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Biofluid dynamics

Petra Bilić, Nicolas Guillemin, Alan Kovačević, Blanka Beer Ljubić, Ines Jović, Asier Galan, Peter David Eckersall, Richard Burchmore, Vladimir Mrljak
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...
March 9, 2018: Journal of Proteomics
John A Carver, Heath Ecroyd, Roger J W Truscott, David C Thorn, Carl Holt
Molecular chaperone proteins perform a diversity of roles inside and outside the cell. One of the most important is the stabilization of misfolding proteins to prevent their aggregation, a process that is potentially detrimental to cell viability. Diseases such as Alzheimer's, Parkinson's, and cataract are characterized by the accumulation of protein aggregates. In vivo, many proteins are metastable and therefore under mild destabilizing conditions have an inherent tendency to misfold, aggregate, and hence lose functionality...
February 14, 2018: Accounts of Chemical Research
Hechuan Jiang, Xiaojue Zhu, Varghese Mathai, Roberto Verzicco, Detlef Lohse, Chao Sun
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...
January 26, 2018: Physical Review Letters
Yan Wang, Lei Hua, Jichun Jiang, Yuanyuan Xie, Keyong Hou, Qingyun Li, Chenxin Wu, Haiyang Li
Small molecule metabolites are widely used as biomarkers in the research field of metabolomics for disease diagnosis and exposure assessment. As a readily available biofluid containing plenty of volatile organic metabolites (VOMs), urine is ideal for non-invasive metabolomic analysis; however, there is still lack of rapid analysis method for VOMs in urine. Here we report a kind of rapid method for urine analysis by employing high-pressure photon ionization time-of-flight mass spectrometry (HPPI-TOFMS) combined with dynamic purge-injection...
May 30, 2018: Analytica Chimica Acta
Ezel Boyacı, Barbara Bojko, Nathaly Reyes-Garcés, Justen J Poole, Germán Augusto Gómez-Ríos, Alexandre Teixeira, Beate Nicol, Janusz Pawliszyn
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...
January 18, 2018: Scientific Reports
Immanuel P Seitz, Stylianos Michalakis, Barbara Wilhelm, Felix F Reichel, G Alex Ochakovski, Eberhart Zrenner, Marius Ueffing, Martin Biel, Bernd Wissinger, Karl U Bartz-Schmidt, Tobias Peters, M Dominik Fischer
Purpose: To investigate shedding and biodistribution characteristics of recombinant adeno-associated virus serotype 8 (rAAV8) after single-dose subretinal or intravitreal injection in nonhuman primates (NHP, Macaca fascicularis) as a surrogate for environmental hazard and patient safety. Methods: In a study for regulatory submission, 22 NHP were divided into four cohorts receiving either single subretinal injections of vehicle or clinical grade rAAV8 (1 × 1011 or 1 × 1012 vector genomes [vg]) versus single intravitreal application of 1 × 1012 vg...
November 1, 2017: Investigative Ophthalmology & Visual Science
Haixia Wang, Youhui Lin, Karin Nienhaus, G Ulrich Nienhaus
Most surfaces of engineered nanoparticles (NPs) are reactive toward biomolecules. Therefore, whenever NPs become immersed in biological fluids, proteins and other biomolecules bind to the NP surface, forming an adsorption layer (biomolecular corona) that modifies the NPs' physicochemical properties and subsequent interactions with living systems. Its exploration is a formidable endeavor owing to the enormous diversity of engineered NPs in terms of their physicochemical properties and the vast number of biomolecules available in biofluids that may bind to NPs with widely different strengths...
October 26, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
Paul Dowling, Kay Ohlendieck
This chapter will focus on upstream immunodepletion of high abundant proteins from plasma samples and subsequent analysis by difference gel electrophoresis (DIGE). The abundances of proteins in biofluid proteomes, such as serum, plasma, saliva, and bronchoalveolar lavage fluid (BALF), can exceed 10 orders of magnitude. This substantial dynamic range is problematic for the detection of medium and low abundance proteins by DIGE analysis. To increase the detection, quantification, and identification of medium-low abundant proteins, the targeted depletion of known abundant proteins with antibody columns has been successfully employed...
2018: Methods in Molecular Biology
Sandra Murphy, Paul Dowling
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically difference gel electrophoresis (DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins...
2018: Methods in Molecular Biology
Mariano Provencio, María Torrente, Virgina Calvo, Lourdes Gutiérrez, David Pérez-Callejo, Clara Pérez-Barrios, Miguel Barquín, Ana Royuela, Begoña Rodriguez-Alfonso, Miguel Sotelo, Juan Luis Cruz-Bermúdez, Miriam Mendez, Alberto Cruz-Bermúdez, Atocha Romero
BACKGROUND: Liquid biopsy has evolved from being a promising line to becoming a validated approach for biomarker testing. However, its utility for individualization of therapy has been scarcely reported. In this study, we show how monitoring levels of EGFR mutation in plasma can be useful for the individualization of treatment. RESULTS: Longitudinal EGFR mutation levels in plasma always correlated with tumor response ascertained by RECIST criteria. Moreover, decreasing EGFR mutation levels were detected in all patients benefiting from locoregional radiotherapy, whereas the opposite occurred when a patient progressed soon after radiotherapy treatment...
September 1, 2017: Oncotarget
P Khanna, K L Johnson, J L Maron
It is difficult to identify reliable reference genes for transcriptomic analyses in biofluids such as saliva. This situation is particularly relevant for the newborn population, where rapid development is associated with dynamic changes in gene expression. Real-time gene expression monitoring holds great promise for elucidating disrupted pathways that result in morbidities unique to this population, such as retinopathy of prematurity, but its impact depends on identifying stable and consistently expressed genes across a wide range of gestational ages...
September 14, 2017: Biotechnic & Histochemistry: Official Publication of the Biological Stain Commission
Márkó Grabarics, Orsolya Csernák, Réka Balogh, Szabolcs Béni
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)...
August 31, 2017: Journal of Pharmaceutical and Biomedical Analysis
Raymond Y Lo
Alzheimer's disease (AD) has become a global health issue as the population ages. There is no effective treatment to protect against its occurrence or progression. Some argue that the lack of treatment response is due to delays in diagnosis. By the time a diagnosis of AD is made, neurodegenerative changes are at the stage where very few neurons can be salvaged by medication. The AD research community has developed the idea of mild cognitive impairment (MCI) in an attempt to find predementia patients who might benefit from potentially therapeutic drugs that have proven ineffective in the past...
April 2017: Ci Ji Yi Xue za Zhi, Tzu-chi Medical Journal
Ting Ye, Nhan Phan-Thien, Chwee Teck Lim, Lina Peng, Huixin Shi
In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. The smoothed dissipative particle dynamics (SDPD), a particle-based method, is one of the easy and flexible methods to model such complex structure fluids. It couples the best features of the smoothed particle hydrodynamics (SPH) and dissipative particle dynamics (DPD), with parameters having specific physical meaning (coming from SPH discretization of the Navier-Stokes equations), combined with thermal fluctuations in a mesoscale simulation, in a similar manner to the DPD...
June 2017: Physical Review. E
Vijay K Samineni, Jangyeol Yoon, Kaitlyn E Crawford, Yu Ra Jeong, Kajanna C McKenzie, Gunchul Shin, Zhaoqian Xie, Saranya S Sundaram, Yuhang Li, Min Young Yang, Jeonghyun Kim, Di Wu, Yeguang Xue, Xue Feng, Yonggang Huang, Aaron D Mickle, Anthony Banks, Jeong Sook Ha, Judith P Golden, John A Rogers, Robert W Gereau
The advent of optogenetic tools has allowed unprecedented insights into the organization of neuronal networks. Although recently developed technologies have enabled implementation of optogenetics for studies of brain function in freely moving, untethered animals, wireless powering and device durability pose challenges in studies of spinal cord circuits where dynamic, multidimensional motions against hard and soft surrounding tissues can lead to device degradation. We demonstrate here a fully implantable optoelectronic device powered by near-field wireless communication technology, with a thin and flexible open architecture that provides excellent mechanical durability, robust sealing against biofluid penetration and fidelity in wireless activation, thereby allowing for long-term optical stimulation of the spinal cord without constraint on the natural behaviors of the animals...
November 2017: Pain
Julie A Reisz, Katelyn M Chessler, Monika Dzieciatkowska, Angelo D'Alessandro, Kirk C Hansen
Proteome profiling using mass spectrometry is extensively utilized to understand the physiological characteristics of cells, tissues, fluids, and many other biological matrices. From the earliest days of the proteomics era, exploratory analyses of the blood protein complement have attracted a great deal of interest, owing to the pivotal importance of blood cells and biofluids (serum, plasma) for research and biomedical purposes. Once challenged by the high dynamic range of protein concentrations, low sensitivity of mass spectrometers, and poor annotation of proteomics databases, the techniques in this field have quickly evolved in recent years, particularly in the areas of absolute quantification of proteins and in mapping of posttranslational modifications...
2017: Methods in Molecular Biology
José M Amigó, Michael Small
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...
June 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Wei Feng, Qiuju Dong, Minyan Liu, Si Li, Ting Liu, Xinguo Wang, Liying Niu
Zhi-zi-chi decoction (ZZCD) is a classical formula widely used in Chinese clinical application. In the present study, a novel and efficient strategy has been developed for screening and identification of multiple constituents and their metabolites of ZZCD using ultra-high-performance liquid chromatography combined with triple time-of-flight mass spectrometry. The novel approach of an online data acquisition method dependent on multiple mass defect filter and dynamic background subtraction is combined with multiple data processing techniques...
October 2017: Biomedical Chromatography: BMC
M Simão, J M Ferreira, J Mora-Rodriguez, H M Ramos
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...
June 2017: Computer Methods in Biomechanics and Biomedical Engineering
Sergio A Hassan
Nanoparticle (NP) aggregation can lead to prolonged retention in tissues or embolism, among other adverse effects. Successful use in biomedicine thus requires the capability to make NPs with limited aggregative potential. Rational design is presently a challenge due to incomplete knowledge of their interactions in biofluids. Recently, ultrasmall gold NPs passivated with endogenous antioxidant glutathione have shown promise for use in vivo. Computer simulations are here conducted to identify the forces underlying aggregation (or lack thereof) of these NPs in a cell culture...
April 25, 2017: ACS Nano
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