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Biofluid dynamics

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https://www.readbyqxmd.com/read/27813239/combined-tissue-and-fluid-proteomics-with-tandem-mass-tags-to-identify-low-abundant-protein-biomarkers-of-disease-in-peripheral-body-fluid-an-alzheimer-s-disease-case-study
#1
Claire L Russell, Amanda Heslegrave, Vikram Mitra, Henrik Zetterberg, Jennifer M Pocock, Malcolm A Ward, Ian Pike
RATIONALE: Ideal biomarkers are present in readily accessible samples including plasma and CSF, and are directly derived from diseased tissue, therefore likely to be of relatively low abundance. Traditional unbiased proteomic approaches for biomarker discovery have struggled to detect low abundance markers due to the high dynamic range of proteins, the predominance of hyper-abundant proteins, and the use of data-dependent acquisition MS. To overcome these limitations and improve biomarker discovery in peripheral fluids, we have developed TMTcalibrator™; a novel MS workflow combining isobarically labelled diseased tissue digests in parallel with an appropriate set of labelled body fluids to increase the chance of identifying low abundance, tissue-derived biomarkers...
November 4, 2016: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/27649337/lithotripter-shock-wave-interaction-with-a-bubble-near-various-biomaterials
#2
S W Ohl, E Klaseboer, A J Szeri, B C Khoo
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...
October 7, 2016: Physics in Medicine and Biology
https://www.readbyqxmd.com/read/27633951/detergents-friends-not-foes-for-high-performance-membrane-proteomics-toward-precision-medicine
#3
REVIEW
Xi Zhang
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...
September 16, 2016: Proteomics
https://www.readbyqxmd.com/read/27630182/defining-glomerular-disease-in-mechanistic-terms-implementing-an-integrative-biology-approach-in-nephrology
#4
Laura H Mariani, William F Pendergraft, Matthias Kretzler
Advances in biomedical research allow for the capture of an unprecedented level of genetic, molecular, and clinical information from large patient cohorts, where the quest for precision medicine can be pursued. An overarching goal of precision medicine is to integrate the large-scale genetic and molecular data with deep phenotypic information to identify a new mechanistic disease classification. This classification can ideally be used to meet the clinical goal of the right medication for the right patient at the right time...
September 14, 2016: Clinical Journal of the American Society of Nephrology: CJASN
https://www.readbyqxmd.com/read/27154709/direct-detection-of-circulating-free-dna-extracted-from-serum-samples-of-breast-cancer-using-locked-nucleic-acid-molecular-beacon
#5
Zhen Gui, Quanbo Wang, Jinchang Li, Mingchen Zhu, Lili Yu, Tang Xun, Feng Yan, Huangxian Ju
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)...
July 1, 2016: Talanta
https://www.readbyqxmd.com/read/27094208/analyses-of-endothelial-cells-and-endothelial-progenitor-cells-released-microvesicles-by-using-microbead-and-q-dot-based-nanoparticle-tracking-analysis
#6
Jinju Wang, Yun Zhong, Xiaotang Ma, Xiang Xiao, Chuanfang Cheng, Yusen Chen, Ifeanyi Iwuchukwu, Kenneth J Gaines, Bin Zhao, Shiming Liu, Jeffrey B Travers, Ji C Bihl, Yanfang Chen
Accurate analysis of specific microvesicles (MVs) from biofluids is critical and challenging. Here we described novel methods to purify and detect MVs shed from endothelial cells (ECs) and endothelial progenitor cells (EPCs) by combining microbeads with fluorescence quantum dots (Q-dots) coupled nanoparticle tracking analysis (NTA). In the in vitro screening systems, we demonstrated that 1) anti-CD105 (EC marker) and anti-CD34 (EPC marker) conjugated-microbeads had the highest sensitivity and specificity for isolating respective MVs, which were confirmed with negative controls, CD41 and CD235a; 2) anti-CD144 (EC marker) and anti-KDR (EPC marker) conjugated-Q-dots exhibited the best sensitivity and specificity for their respective MV NTA detection, which were confirmed with positive control, anti-Annexin V (MV universal marker)...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27038173/dynamic-assessment-of-functional-lipidomic-analysis-in-human-urine
#7
Hannah E Rockwell, Fei Gao, Emily Y Chen, Justice McDaniel, Rangaprasad Sarangarajan, Niven R Narain, Michael A Kiebish
The development of enabling mass spectrometry platforms for the quantification of diverse lipid species in human urine is of paramount importance for understanding metabolic homeostasis in normal and pathophysiological conditions. Urine represents a non-invasive biofluid that can capture distinct differences in an individual's physiological status. However, currently there is a lack of quantitative workflows to engage in high throughput lipidomic analysis. This study describes the development of a MS/MS(ALL) shotgun lipidomic workflow and a micro liquid chromatography-high resolution tandem mass spectrometry (LC-MS/MS) workflow for urine structural and mediator lipid analysis, respectively...
July 2016: Lipids
https://www.readbyqxmd.com/read/26868616/contributions-of-immunoaffinity-chromatography-to-deep-proteome-profiling-of-human-biofluids
#8
Chaochao Wu, Jicheng Duan, Tao Liu, Richard D Smith, Wei-Jun Qian
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...
May 15, 2016: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/26718583/integrated-epcam-independent-subtraction-enrichment-and-ifish-strategies-to-detect-and-classify-disseminated-and-circulating-tumors-cells
#9
Peter Ping Lin
Application of tumor cell surface adhesion molecule Anti-epithelial cell adhesion molecule (EpCAM)-dependent antibody capture, and intracellular cytokeratins (CKs)-dependent immunostaining strategies to detect disseminated or circulating tumor cells (DTCs or CTCs), is limited by highly heterogeneous and dynamic expression or absence of EpCAM and/or CKs in CTCs and DTCs, particularly in their capturing and identifying CTCs/DTCs shed from diverse types of solid tumor, thus being biased and restricted to the only both EpCAM and CK positive cancer cells...
December 2015: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/26593324/hemodynamic-characterization-of-geometric-cerebral-aneurysm-templates-treated-with-embolic-coils
#10
Priya Nair, Brian W Chong, Aprinda Indahlastari, Justin Ryan, Christopher Workman, M Haithem Babiker, Hooman Yadollahi Farsani, Carlos E Baccin, David Frakes
Embolic coiling is one of the most effective treatments for cerebral aneurysms (CAs), largely due to the hemodynamic modifications that the treatment effects in the aneurysmal environment. However, coiling can have very different hemodynamic outcomes in aneurysms with different geometries. Previous work in the field of biofluid mechanics has demonstrated on a general level that geometry is a driving factor behind aneurysmal hemodynamics. The goal of this study was to relate two specific geometric factors that describe CAs (i...
February 2016: Journal of Biomechanical Engineering
https://www.readbyqxmd.com/read/26369869/personalized-liposome-protein-corona-in-the-blood-of-breast-gastric-and-pancreatic-cancer-patients
#11
Valentina Colapicchioni, Martina Tilio, Luca Digiacomo, Valentina Gambini, Sara Palchetti, Cristina Marchini, Daniela Pozzi, Sergio Occhipinti, Augusto Amici, Giulio Caracciolo
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...
June 2016: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/26354827/dynamic-footprint-of-sequestration-in-the-molecular-fluctuations-of-osteopontin
#12
S Lenton, T Seydel, T Nylander, C Holt, M Härtlein, S Teixeira, G Zaccai
The sequestration of calcium phosphate by unfolded proteins is fundamental to the stabilization of biofluids supersaturated with respect to hydroxyapatite, such as milk, blood or urine. The unfolded state of osteopontin (OPN) is thought to be a prerequisite for this activity, which leads to the formation of core-shell calcium phosphate nanoclusters. We report on the structures and dynamics of a native OPN peptide from bovine milk, studied by neutron spectroscopy and small-angle X-ray and neutron scattering...
September 6, 2015: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/26313857/optical-characterization-of-core-shell-quantum-dots-embedded-in-synthetic-saliva-temporal-dynamics
#13
Juliana F de Santana, Viviane Pilla, Anielle C A Silva, Noelio O Dantas, Djalmir N Messias, Acácio A Andrade
The present work reports the spectroscopic and thermo-optical properties of CdSe/ZnS and CdSe/CdS core-shell quantum dots (QDs) embedded in synthetic saliva. Spectroscopy studies were performed applying nonfunctionalized CdSe/ZnS QDs (3.4, 3.9 and 5.1 nm cores) and hydroxyl group-functionalized ultrasmall CdSe/CdS core-shell quantum dots (1.6 nm core) suspended in artificial saliva at different potential of hydrogen (pH) values. Saliva was chosen because it is important in a variety of functions such as protecting teeth through the buffering capacity of the formed biofilm, hydration, and dental remineralization...
October 2015: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/26290610/metabolic-profiling-in-human-exposome-studies
#14
REVIEW
Toby J Athersuch, Hector C Keun
The human metabolome-the complement of small molecule metabolites present in biofluids and tissues-represents a significant part of the internal chemical milieu and is therefore an important aspect of the human exposome. Metabolic profiling approaches, commonly referred to as metabonomics or metabolomics, permit detailed and efficient characterisation of human biospecimens; application to population studies holds great promise for uncovering new associations and causal relationships between environmental factors and chronic disease...
November 2015: Mutagenesis
https://www.readbyqxmd.com/read/26267323/enhanced-detection-and-comprehensive-in-situ-phenotypic-characterization-of-circulating-and-disseminated-heteroploid-epithelial-and-glioma-tumor-cells
#15
Feng Ge, Haishi Zhang, Daisy Dandan Wang, Linda Li, Peter Ping Lin
Conventional strategy of anti-EpCAM capture and immunostaining of cytokeratins (CKs) to detect circulating tumor cells (CTCs) is limited by highly heterogeneous and dynamic expression or absence of EpCAM and/or CKs in CTCs. In this study, a novel integrated cellular and molecular approach of subtraction enrichment (SE) and immunostaining-FISH (iFISH) was successfully developed. Both large or small size CTCs and circulating tumor microemboli (CTM) in various biofluid samples including cerebrospinal fluid (CSF) of cancer patients and patient-derived-xenograft (PDX) mouse models were efficiently enriched and comprehensively identified and characterized by SE-iFISH...
September 29, 2015: Oncotarget
https://www.readbyqxmd.com/read/26212450/real-time-monitoring-of-alzheimer-s-related-amyloid-aggregation-via-probe-enhancement-fluorescence-correlation-spectroscopy
#16
Yinghua Guan, Kevin J Cao, Adam Cantlon, Kristyna Elbel, Emmanuel A Theodorakis, Dominic M Walsh, Jerry Yang, Jagesh V Shah
This work describes the use of fluorescence correlation spectroscopy (FCS) and a novel amyloid-binding fluorescent probe, ARCAM 1, to monitor the aggregation of the Alzheimer's disease-associated amyloid β-peptide (Aβ). ARCAM 1 exhibits a large increase in fluorescence emission upon binding to Aβ assemblies, making it an excellent candidate for probe enhancement FCS (PE-FCS). ARCAM 1 binding does not change Aβ aggregation kinetics. It also exhibits greater dynamic range as a probe in reporting aggregate size by FCS in Aβ, when compared to thioflavin T (ThT) or an Aβ peptide modified with a fluorophore...
September 16, 2015: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/26070325/direct-detection-of-%C3%AE-1-antitrypsin-in-serum-samples-using-surface-plasmon-resonance-with-a-new-aptamer-antibody-sandwich-assay
#17
Suhee Kim, Hye Jin Lee
The challenges associated with performing surface plasmon resonance (SPR) based measurements in serum and other biofluids have continued to limit the applicability of this valuable sensing technology for sensitive bioaffinity measurements of proteins in clinically relevant samples. In this paper, a new sandwich assay is introduced for the quantitative SPR analysis of α-1 antitrypsin (AAT), which is a recognized biomarker for Alzheimer's disease. Detection was performed via the specific adsorption of AAT onto a gold chip surface modified with a DNA aptamer...
July 21, 2015: Analytical Chemistry
https://www.readbyqxmd.com/read/26065667/controlled-microfluidic-environment-for-dynamic-investigation-of-red-blood-cell-aggregation
#18
Rym Mehri, Catherine Mavriplis, Marianne Fenech
Blood, as a non-Newtonian biofluid, represents the focus of numerous studies in the hemorheology field. Blood constituents include red blood cells, white blood cells and platelets that are suspended in blood plasma. Due to the abundance of the RBCs (40% to 45% of the blood volume), their behavior dictates the rheological behavior of blood especially in the microcirculation. At very low shear rates, RBCs are seen to assemble and form entities called aggregates, which causes the non-Newtonian behavior of blood...
2015: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/25883534/extracellular-vesicles-potential-applications-in-cancer-diagnosis-prognosis-and-epidemiology
#19
Mukesh Verma, Tram Kim Lam, Elizabeth Hebert, Rao L Divi
Both normal and diseased cells continuously shed extracellular vesicles (EVs) into extracellular space, and the EVs carry molecular signatures and effectors of both health and disease. EVs reflect dynamic changes that are occurring in cells and tissue microenvironment in health and at a different stage of a disease. EVs are capable of altering the function of the recipient cells. Trafficking and reciprocal exchange of molecular information by EVs among different organs and cell types have been shown to contribute to horizontal cellular transformation, cellular reprogramming, functional alterations, and metastasis...
2015: BMC Clinical Pathology
https://www.readbyqxmd.com/read/25784267/metabonomic-changes-associated-with-atherosclerosis-progression-for-ldlr-mice
#20
Dan Li, Lulu Zhang, Fangcong Dong, Yan Liu, Ning Li, Huihui Li, Hehua Lei, Fuhua Hao, Yulan Wang, Yi Zhu, Huiru Tang
Atherosclerosis resulting from hyperlipidemia causes many serious cardiovascular diseases. To understand the systems changes associated with pathogenesis and progression of atherosclerosis, we comprehensively analyzed the dynamic metabonomic changes in multiple biological matrices of LDLR(-/-) mice using NMR and GC-FID/MS with gene expression, clinical chemistry, and histopathological data as well. We found that 12 week "Western-type" diet (WD) treatment caused obvious aortic lesions, macrophage infiltration, and collagen level elevation in LDLR(-/-) mice accompanied by up-regulation of inflammatory factors including aortic ICAM-1, MCP-1, iNOS, MMP2, and hepatic TNFα and IL-1β...
May 1, 2015: Journal of Proteome Research
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