disease states. Here we describe a novel and straightforward method to clone cDNA libraries from small quantities of input RNA. This method permits the generation of cDNA libraries from sub-picogram quantities of RNA robustly, efficiently and reproducibly. We demonstrate that the method provides a significant improvement in sensitivity compared to previous cloning methods while maintaining reproducible identification of diverse small RNA species. This method should have widespread applications in a variety of contexts, including biomarker discovery from scarce samples of human tissue or body fluids. PMID:25056322

Silk-based blood stabilization for diagnostics.

PubMed

Kluge, Jonathan A; Li, Adrian B; Kahn, Brooke T; Michaud, Dominique S; Omenetto, Fiorenzo G; Kaplan, David L

2016-05-24

Advanced personalized medical diagnostics depend on the availability of high-quality biological samples. These are typically biofluids, such as blood, saliva, or urine; and their collection and storage is critical to obtain reliable results. Without proper temperature regulation, protein biomarkers in particular can degrade rapidly in blood samples, an effect that ultimately compromises the quality and reliability of laboratory tests. Here, we present the use of silk fibroin as a solid matrix to encapsulate blood analytes, protecting them from thermally induced damage that could be encountered during nonrefrigerated transportation or freeze-thaw cycles. Blood samples are recovered by simple dissolution of the silk matrix in water. This process is demonstrated to be compatible with a number of immunoassays and provides enhanced sample preservation in comparison with traditional air-drying paper approaches. Additional processing can remediate interactions with conformational structures of the silk protein to further enhance blood stabilization and recovery. This approach can provide expanded utility for remote collection of blood and other biospecimens empowering new modalities of temperature-independent remote diagnostics.

A platform for discovery: The University of Pennsylvania Integrated Neurodegenerative Disease Biobank

PubMed Central

Toledo, Jon B.; Van Deerlin, Vivianna M.; Lee, Edward B.; Suh, EunRan; Baek, Young; Robinson, John L.; Xie, Sharon X.; McBride, Jennifer; Wood, Elisabeth M.; Schuck, Theresa; Irwin, David J.; Gross, Rachel G.; Hurtig, Howard; McCluskey, Leo; Elman, Lauren; Karlawish, Jason; Schellenberg, Gerard; Chen-Plotkin, Alice; Wolk, David; Grossman, Murray; Arnold, Steven E.; Shaw, Leslie M.; Lee, Virginia M.-Y.; Trojanowski, John Q.

2014-01-01

Neurodegenerative diseases (NDs) are defined by the accumulation of abnormal protein deposits in the central nervous system (CNS), and only neuropathological examination enables a definitive diagnosis. Brain banks and their associated scientific programs have shaped the actual knowledge of NDs, identifying and characterizing the CNS deposits that define new diseases, formulating staging schemes, and establishing correlations between neuropathological changes and clinical features. However, brain banks have evolved to accommodate the banking of biofluids as well as DNA and RNA samples. Moreover, the value of biobanks is greatly enhanced if they link all the multidimensional clinical and laboratory information of each case, which is accomplished, optimally, using systematic and standardized operating procedures, and in the framework of multidisciplinary teams with the support of a flexible and user-friendly database system that facilitates the sharing of information of all the teams in the network. We describe a biobanking system that is a platform for discovery research at the Center for Neurodegenerative Disease Research at the University of Pennsylvania. PMID:23978324

Understanding carbon nanotube channel formation in the lipid membrane

NASA Astrophysics Data System (ADS)

Choi, Moon-ki; Kim, Hyunki; Lee, Byung Ho; Kim, Teayeop; Rho, Junsuk; Kim, Moon Ki; Kim, Kyunghoon

2018-03-01

Carbon nanotubes (CNTs) have been considered a prominent nano-channel in cell membranes because of their prominent ion-conductance and ion-selectivity, offering agents for a biomimetic channel platform. Using a coarse-grained molecular dynamics simulation, we clarify a construction mechanism of vertical CNT nano-channels in a lipid membrane for a long period, which has been difficult to observe in previous CNT-lipid interaction simulations. The result shows that both the lipid coating density and length of CNT affect the suitable fabrication condition for a vertical and stable CNT channel. Also, simulation elucidated that a lipid coating on the surface of the CNT prevents the CNT from burrowing into the lipid membrane and the vertical channel is stabilized by the repulsion force between the lipids in the coating and membrane. Our study provides an essential understanding of how CNTs can form stable and vertical channels in the membrane, which is important for designing new types of artificial channels as biosensors for bio-fluidic studies.

Business Process Flow Diagrams in Tissue Bank Informatics System Design, and Identification and Communication of Best Practices: The Pharmaceutical Industry Experience.

PubMed

McDonald, Sandra A; Velasco, Elizabeth; Ilasi, Nicholas T

2010-12-01

Pfizer, Inc.'s Tissue Bank, in conjunction with Pfizer's BioBank (biofluid repository), endeavored to create an overarching internal software package to cover all general functions of both research facilities, including sample receipt, reconciliation, processing, storage, and ordering. Business process flow diagrams were developed by the Tissue Bank and Informatics teams as a way of characterizing best practices both within the Bank and in its interactions with key internal and external stakeholders. Besides serving as a first step for the software development, such formalized process maps greatly assisted the identification and communication of best practices and the optimization of current procedures. The diagrams shared here could assist other biospecimen research repositories (both pharmaceutical and other settings) for comparative purposes or as a guide to successful informatics design. Therefore, it is recommended that biorepositories consider establishing formalized business process flow diagrams for their laboratories, to address these objectives of communication and strategy.

Label-Free Discovery Array Platform for the Characterization of Glycan Binding Proteins and Glycoproteins.

PubMed

Gray, Christopher J; Sánchez-Ruíz, Antonio; Šardzíková, Ivana; Ahmed, Yassir A; Miller, Rebecca L; Reyes Martinez, Juana E; Pallister, Edward; Huang, Kun; Both, Peter; Hartmann, Mirja; Roberts, Hannah N; Šardzík, Robert; Mandal, Santanu; Turnbull, Jerry E; Eyers, Claire E; Flitsch, Sabine L

2017-04-18

The identification of carbohydrate-protein interactions is central to our understanding of the roles of cell-surface carbohydrates (the glycocalyx), fundamental for cell-recognition events. Therefore, there is a need for fast high-throughput biochemical tools to capture the complexity of these biological interactions. Here, we describe a rapid method for qualitative label-free detection of carbohydrate-protein interactions on arrays of simple synthetic glycans, more complex natural glycosaminoglycans (GAG), and lectins/carbohydrate binding proteins using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The platform can unequivocally identify proteins that are captured from either purified or complex sample mixtures, including biofluids. Identification of proteins bound to the functionalized array is achieved by analyzing either the intact protein mass or, after on-chip proteolytic digestion, the peptide mass fingerprint and/or tandem mass spectrometry of selected peptides, which can yield highly diagnostic sequence information. The platform described here should be a valuable addition to the limited analytical toolbox that is currently available for glycomics.

Helmholtz-Smoluchowski velocity for viscoelastic electroosmotic flows.

PubMed

Park, H M; Lee, W M

2008-01-15

Many biofluids such as blood and DNA solutions are viscoelastic and exhibit extraordinary flow behaviors, not existing in Newtonian fluids. Adopting appropriate constitutive equations these exotic flow behaviors can be modeled and predicted reasonably using various numerical methods. However, the governing equations for viscoelastic flows are not easily solvable, especially for electroosmotic flows where the streamwise velocity varies rapidly from zero at the wall to a nearly uniform velocity at the outside of the very thin electric double layer. In the present investigation, we have devised a simple method to find the volumetric flow rate of viscoelastic electroosmotic flows through microchannels. It is based on the concept of the Helmholtz-Smoluchowski velocity which is widely adopted in the electroosmotic flows of Newtonian fluids. It is shown that the Helmholtz-Smoluchowski velocity for viscoelastic fluids can be found by solving a simple cubic algebraic equation. The volumetric flow rate obtained using this Helmholtz-Smoluchowski velocity is found to be almost the same as that obtained by solving the governing partial differential equations for various viscoelastic fluids.

Characterization of the canine urinary proteome.

PubMed

Brandt, Laura E; Ehrhart, E J; Scherman, Hataichanok; Olver, Christine S; Bohn, Andrea A; Prenni, Jessica E

2014-06-01

Urine is an attractive biofluid for biomarker discovery as it is easy and minimally invasive to obtain. While numerous studies have focused on the characterization of human urine, much less research has focused on canine urine. The objectives of this study were to characterize the universal canine urinary proteome (both soluble and exosomal), to determine the overlap between the canine proteome and a representative human urinary proteome study, to generate a resource for future canine studies, and to determine the suitability of the dog as a large animal model for human diseases. The soluble and exosomal fractions of normal canine urine were characterized using liquid chromatography tandem mass spectrometry (LC-MS/MS). Biological Networks Gene Ontology (BiNGO) software was utilized to assign the canine urinary proteome to respective Gene Ontology categories, such as Cellular Component, Molecular Function, and Biological Process. Over 500 proteins were confidently identified in normal canine urine. Gene Ontology analysis revealed that exosomal proteins were largely derived from an intracellular location, while soluble proteins included both extracellular and membrane proteins. Exosome proteins were assigned to metabolic processes and localization, while soluble proteins were primarily annotated to specific localization processes. Several proteins identified in normal canine urine have previously been identified in human urine where these proteins are related to various extrarenal and renal diseases. The results of this study illustrate the potential of the dog as an animal model for human disease states and provide the framework for future studies of canine renal diseases. © 2014 American Society for Veterinary Clinical Pathology and European Society for Veterinary Clinical Pathology.

Informatic system for a global tissue–fluid biorepository with a graph theory–oriented graphical user interface

PubMed Central

Butler, William E.; Atai, Nadia; Carter, Bob; Hochberg, Fred

2014-01-01

The Richard Floor Biorepository supports collaborative studies of extracellular vesicles (EVs) found in human fluids and tissue specimens. The current emphasis is on biomarkers for central nervous system neoplasms but its structure may serve as a template for collaborative EV translational studies in other fields. The informatic system provides specimen inventory tracking with bar codes assigned to specimens and containers and projects, is hosted on globalized cloud computing resources, and embeds a suite of shared documents, calendars, and video-conferencing features. Clinical data are recorded in relation to molecular EV attributes and may be tagged with terms drawn from a network of externally maintained ontologies thus offering expansion of the system as the field matures. We fashioned the graphical user interface (GUI) around a web-based data visualization package. This system is now in an early stage of deployment, mainly focused on specimen tracking and clinical, laboratory, and imaging data capture in support of studies to optimize detection and analysis of brain tumour–specific mutations. It currently includes 4,392 specimens drawn from 611 subjects, the majority with brain tumours. As EV science evolves, we plan biorepository changes which may reflect multi-institutional collaborations, proteomic interfaces, additional biofluids, changes in operating procedures and kits for specimen handling, novel procedures for detection of tumour-specific EVs, and for RNA extraction and changes in the taxonomy of EVs. We have used an ontology-driven data model and web-based architecture with a graph theory–driven GUI to accommodate and stimulate the semantic web of EV science. PMID:25317275

Ciprofloxacin by-products in seawater environment in the presence and absence of gilt-head bream.

PubMed

Ziarrusta, Haizea; Mijangos, Leire; Irazola, Mireia; Prieto, Ailette; Etxebarria, Nestor; Anakabe, Eneritz; Olivares, Maitane; Zuloaga, Olatz

2018-04-01

The widespread use of pharmaceuticals has caused a growing concern on the presence of pharmaceuticals such as the antibiotic ciprofloxacin (CIPRO) in the aquatic environment, since they may exert adverse effects on non-target organisms, including fish. In order to study the uptake, distribution in different tissues (liver, muscle, brain and gill) and biofluids (plasma and bile), metabolism and elimination of CIPRO in gilt-head bream (Sparus aurata), controlled dosing experiments for 8 days at 200 μg/L concentration were carried out. CIPRO was only observed in bile at concentration up to 315 ± 4 ng/mL, probably due to its low octanol-water partition coefficient (log P = -2.4 at pH 7.4) and the zwitterionic behavior (pKa 1  = 5.76 and pKa 2  = 8.68). CIPRO by-products (BPs) were also identified in seawater environment, both in presence and absence of fish. The analysis done by means of liquid chromatography-high resolution mass spectrometry (hybrid quadrupole-Orbitrap) permitted the annotation of up to 35 BPs of CIPRO in seawater and bile, from which 30 structures were reported for the first time. These results confirm that CIPRO is very susceptible to photolysis, and that it goes through various phase I and phase II metabolisms in the fish. All these results suggested that, for a complete characterization of CIPRO exposure, BPs should also be included in the biomonitoring campaigns since they might also be toxicologically relevant. Copyright © 2018 Elsevier Ltd. All rights reserved.

Paper based diagnostics for personalized health care: Emerging technologies and commercial aspects.

PubMed

Mahato, Kuldeep; Srivastava, Ananya; Chandra, Pranjal

2017-10-15

Personalized health care (PHC) is being appreciated globally to combat clinical complexities underlying various metabolic or infectious disorders including diabetes, cardiovascular, communicable diseases etc. Effective diagnoses majorly depend on initial identification of the causes which are nowadays being practiced in disease-oriented approach, where personal health profile is often overlooked. The adoption of PHC has shown significantly improved diagnoses in various conditions including emergency, ambulatory, and remote area. PHC includes personalized health monitoring (PHM), which is its integral part and may provide valuable information's on various clinical conditions. In PHC, bio-fluids are analyzed using various diagnostic devices including lab based equipment and biosensors. Among all types of biosensing systems, paper based biosensors are commercially attracted due to its portability, easy availability, cheaper manufacturing cost, and transportability. Not only these, various intrinsic properties of paper has facilitated the development of paper based miniaturized sensors, which has recently gained ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment free, Deliverable to all end-users) status for point of care diagnosis in miniaturized settings. In this review, importance of paper based biosensors and their compatibility for affordable and low cost diagnostics has been elaborated with various examples. Limitations and strategies to overcome the challenges of paper biosensor have also been discussed. We have provided elaborated tables which describe the types, model specifications, sensing mechanisms, target biomarkers, and analytical performance of the paper biosensors with their respective applications in real sample matrices. Different commercial aspects of paper biosensor have also been explained using SWOT (Strength, Weakness, Opportunities, Threats) analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Advances in multiplexed MRM-based protein biomarker quantitation toward clinical utility.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Hardie, Darryl B; Borchers, Christoph H

2014-05-01

Accurate and rapid protein quantitation is essential for screening biomarkers for disease stratification and monitoring, and to validate the hundreds of putative markers in human biofluids, including blood plasma. An analytical method that utilizes stable isotope-labeled standard (SIS) peptides and selected/multiple reaction monitoring-mass spectrometry (SRM/MRM-MS) has emerged as a promising technique for determining protein concentrations. This targeted approach has analytical merit, but its true potential (in terms of sensitivity and multiplexing) has yet to be realized. Described herein is a method that extends the multiplexing ability of the MRM method to enable the quantitation 142 high-to-moderate abundance proteins (from 31mg/mL to 44ng/mL) in undepleted and non-enriched human plasma in a single run. The proteins have been reported to be associated to a wide variety of non-communicable diseases (NCDs), from cardiovascular disease (CVD) to diabetes. The concentrations of these proteins in human plasma are inferred from interference-free peptides functioning as molecular surrogates (2 peptides per protein, on average). A revised data analysis strategy, involving the linear regression equation of normal control plasma, has been instituted to enable the facile application to patient samples, as demonstrated in separate nutrigenomics and CVD studies. The exceptional robustness of the LC/MS platform and the quantitative method, as well as its high throughput, makes the assay suitable for application to patient samples for the verification of a condensed or complete protein panel. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge. © 2013.

Pinched flow coupled shear-modulated inertial microfluidics for high-throughput rare blood cell separation.

PubMed

Bhagat, Ali Asgar S; Hou, Han Wei; Li, Leon D; Lim, Chwee Teck; Han, Jongyoon

2011-06-07

Blood is a highly complex bio-fluid with cellular components making up >40% of the total volume, thus making its analysis challenging and time-consuming. In this work, we introduce a high-throughput size-based separation method for processing diluted blood using inertial microfluidics. The technique takes advantage of the preferential cell focusing in high aspect-ratio microchannels coupled with pinched flow dynamics for isolating low abundance cells from blood. As an application of the developed technique, we demonstrate the isolation of cancer cells (circulating tumor cells (CTCs)) spiked in blood by exploiting the difference in size between CTCs and hematologic cells. The microchannel dimensions and processing parameters were optimized to enable high throughput and high resolution separation, comparable to existing CTC isolation technologies. Results from experiments conducted with MCF-7 cells spiked into whole blood indicate >80% cell recovery with an impressive 3.25 × 10(5) fold enrichment over red blood cells (RBCs) and 1.2 × 10(4) fold enrichment over peripheral blood leukocytes (PBL). In spite of a 20× sample dilution, the fast operating flow rate allows the processing of ∼10(8) cells min(-1) through a single microfluidic device. The device design can be easily customized for isolating other rare cells from blood including peripheral blood leukocytes and fetal nucleated red blood cells by simply varying the 'pinching' width. The advantage of simple label-free separation, combined with the ability to retrieve viable cells post enrichment and minimal sample pre-processing presents numerous applications for use in clinical diagnosis and conducting fundamental studies.

The cancer secretome, current status and opportunities in the lung, breast and colorectal cancer context.

PubMed

Schaaij-Visser, Tieneke B M; de Wit, Meike; Lam, Siu W; Jiménez, Connie R

2013-11-01

Despite major improvements on the knowledge and clinical management, cancer is still a deadly disease. Novel biomarkers for better cancer detection, diagnosis and treatment prediction are urgently needed. Proteins secreted, shed or leaking from the cancer cell, collectively termed the cancer secretome, are promising biomarkers since they might be detectable in blood or other biofluids. Furthermore, the cancer secretome in part represents the tumor microenvironment that plays a key role in tumor promoting processes such as angiogenesis and invasion. The cancer secretome, sampled as conditioned medium from cell lines, tumor/tissue interstitial fluid or tumor proximal body fluids, can be studied comprehensively by nanoLC-MS/MS-based approaches. Here, we outline the importance of current cancer secretome research and describe the mass spectrometry-based analysis of the secretome. Further, we provide an overview of cancer secretome research with a focus on the three most common cancer types: lung, breast and colorectal cancer. We conclude that the cancer secretome research field is a young, but rapidly evolving research field. Up to now, the focus has mainly been on the discovery of novel promising secreted cancer biomarker proteins. An interesting finding that merits attention is that in cancer unconventional secretion, e.g. via vesicles, seems increased. Refinement of current approaches and methods and progress in clinical validation of the current findings are vital in order to move towards applications in cancer management. This article is part of a Special Issue entitled: An Updated Secretome. Copyright © 2013 Elsevier B.V. All rights reserved.

Using Fourier transform IR spectroscopy to analyze biological materials

PubMed Central

Baker, Matthew J; Trevisan, Júlio; Bassan, Paul; Bhargava, Rohit; Butler, Holly J; Dorling, Konrad M; Fielden, Peter R; Fogarty, Simon W; Fullwood, Nigel J; Heys, Kelly A; Hughes, Caryn; Lasch, Peter; Martin-Hirsch, Pierre L; Obinaju, Blessing; Sockalingum, Ganesh D; Sulé-Suso, Josep; Strong, Rebecca J; Walsh, Michael J; Wood, Bayden R; Gardner, Peter; Martin, Francis L

2015-01-01

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing. PMID:24992094

Informatic system for a global tissue-fluid biorepository with a graph theory-oriented graphical user interface.

PubMed

Butler, William E; Atai, Nadia; Carter, Bob; Hochberg, Fred

2014-01-01

The Richard Floor Biorepository supports collaborative studies of extracellular vesicles (EVs) found in human fluids and tissue specimens. The current emphasis is on biomarkers for central nervous system neoplasms but its structure may serve as a template for collaborative EV translational studies in other fields. The informatic system provides specimen inventory tracking with bar codes assigned to specimens and containers and projects, is hosted on globalized cloud computing resources, and embeds a suite of shared documents, calendars, and video-conferencing features. Clinical data are recorded in relation to molecular EV attributes and may be tagged with terms drawn from a network of externally maintained ontologies thus offering expansion of the system as the field matures. We fashioned the graphical user interface (GUI) around a web-based data visualization package. This system is now in an early stage of deployment, mainly focused on specimen tracking and clinical, laboratory, and imaging data capture in support of studies to optimize detection and analysis of brain tumour-specific mutations. It currently includes 4,392 specimens drawn from 611 subjects, the majority with brain tumours. As EV science evolves, we plan biorepository changes which may reflect multi-institutional collaborations, proteomic interfaces, additional biofluids, changes in operating procedures and kits for specimen handling, novel procedures for detection of tumour-specific EVs, and for RNA extraction and changes in the taxonomy of EVs. We have used an ontology-driven data model and web-based architecture with a graph theory-driven GUI to accommodate and stimulate the semantic web of EV science.

The need for non- or minimally-invasive biomonitoring strategies and the development of pharmacokinetic/pharmacodynamic models for quantification

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

Timchalk, Charles; Weber, Thomas J.; Smith, Jordan N.

Advancements in Exposure Science involving the development and deployment of biomarkers of exposure and biological response are anticipated to significantly (and positively) influence health outcomes associated with occupational, environmental and clinical exposure to chemicals/drugs. To achieve this vision, innovative strategies are needed to develop multiplex sensor platforms capable of quantifying individual and mixed exposures (i.e. systemic dose) by measuring biomarkers of dose and biological response in readily obtainable (non-invasive) biofluids. Secondly, the use of saliva (alternative to blood) for biomonitoring coupled with the ability to rapidly analyze multiple samples in real-time offers an innovative opportunity to revolutionize biomonitoring assessments. Inmore » this regard, the timing and number of samples taken for biomonitoring will not be limited as is currently the case. In addition, real-time analysis will facilitate identification of work practices or conditions that are contributing to increased exposures and will make possible a more rapid and successful intervention strategy. The initial development and application of computational models for evaluation of saliva/blood analyte concentration at anticipated exposure levels represents an important opportunity to establish the limits of quantification and robustness of multiplex sensor systems by exploiting a unique computational modeling framework. The use of these pharmacokinetic models will also enable prediction of an exposure dose based on the saliva/blood measurement. This novel strategy will result in a more accurate prediction of exposures and, once validated, can be employed to assess dosimetry to a broad range of chemicals in support of biomonitoring and epidemiology studies.« less

Multicomponent analysis of radiolytic products in human body fluids using high field proton nuclear magnetic resonance (NMR) spectroscopy

NASA Astrophysics Data System (ADS)

Grootveld, Martin C.; Herz, Herman; Haywood, Rachel; Hawkes, Geoffrey E.; Naughton, Declan; Perera, Anusha; Knappitt, Jacky; Blake, David R.; Claxson, Andrew W. D.

1994-05-01

High field proton Hahn spin-echo nuclear magnetic resonance (NMR) spectroscopy has been employed to investigate radiolytic damage to biomolecules present in intact human body fluids. γ-Radiolysis of healthy or rheumatoid human serum (5.00 kGy) in the presence of atmospheric O 2 gave rise to reproducible elevations in the concentration of NMR-detectable acetate which are predominantly ascribable to the prior oxidation of lactate to pyruvate by hydroxyl radical (·OH) followed by oxidative decarboxylation of pyruvate by radiolytically-generated hydrogen peroxide (H 2O 2) and/or further ·OH radical. Increases in the serum levels of non-protein-bound, low-molecular-mass components such as citrate and glutamine were also observed subsequent to γ-radiolysis, an observation which may reflect their mobilisation from protein binding-sites by ·OH radical, superoxide anion and/or H 2O 2. Moreover, substantial radiolytically-mediated elevations in the concentration of serum formate were also detectable. In addition to the above modifications, γ-radiolysis of inflammatory knee-joint synovial fluid (SF) generated a low-molecular-mass oligosaccharide species derived from the radiolytic fragmentation of hyaluronate. The radiolytically-mediated production of acetate in SF samples was markedly greater than that observed in serum samples, a consequence of the much higher levels of ·OH radical-scavenging lactate present. Indeed, increases in SF acetate concentration were detectable at doses as low as 48 Gy. We conclude that high field proton NMR analysis provides much useful information regarding the relative radioprotectant abilities of endogenous components and the nature, status and levels of radiolytic products generated in intact biofluids. We also suggest that NMR-detectable radiolytic products with associated toxicological properties (e.g. formate) may play a role in contributing to the deleterious effects observed following exposure of living organisms to sources of ionising radiation.

Determination of glycine in biofluid by hydrophilic interaction chromatography coupled with tandem mass spectrometry and its application to the quantification of glycine released by embryonal carcinoma stem cells.

PubMed

Tang, Ya-Bin; Teng, Lin; Sun, Fan; Wang, Xiao-Lin; Peng, Liang; Cui, Yong-Yao; Hu, Jin-Jia; Luan, Xin; Zhu, Liang; Chen, Hong-Zhuan

2012-09-15

Because glycine plays a prominent role in living creatures, an accurate and precise quantitative analysis method for the compound is needed. Herein, a new approach to analyze glycine by hydrophilic interaction chromatography (HILIC) coupled with electrospray ionization tandem mass spectrometry (ESI-MS/MS) was developed. This method avoids the use of derivatization and/or ion-pairing reagents. N-methyl-D-aspartate (NMDA) is used as the internal standard (IS). The mobile phase for the isocratic elution consisted of 10 mM ammonium formate in acetonitrile-water (70:30, v/v, adjusted to pH 2.8 with formic acid), and a flow rate of 250 μL/min was used. Two microliters of sample was injected for analysis. The signal was monitored in the positive multiple reaction monitoring (MRM) mode. The total run time was 5 min. The dynamic range was 40-2000 ng/mL for glycine in the biological matrix. The LLOQ (lower limit of quantification) of this method was 40 ng/mL (80 pg on column). The validated method was applied to determine the dynamic release of glycine from P19 embryonal carcinoma stem cells (ECSCs). Glycine spontaneously released from the ECSCs into the intercellular space gradually increased from 331.02±60.36 ng/mL at 2 min in the beginning to 963.52±283.80 ng/mL at 60 min and 948.27±235.09 ng/mL at 120 min, finally reaching a plateau, indicating that ECSCs consecutively release glycine until achieving equilibration between the release and the reuptake of the compound; on the contrary, the negative control NIH/3T3 embryonic fibroblast cells did not release glycine. This finding will help to improve our understanding of the novel effects of neurotransmitters, including glycine, on non-neural systems. Copyright © 2012 Elsevier B.V. All rights reserved.

Extracellular vesicle communication pathways as regulatory targets of oncogenic transformation.

PubMed

Choi, Dongsic; Lee, Tae Hoon; Spinelli, Cristiana; Chennakrishnaiah, Shilpa; D'Asti, Esterina; Rak, Janusz

2017-07-01

Pathogenesis of human cancers bridges intracellular oncogenic driver events and their impact on intercellular communication. Among multiple mediators of this 'pathological connectivity' the role of extracellular vesicles (EVs) and their subsets (exosomes, ectosomes, oncosomes) is of particular interest for several reasons. The release of EVs from cancer cells represents a unique mechanism of regulated expulsion of bioactive molecules, a process that also mediates cell-to-cell transfer of lipids, proteins, and nucleic acids. Biological effects of these processes have been implicated in several aspects of cancer-related pathology, including tumour growth, invasion, angiogenesis, metastasis, immunity and thrombosis. Notably, the emerging evidence suggests that oncogenic mutations may impact several aspects of EV-mediated cell-cell communication including: (i) EV release rate and protein content; (ii) molecular composition of cancer EVs; (iii) the inclusion of oncogenic and mutant macromolecules in the EV cargo; (iv) EV-mediated release of genomic DNA; (v) deregulation of mechanisms responsible for EV biogenesis (vesiculome) and (vi) mechanisms of EV uptake by cancer cells. Intriguingly, EV-mediated intercellular transfer of mutant and oncogenic molecules between subpopulations of cancer cells, their indolent counterparts and stroma may exert profound biological effects that often resemble (but are not tantamount to) oncogenic transformation, including changes in cell growth, clonogenicity and angiogenic phenotype, or cause cell stress and death. However, several biological barriers likely curtail a permanent horizontal transformation of normal cells through EV-mediated mechanisms. The ongoing analysis and targeting of EV-mediated intercellular communication pathways can be viewed as a new therapeutic paradigm in cancer, while the analysis of oncogenic cargo contained in EVs released from cancer cells into biofluids is being developed for clinical use as a biomarker and companion diagnostics. Indeed, studies are underway to further explore the multiple links between molecular causality in cancer and various aspects of cellular vesiculation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Brain Gene Expression Signatures From Cerebrospinal Fluid Exosome RNA Profiling

NASA Technical Reports Server (NTRS)

Zanello, S. B.; Stevens, B.; Calvillo, E.; Tang, R.; Gutierrez Flores, B.; Hu, L.; Skog, J.; Bershad, E.

2016-01-01

While the Visual Impairment and Intracranial Pressure (VIIP) syndrome observations have focused on ocular symptoms, spaceflight has been also associated with a number of other performance and neurologic signs, such as headaches, cognitive changes, vertigo, nausea, sleep/circadian disruption and mood alterations, which, albeit likely multifactorial, can also result from elevation of intracranial pressure (ICP). We therefore hypothesize that these various symptoms are caused by disturbances in the neurophysiology of the brain structures and are correlated with molecular markers in the cerebrospinal fluid (CSF) as indicators of neurophysiological changes. Exosomes are 30-200 nm microvesicles shed into all biofluids, including blood, urine, and CSF, carrying a highly rich source of intact protein and RNA cargo. Exosomes have been identified in human CSF, and their proteome and RNA pool is a potential new reservoir for biomarker discovery in neurological disorders. The purpose of this study is to investigate changes in brain gene expression via exosome analysis in patients suffering from ICP elevation of varied severity (idiopathic intracranial hypertension -IIH), a condition which shares some of the neuroophthalmological features of VIIP, as a first step toward obtaining evidence suggesting that cognitive function and ICP levels can be correlated with biomarkers in the CSF. Our preliminary work, reported last year, validated the exosomal technology applicable to CSF analysis and demonstrated that it was possible to obtain gene expression evidence of inflammation processes in traumatic brain injury patients. We are now recruiting patients with suspected IIH requiring lumbar puncture at Baylor College of Medicine. Both CSF (5 ml) and human plasma (10 ml) are being collected in order to compare the pattern of differentially expressed genes observed in CSF and in blood. Since blood is much more accessible than CSF, we would like to determine whether plasma biomarkers for elevated ICP can be identified. This may eventually lead to a blood test to diagnose intracranial hypertension.

Ebola Check: Delivering molecular diagnostics at the point of need.

PubMed

Moschos, Sterghios A

2015-01-01

The 2013-5 global outbreak of Ebolavirus disease brought to sharp focus the need for diagnostic capacity to be equitably available on a global scale: from the most under-developed areas of resource-limited countries in West Africa to high volume international travel hubs in Europe and the USA. Quick detection of the causal agent of disease is pivotal to containment, contact tracing and clinical action to protect healthcare workers, communities and patients. Nucleic acid testing (NAT) by real time reverse transcription quantitative polymerase chain reaction (RT-PCR) has emerged as the preferred method for reliable patient status confirmation. Presently, this is served through advanced clinical molecular laboratory testing in a <8hr manual process that requires 3.5ml venous blood samples. To meet the demand in West Africa, this has necessitated large-scale mobile laboratory and volunteer biomedical scientist deployment: a solution that has proven eventually adequate, albeit temporary against future re-emergence of this and other haemorrhagic fever disease agents prevalent in the region. The EbolaCheck consortium was formed in August 2014 to address the need for delivering NAT at the point of care. We have developed a novel platform technology that can QUantitatively, RAPidly IDentify (QuRapID) known RNA or DNA targets in viruses, bacteria, or eukaryotic cells directly in crude biofluids, including whole blood, in under 40min using a 5 microliter sample. The portable, battery-operated system lacks microfluidics, pumps or other sensitive/high cost parts making it suitable for the environmental and economic challenges of resource-limited countries. The simple, safe, 5-step sample-to-answer process requires minimal training and informs frontline healthcare workers of diagnostic status, whilst reporting remotely epidemiologically relevant results. Data on biosafety level 2 surrogate Ebolavirus templates presented in encapsulated or enveloped viruses indicate performance comparable to clinical laboratory testing and utility beyond filoviruses. Emerging performance data on live Ebolavirus, non-human primate disease model and patient samples, as well as future development plans will be discussed.

Cold flame on Biofilm - Transport of Plasma Chemistry from Gas to Liquid Phase

NASA Astrophysics Data System (ADS)

Kong, Michael

2014-10-01

One of the most active and fastest growing fields in low-temperature plasma science today is biological effects of gas plasmas and their translation in many challenges of societal importance such as healthcare, environment, agriculture, and nanoscale fabrication and synthesis. Using medicine as an example, there are already three FDA-approved plasma-based surgical procedures for tissue ablation and blood coagulation and at least five phase-II clinical trials on plasma-assisted wound healing therapies. A key driver for realizing the immense application potential of near room-temperature ambient pressure gas plasmas, commonly known as cold atmospheric plasmas or CAP, is to build a sizeable interdisciplinary knowledge base with which to unravel, optimize, and indeed design how reactive plasma species interact with cells and their key components such as protein and DNA. Whilst a logical objective, it is a formidable challenge not least since existing knowledge of gas discharges is largely in the gas-phase and therefore not directly applicable to cell-containing matters that are covered by or embedded in liquid (e.g. biofluid). Here, we study plasma inactivation of biofilms, a jelly-like structure that bacteria use to protect themselves and a major source of antimicrobial resistance. As 60--90% of biofilm is made of water, we develop a holistic model incorporating physics and chemistry in the upstream CAP-generating region, a plasma-exit region as a buffer for as-phase transport, and a downstream liquid region bordering the gas buffer region. A special model is developed to account for rapid chemical reactions accompanied the transport of gas-phase plasma species through the gas-liquid interface and for liquid-phase chemical reactions. Numerical simulation is used to illustrate how key reactive oxygen species (ROS) are transported into the liquid, and this is supported with experimental data of both biofilm inactivation using plasmas and electron spin spectroscopy (ESR) measurement of liquid-phase ROS.

Detection of wild-type EGFR amplification and EGFRvIII mutation in CSF-derived extracellular vesicles of glioblastoma patients.

PubMed

Figueroa, Javier M; Skog, Johan; Akers, Johnny; Li, Hongying; Komotar, Ricardo; Jensen, Randy; Ringel, Florian; Yang, Isaac; Kalkanis, Steven; Thompson, Reid; LoGuidice, Lori; Berghoff, Emily; Parsa, Andrew; Liau, Linda; Curry, William; Cahill, Daniel; Bettegowda, Chetan; Lang, Frederick F; Chiocca, E Antonio; Henson, John; Kim, Ryan; Breakefield, Xandra; Chen, Clark; Messer, Karen; Hochberg, Fred; Carter, Bob S

2017-10-19

RNAs within extracellular vesicles (EVs) have potential as diagnostic biomarkers for patients with cancer and are identified in a variety of biofluids. Glioblastomas (GBMs) release EVs containing RNA into cerebrospinal fluid (CSF). Here we describe a multi-institutional study of RNA extracted from CSF-derived EVs of GBM patients to detect the presence of tumor-associated amplifications and mutations in epidermal growth factor receptor (EGFR). CSF and matching tumor tissue were obtained from patients undergoing resection of GBMs. We determined wild-type (wt)EGFR DNA copy number amplification, as well as wtEGFR and EGFR variant (v)III RNA expression in tumor samples. We also characterized wtEGFR and EGFRvIII RNA expression in CSF-derived EVs. EGFRvIII-positive tumors had significantly greater wtEGFR DNA amplification (P = 0.02) and RNA expression (P = 0.03), and EGFRvIII-positive CSF-derived EVs had significantly more wtEGFR RNA expression (P = 0.004). EGFRvIII was detected in CSF-derived EVs for 14 of the 23 EGFRvIII tissue-positive GBM patients. Conversely, only one of the 48 EGFRvIII tissue-negative patients had the EGFRvIII mutation detected in their CSF-derived EVs. These results yield a sensitivity of 61% and a specificity of 98% for the utility of CSF-derived EVs to detect an EGFRvIII-positive GBM. Our results demonstrate CSF-derived EVs contain RNA signatures reflective of the underlying molecular genetic status of GBMs in terms of wtEGFR expression and EGFRvIII status. The high specificity of the CSF-derived EV diagnostic test gives us an accurate determination of positive EGFRvIII tumor status and is essentially a less invasive "liquid biopsy" that might direct mutation-specific therapies for GBMs. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Neuro-Oncology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Profiles of extracellular miRNA in cerebrospinal fluid and serum from patients with Alzheimer's and Parkinson's diseases correlate with disease status and features of pathology.

PubMed

Burgos, Kasandra; Malenica, Ivana; Metpally, Raghu; Courtright, Amanda; Rakela, Benjamin; Beach, Thomas; Shill, Holly; Adler, Charles; Sabbagh, Marwan; Villa, Stephen; Tembe, Waibhav; Craig, David; Van Keuren-Jensen, Kendall

2014-01-01

The discovery and reliable detection of markers for neurodegenerative diseases have been complicated by the inaccessibility of the diseased tissue--such as the inability to biopsy or test tissue from the central nervous system directly. RNAs originating from hard to access tissues, such as neurons within the brain and spinal cord, have the potential to get to the periphery where they can be detected non-invasively. The formation and extracellular release of microvesicles and RNA binding proteins have been found to carry RNA from cells of the central nervous system to the periphery and protect the RNA from degradation. Extracellular miRNAs detectable in peripheral circulation can provide information about cellular changes associated with human health and disease. In order to associate miRNA signals present in cell-free peripheral biofluids with neurodegenerative disease status of patients with Alzheimer's and Parkinson's diseases, we assessed the miRNA content in cerebrospinal fluid and serum from postmortem subjects with full neuropathology evaluations. We profiled the miRNA content from 69 patients with Alzheimer's disease, 67 with Parkinson's disease and 78 neurologically normal controls using next generation small RNA sequencing (NGS). We report the average abundance of each detected miRNA in cerebrospinal fluid and in serum and describe 13 novel miRNAs that were identified. We correlated changes in miRNA expression with aspects of disease severity such as Braak stage, dementia status, plaque and tangle densities, and the presence and severity of Lewy body pathology. Many of the differentially expressed miRNAs detected in peripheral cell-free cerebrospinal fluid and serum were previously reported in the literature to be deregulated in brain tissue from patients with neurodegenerative disease. These data indicate that extracellular miRNAs detectable in the cerebrospinal fluid and serum are reflective of cell-based changes in pathology and can be used to assess disease progression and therapeutic efficacy.

A Carbon Nanotube Reporter of miRNA Hybridization Events In Vivo

PubMed Central

Harvey, Jackson D.; Jena, Prakrit V.; Baker, Hanan A.; Zerze, Gül H.; Williams, Ryan M.; Galassi, Thomas V.; Roxbury, Daniel; Mittal, Jeetain

2017-01-01

MicroRNAs and other small oligonucleotides in biofluids are promising disease biomarkers, yet conventional assays require complex processing steps that are unsuitable for point-of-care testing or for implantable or wearable sensors. Single-walled carbon nanotubes are an ideal material for implantable sensors, owing to their emission in the near-infrared spectral region, photostability and exquisite sensitivity. Here, we report an engineered carbon-nanotube-based sensor capable of real-time optical quantification of hybridization events of microRNA and other oligonucleotides. The mechanism of the sensor arises from competitive effects between displacement of both oligonucleotide charge groups and water from the nanotube surface, which result in a solvatochromism-like response. The sensor, which allows for detection via single-molecule sensor elements and for multiplexing by using multiple nanotube chiralities, can monitor toehold-based strand-displacement events, which reverse the sensor response and regenerate the sensor complex. We also show that the sensor functions in whole urine and serum, and can non-invasively measure DNA and microRNA after implantation in live mice. PMID:28845337

Simultaneous determination of vinclozolin and detection of its degradation products in mouse plasma, serum and urine, and from rabbit bile, by high-performance liquid chromatography.

PubMed

Dhananjeyan, Mugunthu R; Erhardt, Paul W; Corbitt, Cynthia

2006-05-19

A specific high-performance liquid chromatography method has been developed for simultaneous detection of vinclozolin and its degradation products (M1, M2, and M3). The method has been validated according to ICH guidelines and can be extended to quantitation of vinclozolin. A base-line separation of vinclozolin and its degradation products was found with symmetrical peak shapes on an XTerra MS C18 column using 10 mM ammonium bicarbonate at pH 9.2 and acetonitrile as mobile phase. The retention times of vinclozolin, M1, M2, and M3 were 12.8, 8.1, 11.6, and 11.1 min, respectively. A linear calibration curve was obtained across a range from 5 to 200 microM for vinclozolin. The intra- and inter-day relative standard deviations (%RSD) were <1%. Greater than 90% recoveries of vinclozolin from bio-fluids including mouse plasma, serum and urine, and rabbit bile, were obtained in a single step with a single solvent.

Suspected non-AD pathology in Mild Cognitive Impairment

PubMed Central

Wisse, Laura E.M.; Butala, Nirali; Das, Sandhitsu R.; Davatzikos, Christos; Dickerson, Bradford C.; Vaishnavi, Sanjeev N.; Yushkevich, Paul A.; Wolk, David A.

2015-01-01

We aim to better characterize Mild Cognitive Impairment (MCI) patients with suspected non-Alzheimer’s Disease (AD) pathology (SNAP) based on their longitudinal outcome, cognition, biofluid and neuroimaging profile. MCI participants (n=361) from ADNI-GO/2 were designated ‘amyloid positive’ with abnormal Aβ42 levels (AMY+) and ‘neurodegeneration positive’ (NEU+) with abnormal hippocampal volume or hypometabolism using FDG-PET. SNAP was compared with the other MCI groups and with AMY− controls. AMY−NEU+/SNAP, 16.6%, were older than the NEU− groups, but not AMY− controls. They had a lower conversion rate to AD after 24 months than AMY+NEU+ MCI participants. SNAP MCI participants had similar Aβ42 levels, florbetapir and tau levels, but larger white matter hyperintensity volumes than AMY− controls and AMY−NEU− MCI participants. SNAP participants performed worse on all memory domains and on other cognitive domains, than AMY−NEU− participants, but less so than AMY+NEU+ participants. Subthreshold levels of cerebral amyloidosis are unlikely to play a role in SNAP MCI, but pathologies involving the hippocampus and cerebrovascular disease may underlie the neurodegeneration and cognitive impairment in this group. PMID:26422359

The Human Serum Metabolome

PubMed Central

Psychogios, Nikolaos; Hau, David D.; Peng, Jun; Guo, An Chi; Mandal, Rupasri; Bouatra, Souhaila; Sinelnikov, Igor; Krishnamurthy, Ramanarayan; Eisner, Roman; Gautam, Bijaya; Young, Nelson; Xia, Jianguo; Knox, Craig; Dong, Edison; Huang, Paul; Hollander, Zsuzsanna; Pedersen, Theresa L.; Smith, Steven R.; Bamforth, Fiona; Greiner, Russ; McManus, Bruce; Newman, John W.; Goodfriend, Theodore; Wishart, David S.

2011-01-01

Continuing improvements in analytical technology along with an increased interest in performing comprehensive, quantitative metabolic profiling, is leading to increased interest pressures within the metabolomics community to develop centralized metabolite reference resources for certain clinically important biofluids, such as cerebrospinal fluid, urine and blood. As part of an ongoing effort to systematically characterize the human metabolome through the Human Metabolome Project, we have undertaken the task of characterizing the human serum metabolome. In doing so, we have combined targeted and non-targeted NMR, GC-MS and LC-MS methods with computer-aided literature mining to identify and quantify a comprehensive, if not absolutely complete, set of metabolites commonly detected and quantified (with today's technology) in the human serum metabolome. Our use of multiple metabolomics platforms and technologies allowed us to substantially enhance the level of metabolome coverage while critically assessing the relative strengths and weaknesses of these platforms or technologies. Tables containing the complete set of 4229 confirmed and highly probable human serum compounds, their concentrations, related literature references and links to their known disease associations are freely available at http://www.serummetabolome.ca. PMID:21359215

In-situ Generated Tribomaterial in Metal/Metal Contacts: current understanding and future implications for implants.

PubMed

Espallargas, N; Fischer, A; Muñoz, A Igual; Mischler, S; Wimmer, M A

2017-06-01

Artificial hip joints operate in aqueous biofluids that are highly reactive towards metallic surfaces. The reactivity at the metal interface is enhanced by mechanical interaction due to friction, which can change the near-surface structure of the metal and surface chemistry. There are now several reports in the literature about the in-situ generation of reaction films and tribo-metallurgical transformations on metal-on-metal hip joints. This paper summarizes current knowledge and provides a mechanistic interpretation of the surface chemical and metallurgical phenomena. Basic concepts of corrosion and wear are illustrated and used to interpret available literature on in-vitro and in-vivo studies of metal-on-metal hip joints. Based on this review, three forms of tribomaterial, characterized by different combinations of oxide films and organic layers, can be determined. It is shown that the generation of these tribofilms can be related to specific electrochemical and mechanical phenomena in the metal interface. It is suggested that the generation of this surface reaction layer constitutes a way to minimize (mechanical) wear of MoM hip implants.

Efficient Exploitation of Separation Space in Two-Dimensional Liquid Chromatography System for Comprehensive and Efficient Proteomic Analyses.

PubMed

Lee, Hangyeore; Mun, Dong-Gi; So, Jeong Eun; Bae, Jingi; Kim, Hokeun; Masselon, Christophe; Lee, Sang-Won

2016-12-06

Proteomics aims to achieve complete profiling of the protein content and protein modifications in cells, tissues, and biofluids and to quantitatively determine changes in their abundances. This information serves to elucidate cellular processes and signaling pathways and to identify candidate protein biomarkers and/or therapeutic targets. Analyses must therefore be both comprehensive and efficient. Here, we present a novel online two-dimensional reverse-phase/reverse-phase liquid chromatography separation platform, which is based on a newly developed online noncontiguous fractionating and concatenating device (NCFC fractionator). In bottom-up proteomics analyses of a complex proteome, this system provided significantly improved exploitation of the separation space of the two RPs, considerably increasing the numbers of peptides identified compared to a contiguous 2D-RP/RPLC method. The fully automated online 2D-NCFC-RP/RPLC system bypassed a number of labor-intensive manual processes required with the previously described offline 2D-NCFC RP/RPLC method, and thus, it offers minimal sample loss in a context of highly reproducible 2D-RP/RPLC experiments.

Characterization of a multi-module tunable EC-QCL system for mid-infrared biofluid spectroscopy for hospital use and personalized diabetes technology

NASA Astrophysics Data System (ADS)

Grafen, M.; Nalpantidis, K.; Ostendorf, A.; Ihrig, D.; Heise, H. M.

2016-03-01

Blood glucose monitoring systems are important point-of-care devices for the hospital and personalised diabetes technology. FTIR-spectrometers have been successfully employed for the development of continuous bed-side monitoring systems in combination with micro-dialysis. For implementation in miniaturised portable systems, external-cavity quantum cascade lasers (EC-QCL) are suited. An ultra-broadly tunable pulsed EC-QCL system, covering a spectral range from 1920 to 780 cm-1, has been characterised with regard to the spectral emission profiles and wavenumber scale accuracy. The measurement of glucose in aqueous solution is presented and problems with signal linearity using Peltier-cooled MCT-detectors are discussed. The use of larger optical sample pathlengths for attenuating the laser power in transmission measurements has recently been suggested and implemented, but implications for broad mid-infrared measurements have now been investigated. The utilization of discrete wavenumber variables as an alternative for sweep-tune measurements has also been studied and sparse multivariate calibration models intended for clinical chemistry applications are described for glucose and lactate.

In-situ Generated Tribomaterial in Metal/Metal Contacts: current understanding and future implications for implants

PubMed Central

Espallargas, N.; Fischer, A.; Muñoz, A. Igual; Mischler, S.; Wimmer, M.A.

2017-01-01

Artificial hip joints operate in aqueous biofluids that are highly reactive towards metallic surfaces. The reactivity at the metal interface is enhanced by mechanical interaction due to friction, which can change the near-surface structure of the metal and surface chemistry. There are now several reports in the literature about the in-situ generation of reaction films and tribo-metallurgical transformations on metal-on-metal hip joints. This paper summarizes current knowledge and provides a mechanistic interpretation of the surface chemical and metallurgical phenomena. Basic concepts of corrosion and wear are illustrated and used to interpret available literature on in-vitro and in-vivo studies of metal-on-metal hip joints. Based on this review, three forms of tribomaterial, characterized by different combinations of oxide films and organic layers, can be determined. It is shown that the generation of these tribofilms can be related to specific electrochemical and mechanical phenomena in the metal interface. It is suggested that the generation of this surface reaction layer constitutes a way to minimize (mechanical) wear of MoM hip implants. PMID:28808674

Saliva Liquid Biopsy for Point-of-Care Applications

PubMed Central

Aro, Katri; Wei, Fang; Wong, David T.; Tu, Michael

2017-01-01

Saliva is a non-invasive biofluid, which is easy to collect, transport, and store. Because of its accessibility and connection to systemic diseases, saliva is one of the best candidates for the advancement of point-of-care medicine, where individuals are able to easily monitor their health status by using portable convenient tools such as smartphones. There are a variety of scenarios with which saliva can be used: studies have been conducted on using saliva to measure stress hormones, enzyme levels, developmental disease biomarkers, and even cancer mutations. If validated biomarkers were combined with high-quality detection tools, saliva would open up a new frontier in high-quality healthcare, allowing physicians and patients to work together for real-time health monitoring and high-impact personalized preventative medicine. One of the most exciting emerging frontiers of saliva is liquid biopsy, which is a non-invasive means to assess the presence and characteristics of cancer in a patient. This article will review current basic knowledge of biomarkers, review their relation to different diseases and conditions, and explore liquid biopsy for point-of-care applications. PMID:28443278

A multi-channel clogging-resistant lab-on-a-chip cell counter and analyzer

NASA Astrophysics Data System (ADS)

Dai, Jie; Chiu, Yu-Jui; Lian, Ian; Wu, Tsung-Feng; Yang, Kecheng; Lo, Yu-Hwa

2016-02-01

Early signs of diseases can be revealed from cell detection in biofluids, such as detection of white blood cells (WBCs) in the peritoneal fluid for peritonitis. A lab-on-a-chip microfluidic device offers an attractive platform for such applications because of its small size, low cost, and ease of use provided the device can meet the performance requirements which many existing LoC devices fail to satisfy. We report an integrated microfluidic device capable of accurately counting low concentration of white blood cells in peritoneal fluid at 150 μl min-1 to offer an accurate (<3% error) and fast (~10 min/run) WBC count. Utilizing the self-regulating hydrodynamic properties and a unique architecture in the design, the device can achieve higher flow rate (500-1000 μl min-1), continuous running for over 5 h without clogging, as well as excellent signal quality for unambiguous WBC count and WBC classification for certain diseases. These properties make the device a promising candidate for point-of-care applications.

An Outlook on Biothermodynamics: Needs, Problems, and New Developments. I. Stability and Hydration of Proteins

NASA Astrophysics Data System (ADS)

Keller, Jürgen U.

2008-12-01

The application of concepts, principles, and methods of thermodynamics of equilibria and processes to bioengineering systems has led to a new and growing field: engineering biothermodynamics. This article, which is meant as the first in a series, gives an outline of basic aspects, changes, and actual examples in this field. After a few introductory remarks, the basic concepts and laws of thermodynamics extended to systems with internal variables, which serve as models for biofluids and other biosystems, are given. The method of thermodynamics is then applied to the problem of thermal stability of aqueous protein solutions, especially to that of myoglobin solutions. After this, the phenomenon of hydration of proteins by adsorption and intrusion of water molecules is considered. Several other phenomena like the adsorption of proteins on solid surfaces or cell membranes and their temperature and pressure-related behavior represented by an equation of state, or the thermodynamics of bacterial solutions including chemical reactions like wine fermentation, etc., will be presented in Parts II and III of this article.

Detection of circulatory microRNAs in prostate cancer.

PubMed

Srivastava, Anvesha; Goldberger, Helle; Afzal, Zainab; Suy, Simeng; Collins, Sean P; Kumar, Deepak

2015-01-01

Prostate cancer (PCa) is one of the most common cancer worldwide and accounts for 14.4 % of all new cancer cases. The clinical outcome and management of PCa can be significantly improved by use of biomarker assays for early detection, prognosis and also for prediction and monitoring of treatment response. MiRNAs are short, endogenous, single-stranded RNA molecules that play important role in regulation of gene expression and can modulate a number of cellular processes. Discovery of miRNAs in circulation has not only facilitated understanding their role in various diseases but also paved new avenues for biomarker discovery due to their ease of access and stability. The fact that a minimally invasive test based on miRNAs profiles can distinguish the presence or absence of disease illustrates immense potential of these molecules as predictive biomarkers.In this chapter, we have summarized the presumed mechanisms of miRNA release into the circulation and systematically summarized the studies of circulatory miRNAs in PCa. Also, we have mainly focused on the methodology of identification of circulatory miRNAs from biofluids.

High definition infrared chemical imaging of colorectal tissue using a Spero QCL microscope.

PubMed

Bird, B; Rowlette, J

2017-04-10

Mid-infrared microscopy has become a key technique in the field of biomedical science and spectroscopy. This label-free, non-destructive technique permits the visualisation of a wide range of intrinsic biochemical markers in tissues, cells and biofluids by detection of the vibrational modes of the constituent molecules. Together, infrared microscopy and chemometrics is a widely accepted method that can distinguish healthy and diseased states with high accuracy. However, despite the exponential growth of the field and its research world-wide, several barriers currently exist for its full translation into the clinical sphere, namely sample throughput and data management. The advent and incorporation of quantum cascade lasers (QCLs) into infrared microscopes could help propel the field over these remaining hurdles. Such systems offer several advantages over their FT-IR counterparts, a simpler instrument architecture, improved photon flux, use of room temperature camera systems, and the flexibility of a tunable illumination source. In this current study we explore the use of a QCL infrared microscope to produce high definition, high throughput chemical images useful for the screening of biopsied colorectal tissue.

Solution of the Inverse Problem for Thin Film Patterning by Electrohydrodynamic Forces

NASA Astrophysics Data System (ADS)

Zhou, Chengzhe; Troian, Sandra

2017-11-01

Micro- and nanopatterning techniques for applications ranging from optoelectronics to biofluidics have multiplied in number over the past decade to include adaptations of mature technologies as well as novel lithographic techniques based on periodic spatial modulation of surface stresses. We focus here on one such technique which relies on shape changes in nanofilms responding to a patterned counter-electrode. The interaction of a patterned electric field with the polarization charges at the liquid interface causes a patterned electrostatic pressure counterbalanced by capillary pressure which leads to 3D protrusions whose shape and evolution can be terminated as needed. All studies to date, however, have investigated the evolution of the liquid film in response to a preset counter-electrode pattern. In this talk, we present solution of the inverse problem for the thin film equation governing the electrohydrodynamic response by treating the system as a transient control problem. Optimality conditions are derived and an efficient corresponding solution algorithm is presented. We demonstrate such implementation of film control to achieve periodic, free surface shapes ranging from simple circular cap arrays to more complex square and sawtooth patterns.

A Carbon Nanotube Reporter of miRNA Hybridization Events In Vivo.

PubMed

Harvey, Jackson D; Jena, Prakrit V; Baker, Hanan A; Zerze, Gül H; Williams, Ryan M; Galassi, Thomas V; Roxbury, Daniel; Mittal, Jeetain; Heller, Daniel A

2017-01-01

MicroRNAs and other small oligonucleotides in biofluids are promising disease biomarkers, yet conventional assays require complex processing steps that are unsuitable for point-of-care testing or for implantable or wearable sensors. Single-walled carbon nanotubes are an ideal material for implantable sensors, owing to their emission in the near-infrared spectral region, photostability and exquisite sensitivity. Here, we report an engineered carbon-nanotube-based sensor capable of real-time optical quantification of hybridization events of microRNA and other oligonucleotides. The mechanism of the sensor arises from competitive effects between displacement of both oligonucleotide charge groups and water from the nanotube surface, which result in a solvatochromism-like response. The sensor, which allows for detection via single-molecule sensor elements and for multiplexing by using multiple nanotube chiralities, can monitor toehold-based strand-displacement events, which reverse the sensor response and regenerate the sensor complex. We also show that the sensor functions in whole urine and serum, and can non-invasively measure DNA and microRNA after implantation in live mice.

Wettability and friction of water on a MoS{sub 2} nanosheet

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

Luan, Binquan, E-mail: bluan@us.ibm.com, E-mail: ruhongz@us.ibm.com; Zhou, Ruhong, E-mail: bluan@us.ibm.com, E-mail: ruhongz@us.ibm.com

2016-03-28

The molybdenum disulfide (MoS{sub 2}) nanosheet is a promising two-dimensional (2D) material and has recently been used in biological sensing. While the electronic structure of 2D MoS{sub 2} sheet has been actively studied, the role of its atomic structure and thus the interfacial interactions with bio-fluids are still elusive. Using Molecular dynamics simulations, we developed MoS{sub 2} force field parameters to reproduce the experimentally determined water contact angle of the MoS{sub 2} nanosheet and then predicted the slip-length of water that has not been measured in experiment yet. Simulation results suggest that the MoS{sub 2} nanosheet is a hydrophobic andmore » low-friction surface, despite its seemingly significant charges of surface atoms and relatively strong strength of van der Waals potentials. We expect that the developed force fields for depicting surface atoms of MoS{sub 2} will facilitate future research in understanding biomolecule-MoS{sub 2} interactions in MoS{sub 2}-based biosensors.« less

The epigenetics of prostate cancer diagnosis and prognosis: update on clinical applications.

PubMed

Blute, Michael L; Damaschke, Nathan A; Jarrard, David F

2015-01-01

There is a major deficit in our ability to detect and predict the clinical behavior of prostate cancer (PCa). Epigenetic changes are associated with PCa development and progression. This review will focus on recent results in the clinical application of diagnostic and prognostic epigenetic markers. The development of high throughput technology has seen an enormous increase in the discovery of new markers that encompass epigenetic changes including those in DNA methylation and histone modifications. Application of these findings to urine and other biofluids, but also cancer and noncancerous prostate tissue, has resulted in new biomarkers. There has been a recent commercial development of a DNA methylation-based assay for identifying PCa risk from normal biopsy tissue. Other biomarkers are currently in the validation phase and encompass combinations of multiple genes. Epigenetic changes improve the specificity and sensitivity of PCa diagnosis and have the potential to help determine clinical prognosis. Additional studies will not only provide new and better biomarker candidates, but also have the potential to inform new therapeutic strategies given the reversibility of these processes.

A two-magnet strategy for improved mixing and capture from biofluids

PubMed Central

Doyle, Andrew B.; Haselton, Frederick R.

2016-01-01

Magnetic beads are a popular method for concentrating biomolecules from solution and have been more recently used in multistep pre-arrayed microfluidic cartridges. Typical processing strategies rely on a single magnet, resulting in a tight cluster of beads and requiring long incubation times to achieve high capture efficiencies, especially in highly viscous patient samples. This report describes a two-magnet strategy to improve the interaction of the bead surface with the surrounding fluid inside of a pre-arrayed, self-contained assay-in-a-tube. In the two-magnet system, target biomarker capture occurs at a rate three times faster than the single-magnet system. In clinically relevant biomatrices, we find a 2.5-fold improvement in biomarker capture at lower sample viscosities with the two-magnet system. In addition, we observe a 20% increase in the amount of protein captured at high viscosity for the two-magnet configuration relative to the single magnet approach. The two-magnet approach offers a means to achieve higher biomolecule extraction yields and shorter assay times in magnetic capture assays and in self-contained processor designs. PMID:27158286

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling.

PubMed

Suarez-Diez, Maria; Adam, Jonathan; Adamski, Jerzy; Chasapi, Styliani A; Luchinat, Claudio; Peters, Annette; Prehn, Cornelia; Santucci, Claudio; Spyridonidis, Alexandros; Spyroulias, Georgios A; Tenori, Leonardo; Wang-Sattler, Rui; Saccenti, Edoardo

2017-07-07

Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA-MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids.

Plasma and Serum Metabolite Association Networks: Comparability within and between Studies Using NMR and MS Profiling

PubMed Central

2017-01-01

Blood is one of the most used biofluids in metabolomics studies, and the serum and plasma fractions are routinely used as a proxy for blood itself. Here we investigated the association networks of an array of 29 metabolites identified and quantified via NMR in the plasma and serum samples of two cohorts of ∼1000 healthy blood donors each. A second study of 377 individuals was used to extract plasma and serum samples from the same individual on which a set of 122 metabolites were detected and quantified using FIA–MS/MS. Four different inference algorithms (ARANCE, CLR, CORR, and PCLRC) were used to obtain consensus networks. The plasma and serum networks obtained from different studies showed different topological properties with the serum network being more connected than the plasma network. On a global level, metabolite association networks from plasma and serum fractions obtained from the same blood sample of healthy people show similar topologies, and at a local level, some differences arise like in the case of amino acids. PMID:28517934

Saliva exosomes from pancreatic tumor-bearing mice modulate NK cell phenotype and antitumor cytotoxicity.

PubMed

Katsiougiannis, Stergios; Chia, David; Kim, Yong; Singh, Ram P; Wong, David T W

2017-03-01

Tumor exosomes are emerging as antitumor immunity regulators; however, their effects on secondary exosome secretion by distal organs have not been explored. We have previously demonstrated that suppression of exosomes at the distal tumor site of pancreatic ductal adenocarcinoma (PDAC) ablated the development of salivary biomarker profile. Here, we explore the function of salivary exosomes from tumor-bearing mice in immune surveillance. We provide evidence that salivary exosomes from mice with PDAC exhibit a suppressive effect that results in reduced tumor-killing capacity by NK cells. Salivary exosomes from mice with PDAC where pancreatic tumors were engineered to suppress exosome biogenesis failed to suppress NK cell cytotoxic potential against tumor cells, as opposed to salivary exosomes from mice with PDAC with normal tumor exosome biogenesis. These results reveal an important and previously unknown mechanism of antitumor immune regulation and provide new insights into our understanding of the alterations of this biofluid during tumor development.-Katsiougiannis, S., Chia, D., Kim, Y., Singh, R. P., Wong, D. T. W. Saliva exosomes from pancreatic tumor-bearing mice modulate NK cell phenotype and antitumor cytotoxicity. © FASEB.

Metabolic phenotyping in the mouse model of urinary tract infection shows that 3-hydroxybutyrate in plasma is associated with infection

PubMed Central

Xie, Yumin; Yang, Wu; Wang, Yaoyao; Xiang, Wenying; Hylands, Peter J.

2017-01-01

Urinary tract infection is one of the most common bacterial infections worldwide. Current diagnosis of urinary tract infection chiefly relies on its clinical presentation, urine dipstick tests and urine culture. Small molecules found in bio-fluids related with both infection and recovery would facilitate diagnosis and management of UTI. Mass spectrometry-based fingerprinting of plasma and urine at 3 time points, pre-infection (t = -24h), infection (t = 24h) and post 3-day treatment (t = 112h), were acquired in the following four groups: mice which were healthy, infected but not treated, infected and treated with ciprofloxacin, and infected and treated with Relinqing® granules (n = 6 per group). A metabolomics workflow including multivariate analysis and ROC regression was employed to select metabolic features that correlated with UTI and its treatment. Circa 4,000 molecular features were acquired for each sample. The small acid 3-hydroxybutyrate in plasma was found to be differentiated for urinary tract infection, with an area under the curve = 0.97 (95% confidence interval: 0.93–1.00, accuracy = 0.91, sensitivity = 0.92 and specificity = 0.91). The level of 3-hydroxybutyrate in plasma was depleted after infection with a fold change of -22 (q < 0.0001). Correlation between plasma 3-hydroxybutyrate and urine bacterial number in all groups and time points was r = -0.753 (p < 0.0001). The findings show that 3-hydroxybutyrate is depleted in blood and strongly associated with UTI at both infection and post-treatment stage in a UTI mouse model. Further work is envisaged to assess the clinical potential of blood tests to assist with UTI management. PMID:29036204

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles.

PubMed

Sugimoto, Masahiro; Wong, David T; Hirayama, Akiyoshi; Soga, Tomoyoshi; Tomita, Masaru

2010-03-01

Saliva is a readily accessible and informative biofluid, making it ideal for the early detection of a wide range of diseases including cardiovascular, renal, and autoimmune diseases, viral and bacterial infections and, importantly, cancers. Saliva-based diagnostics, particularly those based on metabolomics technology, are emerging and offer a promising clinical strategy, characterizing the association between salivary analytes and a particular disease. Here, we conducted a comprehensive metabolite analysis of saliva samples obtained from 215 individuals (69 oral, 18 pancreatic and 30 breast cancer patients, 11 periodontal disease patients and 87 healthy controls) using capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS). We identified 57 principal metabolites that can be used to accurately predict the probability of being affected by each individual disease. Although small but significant correlations were found between the known patient characteristics and the quantified metabolites, the profiles manifested relatively higher concentrations of most of the metabolites detected in all three cancers in comparison with those in people with periodontal disease and control subjects. This suggests that cancer-specific signatures are embedded in saliva metabolites. Multiple logistic regression models yielded high area under the receiver-operating characteristic curves (AUCs) to discriminate healthy controls from each disease. The AUCs were 0.865 for oral cancer, 0.973 for breast cancer, 0.993 for pancreatic cancer, and 0.969 for periodontal diseases. The accuracy of the models was also high, with cross-validation AUCs of 0.810, 0.881, 0.994, and 0.954, respectively. Quantitative information for these 57 metabolites and their combinations enable us to predict disease susceptibility. These metabolites are promising biomarkers for medical screening. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-009-0178-y) contains supplementary material, which is available to authorized users.

MALDI Mass Spectral Imaging of Bile Acids Observed as Deprotonated Molecules and Proton-Bound Dimers from Mouse Liver Sections

NASA Astrophysics Data System (ADS)

Rzagalinski, Ignacy; Hainz, Nadine; Meier, Carola; Tschernig, Thomas; Volmer, Dietrich A.

2018-02-01

Bile acids (BAs) play two vital roles in living organisms, as they are involved in (1) the secretion of cholesterol from liver, and (2) the lipid digestion/absorption in the intestine. Abnormal bile acid synthesis or secretion can lead to severe liver disorders. Even though there is extensive literature on the mass spectrometric determination of BAs in biofluids and tissue homogenates, there are no reports on the spatial distribution in the biliary network of the liver. Here, we demonstrate the application of high mass resolution/mass accuracy matrix-assisted laser desorption/ionization (MALDI)-Fourier-transform ion cyclotron resonance (FTICR) to MS imaging (MSI) of BAs at high spatial resolutions (pixel size, 25 μm). The results show chemical heterogeneity of the mouse liver sections with a number of branching biliary and blood ducts. In addition to ion signals from deprotonation of the BA molecules, MALDI-MSI generated several further intense signals at larger m/z for the BAs. These signals were spatially co-localized with the deprotonated molecules and easily misinterpreted as additional products of BA biotransformations. In-depth analysis of accurate mass shifts and additional electrospray ionization and MALDI-FTICR experiments, however, confirmed them as proton-bound dimers. Interestingly, dimers of bile acids, but also unusual mixed dimers of different taurine-conjugated bile acids and free taurine, were identified. Since formation of these complexes will negatively influence signal intensities of the desired [M - H]- ions and significantly complicate mass spectral interpretations, two simple broadband techniques were proposed for non-selective dissociation of dimers that lead to increased signals for the deprotonated BAs. [Figure not available: see fulltext.

Analytical characterization of human milk oligosaccharides - potential applications in pharmaceutical analysis.

PubMed

Grabarics, Márkó; Csernák, Orsolya; Balogh, Réka; Béni, Szabolcs

2017-11-30

Human breast milk is the gold standard for infant feeding and the best possible nourishment a new-born could have. Breastfeeding is the natural way to provide optimal nutritional, immunological and emotional nurturing for the healthy growth and development of infants. Human milk is a complex and dynamic biofluid comprised of many hundreds to thousands of distinct bioactive structures, among which one of the most abundant substances are the non-conjugated complex carbohydrates referred to as human milk oligosaccharides (HMOs). Due to their structural diversity and abundance, HMOs possess many beneficial biological functions. In order to understand human milk composition and HMO functions, state-of-the-art glycomic methods are inevitable. The industrial, large scale chemoenzymatic production of the most abundant HMOs became a reality in the last years and it evokes the need for straightforward and genuine analytical procedures to monitor the synthetic process and the quality of the products. It is obvious, that HMOs represent the next breakthrough in infant nutrition, as the addition of HMOs (such as 2'-fucosyllactose or lacto-N-neotetraose) to infant- and follow-on formulas, processed cereal-based food and baby foods for infants and young children etc. will revolutionize this field. This review highlights the potential applications of HMOs in the (bio)pharmaceutical industry, also summarizes the analytical methods available for the characterization of HMOs. An overview of the structure and function of HMOs along with their determination methods in complex matrices are provided. Various separation methods including liquid- and gas chromatography and capillary electrophoresis for the characterization and novel approaches for the quantitation of HMOs are discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

A Community-Based IoT Personalized Wireless Healthcare Solution Trial.

PubMed

Catherwood, Philip A; Steele, David; Little, Mike; Mccomb, Stephen; Mclaughlin, James

2018-01-01

This paper presents an advanced Internet of Things point-of-care bio-fluid analyzer; a LoRa/Bluetooth-enabled electronic reader for biomedical strip-based diagnostics system for personalized monitoring. We undertake test simulations (technology trial without patient subjects) to demonstrate potential of long-range analysis, using a disposable test 'key' and companion Android app to form a diagnostic platform suitable for remote point-of-care screening for urinary tract infection (UTI). The 868 MHz LoRaWAN-enabled personalized monitor demonstrated sound potential with UTI test results being correctly diagnosed and transmitted to a remote secure cloud server in every case. Tests ranged over distances of 1.1-6.0 Km with radio path losses from 119-141 dB. All tests conducted were correctly and robustly received at the base station and relayed to the secure server for inspection. The UTI test strips were visually inspected for correct diagnosis based on color change and verified as 100% accurate. Results from testing across a number of regions indicate that such an Internet of Things medical solution is a robust and simple way to deliver next generation community-based smart diagnostics and disease management to best benefit patients and clinical staff alike. This significant step can be applied to any type of home or region, particularly those lacking suitable mobile signals, broadband connections, or even landlines. It brings subscription-free long-range bio-telemetry to healthcare providers and offers savings on regular clinician home visits or frequent clinic visits by the chronically ill. This paper highlights practical hurdles in establishing an Internet of Medical Things network, assisting informed deployment of similar future systems.

A Community-Based IoT Personalized Wireless Healthcare Solution Trial

PubMed Central

Steele, David; Little, Mike; Mccomb, Stephen; Mclaughlin, James

2018-01-01

This paper presents an advanced Internet of Things point-of-care bio-fluid analyzer; a LoRa/Bluetooth-enabled electronic reader for biomedical strip-based diagnostics system for personalized monitoring. We undertake test simulations (technology trial without patient subjects) to demonstrate potential of long-range analysis, using a disposable test ‘key’ and companion Android app to form a diagnostic platform suitable for remote point-of-care screening for urinary tract infection (UTI). The 868 MHz LoRaWAN-enabled personalized monitor demonstrated sound potential with UTI test results being correctly diagnosed and transmitted to a remote secure cloud server in every case. Tests ranged over distances of 1.1–6.0 Km with radio path losses from 119–141 dB. All tests conducted were correctly and robustly received at the base station and relayed to the secure server for inspection. The UTI test strips were visually inspected for correct diagnosis based on color change and verified as 100% accurate. Results from testing across a number of regions indicate that such an Internet of Things medical solution is a robust and simple way to deliver next generation community-based smart diagnostics and disease management to best benefit patients and clinical staff alike. This significant step can be applied to any type of home or region, particularly those lacking suitable mobile signals, broadband connections, or even landlines. It brings subscription-free long-range bio-telemetry to healthcare providers and offers savings on regular clinician home visits or frequent clinic visits by the chronically ill. This paper highlights practical hurdles in establishing an Internet of Medical Things network, assisting informed deployment of similar future systems. PMID:29888145

Investigation of pumping mechanism for non-Newtonian blood flow with AC electrothermal forces in a microchannel by hybrid boundary element method and immersed boundary-lattice Boltzmann method.

PubMed

Ren, Qinlong

2018-02-10

Efficient pumping of blood flow in a microfluidic device is essential for rapid detection of bacterial bloodstream infections (BSI) using alternating current (AC) electrokinetics. Compared with AC electro-osmosis (ACEO) phenomenon, the advantage of AC electrothermal (ACET) mechanism is its capability of pumping biofluids with high electrical conductivities at a relatively high AC voltage frequency. In the current work, the microfluidic pumping of non-Newtonian blood flow using ACET forces is investigated in detail by modeling its multi-physics process with hybrid boundary element method (BEM) and immersed boundary-lattice Boltzmann method (IB-LBM). The Carreau-Yasuda model is used to simulate the realistic rheological behavior of blood flow. The ACET pumping efficiency of blood flow is studied in terms of different AC voltage magnitudes and frequencies, thermal boundary conditions of electrodes, electrode configurations, channel height, and the channel length per electrode pair. Besides, the effect of rheological behavior on the blood flow velocity is theoretically analyzed by comparing with the Newtonian fluid flow using scaling law analysis under the same physical conditions. The results indicate that the rheological behavior of blood flow and its frequency-dependent dielectric property make the pumping phenomenon of blood flow different from that of the common Newtonian aqueous solutions. It is also demonstrated that using a thermally insulated electrode could enhance the pumping efficiency dramatically. Besides, the results conclude that increasing the AC voltage magnitude is a more economical pumping approach than adding the number of electrodes with the same energy consumption when the Joule heating effect is acceptable. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Influence of the Surface Functional Group Density on the Carbon-Nanotube-Induced α-Chymotrypsin Structure and Activity Alterations.

PubMed

Zhao, Xingchen; Hao, Fang; Lu, Dawei; Liu, Wei; Zhou, Qunfang; Jiang, Guibin

2015-08-26

Because of the special properties of carbon nanotubes (CNTs), their applications have been introduced to many fields. The biosafety of these emerging materials is of high concern concomitantly. Because CNTs may initially bind with proteins in biofluids before they exert biological effects, it is of great importance to understand how the target proteins interact with these exogenous nanomaterials. Here we investigated the interaction between α-chymotrypsin (α-ChT) and carboxylized multiwalled CNTs in a simulated biophysical environment utilizing the techniques of fluorescence, UV-vis, circular dichroism spectroscopy, ζ potential, atomic force microscopy, and bicinchoninic acid analysis. It was demonstrated that CNTs interacted with α-ChT through electrostatic forces, causing a decrement in the α-helix and an increment in the β-sheet content of the protein. The protein fluorescence was quenched in a static mode. The increase in the surface modification density of CNTs enhanced the protein absorption and decreased the enzymatic activity correspondingly. α-ChT activity inhibition induced by CNTs with low surface modification density exhibited noncompetitive characteristics; however, a competitive feature was observed when CNTs with high surface modification density interacted with the protein. An increase of the ionic strength in the reaction buffer may help to reduce the interaction between CNTs and α-ChT because the high ionic strength may favor the release of the protein from binding on a CNT surface modified with functional groups. Accordingly, the functionalization density on the CNT surface plays an important role in the regulation of their biological effects and is worthy of concern when new modified CNTs are developed.

Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species.

PubMed

Ferrero, Giulio; Cordero, Francesca; Tarallo, Sonia; Arigoni, Maddalena; Riccardo, Federica; Gallo, Gaetano; Ronco, Guglielmo; Allasia, Marco; Kulkarni, Neha; Matullo, Giuseppe; Vineis, Paolo; Calogero, Raffaele A; Pardini, Barbara; Naccarati, Alessio

2018-01-09

The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans. By analysing small RNA-sequencing data from 243 samples, we have identified and compared the most abundantly and uniformly expressed miRNAs and non-miRNA species of comparable size with the library preparation in four different specimens (plasma exosomes, stool, urine, and cervical scrapes). Eleven miRNAs were commonly detected among all different specimens while 231 miRNAs were globally unique across them. Classification analysis using these miRNAs provided an accuracy of 99.6% to recognize the sample types. piRNAs and tRNAs were the most represented non-miRNA small RNAs detected in all specimen types that were analysed, particularly in urine samples. With the present data, the most uniformly expressed small RNAs in each sample type were also identified. A signature of small RNAs for each specimen could represent a reference gene set in validation studies by RT-qPCR. Overall, the data reported hereby provide an insight of the constitution of the human miRNome and of other small non-coding RNAs in various specimens of healthy individuals.

Comparative Proteomic Analysis of Whole-Gut Lavage Fluid and Pancreatic Juice Reveals a Less Invasive Method of Sampling Pancreatic Secretions

PubMed Central

Rocker, Jana M; Tan, Marcus C; Thompson, Lee W; Contreras, Carlo M; DiPalma, Jack A; Pannell, Lewis K

2016-01-01

OBJECTIVES: There are currently no reliable, non-invasive screening tests for pancreatic ductal adenocarcinoma. The fluid secreted from the pancreatic ductal system (“pancreatic juice”) has been well-studied as a potential source of cancer biomarkers. However, it is invasive to collect. We recently observed that the proteomic profile of intestinal effluent from the bowel in response to administration of an oral bowel preparation solution (also known as whole-gut lavage fluid, WGLF) contains large amounts of pancreas-derived proteins. We therefore hypothesized that the proteomic profile is similar to that of pancreatic juice. In this study, we compared the proteomic profiles of 77 patients undergoing routine colonoscopy with the profiles of 19 samples of pure pancreatic juice collected during surgery. METHODS: WGLF was collected from patients undergoing routine colonoscopy, and pancreatic juice was collected from patients undergoing pancreatic surgery. Protein was isolated from both samples using an optimized method and analyzed by LC-MS/MS. Identified proteins were compared between samples and groups to determine similarity of the two fluids. We then compared our results with literature reports of pancreatic juice-based studies to determine similarity. RESULTS: We found 104 proteins in our pancreatic juice samples, of which 90% were also found in our WGLF samples. The majority (67%) of the total proteins found in the WGLF were common to pancreatic juice, with intestine-specific proteins making up a smaller proportion. CONCLUSIONS: WGLF and pancreatic juice appear to have similar proteomic profiles. This supports the notion that WGLF is a non-invasive, surrogate bio-fluid for pancreatic juice. Further studies are required to further elucidate its role in the diagnosis of pancreatic cancer. PMID:27228405

Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine.

PubMed

Zhang, Xi

2017-02-01

Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Circulating microRNAs as Potential Biomarkers of Infectious Disease

PubMed Central

Correia, Carolina N.; Nalpas, Nicolas C.; McLoughlin, Kirsten E.; Browne, John A.; Gordon, Stephen V.; MacHugh, David E.; Shaughnessy, Ronan G.

2017-01-01

microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease. PMID:28261201

Wetting and spreading behaviors of impinging microdroplets on textured surfaces

NASA Astrophysics Data System (ADS)

Kwon, Dae Hee; Lee, Sang Joon; CenterBiofluid and Biomimic Reseach Team

2012-11-01

Textured surfaces having an array of microscale pillars have been receiving large attention because of their potential uses for robust superhydrophobic and superoleophobic surfaces. In many practical applications, the textured surfaces usually accompany impinging small-scale droplets. To better understand the impinging phenomena on the textured surfaces, the wetting and spreading behaviors of water microdroplets are investigated experimentally. Microdroplets with diameter less than 50 μm are ejected from a piezoelectric printhead with varying Weber number. The final wetting state of an impinging droplet can be estimated by comparing the wetting pressures of the droplet and the capillary pressure of the textured surface. The wetting behaviors obtained experimentally are well agreed with the estimated results. In addition, the transition from bouncing to non-bouncing behaviors in the partially penetrated wetting state is observed. This transition implies the possibility of withdrawal of the penetrated liquid from the inter-pillar space. The maximum spreading factors (ratio of the maximum spreading diameter to the initial diameter) of the impinging droplets have close correlation with the texture area fraction of the surfaces. This work was supported by Creative Research Initiatives (Diagnosis of Biofluid Flow Phenomena and Biomimic Research) of MEST/KOSEF.

Development of a Targeted Urine Proteome Assay for kidney diseases.

PubMed

Cantley, Lloyd G; Colangelo, Christopher M; Stone, Kathryn L; Chung, Lisa; Belcher, Justin; Abbott, Thomas; Cantley, Jennifer L; Williams, Kenneth R; Parikh, Chirag R

2016-01-01

Since human urine is the most readily available biofluid whose proteome changes in response to disease, it is a logical sample for identifying protein biomarkers for kidney diseases. Potential biomarkers were identified by using a multiproteomics workflow to compare urine proteomes of kidney transplant patients with immediate and delayed graft function. Differentially expressed proteins were identified, and corresponding stable isotope labeled internal peptide standards were synthesized for scheduled MRM. The Targeted Urine Proteome Assay (TUPA) was then developed by identifying those peptides for which there were at least two transitions for which interference in a urine matrix across 156 MRM runs was <30%. This resulted in an assay that monitors 224 peptides from 167 quantifiable proteins. TUPA opens the way for using a robust mass spectrometric technology, MRM, for quantifying and validating biomarkers from among 167 urinary proteins. This approach, while developed using differentially expressed urinary proteins from patients with delayed versus immediate graft function after kidney transplant, can be expanded to include differentially expressed urinary proteins in multiple kidney diseases. Thus, TUPA could provide a single assay to help diagnose, prognose, and manage many kidney diseases. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Extracellular vesicles for personalized therapy decision support in advanced metastatic cancers and its potential impact for prostate cancer.

PubMed

Soekmadji, Carolina; Corcoran, Niall M; Oleinikova, Irina; Jovanovic, Lidija; Ramm, Grant A; Nelson, Colleen C; Jenster, Guido; Russell, Pamela J

2017-10-01

The use of circulating tumor cells (CTCs) and circulating extracellular vesicles (EVs), such as exosomes, as liquid biopsy-derived biomarkers for cancers have been investigated. CTC enumeration using the CellSearch based platform provides an accurate insight on overall survival where higher CTC counts indicate poor prognosis for patients with advanced metastatic cancer. EVs provide information based on their lipid, protein, and nucleic acid content and can be isolated from biofluids and analyzed from a relatively small volume, providing a routine and non-invasive modality to monitor disease progression. Our pilot experiment by assessing the level of two subpopulations of small EVs, the CD9 positive and CD63 positive EVs, showed that the CD9 positive EV level is higher in plasma from patients with advanced metastatic prostate cancer with detectable CTCs. These data show the potential utility of a particular EV subpopulation to serve as biomarkers for advanced metastatic prostate cancer. EVs can potentially be utilized as biomarkers to provide accurate genotypic and phenotypic information for advanced prostate cancer, where new strategies to design a more personalized therapy is currently the focus of considerable investigation. © 2017 Wiley Periodicals, Inc.

Suspected non-AD pathology in mild cognitive impairment.

PubMed

Wisse, Laura E M; Butala, Nirali; Das, Sandhitsu R; Davatzikos, Christos; Dickerson, Bradford C; Vaishnavi, Sanjeev N; Yushkevich, Paul A; Wolk, David A

2015-12-01

We aim to better characterize mild cognitive impairment (MCI) patients with suspected non-Alzheimer's disease (AD) pathology (SNAP) based on their longitudinal outcome, cognition, biofluid, and neuroimaging profile. MCI participants (n = 361) from ADNI-GO/2 were designated "amyloid positive" with abnormal amyloid-beta 42 levels (AMY+) and "neurodegeneration positive" (NEU+) with abnormal hippocampal volume or hypometabolism using fluorodeoxyglucose-positron emission tomography. SNAP was compared with the other MCI groups and with AMY- controls. AMY-NEU+/SNAP, 16.6%, were older than the NEU- groups but not AMY- controls. They had a lower conversion rate to AD after 24 months than AMY+NEU+ MCI participants. SNAP-MCI participants had similar amyloid-beta 42 levels, florbetapir and tau levels, but larger white matter hyperintensity volumes than AMY- controls and AMY-NEU- MCI participants. SNAP participants performed worse on all memory domains and on other cognitive domains, than AMY-NEU- participants but less so than AMY+NEU+ participants. Subthreshold levels of cerebral amyloidosis are unlikely to play a role in SNAP-MCI, but pathologies involving the hippocampus and cerebrovascular disease may underlie the neurodegeneration and cognitive impairment in this group. Copyright © 2015 Elsevier Inc. All rights reserved.

Cylinders vs. Spheres: Biofluid Shear Thinning in Driven Nanoparticle Transport

PubMed Central

Cribb, Jeremy A.; Meehan, Timothy D.; Shah, Sheel M.; Skinner, Kwan; Superfine, Richard

2011-01-01

Increasingly, the research community applies magnetophoresis to micro and nanoscale particles for drug delivery applications and the nanoscale rheological characterization of complex biological materials. Of particular interest is the design and transport of these magnetic particles through entangled polymeric fluids commonly found in biological systems. We report the magnetophoretic transport of spherical and rod-shaped particles through viscoelastic, entangled solutions using lambda-phage DNA (λ-DNA) as a model system. In order to understand and predict the observed phenomena, we fully characterize three fundamental components: the magnetic field and field gradient, the shape and magnetic properties of the probe particles, and the macroscopic rheology of the solution. Particle velocities obtained in Newtonian solutions correspond to macroscale rheology, with forces calculated via Stokes Law. In λ-DNA solutions, nanorod velocities are 100 times larger than predicted by measured zero-shear viscosity. These results are consistent with particles experiencing transport through a shear thinning fluid, indicating magnetically driven transport in shear thinning may be especially effective and favor narrow diameter, high aspect ratio particles. A complete framework for designing single-particle magnetic-based delivery systems results when we combine a quantified magnetic system with qualified particles embedded in a characterized viscoelastic medium. PMID:20571853

Limits of linearity and detection for some drugs of abuse.

PubMed

Needleman, S B; Romberg, R W

1990-01-01

The limits of linearity (LOL) and detection (LOD) are important factors in establishing the reliability of an analytical procedure for accurately assaying drug concentrations in urine specimens. Multiple analyses of analyte over an extended range of concentrations provide a measure of the ability of the analytical procedure to correctly identify known quantities of drug in a biofluid matrix. Each of the seven drugs of abuse gives linear analytical responses from concentrations at or near their LOD to concentrations several-fold higher than those generally encountered in the drug screening laboratory. The upper LOL exceeds the Department of Navy (DON) cutoff values by factors of approximately 2 to 160. The LOD varies from 0.4 to 5.0% of the DON cutoff value for each drug. The limit of quantitation (LOQ) is calculated as the LOD + 7 SD. The range for LOL is greater for drugs analyzed with deuterated internal standards compared with those using conventional internal standards. For THC acid, cocaine, PCP, and morphine, LOLs are 8 to 160-fold greater than the defined cutoff concentrations. For the other drugs, the LOL's are only 2 to 4-fold greater than the defined cutoff concentrations.

Paper pump for passive and programmable transport

PubMed Central

Wang, Xiao; Hagen, Joshua A.; Papautsky, Ian

2013-01-01

In microfluidic systems, a pump for fluid-driving is often necessary. To keep the size of microfluidic systems small, a pump that is small in size, light-weight and needs no external power source is advantageous. In this work, we present a passive, simple, ultra-low-cost, and easily controlled pumping method based on capillary action of paper that pumps fluid through conventional polymer-based microfluidic channels with steady flow rate. By using inexpensive cutting tools, paper can be shaped and placed at the outlet port of a conventional microfluidic channel, providing a wide range of pumping rates. A theoretical model was developed to describe the pumping mechanism and aid in the design of paper pumps. As we show, paper pumps can provide steady flow rates from 0.3 μl/s to 1.7 μl/s and can be cascaded to achieve programmable flow-rate tuning during the pumping process. We also successfully demonstrate transport of the most common biofluids (urine, serum, and blood). With these capabilities, the paper pump has the potential to become a powerful fluid-driving approach that will benefit the fielding of microfluidic systems for point-of-care applications. PMID:24403999

Biomonitoring of perfluorinated compounds in a drop of blood.

PubMed

Mao, Pan; Wang, Daojing

2015-06-02

Biomonitoring of pollutants and their metabolites and derivatives using biofluids provides new opportunities for spatiotemporal assessment of human risks to environmental exposures. Perfluorinated compounds (PFCs) have been used widely in industry and pose significant environmental concerns due to their stability and bioaccumulation in humans and animals. However, current methods for extraction and measurement of PFCs require relatively large volumes (over one hundred microliters) of blood samples, and therefore, are not suitable for frequent blood sampling and longitudinal biomonitoring of PFCs. We have developed a new microassay, enabled by our silicon microfluidic chip platform, for analyzing PFCs in small volumes (less than five microliters) of blood. Our assay integrates on-chip solid-phase extraction (SPE) with online nanoflow liquid chromatography-electrospray ionization-mass spectrometry (nanoLC-ESI-MS) detection. We demonstrated high sample recovery, excellent interday and intraday accuracy and precision, and a limit of detection down to 50 femtogram of PFCs, in one microliter of human plasma. We validated our assay performance using pooled human plasma and NIST SRM 1950 samples. Our microfluidic chip-based assay may enable frequent longitudinal biomonitoring of PFCs and other environmental toxins using a finger prick of blood, thereby providing new insights into their bioaccumulation, bioavailability, and toxicity.

Dissolution of Monocrystalline Silicon Nanomembranes and Their Use as Encapsulation Layers and Electrical Interfaces in Water-Soluble Electronics.

PubMed

Lee, Yoon Kyeung; Yu, Ki Jun; Song, Enming; Barati Farimani, Amir; Vitale, Flavia; Xie, Zhaoqian; Yoon, Younghee; Kim, Yerim; Richardson, Andrew; Luan, Haiwen; Wu, Yixin; Xie, Xu; Lucas, Timothy H; Crawford, Kaitlyn; Mei, Yongfeng; Feng, Xue; Huang, Yonggang; Litt, Brian; Aluru, Narayana R; Yin, Lan; Rogers, John A

2017-12-26

The chemistry that governs the dissolution of device-grade, monocrystalline silicon nanomembranes into benign end products by hydrolysis serves as the foundation for fully eco/biodegradable classes of high-performance electronics. This paper examines these processes in aqueous solutions with chemical compositions relevant to groundwater and biofluids. The results show that the presence of Si(OH) 4 and proteins in these solutions can slow the rates of dissolution and that ion-specific effects associated with Ca 2+ can significantly increase these rates. This information allows for effective use of silicon nanomembranes not only as active layers in eco/biodegradable electronics but also as water barriers capable of providing perfect encapsulation until their disappearance by dissolution. The time scales for this encapsulation can be controlled by introduction of dopants into the Si and by addition of oxide layers on the exposed surfaces.The former possibility also allows the doped silicon to serve as an electrical interface for measuring biopotentials, as demonstrated in fully bioresorbable platforms for in vivo neural recordings. This collection of findings is important for further engineering development of water-soluble classes of silicon electronics.

The Alzheimer’s Disease Neuroimaging Initiative 2 Biomarker Core: A review of progress and plans

PubMed Central

Kang, Ju-Hee; Korecka, Magdalena; Figurski, Michal J.; Toledo, Jon B.; Blennow, Kaj; Zetterberg, Henrik; Waligorska, Teresa; Brylska, Magdalena; Fields, Leona; Shah, Nirali; Soares, Holly; Dean, Robert A.; Vanderstichele, Hugo; Petersen, Ronald C.; Aisen, Paul S.; Saykin, Andrew J.; Weiner, Michael W.; Trojanowski, John Q.; Shaw, Leslie M.

2016-01-01

Introduction We describe Alzheimer’s Disease Neuroimaging Initiative (ADNI) Biomarker Core progress including: the Biobank; cerebrospinal fluid (CSF) amyloid beta (Aβ1–42), t-tau, and p-tau181 analytical performance, definition of Alzheimer’s disease (AD) profile for plaque, and tangle burden detection and increased risk for progression to AD; AD disease heterogeneity; progress in standardization; and new studies using ADNI biofluids. Methods Review publications authored or coauthored by ADNI Biomarker core faculty and selected non-ADNI studies to deepen the understanding and interpretation of CSF Aβ1–42, t-tau, and p-tau181 data. Results CSFAD biomarker measurements with the qualified AlzBio3 immunoassay detects neuropathologic AD hallmarks in preclinical and prodromal disease stages, based on CSF studies in non-ADNI living subjects followed by the autopsy confirmation of AD. Collaboration across ADNI cores generated the temporal ordering model of AD biomarkers varying across individuals because of genetic/environmental factors that increase/decrease resilience to AD pathologies. Discussion Further studies will refine this model and enable the use of biomarkers studied in ADNI clinically and in disease-modifying therapeutic trials. PMID:26194312

Microfluidic Diatomite Analytical Devices for Illicit Drug Sensing with ppb-Level Sensitivity.

PubMed

Kong, Xianming; Chong, Xinyuan; Squire, Kenny; Wang, Alan X

2018-04-15

The escalating research interests in porous media microfluidics, such as microfluidic paper-based analytical devices, have fostered a new spectrum of biomedical devices for point-of-care (POC) diagnosis and biosensing. In this paper, we report microfluidic diatomite analytical devices (μDADs), which consist of highly porous photonic crystal biosilica channels, as an innovative lab-on-a-chip platform to detect illicit drugs. The μDADs in this work are fabricated by spin-coating and tape-stripping diatomaceous earth on regular glass slides with cross section of 400×30µm 2 . As the most unique feature, our μDADs can simultaneously perform on-chip chromatography to separate small molecules from complex biofluidic samples and acquire the surface-enhanced Raman scattering spectra of the target chemicals with high specificity. Owing to the ultra-small dimension of the diatomite microfluidic channels and the photonic crystal effect from the fossilized diatom frustules, we demonstrate unprecedented sensitivity down to part-per-billion (ppb) level when detecting pyrene (1ppb) from mixed sample with Raman dye and cocaine (10 ppb) from human plasma. This pioneering work proves the exclusive advantage of μDADs as emerging microfluidic devices for chemical and biomedical sensing, especially for POC drug screening.

The expanding roles of microRNAs in kidney pathophysiology.

PubMed

Metzinger-Le Meuth, Valérie; Fourdinier, Ophélie; Charnaux, Nathalie; Massy, Ziad A; Metzinger, Laurent

2018-05-25

MicroRNAs (miRNAs) are short single-stranded RNAs that control gene expression through base pairing with regions within the 3'-untranslated region of target mRNAs. These small non-coding RNAs are now increasingly known to be involved in kidney physiopathology. In this review we will describe how miRNAs were in recent years implicated in cellular and animal models of kidney disease but also in chronic kidney disease, haemodialysed and grafted patients, acute kidney injury patients and so on. At the moment miRNAs are considered as potential biomarkers in nephrology, but larger cohorts as well as the standardization of methods of measurement will be needed to confirm their usefulness. It will further be of the utmost importance to select specific tissues and biofluids to make miRNAs appropriate in day-to-day clinical practice. In addition, up- or down-regulating miRNAs that were described as deregulated in kidney diseases may represent innovative therapeutic methods to cure these disorders. We will enumerate in this review the most recent methods that can be used to deliver miRNAs in a specific and suitable way in kidney and other organs damaged by kidney failure, such as the cardiovascular system.

A Thrombus Generation Model Applied to Aneurysms Treated with Shape Memory Polymer Foam and Metal Coils

NASA Astrophysics Data System (ADS)

Horn, John; Ortega, Jason; Hartman, Jonathan; Maitland, Duncan

2015-11-01

To prevent their rupture, intracranial aneurysms are often treated with endovascular metal coils which fill the aneurysm sac and isolate it from the arterial flow. Despite its widespread use, this method can result in suboptimal outcomes leading to aneurysm recurrence. Recently, shape memory polymer foam has been proposed as an alternative aneurysm filler. In this work, a computational model has been developed to predict thrombus formation in blood in response to such cardiovascular implantable devices. The model couples biofluid and biochemical phenomena present as the blood interacts with a device and stimulates thrombus formation. This model is applied to simulations of both metal coil and shape memory polymer foam treatments within an idealized 2D aneurysm geometry. Using the predicted thrombus responses, the performance of these treatments is evaluated and compared. The results suggest that foam-treated aneurysms may fill more quickly and more completely with thrombus than coil-filled aneurysms, potentially leading to improved long-term aneurysm healing. This work was performed in part under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Current status of fluid biomarkers in mild traumatic brain injury

PubMed Central

Kulbe, Jacqueline R.; Geddes, James W.

2015-01-01

Mild traumatic brain injury (mTBI) affects millions of people annually and is difficult to diagnose. Mild injury is insensitive to conventional imaging techniques and diagnoses are often made using subjective criteria such as self-reported symptoms. Many people who sustain a mTBI develop persistent post-concussive symptoms. Athletes and military personnel are at great risk for repeat injury which can result in second impact syndrome or chronic traumatic encephalopathy. An objective and quantifiable measure, such as a serum biomarker, is needed to aid in mTBI diagnosis, prognosis, return to play/duty assessments, and would further elucidate mTBI pathophysiology. The majority of TBI biomarker research focuses on severe TBI with few studies specific to mild injury. Most studies use a hypothesis-driven approach, screening biofluids for markers known to be associated with TBI pathophysiology. This approach has yielded limited success in identifying markers that can be used clinically, additional candidate biomarkers are needed. Innovative and unbiased methods such as proteomics, microRNA arrays, urinary screens, autoantibody identification and phage display would complement more traditional approaches to aid in the discovery of novel mTBI biomarkers. PMID:25981889

Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow.

PubMed

Kulkarni, Shilpa; Koller, Antonius; Mani, Kartik M; Wen, Ruofeng; Alfieri, Alan; Saha, Subhrajit; Wang, Jian; Patel, Purvi; Bandeira, Nuno; Guha, Chandan; Chen, Emily I

2016-11-01

Early and accurate assessment of radiation injury by radiation-responsive biomarkers is critical for triage and early intervention. Biofluids such as urine and serum are convenient for such analysis. Recent research has also suggested that exosomes are a reliable source of biomarkers in disease progression. In the present study, we analyzed total urine proteome and exosomes isolated from urine or serum for potential biomarkers of acute and persistent radiation injury in mice exposed to lethal whole body irradiation (WBI). For feasibility studies, the mice were irradiated at 10.4 Gy WBI, and urine and serum samples were collected 24 and 72 hours after irradiation. Exosomes were isolated and analyzed using liquid chromatography mass spectrometry/mass spectrometry-based workflow for radiation exposure signatures. A data dependent acquisition and SWATH-MS combined workflow approach was used to identify significantly exosome biomarkers indicative of acute or persistent radiation-induced responses. For the validation studies, mice were exposed to 3, 6, 8, or 10 Gy WBI, and samples were analyzed for comparison. A comparison between total urine proteomics and urine exosome proteomics demonstrated that exosome proteomic analysis was superior in identifying radiation signatures. Feasibility studies identified 23 biomarkers from urine and 24 biomarkers from serum exosomes after WBI. Urinary exosome signatures identified different physiological parameters than the ones obtained in serum exosomes. Exosome signatures from urine indicated injury to the liver, gastrointestinal, and genitourinary tracts. In contrast, serum showed vascular injuries and acute inflammation in response to radiation. Selected urinary exosomal biomarkers also showed changes at lower radiation doses in validation studies. Exosome proteomics revealed radiation- and time-dependent protein signatures after WBI. A total of 47 differentially secreted proteins were identified in urinary and serum exosomes. Together, these data showed the feasibility of defining biomarkers that could elucidate tissue-associated and systemic response caused by high-dose ionizing radiation. This is the first report using an exosome proteomics approach to identify radiation signatures. Copyright © 2016 Elsevier Inc. All rights reserved.

Identifying Urinary and Serum Exosome Biomarkers for Radiation Exposure Using a Data Dependent Acquisition and SWATH-MS Combined Workflow

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

Kulkarni, Shilpa; Koller, Antonius; Proteomics Shared Resource, Herbert Irving Comprehensive Cancer Center, New York, New York

Purpose: Early and accurate assessment of radiation injury by radiation-responsive biomarkers is critical for triage and early intervention. Biofluids such as urine and serum are convenient for such analysis. Recent research has also suggested that exosomes are a reliable source of biomarkers in disease progression. In the present study, we analyzed total urine proteome and exosomes isolated from urine or serum for potential biomarkers of acute and persistent radiation injury in mice exposed to lethal whole body irradiation (WBI). Methods and Materials: For feasibility studies, the mice were irradiated at 10.4 Gy WBI, and urine and serum samples were collected 24more » and 72 hours after irradiation. Exosomes were isolated and analyzed using liquid chromatography mass spectrometry/mass spectrometry-based workflow for radiation exposure signatures. A data dependent acquisition and SWATH-MS combined workflow approach was used to identify significantly exosome biomarkers indicative of acute or persistent radiation-induced responses. For the validation studies, mice were exposed to 3, 6, 8, or 10 Gy WBI, and samples were analyzed for comparison. Results: A comparison between total urine proteomics and urine exosome proteomics demonstrated that exosome proteomic analysis was superior in identifying radiation signatures. Feasibility studies identified 23 biomarkers from urine and 24 biomarkers from serum exosomes after WBI. Urinary exosome signatures identified different physiological parameters than the ones obtained in serum exosomes. Exosome signatures from urine indicated injury to the liver, gastrointestinal, and genitourinary tracts. In contrast, serum showed vascular injuries and acute inflammation in response to radiation. Selected urinary exosomal biomarkers also showed changes at lower radiation doses in validation studies. Conclusions: Exosome proteomics revealed radiation- and time-dependent protein signatures after WBI. A total of 47 differentially secreted proteins were identified in urinary and serum exosomes. Together, these data showed the feasibility of defining biomarkers that could elucidate tissue-associated and systemic response caused by high-dose ionizing radiation. This is the first report using an exosome proteomics approach to identify radiation signatures.« less

Simultaneous analysis method for GHB, ketamine, norketamine, phenobarbital, thiopental, zolpidem, zopiclone and phenytoin in urine, using C18 poroshell column.

PubMed

Anilanmert, Beril; Çavuş, Fatma; Narin, Ibrahim; Cengiz, Salih; Sertler, Şefika; Özdemir, Ali Acar; Açikkol, Münevver

2016-06-01

Date-rape drugs have the potential to be used in drug-facilitated sexual assault, organ theft and property theft. Since they are colorless, tasteless and odorless, victims can drink without noticing, when added to the beverages. These drugs must be detected in time, before they are cleared up from the biofluids. A simultaneous extraction and determination method in urine for GHB, ketamine, norketamine, phenobarbital, thiopental, zolpidem, zopiclone and phenytoin (an anticonvulsant and antiepileptic drug) with LC-MS/MS was developed for the first time with analytically acceptable recoveries and validated. A 4 steps liquid-liquid extraction was applied, using only 1.000mL urine. A new age commercial C18 poroshell column with high column efficiency was used for LC-MS/MS analysis with a fast isocratic elution as 5.5min. A new MS transition were introduced for barbital. 222.7>179.8 with the effect of acetonitrile. Recoveries (%) were between 80.98-99.27 for all analytes, except for GHB which was 71.46. LOD and LOQ values were found in the ranges of 0.59-49.50 and 9.20-80.80ngmL(-1) for all the analytes (except for GHB:3.44 and 6.00μgmL(-1)). HorRat values calculated (between 0.25-1.21), revealed that the inter-day and interanalist precisions (RSD%≤14.54%) acceptable. The simultaneous extraction and determination of these 8 analytes in urine is challenging because of the difficulty arising from the different chemical properties of some. Since the procedure can extract drugs from a wide range of polarity and pKa, it increases the window of detection. Group representatives from barbiturates, z-drugs, ketamine, phenytoin and polar acidic drugs (GHB) have been successfully analyzed in this study with low detection limits. The method is important from the point of determining the combined or single use of these drugs in crimes and finding out the reasons of deaths related to these drugs. Copyright © 2016 Elsevier B.V. All rights reserved.

Surface charge effects in protein adsorption on nanodiamonds

NASA Astrophysics Data System (ADS)

Aramesh, M.; Shimoni, O.; Ostrikov, K.; Prawer, S.; Cervenka, J.

2015-03-01

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids. Electronic supplementary information (ESI) available: The FTIR spectrum of nanodiamonds, QCM-D profiles of 50 nm nanodiamond adsorption on silica surfaces, QCM-D profiles of protein desorption after rinsing with water (rinsing experiment) and the full FTIR spectrum of proteins before and after adsorption on ND particles. See DOI: 10.1039/c5nr00250h

MS Based Metabonomics

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

Want, Elizabeth J.; Metz, Thomas O.

Metabonomics is the latest and least mature of the systems biology triad, which also includes genomics and proteomics, and has its origins in the early orthomolecular medicine work pioneered by Linus Pauling and Arthur Robinson. It was defined by Nicholson and colleagues in 1999 as the quantitative measurement of perturbations in the metabolite complement of an integrated biological system in response to internal or external stimuli, and is often used today to describe many non-global types of metabolite analyses. Applications of metabonomics are extensive and include toxicology, nutrition, pharmaceutical research and development, physiological monitoring and disease diagnosis. For example, bloodmore » samples from millions of neonates are tested routinely by mass spectrometry (MS) as a diagnostic tool for inborn errors of metabolism. The metabonome encompasses a wide range of structurally diverse metabolites; therefore, no single analytical platform will be sufficient. Specialized sample preparation and detection techniques are required, and advances in NMR and MS technologies have led to enhanced metabonome coverage, which in turn demands improved data analysis approaches. The role of MS in metabonomics is still evolving as instrumentation and software becomes more sophisticated and as researchers realize the strengths and limitations of current technology. MS offers a wide dynamic range, high sensitivity, and reproducible, quantitative analysis. These attributes are essential for addressing the challenges of metabonomics, as the range of metabolite concentrations easily exceeds nine orders of magnitude in biofluids, and the diversity of molecular species ranges from simple amino and organic acids to lipids and complex carbohydrates. Additional challenges arise in generating a comprehensive metabolite profile, downstream data processing and analysis, and structural characterization of important metabolites. A typical workflow of MS-based metabonomics is shown in Figure 1. Gas chromatography-(GC)-MS was the most commonly used MS-based method for small molecule analysis in the 1970s and 1980s. It is still used today for the detection of many metabolic disorders and plays a strong role in plant metabonomics. Liquid chromatography (LC)-MS approaches have grown in popularity for metabolite studies, due to simpler sample preparation, reduced analysis times through the introduction of ultra-high performance liquid chromatography (UPLC)-MS and the ability to observe a wider range of metabolites. This chapter will discuss the role of MS in metabonomics, the techniques involved in this exciting area, and the current and future applications of the field. The various bioinformatics tools and multivariate analysis techniques used to maximize information recovery and to aid in the interpretation of the very large data sets typically obtained in metabonomics studies will also be discussed. While there are many different MS-based approaches utilized in metabonomics studies, emphasis will be placed on more established methods.« less

PREFACE: Introductory remarks from the Editors Introductory remarks from the Editors

NASA Astrophysics Data System (ADS)

Knobloch, E.; Meseguer, A.; Marques, F.

2012-06-01

The local organizers of the 4th BIFD (Bifurcations and Instabilities in Fluid Dynamics) Symposium held in Barcelona on 18-21 July 2011 would like to thank the editors of Fluid Dynamics Research for offering us the opportunity of publishing a peer-reviewed special issue of the journal with a selection of the contributions presented at this conference. We thank both the authors and the referees for working with us on the rather tight schedule necessary to release the issue within one year of the date of the conference. We also thank the invited speakers, B Eckhardt, L Tuckerman, and J M Vega, for contributing keynote papers to this special issue. The series of BIFD symposia started as a small workshop in Madeira, Portugal, in 2004 with no more than 20 participants. This number increased rapidly during the second and third symposia held in 2006 (Denmark) and 2009 (United Kingdom), with 40 and 110 participants, respectively. The 4th BIFD symposium has consolidated this event as one of the leading conferences in hydrodynamic stability, with nearly 200 participants from around the world. The main goal of this conference is to bring together scientists and engineers from different disciplines directly or indirectly related to fluid dynamics, bifurcation theory and hydrodynamic stability theory. The conference covered many research areas within the aforementioned fields, ranging from thermal, shear and centrifugal flows to biofluids, films, drops, viscoelastic flows and magnetohydrodynamics. The structure of the conference, with invited plenary talks and focused sessions, helped the participants find their home in the conference and share state-of-the-art knowledge within the field of hydrodynamic instabilities. The financial support from MICINN (Spanish Ministry of Science and Innovation, Grant no FIS2009-08065-E) and UPC (Universitat Politècnica de Catalunya) is greatly appreciated. The local organizers would also like to thank ETSAB (Barcelona School of Architecture) for providing their facilities and support staff, as well as CIMNE (Center for Numerical Methods in Engineering) for helping us with the administrative tasks and management of this event.

A validated inductively coupled plasma mass spectrometry (ICP-MS) method for the quantification of total platinum content in plasma, plasma ultrafiltrate, urine and peritoneal fluid.

PubMed

Lemoine, Lieselotte; Thijssen, Elsy; Noben, Jean-Paul; Adriaensens, Peter; Carleer, Robert; Speeten, Kurt Van der

2018-04-15

Oxaliplatin is a platinum (Pt) 1 containing antineoplastic agent that is applied in current clinical practice for the treatment of colon and appendiceal neoplasms. A fully validated, highly sensitive, high throughput inductively coupled plasma mass spectrometry (ICP-MS) method is provided to quantify the total Pt content in plasma, plasma ultrafiltrate, urine and peritoneal fluid. In this ICP-MS approach, the only step of sample preparation is a 1000-fold dilution in 0.5% nitric acid, allowing the analysis of 17 samples per hour. Detection of Pt was achieved over a linear range of 0.01-100 ng/mL. The limit of quantification was 18.0 ng/mL Pt in plasma, 8.0 ng/mL in ultrafiltrate and 6.1 ng/mL in urine and peritoneal fluid. The ICP-MS method was further validated for inter-and intraday precision and accuracy (≤15%), recovery, robustness and stability. Short-term storage of the biofluids, for 14 days, can be performed at -4 °C, -24 °C and -80 °C. As to long-term stability, up to 5 months, storage at -80 °C is encouraged. Furthermore, a timeline assessing the total and unbound Pt fraction in plasma and ultrafiltrate over a period of 45 h is provided. Following an incubation period of 5 h at 37 °C, 19-21% of Pt was recovered in the ultrafiltrate, emphasizing the extensive and rapid binding of oxaliplatin-derived Pt to plasma proteins. The described method can easily be implemented in a routine setting for pharmacokinetic studies in patients treated with oxaliplatin-based hyperthermic intraperitoneal perioperative chemotherapy. Copyright © 2018 Elsevier B.V. All rights reserved.

The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices

PubMed Central

Lee, Jeong-A; Kim, Mi-Kyung; Kim, Hyoung-Mi; Lee, Jong Kwon; Jeong, Jayoung; Kim, Young-Rok; Oh, Jae-Min; Choi, Soo-Jin

2015-01-01

Background Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics. Methods We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m2/g, respectively) on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats. Results N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen, were the major corona proteins, regardless of particle size. A biokinetic study revealed that orally delivered N-Cal was more rapidly absorbed into the blood stream than B-Cal, but no significant differences were observed between the two in terms of absorption efficiencies or tissue distributions. Both calcium carbonates were primarily present as particulate forms in gastrointestinal fluids but enter the circulatory system in dissolved Ca2+, although both types showed partial phase transformation to dicalcium phosphate dihydrate. Relatively low dissolution (about 4%), no remarkable protein–particle interaction, and the major particulate fate of calcium carbonate in vivo gastrointestinal fluids can explain its low oral absorption (about 4%) regardless of particle size. Conclusion We conclude that calcium carbonate nanoparticles can act more actively with biological matrices in vitro and ex vivo, but that in vivo, their biological interactions and biokinetics are not affected by particle size. PMID:25848250

The fate of calcium carbonate nanoparticles administered by oral route: absorption and their interaction with biological matrices.

PubMed

Lee, Jeong-A; Kim, Mi-Kyung; Kim, Hyoung-Mi; Lee, Jong Kwon; Jeong, Jayoung; Kim, Young-Rok; Oh, Jae-Min; Choi, Soo-Jin

2015-01-01

Orally administered particles rapidly interact with biological fluids containing proteins, enzymes, electrolytes, and other biomolecules to eventually form particles covered by a corona, and this corona potentially affects particle uptake, fate, absorption, distribution, and elimination in vivo. This study explored relationships between the biological interactions of calcium carbonate particles and their biokinetics. We examined the effects of food grade calcium carbonates of different particle size (nano [N-Cal] and bulk [B-Cal]: specific surface areas of 15.8 and 0.83 m(2)/g, respectively) on biological interactions in in vitro simulated physiological fluids, ex vivo biofluids, and in vivo in gastrointestinal fluid. Moreover, absorption and tissue distribution of calcium carbonates were evaluated following a single dose oral administration to rats. N-Cal interacted more with biomatrices than bulk materials in vitro and ex vivo, as evidenced by high fluorescence quenching ratios, but it did not interact more actively with biomatrices in vivo. Analysis of coronas revealed that immunoglobulin, apolipoprotein, thrombin, and fibrinogen, were the major corona proteins, regardless of particle size. A biokinetic study revealed that orally delivered N-Cal was more rapidly absorbed into the blood stream than B-Cal, but no significant differences were observed between the two in terms of absorption efficiencies or tissue distributions. Both calcium carbonates were primarily present as particulate forms in gastrointestinal fluids but enter the circulatory system in dissolved Ca(2+), although both types showed partial phase transformation to dicalcium phosphate dihydrate. Relatively low dissolution (about 4%), no remarkable protein-particle interaction, and the major particulate fate of calcium carbonate in vivo gastrointestinal fluids can explain its low oral absorption (about 4%) regardless of particle size. We conclude that calcium carbonate nanoparticles can act more actively with biological matrices in vitro and ex vivo, but that in vivo, their biological interactions and biokinetics are not affected by particle size.

Photocleavage-based affinity purification of biomarkers from serum: Application to multiplex allergy testing.

PubMed

Wan, Zhi; Ostendorff, Heather P; Liu, Ziying; Schneider, Lynda C; Rothschild, Kenneth J; Lim, Mark J

2018-01-01

Multiplex serological immunoassays, such as implemented on microarray or microsphere-based platforms, provide greater information content and higher throughput, while lowering the cost and blood volume required. These features are particularly attractive in pediatric food allergy testing to facilitate high throughput multi-allergen analysis from finger- or heel-stick collected blood. However, the miniaturization and microfluidics necessary for creating multiplex assays make them highly susceptible to the "matrix effect" caused by interference from non-target agents in serum and other biofluids. Such interference can result in lower sensitivity, specificity, reproducibility and quantitative accuracy. These problems have in large part prevented wide-spread implementation of multiplex immunoassays in clinical laboratories. We report the development of a novel method to eliminate the matrix effect by utilizing photocleavable capture antibodies to purify and concentrate blood-based biomarkers (a process termed PC-PURE) prior to detection in a multiplex immunoassay. To evaluate this approach, it was applied to blood-based allergy testing. Patient total IgE was purified and enriched using PC-PURE followed by multiplex microsphere-based detection of allergen-specific IgEs (termed the AllerBead assay). AllerBead was formatted to detect the eight most common pediatric food allergens: milk, soy, wheat, egg, peanuts, tree nuts, fin fish and shellfish, which account for >90% of all pediatric food allergies. 205 serum samples obtained from Boston Children's Hospital were evaluated. When PC-PURE was employed with AllerBead, excellent agreement was obtained with the standard, non-multiplex, ImmunoCAP® assay (average sensitivity above published negative predictive cutoffs = 96% and average Pearson r = 0.90; average specificity = 97%). In contrast, poor ImmunoCAP®-correlation was observed when PC-PURE was not utilized (average sensitivity above published negative predictive cutoffs = 59% and average Pearson r = 0.61; average specificity = 97%). This approach should be adaptable to improve a wide range of multiplex immunoassays such as in cancer, infectious disease and autoimmune disease.

Photocleavage-based affinity purification of biomarkers from serum: Application to multiplex allergy testing

PubMed Central

Wan, Zhi; Ostendorff, Heather P.; Liu, Ziying; Schneider, Lynda C.; Rothschild, Kenneth J.

2018-01-01

Multiplex serological immunoassays, such as implemented on microarray or microsphere-based platforms, provide greater information content and higher throughput, while lowering the cost and blood volume required. These features are particularly attractive in pediatric food allergy testing to facilitate high throughput multi-allergen analysis from finger- or heel-stick collected blood. However, the miniaturization and microfluidics necessary for creating multiplex assays make them highly susceptible to the “matrix effect” caused by interference from non-target agents in serum and other biofluids. Such interference can result in lower sensitivity, specificity, reproducibility and quantitative accuracy. These problems have in large part prevented wide-spread implementation of multiplex immunoassays in clinical laboratories. We report the development of a novel method to eliminate the matrix effect by utilizing photocleavable capture antibodies to purify and concentrate blood-based biomarkers (a process termed PC-PURE) prior to detection in a multiplex immunoassay. To evaluate this approach, it was applied to blood-based allergy testing. Patient total IgE was purified and enriched using PC-PURE followed by multiplex microsphere-based detection of allergen-specific IgEs (termed the AllerBead assay). AllerBead was formatted to detect the eight most common pediatric food allergens: milk, soy, wheat, egg, peanuts, tree nuts, fin fish and shellfish, which account for >90% of all pediatric food allergies. 205 serum samples obtained from Boston Children’s Hospital were evaluated. When PC-PURE was employed with AllerBead, excellent agreement was obtained with the standard, non-multiplex, ImmunoCAP® assay (average sensitivity above published negative predictive cutoffs = 96% and average Pearson r = 0.90; average specificity = 97%). In contrast, poor ImmunoCAP®-correlation was observed when PC-PURE was not utilized (average sensitivity above published negative predictive cutoffs = 59% and average Pearson r = 0.61; average specificity = 97%). This approach should be adaptable to improve a wide range of multiplex immunoassays such as in cancer, infectious disease and autoimmune disease. PMID:29389948

Evaluation of commercially available small RNASeq library preparation kits using low input RNA.

PubMed

Yeri, Ashish; Courtright, Amanda; Danielson, Kirsty; Hutchins, Elizabeth; Alsop, Eric; Carlson, Elizabeth; Hsieh, Michael; Ziegler, Olivia; Das, Avash; Shah, Ravi V; Rozowsky, Joel; Das, Saumya; Van Keuren-Jensen, Kendall

2018-05-05

Evolving interest in comprehensively profiling the full range of small RNAs present in small tissue biopsies and in circulating biofluids, and how the profile differs with disease, has launched small RNA sequencing (RNASeq) into more frequent use. However, known biases associated with small RNASeq, compounded by low RNA inputs, have been both a significant concern and a hurdle to widespread adoption. As RNASeq is becoming a viable choice for the discovery of small RNAs in low input samples and more labs are employing it, there should be benchmark datasets to test and evaluate the performance of new sequencing protocols and operators. In a recent publication from the National Institute of Standards and Technology, Pine et al., 2018, the investigators used a commercially available set of three tissues and tested performance across labs and platforms. In this paper, we further tested the performance of low RNA input in three commonly used and commercially available RNASeq library preparation kits; NEB Next, NEXTFlex, and TruSeq small RNA library preparation. We evaluated the performance of the kits at two different sites, using three different tissues (brain, liver, and placenta) with high (1 μg) and low RNA (10 ng) input from tissue samples, or 5.0, 3.0, 2.0, 1.0, 0.5, and 0.2 ml starting volumes of plasma. As there has been a lack of robust validation platforms for differentially expressed miRNAs, we also compared low input RNASeq data with their expression profiles on three different platforms (Abcam Fireplex, HTG EdgeSeq, and Qiagen miRNome). The concordance of RNASeq results on these three platforms was dependent on the RNA expression level; the higher the expression, the better the reproducibility. The results provide an extensive analysis of small RNASeq kit performance using low RNA input, and replication of these data on three downstream technologies.

HPLC-MS/MS methods for the quantitative analysis of 5-oxoproline (pyroglutamate) in rat plasma and hepatic cell line culture medium.

PubMed

Geenen, Suzanne; Guallar-Hoyas, Cristina; Michopoulos, Filippos; Kenna, J Gerry; Kolaja, Kyle L; Westerhoff, Hans V; Thomas, Paul; Wilson, Ian D

2011-11-01

5-Oxoproline (5-OP; pyroglutamate) is an intermediate in the biosynthesis of the endogenous tripeptide glutathione and has been seen to be elevated in the biofluids and tissues of rats following the administration of glutathione-depleting hepatotoxic xenobiotics such as acetaminophen (paracetamol), bromobenzene and ethionine. As 5-OP is a potential biomarker for hepatotoxicity HPLC-MS/MS methods have been developed for its quantification in in vitro cell culture media and rat plasma. For the cell culture media the lower limit of quantification (LLOQ), defined as the lowest concentration on the calibration curve, was 10 ng/ml. Minimal carry over was observed for cell culture media between injections (less than 5% at all concentrations examined), precision and accuracy were generally better than 20% for within and between day analyses. For rat plasma a LLOQ of 50 ng/ml was obtained. Carry over for plasma was less than 5% for all concentrations, within and between batch accuracy and precision were generally better than 20%. The methods were linear for both sample types from the LLOQ up to 1 μg/ml. For samples obtained from rats subjected to chronic administration of the hepatotoxin methapyrilene, concentrations of 5-OP were not observed to increase significantly at any time point compared to controls. 5-OP was also determined in the culture media of human liver epithelial (THLE) cells transfected with cytochrome P450 2E1 (THLE-2E1). Following exposure of THLE-2E1 cells to acetaminophen, large increases in the concentrations of 5-OP were observed, which correlated with reduced cellular glutathione content and with cell toxicity. These results show that LC-MS/MS can be used to perform rapid, sensitive, and quantitative determination of 5-OP in vivo and in vitro and will enable additional investigations into the utility of 5-OP as a biomarker of liver drug-induced liver injury. Copyright © 2011 Elsevier B.V. All rights reserved.

Oxygen and oxidative stress in the perinatal period.

PubMed

Torres-Cuevas, Isabel; Parra-Llorca, Anna; Sánchez-Illana, Angel; Nuñez-Ramiro, Antonio; Kuligowski, Julia; Cháfer-Pericás, Consuelo; Cernada, María; Escobar, Justo; Vento, Máximo

2017-08-01

Fetal life evolves in a hypoxic environment. Changes in the oxygen content in utero caused by conditions such as pre-eclampsia or type I diabetes or by oxygen supplementation to the mother lead to increased free radical production and correlate with perinatal outcomes. In the fetal-to-neonatal transition asphyxia is characterized by intermittent periods of hypoxia ischemia that may evolve to hypoxic ischemic encephalopathy associated with neurocognitive, motor, and neurosensorial impairment. Free radicals generated upon reoxygenation may notably increase brain damage. Hence, clinical trials have shown that the use of 100% oxygen given with positive pressure in the airways of the newborn infant during resuscitation causes more oxidative stress than using air, and increases mortality. Preterm infants are endowed with an immature lung and antioxidant system. Clinical stabilization of preterm infants after birth frequently requires positive pressure ventilation with a gas admixture that contains oxygen to achieve a normal heart rate and arterial oxygen saturation. In randomized controlled trials the use high oxygen concentrations (90% to 100%) has caused more oxidative stress and clinical complications that the use of lower oxygen concentrations (30-60%). A correlation between the amount of oxygen received during resuscitation and the level of biomarkers of oxidative stress and clinical outcomes was established. Thus, based on clinical outcomes and analytical results of oxidative stress biomarkers relevant changes were introduced in the resuscitation policies. However, it should be underscored that analysis of oxidative stress biomarkers in biofluids has only been used in experimental and clinical research but not in clinical routine. The complexity of the technical procedures, lack of automation, and cost of these determinations have hindered the routine use of biomarkers in the clinical setting. Overcoming these technical and economical difficulties constitutes a challenge for the immediate future since accurate evaluation of oxidative stress would contribute to improve the quality of care of our neonatal patients. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism.

PubMed

Gevi, Federica; Zolla, Lello; Gabriele, Stefano; Persico, Antonio M

2016-01-01

Autism spectrum disorder (ASD) is still diagnosed through behavioral observation, due to a lack of laboratory biomarkers, which could greatly aid clinicians in providing earlier and more reliable diagnoses. Metabolomics on human biofluids provides a sensitive tool to identify metabolite profiles potentially usable as biomarkers for ASD. Initial metabolomic studies, analyzing urines and plasma of ASD and control individuals, suggested that autistic patients may share some metabolic abnormalities, despite several inconsistencies stemming from differences in technology, ethnicity, age range, and definition of "control" status. ASD-specific urinary metabolomic patterns were explored at an early age in 30 ASD children and 30 matched controls (age range 2-7, M:F = 22:8) using hydrophilic interaction chromatography (HILIC)-UHPLC and mass spectrometry, a highly sensitive, accurate, and unbiased approach. Metabolites were then subjected to multivariate statistical analysis and grouped by metabolic pathway. Urinary metabolites displaying the largest differences between young ASD and control children belonged to the tryptophan and purine metabolic pathways. Also, vitamin B 6 , riboflavin, phenylalanine-tyrosine-tryptophan biosynthesis, pantothenate and CoA, and pyrimidine metabolism differed significantly. ASD children preferentially transform tryptophan into xanthurenic acid and quinolinic acid (two catabolites of the kynurenine pathway), at the expense of kynurenic acid and especially of melatonin. Also, the gut microbiome contributes to altered tryptophan metabolism, yielding increased levels of indolyl 3-acetic acid and indolyl lactate. The metabolic pathways most distinctive of young Italian autistic children largely overlap with those found in rodent models of ASD following maternal immune activation or genetic manipulations. These results are consistent with the proposal of a purine-driven cell danger response, accompanied by overproduction of epileptogenic and excitotoxic quinolinic acid, large reductions in melatonin synthesis, and gut dysbiosis. These metabolic abnormalities could underlie several comorbidities frequently associated to ASD, such as seizures, sleep disorders, and gastrointestinal symptoms, and could contribute to autism severity. Their diagnostic sensitivity, disease-specificity, and interethnic variability will merit further investigation.

Untargeted mass spectrometry-based metabolomic profiling of pleural effusions: fatty acids as novel cancer biomarkers for malignant pleural effusions.

PubMed

Lam, Ching-Wan; Law, Chun-Yiu

2014-09-05

Untargeted mass spectrometry-based metabolomic profiling is a powerful analytical method used for broad-spectrum identification and quantification of metabolites in biofluids in human health and disease states. In this study, we exploit metabolomic profiling for cancer biomarker discovery for diagnosis of malignant pleural effusions. We envisage the result will be clinically useful since currently there are no cancer biomarkers that are accurate enough for the diagnosis of malignant pleural effusions. Metabolomes of 32 malignant pleural effusions from lung cancer patients and 18 benign effusions from patients with pulmonary tuberculosis were analyzed using reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) using AB SCIEX TripleTOF 5600. MS spectra were analyzed using XCMS, PeakView, and LipidView. Metabolome-Wide Association Study (MWAS) was performed by Receiver Operating Characteristic Curve Explorer and Tester (ROCCET). Insignificant markers were filtered out using a metabolome-wide significance level (MWSL) with p-value < 2 × 10(-5) for t test. Only compounds in Human Metabolome Database (HMDB) will be used as cancer biomarkers. ROCCET analysis of ESI positive and negative MS spectra revealed free fatty acid (FFA) 18:1 (oleic acid) had the largest area-under-ROC of 0.96 (95% CI = 0.87-1.00) in malignant pleural effusions. Using a ratio of FFA 18:1-to-ceramide (d18:1/16:0), the area-under-ROC was further increased to 0.99 (95% CI = 0.91-1.00) with sensitivity 93.8% and specificity 100.0%. Using untargeted metabolomic profiling, the diagnostic cancer biomarker with the largest area-under-ROC can be determined objectively. This lipogenic phenotype could be explained by overexpression of fatty acid synthase (FASN) in cancer cells. The diagnostic performance of FFA 18:1-to-ceramide (d18:1/16:0) ratio supports its use for diagnosis of malignant pleural effusions.

Metabolomics studies in brain tissue: A review.

PubMed

Gonzalez-Riano, Carolina; Garcia, Antonia; Barbas, Coral

2016-10-25

Brain is still an organ with a composition to be discovered but beyond that, mental disorders and especially all diseases that curse with dementia are devastating for the patient, the family and the society. Metabolomics can offer an alternative tool for unveiling new insights in the discovery of new treatments and biomarkers of mental disorders. Until now, most of metabolomic studies have been based on biofluids: serum/plasma or urine, because brain tissue accessibility is limited to animal models or post mortem studies, but even so it is crucial for understanding the pathological processes. Metabolomics studies of brain tissue imply several challenges due to sample extraction, along with brain heterogeneity, sample storage, and sample treatment for a wide coverage of metabolites with a wide range of concentrations of many lipophilic and some polar compounds. In this review, the current analytical practices for target and non-targeted metabolomics are described and discussed with emphasis on critical aspects: sample treatment (quenching, homogenization, filtration, centrifugation and extraction), analytical methods, as well as findings considering the used strategies. Besides that, the altered analytes in the different brain regions have been associated with their corresponding pathways to obtain a global overview of their dysregulation, trying to establish the link between altered biological pathways and pathophysiological conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluid models and simulations of biological cell phenomena

NASA Technical Reports Server (NTRS)

Greenspan, H. P.

1982-01-01

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

The Role of Proteomics in Biomarker Development for Improved Patient Diagnosis and Clinical Decision Making in Prostate Cancer

PubMed Central

Tonry, Claire L.; Leacy, Emma; Raso, Cinzia; Finn, Stephen P.; Armstrong, John; Pennington, Stephen R.

2016-01-01

Prostate Cancer (PCa) is the second most commonly diagnosed cancer in men worldwide. Although increased expression of prostate-specific antigen (PSA) is an effective indicator for the recurrence of PCa, its intended use as a screening marker for PCa is of considerable controversy. Recent research efforts in the field of PCa biomarkers have focused on the identification of tissue and fluid-based biomarkers that would be better able to stratify those individuals diagnosed with PCa who (i) might best receive no treatment (active surveillance of the disease); (ii) would benefit from existing treatments; or (iii) those who are likely to succumb to disease recurrence and/or have aggressive disease. The growing demand for better prostate cancer biomarkers has coincided with the development of improved discovery and evaluation technologies for multiplexed measurement of proteins in bio-fluids and tissues. This review aims to (i) provide an overview of these technologies as well as describe some of the candidate PCa protein biomarkers that have been discovered using them; (ii) address some of the general limitations in the clinical evaluation and validation of protein biomarkers; and (iii) make recommendations for strategies that could be adopted to improve the successful development of protein biomarkers to deliver improvements in personalized PCa patient decision making. PMID:27438858

Pseudomonas aeruginosa quorum sensing molecules correlate with clinical status in cystic fibrosis.

PubMed

Barr, Helen L; Halliday, Nigel; Cámara, Miguel; Barrett, David A; Williams, Paul; Forrester, Douglas L; Simms, Rebecca; Smyth, Alan R; Honeybourne, David; Whitehouse, Joanna L; Nash, Edward F; Dewar, Jane; Clayton, Andrew; Knox, Alan J; Fogarty, Andrew W

2015-10-01

Pseudomonas aeruginosa produces quorum sensing signal molecules that are potential biomarkers for infection.A prospective study of 60 cystic fibrosis patients with chronic P. aeruginosa, who required intravenous antibiotics for pulmonary exacerbations, was undertaken. Clinical measurements and biological samples were obtained at the start and end of the treatment period. Additional data were available for 29 of these patients when they were clinically stable.Cross-sectionally, quorum sensing signal molecules were detectable in the sputum, plasma and urine of 86%, 75% and 83% patients, respectively. They were positively correlated between the three biofluids. Positive correlations were observed for most quorum sensing signal molecules in sputum, plasma and urine, with quantitative measures of pulmonary P. aeruginosa load at the start of a pulmonary exacerbation. Plasma concentrations of 2-nonyl-4-hydroxy-quinoline (NHQ) were significantly higher at the start of a pulmonary exacerbation compared to clinical stability (p<0.01). Following the administration of systemic antibiotics, plasma 2-heptyl-4-hydroxyquinoline (p=0.02) and NHQ concentrations (p<0.01) decreased significantly.In conclusion, quorum sensing signal molecules are detectable in cystic fibrosis patients with pulmonary P. aeruginosa infection and are positively correlated with quantitative measures of P. aeruginosa. NHQ correlates with clinical status and has potential as a novel biomarker for P. aeruginosa infection. Copyright ©ERS 2015.

A green and facile approach for synthesizing imine to develop optical biosensor for wide range detection of bilirubin in human biofluids.

PubMed

Ellairaja, Sundaram; Shenbagavalli, Kathiravan; Ponmariappan, Sarkaraisamy; Vasantha, Vairathevar Sivasamy

2017-05-15

Bilirubin, a key biomarker for the jaundice and its clinical diagnosis needs a better analytical tool. A novel and simple fluorescent platform based on (2,2'-((1E,1'E)-((6-bromopyridine-2,3-diyl) bis(azanylylidene)) bis(methanylylidene diphenol) (BAMD) was designed. BAMD showed a remarkable fluorescent intensity with a very good quantum yield of 0.85 and lifetime of 870ps. Hence, it was applied for the determination of bilirubin using both colorimetric and fluorimetric techniques in physiological and basic pH. Under optimized experimental conditions, the probe detects bilirubin selectively in the presence of other interfering biomolecules and metal ions. The linear range of detection is 1pM-500µM at pH=7.4 and LOD is 2.8 and 3.3 pM at pH=7.4 and 9.0, respectively, which were reported so far. The probe detects the bilirubin through FRET mechanism. The practical application of the probe was successfully tested in the human blood and urine samples. Based on all above advantages, this simple idea can be applied to design a simple clinical diagnostic tool for jaundice. Copyright © 2016. Published by Elsevier B.V.

Overcoming biofluid protein complexity during targeted mass spectrometry detection and quantification of protein biomarkers by MRM cubed (MRM3).

PubMed

Jeudy, Jeremy; Salvador, Arnaud; Simon, Romain; Jaffuel, Aurore; Fonbonne, Catherine; Léonard, Jean-François; Gautier, Jean-Charles; Pasquier, Olivier; Lemoine, Jerome

2014-02-01

Targeted mass spectrometry in the so-called multiple reaction monitoring mode (MRM) is certainly a promising way for the precise, accurate, and multiplexed measurement of proteins and their genetic or posttranslationally modified isoforms. MRM carried out on a low-resolution triple quadrupole instrument faces a lack of specificity when addressing the quantification of weakly concentrated proteins. In this case, extensive sample fractionation or immunoenrichment alleviates signal contamination by interferences, but in turn decreases assay performance and throughput. Recently, MRM(3) was introduced as an alternative to MRM to improve the limit of quantification of weakly concentrated protein biomarkers. In the present work, we compare MRM and MRM(3) modes for the detection of biomarkers in plasma and urine. Calibration curves drawn with MRM and MRM(3) showed a similar range of linearity (R(2) > 0.99 for both methods) with protein concentrations above 1 μg/mL in plasma and a few nanogram per milliliter in urine. In contrast, optimized MRM(3) methods improve the limits of quantification by a factor of 2 to 4 depending on the targeted peptide. This gain arises from the additional MS(3) fragmentation step, which significantly removes or decreases interfering signals within the targeted transition channels.

Non-Invasive Electromagnetic Skin Patch Sensor to Measure Intracranial Fluid–Volume Shifts

PubMed Central

Griffith, Jacob; Cluff, Kim; Eckerman, Brandon; Aldrich, Jessica; Becker, Ryan; Moore-Jansen, Peer; Patterson, Jeremy

2018-01-01

Elevated intracranial fluid volume can drive intracranial pressure increases, which can potentially result in numerous neurological complications or death. This study’s focus was to develop a passive skin patch sensor for the head that would non-invasively measure cranial fluid volume shifts. The sensor consists of a single baseline component configured into a rectangular planar spiral with a self-resonant frequency response when impinged upon by external radio frequency sweeps. Fluid volume changes (10 mL increments) were detected through cranial bone using the sensor on a dry human skull model. Preliminary human tests utilized two sensors to determine feasibility of detecting fluid volume shifts in the complex environment of the human body. The correlation between fluid volume changes and shifts in the first resonance frequency using the dry human skull was classified as a second order polynomial with R2 = 0.97. During preliminary and secondary human tests, a ≈24 MHz and an average of ≈45.07 MHz shifts in the principal resonant frequency were measured respectively, corresponding to the induced cephalad bio-fluid shifts. This electromagnetic resonant sensor may provide a non-invasive method to monitor shifts in fluid volume and assist with medical scenarios including stroke, cerebral hemorrhage, concussion, or monitoring intracranial pressure. PMID:29596338

Metabolomics, Nutrition, and Potential Biomarkers of Food Quality, Intake, and Health Status.

PubMed

Sébédio, Jean-Louis

Diet, dietary patterns, and other environmental factors such as exposure to toxins are playing an important role in the prevention/development of many diseases, like obesity, type 2 diabetes, and consequently on the health status of individuals. A major challenge nowadays is to identify novel biomarkers to detect as early as possible metabolic dysfunction and to predict evolution of health status in order to refine nutritional advices to specific population groups. Omics technologies such as genomics, transcriptomics, proteomics, and metabolomics coupled with statistical and bioinformatics tools have already shown great potential in this research field even if so far only few biomarkers have been validated. For the past two decades, important analytical techniques have been developed to detect as many metabolites as possible in human biofluids such as urine, blood, and saliva. In the field of food science and nutrition, many studies have been carried out for food authenticity, quality, and safety, as well as for food processing. Furthermore, metabolomic investigations have been carried out to discover new early biomarkers of metabolic dysfunction and predictive biomarkers of developing pathologies (obesity, metabolic syndrome, type-2 diabetes, etc.). Great emphasis is also placed in the development of methodologies to identify and validate biomarkers of nutrients exposure. © 2017 Elsevier Inc. All rights reserved.

AC electrothermal mixing for high conductive biofluids by arc-electrodes

NASA Astrophysics Data System (ADS)

Meng, Jiyu; Li, Shanshan; Li, Junwei; Yu, Chengzhuang; Wei, Chunyang; Dai, Shijie

2018-06-01

As a platform to mix the bioagents (i.e. serum, urine), we take advantage of the alternating current electrothermal (ACET) effect which is quite suitable for rapid pumping/mixing of high conductive biomicrofluids. Here we demonstrate the concept of a high-efficient mixing microfluidic chip as a basic unit to provide rapid mixing for lab-on-a-chip applications. As an active mixer, two streams are introduced into a ring-shape microchamber by a passive flow rate regulator, and then the microfluids in the chamber are actuated by a nonuniform electric field with a phase shift of 180°. It shows perfect mixing performance by arranging four arc-electrodes around the ring-shape microchamber subsequently. Taking the Joule heating and conductivity/permittivity changes into consideration, a temperature dependent fully coupled numerical model is presented. Then, the effects of applied voltages on mixing performance and temperature rise are provided to get an optimized design for ACET mixer. Moreover, the arrangement of the electrode array is analyzed to show the effects of electrode patterns on the swirls and mixing efficiencies. Since all the electrodes here are located along a ring-shape central microchamber, the ring-shape micromixer is quite suitable to function as a compact element modular for integrated microfluidic chips.

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling.

PubMed

Castagné, Raphaële; Boulangé, Claire Laurence; Karaman, Ibrahim; Campanella, Gianluca; Santos Ferreira, Diana L; Kaluarachchi, Manuja R; Lehne, Benjamin; Moayyeri, Alireza; Lewis, Matthew R; Spagou, Konstantina; Dona, Anthony C; Evangelos, Vangelis; Tracy, Russell; Greenland, Philip; Lindon, John C; Herrington, David; Ebbels, Timothy M D; Elliott, Paul; Tzoulaki, Ioanna; Chadeau-Hyam, Marc

2017-10-06

1 H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1 H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies.

Improving Visualization and Interpretation of Metabolome-Wide Association Studies: An Application in a Population-Based Cohort Using Untargeted 1H NMR Metabolic Profiling

PubMed Central

2017-01-01

1H NMR spectroscopy of biofluids generates reproducible data allowing detection and quantification of small molecules in large population cohorts. Statistical models to analyze such data are now well-established, and the use of univariate metabolome wide association studies (MWAS) investigating the spectral features separately has emerged as a computationally efficient and interpretable alternative to multivariate models. The MWAS rely on the accurate estimation of a metabolome wide significance level (MWSL) to be applied to control the family wise error rate. Subsequent interpretation requires efficient visualization and formal feature annotation, which, in-turn, call for efficient prioritization of spectral variables of interest. Using human serum 1H NMR spectroscopic profiles from 3948 participants from the Multi-Ethnic Study of Atherosclerosis (MESA), we have performed a series of MWAS for serum levels of glucose. We first propose an extension of the conventional MWSL that yields stable estimates of the MWSL across the different model parameterizations and distributional features of the outcome. We propose both efficient visualization methods and a strategy based on subsampling and internal validation to prioritize the associations. Our work proposes and illustrates practical and scalable solutions to facilitate the implementation of the MWAS approach and improve interpretation in large cohort studies. PMID:28823158

Circulating exosomes as new biomarkers for brain disease and injury

NASA Astrophysics Data System (ADS)

Graner, Michael W.; Epple, Laura M.; Dusto, Nathaniel L.; Lencioni, Alex M.; Nega, Meheret; Herring, Matthew; Winston, Ben; Madsen, Helen; Bemis, Lynne T.; Anchordoquy, Thomas J.

2013-05-01

Brain diseases such as cancers, neurodegenerative disorders, or trauma are frequently diagnosed with imaging modalities and sometimes with intracranial biopsies. Treatment response is similarly monitored, along with clinical indications. While these technologies provide important windows into the disease state, they fail to provide us a detailed molecular portrait of the disease and of the changes taking place during therapy. Exosomes are virus-sized nanovesicles derived from the endosomal system and are released extracellularly from essentially all cell types. Exosomes contain intracellular entities (proteins, nucleic acids, metabolites), membrane proteins and lipids, and even extracellular proteins bound to them. Exosomes may be considered as mini-surrogates of their cells of origin, with some content common to all cells/exosomes, but some of the content would be cell-specific. These vesicles are found in all biofluids in humans, and are thus accessible to "liquid biopsy" with harvest of vesicles from such fluids. Current challenges are to identify disease-related markers or panels of markers to distinguish the disease state. Here we will show examples of brain tumor markers found in/on exosomes from cell culture and patient sera, and we will suggest that aspects of the biology of disease may have a relevant place in the search for biomarkers.

Electrowetting on plasma-deposited fluorocarbon hydrophobic films for biofluid transport in microfluidics

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

Bayiati, P.; Tserepi, A.; Petrou, P. S.

2007-05-15

The present work focuses on the plasma deposition of fluorocarbon (FC) films on surfaces and the electrostatic control of their wettability (electrowetting). Such films can be employed for actuation of fluid transport in microfluidic devices, when deposited over patterned electrodes. Here, the deposition was performed using C{sub 4}F{sub 8} and the plasma parameters that permit the creation of films with optimized properties desirable for electrowetting were established. The wettability of the plasma-deposited surfaces was characterized by means of contact angle measurements (in the static and dynamic mode). The thickness of the deposited films was probed in situ by means ofmore » spectroscopic ellipsometry, while the surface roughness was provided by atomic force microscopy. These plasma-deposited FC films in combination with silicon nitride, a material of high dielectric constant, were used to create a dielectric structure that requires reduced voltages for successful electrowetting. Electrowetting experiments using protein solutions were conducted on such optimized dielectric structures and were compared with similar structures bearing commercial spin-coated Teflon registered amorphous fluoropolymer (AF) film as the hydrophobic top layer. Our results show that plasma-deposited FC films have desirable electrowetting behavior and minimal protein adsorption, a requirement for successful transport of biological solutions in 'digital' microfluidics.« less

Label free detection of phospholipids by infrared absorption spectroscopy

NASA Astrophysics Data System (ADS)

Ahmed, Tahsin; Foster, Erick; Vigil, Genevieve; Khan, Aamir A.; Bohn, Paul; Howard, Scott S.

2014-08-01

We present our study on compact, label-free dissolved lipid sensing by combining capillary electrophoresis separation in a PDMS microfluidic chip online with mid-infrared (MIR) absorption spectroscopy for biomarker detection. On-chip capillary electrophoresis is used to separate the biomarkers without introducing any extrinsic contrast agent, which reduces both cost and complexity. The label free biomarker detection could be done by interrogating separated biomarkers in the channel by MIR absorption spectroscopy. Phospholipids biomarkers of degenerative neurological, kidney, and bone diseases are detectable using this label free technique. These phospholipids exhibit strong absorption resonances in the MIR and are present in biofluids including urine, blood plasma, and cerebrospinal fluid. MIR spectroscopy of a 12-carbon chain phosphatidic acid (PA) (1,2-dilauroyl-snglycero- 3-phosphate (sodium salt)) dissolved in N-methylformamide, exhibits a strong amide peak near wavenumber 1660 cm-1 (wavelength 6 μm), arising from the phosphate headgroup vibrations within a low-loss window of the solvent. PA has a similar structure to many important phospholipids molecules like phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylserine (PS), making it an ideal molecule for initial proof-of-concept studies. This newly proposed detection technique can lead us to minimal sample preparation and is capable of identifying several biomarkers from the same sample simultaneously.

A label-free aptamer-fluorophore assembly for rapid and specific detection of cocaine in biofluids.

PubMed

Roncancio, Daniel; Yu, Haixiang; Xu, Xiaowen; Wu, Shuo; Liu, Ran; Debord, Joshua; Lou, Xinhui; Xiao, Yi

2014-11-18

We report a rapid and specific aptamer-based method for one-step cocaine detection with minimal reagent requirements. The feasibility of aptamer-based detection has been demonstrated with sensors that operate via target-induced conformational change mechanisms, but these have generally exhibited limited target sensitivity. We have discovered that the cocaine-binding aptamer MNS-4.1 can also bind the fluorescent molecule 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) and thereby quench its fluorescence. We subsequently introduced sequence changes into MNS-4.1 to engineer a new cocaine-binding aptamer (38-GC) that exhibits higher affinity to both ligands, with reduced background signal and increased signal gain. Using this aptamer, we have developed a new sensor platform that relies on the cocaine-mediated displacement of ATMND from 38-GC as a result of competitive binding. We demonstrate that our sensor can detect cocaine within seconds at concentrations as low as 200 nM, which is 50-fold lower than existing assays based on target-induced conformational change. More importantly, our assay achieves successful cocaine detection in body fluids, with a limit of detection of 10.4, 18.4, and 36 μM in undiluted saliva, urine, and serum samples, respectively.

Pseudomonas aeruginosa quorum sensing molecules correlate with clinical status in cystic fibrosis

PubMed Central

Halliday, Nigel; Cámara, Miguel; Barrett, David A.; Williams, Paul; Forrester, Douglas L.; Simms, Rebecca; Smyth, Alan R.; Honeybourne, David; Whitehouse, Joanna L.; Nash, Edward F.; Dewar, Jane; Clayton, Andrew; Knox, Alan J.; Fogarty, Andrew W.

2015-01-01

Pseudomonas aeruginosa produces quorum sensing signal molecules that are potential biomarkers for infection. A prospective study of 60 cystic fibrosis patients with chronic P. aeruginosa, who required intravenous antibiotics for pulmonary exacerbations, was undertaken. Clinical measurements and biological samples were obtained at the start and end of the treatment period. Additional data were available for 29 of these patients when they were clinically stable. Cross-sectionally, quorum sensing signal molecules were detectable in the sputum, plasma and urine of 86%, 75% and 83% patients, respectively. They were positively correlated between the three biofluids. Positive correlations were observed for most quorum sensing signal molecules in sputum, plasma and urine, with quantitative measures of pulmonary P. aeruginosa load at the start of a pulmonary exacerbation. Plasma concentrations of 2-nonyl-4-hydroxy-quinoline (NHQ) were significantly higher at the start of a pulmonary exacerbation compared to clinical stability (p<0.01). Following the administration of systemic antibiotics, plasma 2-heptyl-4-hydroxyquinoline (p=0.02) and NHQ concentrations (p<0.01) decreased significantly. In conclusion, quorum sensing signal molecules are detectable in cystic fibrosis patients with pulmonary P. aeruginosa infection and are positively correlated with quantitative measures of P. aeruginosa. NHQ correlates with clinical status and has potential as a novel biomarker for P. aeruginosa infection. PMID:26022946

Surface charge effects in protein adsorption on nanodiamonds.

PubMed

Aramesh, M; Shimoni, O; Ostrikov, K; Prawer, S; Cervenka, J

2015-03-19

Understanding the interaction of proteins with charged diamond nanoparticles is of fundamental importance for diverse biomedical applications. Here we present a thorough study of protein binding, adsorption kinetics and structure on strongly positively (hydrogen-terminated) and negatively (oxygen-terminated) charged nanodiamond particles using a quartz crystal microbalance by dissipation and infrared spectroscopy. By using two model proteins (bovine serum albumin and lysozyme) of different properties (charge, molecular weight and rigidity), the main driving mechanism responsible for the protein binding to the charged nanoparticles was identified. Electrostatic interactions were found to dominate the protein adsorption dynamics, attachment and conformation. We developed a simple electrostatic model that can qualitatively explain the observed adsorption behaviour based on charge-induced pH modifications near the charged nanoparticle surfaces. Under neutral conditions, the local pH around the positively and negatively charged nanodiamonds becomes very high (11-12) and low (1-3) respectively, which has a profound impact on the protein charge, hydration and affinity to the nanodiamonds. Small proteins (lysozyme) were found to form multilayers with significant conformational changes to screen the surface charge, while larger proteins (albumin) formed monolayers with minor conformational changes. The findings of this study provide a step forward toward understanding and eventually predicting nanoparticle interactions with biofluids.

The microfluidics of the eccrine sweat gland, including biomarker partitioning, transport, and biosensing implications

PubMed Central

Sonner, Z.; Wilder, E.; Heikenfeld, J.; Kasting, G.; Beyette, F.; Swaile, D.; Sherman, F.; Joyce, J.; Hagen, J.; Kelley-Loughnane, N.; Naik, R.

2015-01-01

Non-invasive and accurate access of biomarkers remains a holy grail of the biomedical community. Human eccrine sweat is a surprisingly biomarker-rich fluid which is gaining increasing attention. This is especially true in applications of continuous bio-monitoring where other biofluids prove more challenging, if not impossible. However, much confusion on the topic exists as the microfluidics of the eccrine sweat gland has never been comprehensively presented and models of biomarker partitioning into sweat are either underdeveloped and/or highly scattered across literature. Reported here are microfluidic models for eccrine sweat generation and flow which are coupled with review of blood-to-sweat biomarker partition pathways, therefore providing insights such as how biomarker concentration changes with sweat flow rate. Additionally, it is shown that both flow rate and biomarker diffusion determine the effective sampling rate of biomarkers at the skin surface (chronological resolution). The discussion covers a broad class of biomarkers including ions (Na+, Cl−, K+, NH4+), small molecules (ethanol, cortisol, urea, and lactate), and even peptides or small proteins (neuropeptides and cytokines). The models are not meant to be exhaustive for all biomarkers, yet collectively serve as a foundational guide for further development of sweat-based diagnostics and for those beginning exploration of new biomarker opportunities in sweat. PMID:26045728

Particle image velocimetry of a flow at a vaulted wall.

PubMed

Kertzscher, U; Berthe, A; Goubergrits, L; Affeld, K

2008-05-01

The assessment of flow along a vaulted wall (with two main finite radii of curvature) is of general interest; in biofluid mechanics, it is of special interest. Unlike the geometry of flows in engineering, flow geometry in nature is often determined by vaulted walls. Specifically the flow adjacent to the wall of blood vessels is particularly interesting since this is where either thrombi are formed or atherosclerosis develops. Current measurement methods have problems assessing the flow along vaulted walls. In contrast with conventional particle image velocimetry (PIV), this new method, called wall PIV, allows the investigation of a flow adjacent to transparent flexible surfaces with two finite radii of curvature. Using an optical method which allows the observation of particles up to a predefined depth enables the visualization solely of the boundary layer flow. This is accomplished by adding a specific dye to the fluid which absorbs the monochromatic light used to illuminate the region of observation. The obtained images can be analysed with the methods of conventional PIV and result in a vector field of the velocities along the wall. With wall PIV, the steady flow adjacent to the vaulted wall of a blood pump was investigated and the resulting velocity field as well as the velocity fluctuations were assessed.

Monitoring of interstitial buffer systems using micro-dialysis and infrared spectrometry

NASA Astrophysics Data System (ADS)

Heise, H. M.; Cocchieri, L.; Vahlsing, T.; Ihrig, D.; Elm, J.

2017-02-01

Nowadays, continuous sensing systems are important point-of-care devices for the hospital and personalized patient technology. FTIR-spectrometers have been successfully employed for the development of bed-side systems. In-vivo applications for critically ill patients can be envisaged for analytes and parameters, which are of interest for intensive care such as lactate, urea, pCO2 and pH. The human body maintains the blood pH around 7.4, but for severe pH level changes acidosis or alkalosis can lead to serious health problems. Three different buffer systems exist based on bicarbonate, phosphate and proteins; for the most important bicarbonate and phosphate systems infrared transmission spectra were recorded. By using the CO2 and HCO3 - bands of the bicarbonate spectra, the pH of the harvested biofluid can be predicted using the Henderson-Hasselbalch equation. Furthermore, we studied the solubility of CO2 in aqueous solutions using gas mixtures of N2 and CO2 with known composition within partial pressures of CO2 as relevant for invivo conditions. Thus, values of pCO2 up to 150 mm Hg (200 hPa) with distilled water and a Ringer solution, which is an isotonic electrolyte solution used for medical infusion, were measured at 25 °C and 37 °C (normal body temperature).

Raman spectroscopy of dried synovial fluid droplets as a rapid diagnostic for knee joint damage

NASA Astrophysics Data System (ADS)

Esmonde-White, Karen A.; Mandair, Gurjit S.; Raaii, Farhang; Roessler, Blake J.; Morris, Michael D.

2008-02-01

Human synovial fluid droplets were investigated using drop deposition in combination with Raman spectroscopy. Following informed consent, synovial fluid was obtained from forty human patients with various severities of knee pain and/or osteoarthritis at the time of knee arthroscopy or total joint replacement. Synovial fluid was aspirated from the knee joint of each patient and stored at -80°C until examination by near-infrared Raman spectroscopy. Synovial fluid aspirates from the knee joint of each patient were deposited onto a clean fused silica microscope slide and the droplet dried under ambient laboratory conditions. Each droplet was illuminated by a line-focused or a ring-focused 785 nm laser. As the droplet dries, biofluid components segregated based on solubility differences and a deposit that is spatially heterogeneous was made. Spectra taken from the droplet edges and center were dominated by protein bands and showed the presence of at least two protein moieties in the droplet. Band area and band height ratios (1410 cm -1/1450 cm -1) showed the greatest change between specimens from patients with mild/early osteoarthritis compared to those with severe/late stage osteoarthritis. The greatest differences were found in the center of the droplet, which contains more soluble protein components than the edges.

Joule heating effects on electromagnetohydrodynamic flow through a peristaltically induced micro-channel with different zeta potential and wall slip

NASA Astrophysics Data System (ADS)

Ranjit, N. K.; Shit, G. C.

2017-09-01

This paper aims to develop a mathematical model for magnetohydrodynamic flow of biofluids through a hydrophobic micro-channel with periodically contracting and expanding walls under the influence of an axially applied electric field. The velocity slip effects have been taken into account at the channel walls by employing different slip lengths due to hydrophobic gating. Different temperature jump factors have also been used to investigate the thermomechanical interactions at the fluid-solid interface. The electromagnetohydrodynamic flow in a microchannel is simplified under the framework of Debye-Hückel linearization approximation. We have derived the closed-form solutions for the linearized dimensionless boundary value problem under the assumptions of long wave length and low Reynolds number. The axial velocity, temperature, pressure distribution, stream function, wall shear stress and the Nusselt number have been appraised for diverse values of the parameters approaching into the problem. Our main focus is to determine the effects of different zeta potential on the axial velocity and temperature distribution under electromagnetic environment. This study puts forward an important observation that the different zeta potential plays an important role in controlling fluid velocity. The study further reveals that the temperature increases significantly with the Joule heating parameter and the Brinkman number (arises due to the dissipation of energy).

Peptidomics of urine and other biofluids for cancer diagnostics.

PubMed

Bauça, Josep Miquel; Martínez-Morillo, Eduardo; Diamandis, Eleftherios P

2014-08-01

Cancer is a leading cause of death worldwide. The low diagnostic sensitivity and specificity of most current cancer biomarkers make early cancer diagnosis a challenging task. The comprehensive study of peptides and small proteins in a living system, known as "peptidomics," represents an alternative technological approach to the discovery of potential biomarkers for the assessment of a wide variety of pathologies. This review examines the current status of peptidomics for several body fluids, with a focus on urine, for cancer diagnostics applications. Several studies have used high-throughput technologies to characterize the peptide content of different body fluids. Because of its noninvasive collection and high stability, urine is a valuable source of candidate cancer biomarkers. A wide variety of preanalytical issues concerning patient selection and sample handling need to be considered, because not doing so can affect the quality of the results by introducing bias and artifacts. Optimization of both the analytical strategies and the processing of bioinformatics data is also essential to minimize the false-discovery rate. Peptidomics-based studies of urine and other body fluids have yielded a number of biomolecules and peptide panels with potential for diagnosing different types of cancer, especially of the ovary, prostate, and bladder. Large-scale studies are needed to validate these molecules as cancer biomarkers. © 2013 American Association for Clinical Chemistry.

CREATININE DETERMINATION IN URINE BY LIQUID CHROMATOGRAPHY-ELECTROSPRAY IONIZATION-TANDEM MASS SPECTROMETRY METHOD.

PubMed

Dereziński, Paweł; Klupczyńska, Agnieszka; Sawicki, Wojciech; Kokot, Zenon J

2016-01-01

Creatinine determination in urine is used to estimate the completeness of the 24-h urine collection, compensation for variable diuresis and as a preliminary step in protein profiling in urine. Despite the fact that a wide range of methods of measuring creatinine level in biofluids has been developed, many of them are adversely affected by interfering substances. A new liquid chromatography-tandem mass spectrometry method for creatinine determination in urine has been developed. Chromatographic separation was performed by applying C18 column and a gradient elution. Analyses were carried out on a triple quadrupole mass spectrometer equipped with an electrospray ion source. The developed method was fully validated according to the international guidelines. The quantification range of the method was 5-1500 ng/mL, which corresponds to 1-300 mg/dL in urine. Limit of detection and quantitation were 2 and 5 ng/mL, respectively. Additionally, the comparison of creatinine determination by newly developed method to the colorimetric method was performed. The method enables the determination of creatinine in urine samples with a minimal sample preparation, excellent sensitivity and prominent selectivity. Since mass spectrometry allows to measure a number of compounds simultaneously, a future perspective would be to incorporate the determination of other clinically important compounds excreted in urine.

Biophysics and biofluid dynamics of primary cilia: evidence for and against the flow-sensing function.

PubMed

Nag, Subhra; Resnick, Andrew

2017-09-01

Primary cilia have been called "the forgotten organelle" for over 20 yr. As cilia now have their own journal and several books devoted to their study, perhaps it is time to reconsider the moniker "forgotten organelle." In fact, during the drafting of this review, 12 relevant publications have been issued; we therefore apologize in advance for any relevant work we inadvertently omitted. What purpose is yet another ciliary review? The primary goal of this review is to specifically examine the evidence for and against the hypothesized flow-sensing function of primary cilia expressed by differentiated epithelia within a kidney tubule, bringing together differing disciplines and their respective conceptual and experimental approaches. We will show that understanding the biophysics/biomechanics of primary cilia provides essential information for understanding any potential role of ciliary function in disease. We will summarize experimental and mathematical models used to characterize renal fluid flow and incident force on primary cilia and to characterize the mechanical response of cilia to an externally applied force and discuss possible ciliary-mediated cell signaling pathways triggered by flow. Throughout, we stress the importance of separating the effects of fluid shear and stretch from the action of hydrodynamic drag. Copyright © 2017 the American Physiological Society.

The NASA Microgravity Fluid Physics Program: Research Plans for the ISS

NASA Technical Reports Server (NTRS)

Kohl, Fred J.; Singh, Bhim S.; Shaw, Nancy J.; Chiaramonte, Francis P.

2003-01-01

Building on over four decades of research and technology development related to the behavior of fluids in low gravity environments, the current NASA Microgravity Fluid Physics Program continues the quest for knowledge to further understand and design better fluids systems for use on earth and in space. NASA's Biological and Physical Research Enterprise seeks to exploit the space environment to conduct research supporting human exploration of space (strategic research), research of intrinsic scientific importance and impact (fundamental research), and commercial research. The strategic research thrust will build the vital knowledge base needed to enable NASA's mission to explore the Universe and search for life. There are currently five major research areas in the Microgravity Fluid Physics Program: complex fluids, niultiphase flows and phase change, interfacial phenomena, biofluid mechanics, and dynamics and instabilities. Numerous investigations into these areas are being conducted in both ground-based laboratories and facilities and in the flight experiments program. Most of the future NASA- sponsored flight experiments in microgravity fluid physics and transport phenomena will be carried out on the International Space Station (ISS) in the Fluids Integrated Rack (FIR), in the Microgravity Science Glovebox (MSG), in EXPRESS racks, and in other facilities provided by international partners. This paper presents an overview of the near- and long-term visions for NASA's Microgravity Fluid Physics Research Program and brief descriptions of hardware systems planned to enable this research.

Pea Fiber and Wheat Bran Fiber Show Distinct Metabolic Profiles in Rats as Investigated by a 1H NMR-Based Metabolomic Approach

PubMed Central

Liu, Guangmang; Xiao, Liang; Fang, Tingting; Cai, Yimin; Jia, Gang; Zhao, Hua; Wang, Jing; Chen, Xiaoling; Wu, Caimei

2014-01-01

This study aimed to examine the effect of pea fiber (PF) and wheat bran fiber (WF) supplementation in rat metabolism. Rats were assigned randomly to one of three dietary groups and were given a basal diet containing 15% PF, 15% WF, or no supplemental fiber. Urine and plasma samples were analyzed by NMR-based metabolomics. PF significantly increased the plasma levels of 3-hydroxybutyrate, and myo-inositol as well as the urine levels of alanine, hydroxyphenylacetate, phenylacetyglycine, and α-ketoglutarate. However, PF significantly decreased the plasma levels of isoleucine, leucine, lactate, and pyruvate as well as the urine levels of allantoin, bile acids, and trigonelline. WF significantly increased the plasma levels of acetone, isobutyrate, lactate, myo-inositol, and lipids as well as the urine levels of alanine, lactate, dimethylglycine, N-methylniconamide, and α-ketoglutarate. However, WF significantly decreased the plasma levels of amino acids, and glucose as well as the urine levels of acetate, allantoin, citrate, creatine, hippurate, hydroxyphenylacetate, and trigonelline. Results suggest that PF and WF exposure can promote antioxidant activity and can exhibit common systemic metabolic changes, including lipid metabolism, energy metabolism, glycogenolysis and glycolysis metabolism, protein biosynthesis, and gut microbiota metabolism. PF can also decrease bile acid metabolism. These findings indicate that different fiber diet may cause differences in the biofluid profile in rats. PMID:25541729

Laser surface treatment for porous and textured Ca-P bio-ceramic coating on Ti-6Al-4V.

PubMed

Paital, Sameer R; Dahotre, Narendra B

2007-12-01

In the present paper the feasibility of depositing a porous calcium phosphate (CaP) bio-ceramic coating using a continuous wave Nd:YAG laser on a Ti-6Al-4V substrate has been demonstrated. The advantages offered by such porous bio-ceramic coating are its inertness combined with the mechanical stability of the highly convoluted interface that develops when bone grows into the pores of ceramic. The formation of different phases with varying laser fluences is studied using x-ray diffraction (XRD). A quantitative estimation of the crystallite size and relative amounts of Ti and other predominant phases such as TiO(2) and alpha-tricalcium phosphate (alpha-TCP) were obtained. An increase in the crystallite size with increasing laser fluence is observed for all the above three phases. It is observed that TiO(2) is the predominant phase for all laser fluences and there is an increase in the alpha-TCP phase with increasing laser fluence. Surface porosity measurements indicated a decreasing trend with increasing laser fluence. Microhardness measurements in the cross section of samples showed a maximum hardness within the coating. The bioactivity of the coatings was further demonstrated by the formation of an apatite-like layer on the surface of the sample after being immersed in a simulated biofluid.

The effect of loading carbon nanotubes onto chitosan films on electrochemical dopamine sensing in the presence of biological interference.

PubMed

Shukla, Sudheesh K; Lavon, Avia; Shmulevich, Offir; Ben-Yoav, Hadar

2018-05-01

In vivo monitoring of the neurotransmitter dopamine can potentially improve the diagnosis of neurological disorders and elucidate their underlying biochemical mechanisms. While electrochemical sensors can detect unlabeled dopamine molecules, their sensing performance is dramatically reduced by electrochemical currents generated by other, interfering molecules (e.g., uric acid) in the biological environment. To overcome this caveat, the surface of the sensor is often modified with electrocatalytic materials, which are encapsulated inside a polymeric film; however, the effect of the encapsulating film on the sensing performance of the electrode has not been systematically studied. This study characterizes the effect of loading carbon nanotubes (CNTs) onto a chitosan film on the electrochemical sensing performance of dopamine in the presence of uric acid. Higher CNT loading increases the diffusion and electron transfer rate coefficients of the sensor and, in the presence of uric acid, provides better sensitivity (3.00µALµmol -1 for 1.75% CNT loading, vs 0.01µALµmol -1 for 1% loading) but a poorer limit-of-detection (2.00µmolL -1 vs 1.00, respectively), as reported here for the first time. These findings can help optimize the sensitivity and the limit-of-detection of electrochemical sensors in complex biofluids to enable an in vivo monitoring of dopamine and other redox-active molecules. Copyright © 2017 Elsevier B.V. All rights reserved.

Resolving Low-Density Lipoprotein (LDL) on the Human Aortic Surface Using Large Eddy Simulation

NASA Astrophysics Data System (ADS)

Lantz, Jonas; Karlsson, Matts

2011-11-01

The prediction and understanding of the genesis of vascular diseases is one of the grand challenges in biofluid engineering. The progression of atherosclerosis is correlated to the build- up of LDL on the arterial surface, which is affected by the blood flow. A multi-physics simulation of LDL mass transport in the blood and through the arterial wall of a subject specific human aorta was performed, employing a LES turbulence model to resolve the turbulent flow. Geometry and velocity measurements from magnetic resonance imaging (MRI) were incorporated to assure physiological relevance of the simulation. Due to the turbulent nature of the flow, consecutive cardiac cycles are not identical, neither in vivo nor in the simulations. A phase average based on a large number of cardiac cycles is therefore computed, which is the proper way to get reliable statistical results from a LES simulation. In total, 50 cardiac cycles were simulated, yielding over 2.5 Billion data points to be post-processed. An inverse relation between LDL and WSS was found; LDL accumulated on locations where WSS was low and vice-versa. Large temporal differences were present, with the concentration level decreasing during systolic acceleration and increasing during the deceleration phase. This method makes it possible to resolve the localization of LDL accumulation in the normal human aorta with its complex transitional flow.

A novel alternating current multiple array electrothermal micropump for lab-on-a-chip applications.

PubMed

Salari, A; Navi, M; Dalton, C

2015-01-01

The AC electrothermal technique is very promising for biofluid micropumping, due to its ability to pump high conductivity fluids. However, compared to electroosmotic micropumps, a lack of high fluid flow is a disadvantage. In this paper, a novel AC multiple array electrothermal (MAET) micropump, utilizing multiple microelectrode arrays placed on the side-walls of the fluidic channel of the micropump, is introduced. Asymmetric coplanar microelectrodes are placed on all sides of the microfluidic channel, and are actuated in different phases: one, two opposing, two adjacent, three, or all sides at the same time. Micropumps with different combinations of side electrodes and cross sections are numerically investigated in this paper. The effect of the governing parameters with respect to thermal, fluidic, and electrical properties are studied and discussed. To verify the simulations, the AC MAET concept was then fabricated and experimentally tested. The resulted fluid flow achieved by the experiments showed good agreement with the corresponding simulations. The number of side electrode arrays and the actuation patterns were also found to greatly influence the micropump performance. This study shows that the new multiple array electrothermal micropump design can be used in a wide range of applications such as drug delivery and lab-on-a-chip, where high flow rate and high precision micropumping devices for high conductivity fluids are needed.

Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes

PubMed Central

Alsaweed, Mohammed; Lai, Ching Tat; Hartmann, Peter E.; Geddes, Donna T.; Kakulas, Foteini

2016-01-01

Human milk (HM) is a complex biofluid conferring nutritional, protective and developmental components for optimal infant growth. Amongst these are maternal cells, which change in response to feeding and were recently shown to be a rich source of miRNAs. We used next generation sequencing to characterize the cellular miRNA profile of HM collected before and after feeding. HM cells conserved higher miRNA content than the lipid and skim HM fractions or other body fluids, in accordance with previous studies. In total, 1467 known mature and 1996 novel miRNAs were identified, with 89 high-confidence novel miRNAs. HM cell content was higher post-feeding (p < 0.05), and was positively associated with total miRNA content (p = 0.014) and species number (p < 0.001). This coincided with upregulation of 29 known and 2 novel miRNAs, and downregulation of 4 known and 1 novel miRNAs post-feeding, but no statistically significant change in expression was found for the remaining miRNAs. These findings suggest that feeding may influence the miRNA content of HM cells. The most highly and differentially expressed miRNAs were key regulators of milk components, with potential diagnostic value in lactation performance. They are also involved in the control of body fluid balance, thirst, appetite, immune response, and development, implicating their functional significance for the infant. PMID:27322254

Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

PubMed Central

Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

2016-01-01

The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

Forecasting Chronic Diseases Using Data Fusion.

PubMed

Acar, Evrim; Gürdeniz, Gözde; Savorani, Francesco; Hansen, Louise; Olsen, Anja; Tjønneland, Anne; Dragsted, Lars Ove; Bro, Rasmus

2017-07-07

Data fusion, that is, extracting information through the fusion of complementary data sets, is a topic of great interest in metabolomics because analytical platforms such as liquid chromatography-mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy commonly used for chemical profiling of biofluids provide complementary information. In this study, with a goal of forecasting acute coronary syndrome (ACS), breast cancer, and colon cancer, we jointly analyzed LC-MS, NMR measurements of plasma samples, and the metadata corresponding to the lifestyle of participants. We used supervised data fusion based on multiple kernel learning and exploited the linearity of the models to identify significant metabolites/features for the separation of healthy referents and the cases developing a disease. We demonstrated that (i) fusing LC-MS, NMR, and metadata provided better separation of ACS cases and referents compared with individual data sets, (ii) NMR data performed the best in terms of forecasting breast cancer, while fusion degraded the performance, and (iii) neither the individual data sets nor their fusion performed well for colon cancer. Furthermore, we showed the strengths and limitations of the fusion models by discussing their performance in terms of capturing known biomarkers for smoking and coffee. While fusion may improve performance in terms of separating certain conditions by jointly analyzing metabolomics and metadata sets, it is not necessarily always the best approach as in the case of breast cancer.

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

Nephron segment specific microRNA biomarkers of pre-clinical drug-induced renal toxicity: Opportunities and challenges

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

Nassirpour, Rounak, E-mail: Rounak.nassirpour@pfiz

Drug-induced nephrotoxicity is a common drug development complication for pharmaceutical companies. Sensitive, specific, translatable and non-invasive biomarkers of renal toxicity are urgently needed to diagnose nephron segment specific injury. The currently available gold standard biomarkers for nephrotoxicity are not kidney-specific, lack sensitivity for early detection, and are not suitable for renal damage localization (glomerular vs tubulointerstitial injury). MicroRNAs (miRNAs) are increasingly gaining momentum as promising biomarkers of various organ toxicities, including drug induced renal injury. This is mostly due to their stability in easily accessible biofluids, ease of developing nucleic acids detection compared to protein detection assays, as well asmore » their interspecies translatability. Increasing concordance of miRNA findings by standardizing methodology most suitable for their detection and quantitation, as well as characterization of their expression pattern in a cell type specific manner, will accelerate progress toward validation of these miRNAs as biomarkers in pre-clinical, and clinical settings. This review aims to highlight the current pre-clinical findings surrounding miRNAs as biomarkers in two important segments of the nephron, the glomerulus and tubules. - Highlights: • miRNAs are promising biomarkers of drug-induced kidney injury. • Summarized pre-clinical miRNA biomarkers of drug-induced nephrotoxicity. • Described the strengths and challenges associated with miRNAs as biomarkers.« less

Comparison of the fatty acid profile of Spanish infant formulas and Galician women breast milk.

PubMed

Barreiro, Rocío; Regal, Patricia; López-Racamonde, Olga; Cepeda, Alberto; Fente, Cristina A

2018-02-01

The importance of dietary lipids during childhood is evident, as they are necessary for correct growth and development of the newborn. When breastfeeding is not possible, infant formulas are designed to mimic human milk as much as possible to fulfill infant's requirements. However, the composition of these dairy products is relatively constant, while human milk is not a uniform bio-fluid and changes according to the requirements of the baby. In this study, breast milk samples were donated by 24 Spanish mothers in different lactation stages and different infant formulas were purchased in supermarkets and pharmacies. Gas chromatography coupled to flame ionization detection was used for the fatty acid determination. Compared to breast milk, first-stage formulas are apparently very similar in composition; however, no major differences were observed in the fatty acid profiles between formulas of different lactation stages. The Galician women breast milk has a fatty acid profile rich in oleic acid, linoleic acid, arachidonic acid, and docosahexaenoic acid. When comparing human milk with formulas, it becomes evident that the manufacturers tend to enrich the formulas with essential fatty acids (especially with α-linolenic acid), but arachidonic and docosahexaenoic acid levels are lower than in breast milk. Additionally, the obtained results demonstrated that after 1 year of lactation, human milk is still a good source of energy, essential fatty acids, and long-chain polyunsaturated fatty acids for the baby.

Identification of compounds in an anti-fibrosis Chinese medicine (Fufang Biejia Ruangan Pill) and its absorbed components in rat biofluids and liver by UPLC-MS.

PubMed

Dong, Qin; Qiu, Ling-Ling; Zhang, Cong-En; Chen, Long-Hu; Feng, Wu-Wen; Ma, Li-Na; Yan, Dan; Niu, Ming; Wang, Jia-Bo; Xiao, Xiao-He

2016-07-15

Liver fibrosis represents a major public health problem worldwide. To date, antifibrotic treatment of fibrosis still remains an unconquered area for western medicine. Fufang Biejia Ruangan Pill (FFBJ) is the first anti-fibrosis drug approved by the China State Food and Drug Administration, and has been demonstrated to have a good antifibrotic efficacy in China. However, the chemical constituents of FFBJ and the absorption and distribution of it in vivo remain unclear, which restricts its research on bioactive components identification and mechanisms of action. In this study, ultra-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UPLC/Q-TOF-MS) combined with ultra-performance liquid chromatography/triple quadrupole mass spectrometry (UPLC/QqQ-MS) was applied to identify compounds in FFBJ and its absorbed components in rat serum, liver and urine samples after intragastric administration of FFBJ. As a result, a total of 32 Chinese material medica components including organic acids, terpenoids, flavonoids, phenylpropanoids and alkaloids, were identified or tentatively characterized, while the distribution of 10 prototype compounds in rat serum, liver and urine were discovered. The identified constituents in FFBJ and the distribution of prototype compounds in rat serum, liver and urine are help for understanding the material bases of its therapeutic effects. Copyright © 2016. Published by Elsevier B.V.

Sensitive SERS-pH sensing in biological media using metal carbonyl functionalized planar substrates.

PubMed

Kong, Kien Voon; Dinish, U S; Lau, Weber Kam On; Olivo, Malini

2014-04-15

Conventional nanoparticle based Surface enhanced Raman scattering (SERS) technique for pH sensing often fails due to the aggregation of particles when detecting in acidic medium or biosamples having high ionic strength. Here, We develop SERS based pH sensing using a novel Raman reporter, arene chromium tricarbonyl linked aminothiophenol (Cr(CO)3-ATP), functionalized onto a nano-roughened planar substrates coated with gold. Unlike the SERS spectrum of the ATP molecule that dominates in the 400-1700 cm(-1) region, which is highly interfered by bio-molecules signals, metal carbonyl-ATP (Cr(CO)3)-ATP) offers the advantage of monitoring the pH dependent strong CO stretching vibrations in the mid-IR (1800-2200 cm(-1)) range. Raman signal of the CO stretching vibrations at ~1820 cm(-1) has strong dependency on the pH value of the environment, where its peak undergo noticeable shift as the pH of the medium is varied from 3.0 to 9.0. The sensor showed better sensitivity in the acidic range of the pH. We also demonstrate the pH sensing in a urine sample, which has high ionic strength and our data closely correlate to the value obtained from conventional sensor. In future, this study may lead to a sensitive chip based pH sensing platform in bio-fluids for the early diagnosis of diseases. © 2013 Published by Elsevier B.V.

Metabolomics identifies a biological response to chronic low-dose natural uranium contamination in urine samples.

PubMed

Grison, Stéphane; Favé, Gaëlle; Maillot, Matthieu; Manens, Line; Delissen, Olivia; Blanchardon, Eric; Banzet, Nathalie; Defoort, Catherine; Bott, Romain; Dublineau, Isabelle; Aigueperse, Jocelyne; Gourmelon, Patrick; Martin, Jean-Charles; Souidi, Maâmar

2013-01-01

Because uranium is a natural element present in the earth's crust, the population may be chronically exposed to low doses of it through drinking water. Additionally, the military and civil uses of uranium can also lead to environmental dispersion that can result in high or low doses of acute or chronic exposure. Recent experimental data suggest this might lead to relatively innocuous biological reactions. The aim of this study was to assess the biological changes in rats caused by ingestion of natural uranium in drinking water with a mean daily intake of 2.7 mg/kg for 9 months and to identify potential biomarkers related to such a contamination. Subsequently, we observed no pathology and standard clinical tests were unable to distinguish between treated and untreated animals. Conversely, LC-MS metabolomics identified urine as an appropriate biofluid for discriminating the experimental groups. Of the 1,376 features detected in urine, the most discriminant were metabolites involved in tryptophan, nicotinate, and nicotinamide metabolic pathways. In particular, N -methylnicotinamide, which was found at a level seven times higher in untreated than in contaminated rats, had the greatest discriminating power. These novel results establish a proof of principle for using metabolomics to address chronic low-dose uranium contamination. They open interesting perspectives for understanding the underlying biological mechanisms and designing a diagnostic test of exposure.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies.

PubMed

Cserhati, Matyas F; Pandey, Sanjit; Beaudoin, James J; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33,017,407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. © The Author(s) 2015. Published by Oxford University Press.

The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies

PubMed Central

Cserhati, Matyas F.; Pandey, Sanjit; Beaudoin, James J.; Baccaglini, Lorena; Guda, Chittibabu; Fox, Howard S.

2015-01-01

We herein present the National NeuroAIDS Tissue Consortium-Data Coordinating Center (NNTC-DCC) database, which is the only available database for neuroAIDS studies that contains data in an integrated, standardized form. This database has been created in conjunction with the NNTC, which provides human tissue and biofluid samples to individual researchers to conduct studies focused on neuroAIDS. The database contains experimental datasets from 1206 subjects for the following categories (which are further broken down into subcategories): gene expression, genotype, proteins, endo-exo-chemicals, morphometrics and other (miscellaneous) data. The database also contains a wide variety of downloadable data and metadata for 95 HIV-related studies covering 170 assays from 61 principal investigators. The data represent 76 tissue types, 25 measurement types, and 38 technology types, and reaches a total of 33 017 407 data points. We used the ISA platform to create the database and develop a searchable web interface for querying the data. A gene search tool is also available, which searches for NCBI GEO datasets associated with selected genes. The database is manually curated with many user-friendly features, and is cross-linked to the NCBI, HUGO and PubMed databases. A free registration is required for qualified users to access the database. Database URL: http://nntc-dcc.unmc.edu PMID:26228431

Spectral relative standard deviation: a practical benchmark in metabolomics.

PubMed

Parsons, Helen M; Ekman, Drew R; Collette, Timothy W; Viant, Mark R

2009-03-01

Metabolomics datasets, by definition, comprise of measurements of large numbers of metabolites. Both technical (analytical) and biological factors will induce variation within these measurements that is not consistent across all metabolites. Consequently, criteria are required to assess the reproducibility of metabolomics datasets that are derived from all the detected metabolites. Here we calculate spectrum-wide relative standard deviations (RSDs; also termed coefficient of variation, CV) for ten metabolomics datasets, spanning a variety of sample types from mammals, fish, invertebrates and a cell line, and display them succinctly as boxplots. We demonstrate multiple applications of spectral RSDs for characterising technical as well as inter-individual biological variation: for optimising metabolite extractions, comparing analytical techniques, investigating matrix effects, and comparing biofluids and tissue extracts from single and multiple species for optimising experimental design. Technical variation within metabolomics datasets, recorded using one- and two-dimensional NMR and mass spectrometry, ranges from 1.6 to 20.6% (reported as the median spectral RSD). Inter-individual biological variation is typically larger, ranging from as low as 7.2% for tissue extracts from laboratory-housed rats to 58.4% for fish plasma. In addition, for some of the datasets we confirm that the spectral RSD values are largely invariant across different spectral processing methods, such as baseline correction, normalisation and binning resolution. In conclusion, we propose spectral RSDs and their median values contained herein as practical benchmarks for metabolomics studies.

The NASA Microgravity Fluid Physics Program: Knowledge for Use on Earth and Future Space Missions

NASA Technical Reports Server (NTRS)

Kohl, Fred J.; Singh, Bhim S.; Alexander, J. Iwan; Shaw, Nancy J.; Hill, Myron E.; Gati, Frank G.

2002-01-01

Building on over four decades of research and technology development related to the behavior of fluids in low gravity environments, the current NASA Microgravity Fluid Physics Program continues the quest for knowledge to further understand and design better fluids systems for use on earth and in space. The purpose of the Fluid Physics Program is to support the goals of NASA's Biological and Physical Research Enterprise which seeks to exploit the space environment to conduct research and to develop commercial opportunities, while building the vital knowledge base needed to enable efficient and effective systems for protecting and sustaining humans during extended space flights. There are currently five major research areas in the Microgravity Fluid Physics Program: complex fluids, multiphase flows and phase change, interfacial phenomena, biofluid mechanics, and dynamics and instabilities. Numerous investigations into these areas are being conducted in both ground-based laboratories and facilities and in the flight experiments program. Most of the future NASA-sponsored fluid physics and transport phenomena studies will be carried out on the International Space Station in the Fluids Integrated Rack, in the Microgravity Science Glovebox, in EXPRESS racks, and in other facilities provided by international partners. This paper will present an overview of the near- and long-term visions for NASA's Microgravity Fluid Physics Research Program and brief descriptions of hardware systems planned to achieve this research.

Serum Dyslipidemia Is Induced by Internal Exposure to Strontium-90 in Mice, Lipidomic Profiling Using a Data-Independent Liquid Chromatography-Mass Spectrometry Approach.

PubMed

Goudarzi, Maryam; Weber, Waylon M; Chung, Juijung; Doyle-Eisele, Melanie; Melo, Dunstana R; Mak, Tytus D; Strawn, Steven J; Brenner, David J; Guilmette, Raymond; Fornace, Albert J

2015-09-04

Despite considerable research into the environmental risks and biological effects of exposure to external beam γ rays, incorporation of radionuclides has largely been understudied. This dosimetry and exposure risk assessment is challenging for first responders in the field during a nuclear or radiological event. Therefore, we have developed a workflow for assessing injury responses in easily obtainable biofluids, such as urine and serum, as the result of exposure to internal emitters cesium-137 ((137)Cs) and strontium-90 ((90)Sr) in mice. Here we report on the results of the untargeted lipidomic profiling of serum from mice exposed to (90)Sr. We also compared these results to those from previously published (137)Cs exposure to determine any differences in cellular responses based on exposure type. The results of this study conclude that there is a gross increase in the serum abundance of triacylglycerides and cholesterol esters, while phostaphatidylcholines and lysophosphatidylcholines displayed decreases in their serum levels postexposure at study days 4, 7, 9, 25, and 30, with corresponding average cumulative skeleton doses ranging from 1.2 ± 0.1 to 5.2 ± 0.73 Gy. The results show significant perturbations in serum lipidome as early as 2 days postexposure persisting until the end of the study (day 30).

Review: Tau in biofluids - relation to pathology, imaging and clinical features.

PubMed

Zetterberg, H

2017-04-01

Tau is a microtubule-binding protein that is important for the stability of neuronal axons. It is normally expressed within neurons and is also secreted into the brain interstitial fluid that communicates freely with cerebrospinal fluid (CSF) and, in a more restricted manner, blood via the glymphatic clearance system of the brain. In Alzheimer's disease (AD), neuroaxonal degeneration results in increased release of tau from neurons. Furthermore, tau is truncated and phosphorylated, which leads to aggregation of tau in neurofibrillary tangles of the proximal axoplasm. Neuroaxonal degeneration and tangle formation are reflected by increased concentrations of total tau (T-tau, measured using assays that detect most forms of tau) and phospho-tau (P-tau, measured using assays with antibodies specific to phosphorylated forms of tau). In AD CSF, both T-tau and P-tau concentrations are increased. In stroke and other CNS disorders with neuroaxonal injury but without tangles, T-tau is selectively increased, whereas P-tau concentration often stays normal. In tauopathies (diseases with both neurodegeneration and neurofibrillary tangles) other than AD, CSF T-tau and P-tau concentrations are typically unaltered, which is a puzzling result that warrants further investigation. In the current review, I discuss the association of T-tau and P-tau concentrations in body fluids with neuropathological changes, imaging findings and clinical features in AD and other CNS diseases. © 2017 British Neuropathological Society.

Moisture-triggered physically transient electronics

PubMed Central

Gao, Yang; Zhang, Ying; Wang, Xu; Sim, Kyoseung; Liu, Jingshen; Chen, Ji; Feng, Xue; Xu, Hangxun; Yu, Cunjiang

2017-01-01

Physically transient electronics, a form of electronics that can physically disappear in a controllable manner, is very promising for emerging applications. Most of the transient processes reported so far only occur in aqueous solutions or biofluids, offering limited control over the triggering and degradation processes. We report novel moisture-triggered physically transient electronics, which exempt the needs of resorption solutions and can completely disappear within well-controlled time frames. The triggered transient process starts with the hydrolysis of the polyanhydride substrate in the presence of trace amounts of moisture in the air, a process that can generate products of corrosive organic acids to digest various inorganic electronic materials and components. Polyanhydride is the only example of polymer that undergoes surface erosion, a distinct feature that enables stable operation of the functional devices over a predefined time frame. Clear advantages of this novel triggered transience mode include that the lifetime of the devices can be precisely controlled by varying the moisture levels and changing the composition of the polymer substrate. The transience time scale can be tuned from days to weeks. Various transient devices, ranging from passive electronics (such as antenna, resistor, and capacitor) to active electronics (such as transistor, diodes, optoelectronics, and memories), and an integrated system as a platform demonstration have been developed to illustrate the concept and verify the feasibility of this design strategy. PMID:28879237

Electrostatically driven resonance energy transfer in "cationic" biocompatible indium phosphide quantum dots.

PubMed

Devatha, Gayathri; Roy, Soumendu; Rao, Anish; Mallick, Abhik; Basu, Sudipta; Pillai, Pramod P

2017-05-01

Indium Phosphide Quantum Dots (InP QDs) have emerged as an alternative to toxic metal ion based QDs in nanobiotechnology. The ability to generate cationic surface charge, without compromising stability and biocompatibility, is essential in realizing the full potential of InP QDs in biological applications. We have addressed this challenge by developing a place exchange protocol for the preparation of cationic InP/ZnS QDs. The quaternary ammonium group provides the much required permanent positive charge and stability to InP/ZnS QDs in biofluids. The two important properties of QDs, namely bioimaging and light induced resonance energy transfer, are successfully demonstrated in cationic InP/ZnS QDs. The low cytotoxicity and stable photoluminescence of cationic InP/ZnS QDs inside cells make them ideal candidates as optical probes for cellular imaging. An efficient resonance energy transfer ( E ∼ 60%) is observed, under physiological conditions, between the cationic InP/ZnS QD donor and anionic dye acceptor. A large bimolecular quenching constant along with a linear Stern-Volmer plot confirms the formation of a strong ground state complex between the cationic InP/ZnS QDs and the anionic dye. Control experiments prove the role of electrostatic attraction in driving the light induced interactions, which can rightfully form the basis for future nano-bio studies between cationic InP/ZnS QDs and anionic biomolecules.

Use of direct gradient analysis to uncover biological hypotheses in 16s survey data and beyond.

PubMed

Erb-Downward, John R; Sadighi Akha, Amir A; Wang, Juan; Shen, Ning; He, Bei; Martinez, Fernando J; Gyetko, Margaret R; Curtis, Jeffrey L; Huffnagle, Gary B

2012-01-01

This study investigated the use of direct gradient analysis of bacterial 16S pyrosequencing surveys to identify relevant bacterial community signals in the midst of a "noisy" background, and to facilitate hypothesis-testing both within and beyond the realm of ecological surveys. The results, utilizing 3 different real world data sets, demonstrate the utility of adding direct gradient analysis to any analysis that draws conclusions from indirect methods such as Principal Component Analysis (PCA) and Principal Coordinates Analysis (PCoA). Direct gradient analysis produces testable models, and can identify significant patterns in the midst of noisy data. Additionally, we demonstrate that direct gradient analysis can be used with other kinds of multivariate data sets, such as flow cytometric data, to identify differentially expressed populations. The results of this study demonstrate the utility of direct gradient analysis in microbial ecology and in other areas of research where large multivariate data sets are involved.

Vortex-based spatiotemporal characterization of nonlinear flows

NASA Astrophysics Data System (ADS)

Byrne, Gregory A.

Although the ubiquity of vortices in nature has been recognized by artists for over seven centuries, it was the work of artist and scientist Leonardo da Vinci that provided the monumental transition from an aesthetic form to a scientific tool. DaVinci used vortices to describe the motions he observed in air currents, flowing water and blood flow in the human heart. Five centuries later, the Navier-Stokes equations allow us to recreate the swirling motions of fluid observed in nature. Computational fluid dynamic (CFD) simulations have provided a lens through which to study the role of vortices in a wide variety of modern day applications. The research summarized below represents an effort to look through this lens and bring into focus the practical use of vortices in describing nonlinear flows. Vortex-based spatiotemporal characterizations are obtained using two specific mathematical tools: vortex core lines (VCL) and proper orthogonal decomposition (POD). By applying these tools, we find that vortices continue to provide new insights in the realm of biofluids, urban flows and the phase space of dynamical systems. The insights we have gained are described in this thesis. Our primary focus is on biofluids. Specifically, we seek to gain new insights into the connection between vortices and vascular diseases in order to provide more effective methods for clinical diagnosis and treatment. We highlight several applications in which VCL and POD are used to characterize the flow conditions in a heart pump, identify stenosis in carotid arteries and validate numerical models against PIV-based experimental data. Next, we quantify the spatial complexity and temporal stability of hemodynamics generated by a database of 210 patient-specific aneurysm geometries. Visual classifications of the hemodynamics are compared to the automated, quantitative classifications. The quantities characterizing the hemodynamics are then compared to clinical data to determine conditions that are most conducive to rupture. Flows that form multiple vortices and undergo large-scale structural changes over the cardiac cycle are found to pose the most significant risk to patients. Concepts from dynamical systems are then applied to explain the formation of large-scale vortical flow structures in cerebral aneurysms. This is done by investigating the role of critical points along vortex core lines. We provide evidence that critical points are created and destroyed in saddle-node bifurcations during the cardiac cycle and that these bifurcations are responsible for changing the large-scale flow structure inside the aneurysm. Uncovering and understanding these mechanisms is the first step towards individualized treatments designed to suppress the creation of specific blood flow patterns that are known to present a risk of rupture. A simple differential dynamical system is used to illustrate the dynamical systems related concepts. Two examples illustrating the use of vortex-based methods in other domains are highlighted at the end of this work. The first example uses realistic CFD modeling of air flow through subway tunnels and stations to study the spread of accidental or planned release of airborne chemical or biological contaminants. Quantities from the vortex-based characterizations are shown to provide clear signatures that correlate to the dispersion and transport of pollutants though the stations. The second example examines swirling flow structures in the phase space of dynamical systems. Descriptions of vortices and their properties are extended to higher dimensions within the special class of differential dynamical systems.

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability

PubMed Central

2013-01-01

Background The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. Methods Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. Results An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. Conclusions We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market. PMID:23445834

Establishing a Southern Swedish Malignant Melanoma OMICS and biobank clinical capability.

PubMed

Welinder, Charlotte; Jönsson, Göran; Ingvar, Christian; Lundgren, Lotta; Olsson, Håkan; Breslin, Thomas; Végvári, Akos; Laurell, Thomas; Rezeli, Melinda; Jansson, Bo; Baldetorp, Bo; Marko-Varga, György

2013-02-27

The objectives and goals of the Southern Swedish Malignant Melanoma (SSMM) are to develop, build and utilize cutting edge biobanks and OMICS platforms to better understand disease pathology and drug mechanisms. The SSMM research team is a truly cross-functional group with members from oncology, surgery, bioinformatics, proteomics, and genomics initiatives. Within the research team there are members who daily diagnose patients with suspect melanomas, do follow-ups on malignant melanoma patients and remove primary or metastatic lesions by surgery. This inter-disciplinary clinical patient care ensures a competence build as well as a best practice procedure where the patient benefits. Clinical materials from patients before, during and after treatments with clinical end points are being collected. Tissue samples as well as bio-fluid samples such as blood fractions, plasma, serum and whole blood will be archived in 384-high density sample tube formats. Standardized approaches for patient selections, patient sampling, sample-processing and analysis platforms with dedicated protein assays and genomics platforms that will hold value for the research community are used. The patient biobank archives are fully automated with novel ultralow temperature biobank storage units and used as clinical resources. An IT-infrastructure using a laboratory information management system (LIMS) has been established, that is the key interface for the research teams in order to share and explore data generated within the project. The cross-site data repository in Lund forms the basis for sample processing, together with biological samples in southern Sweden, including blood fractions and tumor tissues. Clinical registries are associated with the biobank materials, including pathology reports on disease diagnosis on the malignant melanoma (MM) patients. We provide data on the developments of protein profiling and targeted protein assays on isolated melanoma tumors, as well as reference blood standards that is used by the team members in the respective laboratories. These pilot data show biobank access and feasibility of performing quantitative proteomics in MM biobank repositories collected in southern Sweden. The scientific outcomes further strengthen the build of healthcare benefit in the complex challenges of malignant melanoma pathophysiology that is addressed by the novel personalized medicines entering the market.

Dissolvable layered double hydroxide as an efficient nanosorbent for centrifugeless air-agitated dispersive solid-phase extraction of potentially toxic metal ions from bio-fluid samples.

PubMed

Rajabi, Maryam; Arghavani-Beydokhti, Somayeh; Barfi, Behruz; Asghari, Alireza

2017-03-08

In the present work, a novel nanosorbent namely layered double hydroxides with 4-amino-5-hydroxyl-2,7-naphthalendisulfonic acid monosodium salt interlayer anion (Mg-Al-AHNDA-LDH) was synthesized and applied as a dissolvable nanosorbent in a centrifugeless ultrasound-enhanced air-agitated dispersive solid-phase extraction (USE-AA-D-SPE) method. This method was used for the separation and preconcentration of some metal ions including Cd 2+ , Cr 6+ , Pb 2+ , Co 2+ , and Ni 2+ prior to their determination using the micro-sampling flame atomic absorption spectrometry (MS-FAAS) technique. The most interesting aspect of this nanosorbent is its immediate dissolvability at pH values lower than 4. This capability drastically eliminates the elution step, leading to a great improvement in the extraction efficiency and a decrease in the extraction time. Also in this method, the use of a syringe nanofilter eliminates the need for the centrifugation step, which is time-consuming and essentially causes the analysis to be off-line. Several effective parameters governing the extraction efficiency including the sample solution pH, amount of nanosorbent, eluent condition, number of air-agitation cycles, and sonication time were investigated and optimized. Under the optimized conditions, the good linear dynamic ranges of 2-70, 6-360, 7-725, 7-370, and 8-450 ng mL -1 for the Cd 2+ , Cr 6+ , Pb 2+ , Co 2+ and Ni 2+ ions, respectively, with the correlation of determinations (R 2 s) higher than 0.997 were obtained. The limits of detection (LODs) were found to be 0.6, 1.7, 2.0, 2.1, and 2.4 for the Cd 2+ , Cr 6+ , Pb 2+ , Co 2+ , and Ni 2+ ions, respectively. The intra-day and inter-day precisions (percent relative standard deviations (%RSDs) (n = 5)) were below 7.8%. The proposed method was also successfully applied for the extraction and determination of the target ions in different biological fluid and tap water samples. Copyright © 2017 Elsevier B.V. All rights reserved.

48 CFR 47.305-7 - Quantity analysis, direct delivery, and reduction of crosshauling and backhauling.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Quantity analysis, direct... Contracts 47.305-7 Quantity analysis, direct delivery, and reduction of crosshauling and backhauling. (a) Quantity analysis. (1) The requiring activity shall consider the acquisition of carload or truckload...

Alteration of metabolomic markers of amino-acid metabolism in piglets with in-feed antibiotics.

PubMed

Mu, Chunlong; Yang, Yuxiang; Yu, Kaifan; Yu, Miao; Zhang, Chuanjian; Su, Yong; Zhu, Weiyun

2017-04-01

In-feed antibiotics have been used to promote growth in piglets, but its impact on metabolomics profiles associated with host metabolism is largely unknown. In this study, to test the hypothesis that antibiotic treatment may affect metabolite composition both in the gut and host biofluids, metabolomics profiles were analyzed in antibiotic-treated piglets. Piglets were fed a corn-soy basal diet with or without in-feed antibiotics from postnatal day 7 to day 42. The serum biochemical parameters, metabolomics profiles of the serum, urine, and jejunal digesta, and indicators of microbial metabolism (short-chain fatty acids and biogenic amines) were analyzed. Compared to the control group, antibiotics treatment did not have significant effects on serum biochemical parameters except that it increased (P < 0.05) the concentration of urea. Antibiotics treatment increased the relative concentrations of metabolites involved in amino-acid metabolism in the serum, while decreased the relative concentrations of most amino acids in the jejunal content. Antibiotics reduced urinary 2-ketoisocaproate and hippurate. Furthermore, antibiotics decreased (P < 0.05) the concentrations of propionate and butyrate in the feces. Antibiotics significantly affected the concentrations of biogenic amines, which are derived from microbial amino-acid metabolism. The three major amines, putrescine, cadaverine, and spermidine, were all increased (P < 0.05) in the large intestine of antibiotics-treated piglets. These results identified the phenomena that in-feed antibiotics may have significant impact on the metabolomic markers of amino-acid metabolism in piglets.

HMDB 3.0--The Human Metabolome Database in 2013.

PubMed

Wishart, David S; Jewison, Timothy; Guo, An Chi; Wilson, Michael; Knox, Craig; Liu, Yifeng; Djoumbou, Yannick; Mandal, Rupasri; Aziat, Farid; Dong, Edison; Bouatra, Souhaila; Sinelnikov, Igor; Arndt, David; Xia, Jianguo; Liu, Philip; Yallou, Faizath; Bjorndahl, Trent; Perez-Pineiro, Rolando; Eisner, Roman; Allen, Felicity; Neveu, Vanessa; Greiner, Russ; Scalbert, Augustin

2013-01-01

The Human Metabolome Database (HMDB) (www.hmdb.ca) is a resource dedicated to providing scientists with the most current and comprehensive coverage of the human metabolome. Since its first release in 2007, the HMDB has been used to facilitate research for nearly 1000 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 3.0) has been significantly expanded and enhanced over the 2009 release (version 2.0). In particular, the number of annotated metabolite entries has grown from 6500 to more than 40,000 (a 600% increase). This enormous expansion is a result of the inclusion of both 'detected' metabolites (those with measured concentrations or experimental confirmation of their existence) and 'expected' metabolites (those for which biochemical pathways are known or human intake/exposure is frequent but the compound has yet to be detected in the body). The latest release also has greatly increased the number of metabolites with biofluid or tissue concentration data, the number of compounds with reference spectra and the number of data fields per entry. In addition to this expansion in data quantity, new database visualization tools and new data content have been added or enhanced. These include better spectral viewing tools, more powerful chemical substructure searches, an improved chemical taxonomy and better, more interactive pathway maps. This article describes these enhancements to the HMDB, which was previously featured in the 2009 NAR Database Issue. (Note to referees, HMDB 3.0 will go live on 18 September 2012.).

Multiplexed MRM-based quantitation of candidate cancer biomarker proteins in undepleted and non-enriched human plasma.

PubMed

Percy, Andrew J; Chambers, Andrew G; Yang, Juncong; Borchers, Christoph H

2013-07-01

An emerging approach for multiplexed targeted proteomics involves bottom-up LC-MRM-MS, with stable isotope-labeled internal standard peptides, to accurately quantitate panels of putative disease biomarkers in biofluids. In this paper, we used this approach to quantitate 27 candidate cancer-biomarker proteins in human plasma that had not been treated by immunoaffinity depletion or enrichment techniques. These proteins have been reported as biomarkers for a variety of human cancers, from laryngeal to ovarian, with breast cancer having the highest correlation. We implemented measures to minimize the analytical variability, improve the quantitative accuracy, and increase the feasibility and applicability of this MRM-based method. We have demonstrated excellent retention time reproducibility (median interday CV: 0.08%) and signal stability (median interday CV: 4.5% for the analytical platform and 6.1% for the bottom-up workflow) for the 27 biomarker proteins (represented by 57 interference-free peptides). The linear dynamic range for the MRM assays spanned four orders-of-magnitude, with 25 assays covering a 10(3) -10(4) range in protein concentration. The lowest abundance quantifiable protein in our biomarker panel was insulin-like growth factor 1 (calculated concentration: 127 ng/mL). Overall, the analytical performance of this assay demonstrates high robustness and sensitivity, and provides the necessary throughput and multiplexing capabilities required to verify and validate cancer-associated protein biomarker panels in human plasma, prior to clinical use. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.