keyword
MENU ▼
Read by QxMD icon Read
search

quantitative biology

keyword
https://www.readbyqxmd.com/read/28735351/multiple-correlation-analyses-revealed-complex-relationship-between-dna-methylation-and-mrna-expression-in-human-peripheral-blood-mononuclear-cells
#1
Fang-Fei Xie, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Hong Zhu, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Xiao-Wei Zhu, Wei Xia, Lan Wang, Pei He, Peng-Fei Bing, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei
DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes...
July 22, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28735093/stable-isotope-labeling-by-fatty-acids-in-cell-culture-silfac-coupled-with-isotope-pattern-dependent-mass-spectrometry-for-global-screening-of-lipid-hydroperoxide-mediated-protein-modifications
#2
Ryo Takahashi, Shuhei Fujioka, Tomoyuki Oe, Seon Hwa Lee
Lipid hydroperoxide-mediated modifications of proteins are receiving increasing attention because of their possible involvement in various degenerative diseases. These biological effects are attributed to the ability of lipid peroxidation-derived aldehydes to react with the nucleophilic sites of proteins. Here we describe a methodology involving metabolic labeling coupled with mass spectrometry-based proteomic analysis that enables global screening of lipid hydroperoxide-mediated protein modifications in a cell system...
July 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28735000/application-of-pharmacometrics-and-quantitative-systems-pharmacology-to-cancer-therapy-the-example-of-luminal-a-breast-cancer
#3
REVIEW
Brett Fleisher, Kayla Andrews, Ashley A Brown, Sihem Ait-Oudhia
Breast cancer (BC) is the most common cancer in women, and the second most frequent cause of cancer-related deaths in women worldwide. It is a heterogeneous disease composed of multiple subtypes with distinct morphologies and clinical implications. Quantitative systems pharmacology (QSP) is an emerging discipline bridging systems biology with pharmacokinetics (PK) and pharmacodynamics (PD) leveraging the systematic understanding of drugs' efficacy and toxicity. Despite numerous challenges in applying computational methodologies for QSP and mechanism-based PK/PD models to biological, physiological, and pharmacological data, bridging these disciplines has the potential to enhance our understanding of complex disease systems such as BC...
July 19, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28734051/a-user-s-guide-for-%C3%AE-synuclein-biomarker-studies-in-biological-fluids-perianalytical-considerations
#4
REVIEW
Brit Mollenhauer, Richard Batrla, Omar El-Agnaf, Douglas R Galasko, Hilal A Lashuel, Kalpana M Merchant, Lesley M Shaw, Dennis J Selkoe, Robert Umek, Hugo Vanderstichele, Henrik Zetterberg, Jing Zhang, Chelsea Caspell-Garcia, Chris Coffey, Samantha J Hutten, Mark Frasier, Peggy Taylor
Parkinson's disease biomarkers are needed to increase diagnostic accuracy, to objectively monitor disease progression and to assess therapeutic efficacy as well as target engagement when evaluating novel drug and therapeutic strategies. This article summarizes perianalytical considerations for biomarker studies (based on immunoassays) in Parkinson's disease, with emphasis on quantifying total α-synuclein protein in biological fluids. Current knowledge and pitfalls are discussed, and selected perianalytical variables are presented systematically, including different temperature of sample collection and types of collection tubes, gradient sampling, the addition of detergent, aliquot volume, the freezing time, and the different thawing methods...
July 22, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28733924/cellular-mechanosensitivity-to-substrate-stiffness-decreases-with-increasing-dissimilarity-to-cell-stiffness
#5
Tamer Abdalrahman, Laura Dubuis, Jason Green, Neil Davies, Thomas Franz
Computational modelling has received increasing attention to investigate multi-scale coupled problems in micro-heterogeneous biological structures such as cells. In the current study, we investigated for a single cell the effects of (1) different cell-substrate attachment (2) and different substrate modulus [Formula: see text] on intracellular deformations. A fibroblast was geometrically reconstructed from confocal micrographs. Finite element models of the cell on a planar substrate were developed. Intracellular deformations due to substrate stretch of [Formula: see text], were assessed for: (1) cell-substrate attachment implemented as full basal contact (FC) and 124 focal adhesions (FA), respectively, and [Formula: see text]140 KPa and (2) [Formula: see text], 140, 1000, and 10,000 KPa, respectively, and FA attachment...
July 21, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28733819/estimating-environmental-value-losses-from-earth-materials-excavation-and-infilling-for-large-scale-airport-construction-a-case-of-dalian-offshore-airport-dalian-china
#6
Hua-Kun Yan, Nuo Wang, Nuan Wu, Nan-Qi Song, Dao-Li Zhu
Large-scale airport construction removes large quantities of earth materials, resulting in serious environmental pollution and ecosystem damage. However, studies of environmental concerns caused by the materials used in airport construction are still preliminary, and those case studies on the impacts of large-scale offshore airport development are very limited. China's Dalian Offshore Airport is considered here to study the environmental value loss from 240 million m(3) of materials excavations and 21 km(2) of artificial island infillings...
July 21, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28733404/high-throughput-quantitative-genetic-interaction-mapping-in-the-fission-yeast-schizosaccharomyces-pombe
#7
Assen Roguev, Colm J Ryan, Edgar Hartsuiker, Nevan J Krogan
Epistasis mapping, in which the phenotype that emerges from combining pairs of mutations is measured quantitatively, is a powerful tool for unbiased study of gene function. When performed at a large scale, this approach has been used to assign function to previously uncharacterized genes, define functional modules and pathways, and study their cross talk. These experiments rely heavily on methods for rapid sampling of binary combinations of mutant alleles by systematic generation of a series of double mutants...
July 21, 2017: Cold Spring Harbor Protocols
https://www.readbyqxmd.com/read/28733187/a-confidence-building-exercise-in-data-and-identifiability-modeling-cancer-chemotherapy-as-a-case-study
#8
Marisa C Eisenberg, Harsh V Jain
Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions...
July 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28733025/revisiting-historical-khoe-san-skeletal-remains-in-european-collections-a-search-for-identity-through-craniometric-analysis
#9
D Botha, M Steyn, Y Scholtz, I Ribot
As the identity of a large number of Khoe-San skeletal material in European collections recently came into question during its documentation, a re-evaluation of the remains by employing a non-invasive method such as craniometrics was done to investigate the biological affinity. For this purpose, gene flow and population diversity present within the group, as well as between the study sample (N=63) and other modern and historic population groups from southern, central and east Africa were explored. Available comparative groups included the historic Khoe-San from Riet River (N=31), the Sotho-Tswana from southern Africa (N=61), the Basuku from central Africa (N=66) and the Bahutu (N=53) and Teita (N=24) from east Africa...
June 28, 2017: Homo: Internationale Zeitschrift Für die Vergleichende Forschung Am Menschen
https://www.readbyqxmd.com/read/28731516/mir-181d-regulates-human-dendritic-cell-maturation-through-nf-%C3%AE%C2%BAb-pathway
#10
Xian Wei Su, Gang Lu, Chi Kwan Leung, Qiang Liu, Yi Li, Kam Sze Tsang, Shi Dou Zhao, Danny Tat Ming Chan, Hsiang Fu Kung, Wai Sang Poon
OBJECTIVES: MicroRNAs (miRNAs) are considered as the cellular regulators which post-transcriptionally modulate gene expression in diverse biological processes including cell development and immunity. In this study, we investigated functions of miR-181d in dendritic cells (DCs) maturation, and the underlying mechanisms were also explored. MATERIALS AND METHODS: Here we did the miRNA screening in human DCs in response to lipopolysaccharides (LPS) by quantitative real-time PCR (qRT-PCR)...
July 21, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/28731408/defining-the-biological-basis-of-radiomic-phenotypes-in-lung-cancer
#11
Patrick Grossmann, Olya Stringfield, Nehme El-Hachem, Marilyn M Bui, Emmanuel Rios Velazquez, Chintan Parmar, Ralph Th Leijenaar, Benjamin Haibe-Kains, Philippe Lambin, Robert Gillies, Hugo Jwl Aerts
Medical imaging can visualize characteristics of human cancer noninvasively. Radiomics is an emerging field that translates these medical images into quantitative data to enable phenotypic profiling of tumors. While radiomics has been associated with several clinical endpoints, the complex relationships of radiomics, clinical factors, and tumor biology are largely unknown. To this end, we analyzed two independent cohorts of respectively 262 North American and 89 European patients with lung cancer, and consistently identified previously undescribed associations between radiomic imaging features, molecular pathways, and clinical factors...
July 21, 2017: ELife
https://www.readbyqxmd.com/read/28731138/upregulation-of-long-non-coding-rna-dq786243-promotes-the-progression-of-gastric-cancer
#12
Ting Shan, Juanyun Fan, Qin Zhao, Kaiyuan Deng, Jiazeng Xia
Long non‑coding RNAs (lncRNAs) have been identified as key regulatory factors in various biological processes. Their dysregulation has been observed in several types of human cancer, including gastric cancer (GC). The aim of the present study was to investigate the putative roles of the lncRNA DQ786243 in the progression of GC, as well as evaluate its diagnostic and therapeutic potential in GC. The expression of DQ786243 in 82 pairs of GC tissues and adjacent healthy tissues, as well as in three GC cell lines and a human normal gastric epithelial cell line, was assessed using reverse transcription‑quantitative polymerase chain reaction...
July 21, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28731027/ptenp1-acts-as-a-cerna-to-regulate-pten-by-sponging-mir-19b-and-explores-the-biological-role-of-ptenp1-in-breast-cancer
#13
R-K Li, J- Gao, L-H Guo, G-Q Huang, W-H Luo
This study aimed to investigate role of long noncoding RNA PTENP1 regulating PTEN expression via miR-19b to affect breast cancer (BC) progression. We measured expressions of PTENP1, miR-19b and PTEN in 65 matched BC cancerous and noncancerous tissues by quantitative real-time fluorescence PCR (qRT-PCR) and investigated the biological effects of PTENP1 in BC MDA-MB-231 cells by several in vitro experiments including CCK8, wound healing, transwell and Annexin V-FITC/PI analysis. Besides, the competing endogenous RNA (ceRNA) activity of PTENP1 on miR-19b was detected by luciferase reporter assay, and the expressions of related genes and proteins were determined by western blot assay and qRT-PCR...
July 21, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28730495/modeling-of-receptor-tyrosine-kinase-signaling-computational-and-experimental-protocols
#14
Dirk Fey, Edita Aksamitiene, Anatoly Kiyatkin, Boris N Kholodenko
The advent of systems biology has convincingly demonstrated that the integration of experiments and dynamic modelling is a powerful approach to understand the cellular network biology. Here we present experimental and computational protocols that are necessary for applying this integrative approach to the quantitative studies of receptor tyrosine kinase (RTK) signaling networks. Signaling by RTKs controls multiple cellular processes, including the regulation of cell survival, motility, proliferation, differentiation, glucose metabolism, and apoptosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730492/analysis-of-signaling-networks-at-the-single-cell-level-using-mass-cytometry
#15
Shovik Bandyopadhyay, Daniel A C Fisher, Olga Malkova, Stephen T Oh
Mass cytometry is a powerful technology that enables the measurement of >40 parameters at the single-cell level. The inherent spectral limitations of fluorescent flow cytometry are circumvented by the use of antibodies conjugated to metal isotope reporters, which are measured quantitatively using a CyTOF mass cytometer. The high dimensionality of mass cytometry is particularly useful for the analysis of cell signaling networks in complex biological samples. We describe here methods for cell preparation, antibody staining, data acquisition, and analysis of multidimensional data from a mass cytometry experiment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730490/mass-spectrometry-analysis-of-spatial-protein-networks-by-colocalization-analysis-cola
#16
Faraz K Mardakheh
A major challenge in systems biology is comprehensive mapping of protein interaction networks. Crucially, such interactions are often dynamic in nature, necessitating methods that can rapidly mine the interactome across varied conditions and treatments to reveal change in the interaction networks. Recently, we described a fast mass spectrometry-based method to reveal functional interactions in mammalian cells on a global scale, by revealing spatial colocalizations between proteins (COLA) (Mardakheh et al., Mol Biosyst 13:92-105, 2017)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730487/a-methodology-for-comprehensive-analysis-of-toll-like-receptor-signaling-in-macrophages
#17
Marijke Koppenol-Raab, Aleksandra Nita-Lazar
A combination of high-throughput, multiplexed, quantitative methods with computational modeling and statistical approaches is required to obtain system-level understanding of biological function. Mass spectrometry (MS)-based proteomics has emerged as a preferred tool for the analysis of changes in protein abundance and their post-translational modification (PTM) levels at a global scale, comparable with genomic experiments and generating data suitable for use in mathematical modeling of signaling pathways. Here we describe a set of parallel bottom-up proteomic approaches to detect and quantify the global protein changes in total intracellular proteins, their phosphorylation, and the proteins released by active and passive secretion or shedding mechanisms (referred to as the secretome as reviewed in Makridakis and Vlahou, J Proteome 73:2291-2305, 2010) in response to the stimulation of Toll-like receptors (TLRs) with specific ligands in cultured macrophages...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730481/label-free-phosphoproteomic-approach-for-kinase-signaling-analysis
#18
Edmund Wilkes, Pedro R Cutillas
Phosphoproteomics is a powerful platform for the unbiased profiling of kinase-driven signaling pathways. Quantitation of phosphorylation can be performed by means of either labeling or label-free mass spectrometry (MS) methods. Because of their simplicity and universality, label-free methodology is gaining acceptance and popularity in molecular biology research. Analytical workflows for label-free quantification of phosphorylation, however, need to overcome several hurdles for the technique to be accurate and precise...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729949/modeling-the-effect-of-blunt-impact-on-mitochondrial-function-in-cartilage-implications-for-development-of-osteoarthritis
#19
Georgi I Kapitanov, Bruce P Ayati, James A Martin
OBJECTIVE: Osteoarthritis (OA) is a disease characterized by degeneration of joint cartilage. It is associated with pain and disability and is the result of either age and activity related joint wear or an injury. Non-invasive treatment options are scarce and prevention and early intervention methods are practically non-existent. The modeling effort presented in this article is constructed based on an emerging biological hypothesis-post-impact oxidative stress leads to cartilage cell apoptosis and hence the degeneration observed with the disease...
2017: PeerJ
https://www.readbyqxmd.com/read/28728902/role-of-mirnas-in-development-and-disease-lessons-learnt-from-small-organisms
#20
REVIEW
Swati Chandra, Divya Vimal, Divya Sharma, Vipin Rai, Subash Chandra Gupta, D Kar Chowdhuri
MicroRNAs (miRNAs) constitute a class of small (21-24 nucleotides) non-coding RNAs that regulate gene expression at the post-transcriptional level. Caenorhabditis elegans, Drosophila melanogaster, and many other small organisms have been instrumental in deciphering the biological functions of miRNAs. While some miRNAs from small organisms are highly conserved across the taxa, others are organism specific. The miRNAs are known to play a crucial role during development and in various cellular functions such as cell survival, cell proliferation, and differentiation...
July 17, 2017: Life Sciences
keyword
keyword
88719
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"