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quantitative biology

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https://www.readbyqxmd.com/read/28544980/what-we-authors-reviewers-and-editors-of-scientific-work-can-learn-from-the-analytical-history-of-biological-3-nitrotyrosine
#1
REVIEW
Dimitrios Tsikas
Tyrosine and tyrosine residues in proteins are attacked by the reactive oxygen and nitrogen species peroxynitrite (O=N-OO(-)) to generate 3-nitrotyrosine (3-NT) and 3-nitrotyrosine-proteins (3-NTProt), respectively. 3-NT and 3-NTProt are widely accepted as biomarkers of nitr(os)ative stress. Over the years many different analytical methods have been reported for 3-NT and 3-NTProt. Reported concentrations often differ by more than three orders of magnitude, indicative of serious analytical problems. Strategies to overcome pre-analytical and analytical shortcomings and pitfalls have been proposed...
May 13, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28544970/quantitative-chemical-imaging-with-stimulated-raman-scattering-microscopy
#2
REVIEW
Dan Fu
Chemical imaging plays an increasingly important role in studying heterogeneous biological systems. It combines molecular spectroscopy with high-resolution spatial information to create quantitative images of molecular distributions. Here I summarize recent progress in technical developments and biological applications of a specific chemical imaging technique-stimulated Raman scattering (SRS) microscopy. SRS microscopy allows for a wide range of molecules - both endogenous and exogenous - to be imaged at high spatial and temporal resolution in living cells, tissues, and organisms...
May 22, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28544497/cell-tracking-using-gold-nanoparticles-and-computed-tomography-imaging
#3
REVIEW
Rinat Meir, Rachela Popovtzer
Cell-based therapies utilize transplantation of living cells with therapeutic traits to alleviate numerous diseases and disorders. The use of such biological agents is an attractive alternative for diseases that existing medicine cannot effectively treat. Although very promising, translating cell therapy to the clinic has proven to be challenging, due to inconsistent results in preclinical and clinical studies. To examine the underlying cause for these inconsistencies, it is crucial to noninvasively monitor the accuracy of cell injection, and cell survival and migration patterns...
May 24, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28544415/inertial-microfluidic-cell-stretcher-imcs-fully-automated-high-throughput-and-near-real-time-cell-mechanotyping
#4
Yanxiang Deng, Steven P Davis, Fan Yang, Kevin S Paulsen, Maneesh Kumar, Rebecca Sinnott DeVaux, Xianhui Wang, Douglas S Conklin, Assad Oberai, Jason I Herschkowitz, Aram J Chung
Mechanical biomarkers associated with cytoskeletal structures have been reported as powerful label-free cell state identifiers. In order to measure cell mechanical properties, traditional biophysical (e.g., atomic force microscopy, micropipette aspiration, optical stretchers) and microfluidic approaches were mainly employed; however, they critically suffer from low-throughput, low-sensitivity, and/or time-consuming and labor-intensive processes, not allowing techniques to be practically used for cell biology research applications...
May 23, 2017: Small
https://www.readbyqxmd.com/read/28543403/decellularized-human-liver-is-too-heterogeneous-for-designing-a-generic-extracellular-matrix-mimic-hepatic-scaffold
#5
Giorgio Mattei, Chiara Magliaro, Andrea Pirone, Arti Ahluwalia
Decellularized human livers are considered the perfect extracellular matrix (ECM) surrogate because both three-dimensional architecture and biological features of the hepatic microenvironment are thought to be preserved. However, donor human livers are in chronically short supply, both for transplantation or as decellularized scaffolds, and will become even scarcer as life expectancy increases. It is hence of interest to determine the structural and biochemical properties of human hepatic ECM to derive design criteria for engineering biomimetic scaffolds...
May 23, 2017: Artificial Organs
https://www.readbyqxmd.com/read/28543298/synthesis-and-preclinical-pharmacokinetic-study-of-dha-10-a-novel-potential-antifungal-pogostone-analogue
#6
Ming Liu, Yanfen Zhou, Jianwei Zhu, Bo Ma, Zheng Fang, Qi Zhang
OBJECTIVES: The emergence of fungal disease calls for the urgency of development of novel drug. In this study, we developed a novel pogostone analogue, DHA-10 and investigated its preclinical pharmacokinetics, tissue distribution, excretion and protein binding rate in rats. METHODS: DHA-10 was synthesized with dehydroacetic acid (DHA) as the starting material and the structure confirmed by NMR and HRMS. The LC-MS/MS was applied to quantitative analysis of DHA-10 concentrations in the biological samples...
May 23, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28542600/snp-in-human-arhgef3-promoter-is-associated-with-dnase-hypersensitivity-transcript-level-and-platelet-function-and-arhgef3-ko-mice-have-increased-mean-platelet-volume
#7
Siying Zou, Alexandra M Teixeira, Myrto Kostadima, William J Astle, Aparna Radhakrishnan, Lukas Mikolaj Simon, Lucy Truman, Jennifer S Fang, John Hwa, Ping-Xia Zhang, Pim van der Harst, Paul F Bray, Willem H Ouwehand, Mattia Frontini, Diane S Krause
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation...
2017: PloS One
https://www.readbyqxmd.com/read/28542484/simulating-within-vector-generation-of-the-malaria-parasite-diversity
#8
Lauren M Childs, Olivia F Prosper
Plasmodium falciparum, the most virulent human malaria parasite, undergoes asexual reproduction within the human host, but reproduces sexually within its vector host, the Anopheles mosquito. Consequently, the mosquito stage of the parasite life cycle provides an opportunity to create genetically novel parasites in multiply-infected mosquitoes, potentially increasing parasite population diversity. Despite the important implications for disease transmission and malaria control, a quantitative mapping of how parasite diversity entering a mosquito relates to diversity of the parasite exiting, has not been undertaken...
2017: PloS One
https://www.readbyqxmd.com/read/28541666/unveiling-the-molecular-structure-of-pulmonary-surfactant-corona-on-nanoparticles
#9
Qinglin Hu, Xuan Bai, Guoqing Hu, Yi Y Zuo
The growing risk of human exposure to airborne nanoparticles (NPs) causes a general concern on the biosafety of nanotechnology. Inhaled NPs can deposit in the deep lung at which interacting with the pulmonary surfactant (PS). Despite the increasing study of nano-bio interactions, detailed molecular mechanisms by which inhaled NPs interact with the natural PS system remain unclear. Using coarse-grained molecular dynamics simulation, we studied the interaction between NPs and the PS system in the alveolar fluid...
May 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28541365/responses-of-human-adipose-derived-stem-cells-to-interstitial-level-of-extremely-low-shear-flows-regarding-differentiation-morphology-and-proliferation
#10
Sung-Hwan Kim, Kihoon Ahn, Joong Yull Park
Human cells encounter a range of shear stress levels in situ and this natural variability in shear stress implies that realistic investigations of cell type characteristics may depend on nontrivial shear stress models. Human adipose-derived stem cells (hASCs) differentiate near the blood capillary vessels where interstitial flows predominate. However, the effects of interstitial levels of shear on hASCs are not fully understood. In this study, we propose a microfluidic shear generation system, in which a gradient distribution of the interstitial level of shear flow is created to investigate the effects of interstitial-level shear flow on hASCs...
May 25, 2017: Lab on a Chip
https://www.readbyqxmd.com/read/28540805/the-in-vivo-performance-of-a-novel-thermal-accelerant-agent-used-for-augmentation-of-microwave-energy-delivery-within-biologic-tissues-during-image-guided-thermal-ablation-a-porcine-study
#11
William Keun Chan Park, Aaron Wilhelm Palmer Maxwell, Victoria Elizabeth Frank, Michael Patrick Primmer, Jarod Brian Paul, Scott Andrew Collins, Kara Anne Lombardo, Shaolei Lu, Tiffany Marie Borjeson, Grayson Luderman Baird, Damian Edward Dupuy
OBJECTIVES: To investigate the effects of a novel caesium-based thermal accelerant (TA) agent on ablation zone volumes following in vivo microwave ablation of porcine liver and skeletal muscle, and to correlate the effects of TA with target organ perfusion. MATERIALS AND METHODS: This prospective study was performed following institutional animal care and use committee approval. Microwave ablation was performed in liver and resting skeletal muscle in eight Sus scrofa domesticus swine following administration of TA at concentrations of 0 mg/mL (control), 100 mg/mL and 250 mg/mL...
April 24, 2017: International Journal of Hyperthermia
https://www.readbyqxmd.com/read/28540623/qsp-toolbox-computational-implementation-of-integrated-workflow-components-for-deploying-multi-scale-mechanistic-models
#12
Yougan Cheng, Craig J Thalhauser, Shepard Smithline, Jyotsna Pagidala, Marko Miladinov, Heather E Vezina, Manish Gupta, Tarek A Leil, Brian J Schmidt
Quantitative systems pharmacology (QSP) modeling has become increasingly important in pharmaceutical research and development, and is a powerful tool to gain mechanistic insights into the complex dynamics of biological systems in response to drug treatment. However, even once a suitable mathematical framework to describe the pathophysiology and mechanisms of interest is established, final model calibration and the exploration of variability can be challenging and time consuming. QSP models are often formulated as multi-scale, multi-compartment nonlinear systems of ordinary differential equations...
May 24, 2017: AAPS Journal
https://www.readbyqxmd.com/read/28539877/the-social-context-of-do-it-yourself-brain-stimulation-neurohackers-biohackers-and-lifehackers
#13
Anna Wexler
The "do-it-yourself" (DIY) brain stimulation movement began in earnest in late 2011, when lay individuals began building stimulation devices and applying low levels of electricity to their heads for self-improvement purposes. To date, scholarship on the home use of brain stimulation has focused on characterizing the practices of users via quantitative and qualitative studies, and on analyzing related ethical and regulatory issues. In this perspective piece, however, I take the opposite approach: rather than viewing the home use of brain stimulation on its own, I argue that it must be understood within the context of other DIY and citizen science movements...
2017: Frontiers in Human Neuroscience
https://www.readbyqxmd.com/read/28539744/biological-effects-of-hesperetin-on-interleukin-6-phosphorylated-signal-transducer-and-activator-of-transcription-3-pathway-signaling-in-prostate-cancer-pc3-cells
#14
Moein Shirzad, Esfandiar Heidarian, Pezhman Beshkar, Mostafa Gholami-Arjenaki
BACKGROUND: Interleukin-6 (IL-6) is a multifunctional glycoprotein that regulates the growth of some tumors, including prostate carcinomas due to signal transducer and activator of transcription 3 (STAT3), extracellular signal-regulated kinases 1/2 (ERK1/2), and AKT signaling pathways. Hesperetin, as a flavanone, has several biological properties such as antitumor and anti-inflammatory. OBJECTIVE: This study was carried out to evaluate the biological effects of hesperetin on the IL-6 gene expression and phosphorylated STAT3, AKT, and ERK1/2 signaling pathways in PC3 prostate cancer (PC) cells...
April 2017: Pharmacognosy Research
https://www.readbyqxmd.com/read/28539467/b7-h3-expression-in-nsclc-and-its-association-with-b7-h4-pd-l1-and-tumor-infiltrating-lymphocytes
#15
Mehmet Altan, Vasiliki Pelekanou, Kurt A Schalper, Maria I Toki, Patricia Gaule, Konstantinos N Syrigos, Roy S Herbst, David L Rimm
Background and Purpose: <p>The immune checkpoint PD-1 and its receptor B7-H1 (PD-L1) are successful therapeutic targets in cancer but less is known about other B7 family members.  Here, we determined the expression level of B7-H3 protein in non-small cell lung cancer (NSCLC) and evaluated its association with tumor infiltrating lymphocytes (TILs), PD-L1, B7-H4 and major clinico-pathological characteristics is in 3 NSCLC cohorts.</p> <p>Experimental design:</p> <p>We used multiplexed automated quantitative immunofluorescence (QIF) to assess the levels of B7-H3, PD-L1, B7-H4 and TILs in 634 NSCLC cases with validated antibodies...
May 24, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28539121/network-mirroring-for-drug-repositioning
#16
Sunghong Park, Dong-Gi Lee, Hyunjung Shin
BACKGROUND: Although drug discoveries can provide meaningful insights and significant enhancements in pharmaceutical field, the longevity and cost that it takes can be extensive where the success rate is low. In order to circumvent the problem, there has been increased interest in 'Drug Repositioning' where one searches for already approved drugs that have high potential of efficacy when applied to other diseases. To increase the success rate for drug repositioning, one considers stepwise screening and experiments based on biological reactions...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28539064/recent-advances-in-applying-mass-spectrometry-and-systems-biology-to-determine-brain-dynamics
#17
Enzo Scifo, Giulio Calza, Martin Fuhrmann, Rabah Soliymani, Marc Baumann, Maciej Lalowski
Neurological disorders encompass various pathologies which disrupt normal brain physiology and function. Poor understanding of their underlying molecular mechanisms and their societal burden argues for the necessity of novel prevention strategies, early diagnostic techniques and alternative treatment options to reduce the scale of their expected increase. Areas Covered: This review scrutinizes mass spectrometry based approaches used to investigate brain dynamics in various conditions, including neurodegenerative and neuropsychiatric disorders...
May 24, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28536831/abnormal-expression-of-long-non-coding-rnas-in-myocardial-infarction
#18
Tao Wu, Huan-Dong Wu, Zao-Xian Xu, Fei Han, Bi-Qi Zhang, Jian Sun, Shen-Jiang Hu
Myocardial infarction (MI) is the leading cause of fatality worldwide. Our study aimed to investigate the dysregulated long non-coding RNA (lncRNA) in MI and elucidate the mechanism of it in MI. The lncRNA and mRNA expression profiling of the whole left ventricular tissue of MI mice model (8 mice) and Sham group (8 mice) was obtained based on microarray analysis. Differentially expressed lnRNAs/mRNA (DELs/DEMs) were identified in MI. DELs/DEMs co-expression network construction, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were conducted to predict the biological functions of DEMs...
May 23, 2017: Heart and Vessels
https://www.readbyqxmd.com/read/28535261/recruitment-of-a-lineage-specific-virulence-regulatory-pathway-promotes-intracellular-infection-by-a-plant-pathogen-experimentally-evolved-into-a-legume-symbiont
#19
Delphine Capela, Marta Marchetti, Camille Clérissi, Anthony Perrier, Dorian Guetta, Carine Gris, Marc Valls, Alain Jauneau, Stéphane Cruveiller, Eduardo P C Rocha, Catherine Masson-Boivin
Ecological transitions between different lifestyles, such as pathogenicity, mutualism and saprophytism, have been very frequent in the course of microbial evolution, and often driven by horizontal gene transfer. Yet, how genomes achieve the ecological transition initiated by the transfer of complex biological traits remains poorly known. Here we used experimental evolution, genomics, transcriptomics and high-resolution phenotyping to analyze the evolution of the plant pathogen Ralstonia solanacearum into legume symbionts, following the transfer of a natural plasmid encoding the essential mutualistic genes...
May 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28535179/reduced-frequency-of-cells-latently-infected-with-replication-competent-hiv-1-in-virally-suppressed-individuals-living-in-rakai-uganda
#20
Jessica L Prodger, Jun Lai, Steven J Reynolds, Jeanne C Keruly, Richard D Moore, Jingo Kasule, Taddeo Kityamuweesi, Paul Buule, David Serwadda, Martha Nason, Adam A Capoferri, Stephen F Porcella, Robert F Siliciano, Andrew D Redd, Janet D Siliciano, Thomas C Quinn
Background: HIV-1 persists in latently infected resting CD4+ T cells (rCD4), posing a major barrier to curing HIV-1 infection. Previous studies have quantified this pool of latently infected cells in Americans; however, no study has quantified this reservoir in sub-Saharan Africans, who make up the largest population of HIV-1-infected individuals globally. Methods: Peripheral blood was collected from 70 virally suppressed HIV-1-infected individuals from Rakai District, Uganda, who had initiated antiretroviral therapy (ART) during chronic infection...
May 23, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
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