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quantitative biology

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https://www.readbyqxmd.com/read/28103105/evolution-of-earth-like-extrasolar-planetary-atmospheres-assessing-the-atmospheres-and-biospheres-of-early-earth-analog-planets-with-a-coupled-atmosphere-biogeochemical-model
#1
S Gebauer, J L Grenfell, J W Stock, R Lehmann, M Godolt, P von Paris, H Rauer
Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models...
January 2017: Astrobiology
https://www.readbyqxmd.com/read/28103008/quantitative-tracking-of-combinatorially-engineered-populations-with-multiplexed-binary-assemblies
#2
Ramsey Zeitoun, Gur Pines, William C Grau, Ryan T Gill
Advances in synthetic biology and genomics have enabled full-scale genome engineering efforts on laboratory timescales. However, the absence of sufficient approaches for mapping engineered genomes at system-wide scales onto performance has limited the adoption of more sophisticated algorithms for engineering complex biological systems. Here we report on the development and application of a robust approach to quantitatively map combinatorially engineered populations at scales up to several dozen target sites...
January 19, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28101740/improving-parameter-inference-from-frap-data-an-analysis-motivated-by-pattern-formation-in-the-drosophila-wing-disc
#3
Lin Lin, Hans G Othmer
Fluorescence recovery after photobleaching (FRAP) is used to obtain quantitative information about molecular diffusion and binding kinetics at both cell and tissue levels of organization. FRAP models have been proposed to estimate the diffusion coefficients and binding kinetic parameters of species for a variety of biological systems and experimental settings. However, it is not clear what the connection among the diverse parameter estimates from different models of the same system is, whether the assumptions made in the model are appropriate, and what the qualities of the estimates are...
January 18, 2017: Bulletin of Mathematical Biology
https://www.readbyqxmd.com/read/28101613/estimation-of-anaerobic-debromination-rate-constants-of-pbde-pathways-using-an-anaerobic-dehalogenation-model
#4
Filiz Karakas, Ipek Imamoglu
This study aims to estimate anaerobic debromination rate constants (km) of PBDE pathways using previously reported laboratory soil data. km values of pathways are estimated by modifying a previously developed model as Anaerobic Dehalogenation Model. Debromination activities published in the literature in terms of bromine substitutions as well as specific microorganisms and their combinations are used for identification of pathways. The range of estimated km values is between 0.0003 and 0.0241 d(-1). The median and maximum of km values are found to be comparable to the few available biologically confirmed rate constants published in the literature...
January 19, 2017: Bulletin of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/28101283/group-active-engagements-using-quantitative-modeling-of-physiology-concepts-in-large-enrollment-biology-classes
#5
Karen L Carleton, Carly H Rietschel, Gili Marbach-Ad
No abstract text is available yet for this article.
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101282/quantitative-modeling-of-membrane-transport-and-anisogamy-by-small-groups-within-a-large-enrollment-organismal-biology-course
#6
Eric S Haag, Gili Marbach-Ad
No abstract text is available yet for this article.
December 2016: Journal of Microbiology & Biology Education: JMBE
https://www.readbyqxmd.com/read/28101231/the-biological-significance-of-methylome-differences-in-human-papilloma-virus-associated-head-and-neck-cancer
#7
Maria J Worsham, Kang Mei Chen, Indrani Datta, Josena K Stephen, Dhananjay Chitale, Alexandra Gothard, George Divine
In recent years, studies have suggested that promoter methylation in human papilloma virus (HPV) positive head and neck squamous cell carcinoma (HNSCC) has a mechanistic role and has the potential to improve patient survival. The present study aimed to replicate key molecular findings from previous analyses of the methylomes of HPV positive and HPV negative HNSCC in an independent cohort, to assess the reliability of differentially methylated markers in HPV-associated tumors. HPV was measured using real-time quantitative PCR and the biological significance of methylation differences was assessed by Ingenuity Pathway Analysis (IPA)...
December 2016: Oncology Letters
https://www.readbyqxmd.com/read/28100988/simultaneous-analyses-of-n-linked-and-o-linked-glycans-of-ovarian-cancer-cells-using-solid-phase-chemoenzymatic-method
#8
Shuang Yang, Naseruddin Höti, Weiming Yang, Yang Liu, Lijun Chen, Shuwei Li, Hui Zhang
BACKGROUND: Glycans play critical roles in a number of biological activities. Two common types of glycans, N-linked and O-linked, have been extensively analyzed in the last decades. N-glycans are typically released from glycoproteins by enzymes, while O-glycans are released from glycoproteins by chemical methods. It is important to identify and quantify both N- and O-linked glycans of glycoproteins to determine the changes of glycans. METHODS: The effort has been dedicated to study glycans from ovarian cancer cells treated with O-linked glycosylation inhibitor qualitatively and quantitatively...
2017: Clinical Proteomics
https://www.readbyqxmd.com/read/28098896/microrna-194-represses-glioma-cell-epithelial%C3%A2-to%C3%A2-mesenchymal-transition-by-targeting-bmi1
#9
Xi Zhang, Chunyan Wei, Jin Li, Jiali Liu, Jianqiang Qu
MicroRNA-194 (miR-194) is frequently dysregulated in many types of cancer. However, the function of miR-194 in glioma remains unknown. In the present study, we aimed to investigate the biological functions of miR-194 in glioma and the potential molecular mechanism of miR-194 involved in glioma progression. We found that miR-194 expression was significantly reduced in glioma specimens and cell lines, as detected by real-time quantitative polymerase chain reaction (RT-qPCR) analysis. The overexpression of miR-194 inhibited while the suppression of miR-194 promoted cell migration, invasion and epithelial mesenchymal transition (EMT) in glioma cells...
January 17, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28098890/characterization-of-the-microrna-profile-in-early-stage-cervical-squamous-cell-carcinoma-by-next-generation-sequencing
#10
Wansong Lin, Mei Feng, Guilin Chen, Zhifeng Zhou, Jieyu Li, Yunbin Ye
Squamous cell carcinoma (SCC) is histologically the most prominent type of cervical cancer. There is accumulating evidence suggesting that microRNAs (miRNAs) play important regulatory roles in the biological processes of cervical squamous cell carcinoma (CSCC). Deciphering the miRNA regulatory network in CSCC could deepen our understanding at the molecular level of CSCC initiation and progression. In the present study, we performed next‑generation sequencing (NGS) to profile miRNA expression in 3 pairs of early-stage CSCC samples...
January 16, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28098887/mirna%C3%A2-375-regulates-the-cell-survival-and-apoptosis-of-human-non%C3%A2-small-cell-carcinoma-by-targeting-her2
#11
Longqiang Cheng, Bingxiang Zhan, Peng Luo, Baolong Wang
micro (mi)‑RNAs are a class of small non‑coding RNAs that regulate gene expression by binding to the 3'‑untranslated region of mRNA, which may lead to mRNA degradation or transcription regulation. Previous studies indicated that miRNAs are important for the pathogenesis of human cancer. miR‑375 has been implicated in various tumor types; however, the biological activity in human non‑small cell lung carcinoma (NSCLC) cells remains to be fully elucidated. The purpose of the present study was to investigate the biological importance of miR‑375 in human NSCLC cells...
January 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098883/developmental-expression-of-toll%C3%A2-like-receptors-in-the-guinea-pig-lung
#12
Lingjie Ma, Jiali Yang, Li Yang, Juan Shi, Jing Xue, Yong Li, Xiaoming Liu
The guinea pig is a useful model for investigating infectious and non‑infectious lung diseases due to the sensitivity of its respiratory system and susceptibility to infectious agents. Toll‑like receptors (TLRs) are important components of the innate immune response and are critical for lung immune function. In the present study, the differentiation of epithelial cells in the guinea pig lung was examined during gestation by studying anatomic morphology and the major epithelial cell types using cell type‑specific markers...
January 17, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098882/downregulation-of-microrna%C3%A2-34b-is-responsible-for-the-elevation-of-blood-pressure-in-spontaneously-hypertensive-rats
#13
Fan Yang, Haiyu Li, Youyou Du, Qiangwei Shi, Luosha Zhao
The present study aimed to identify the microRNA (miRNA) responsible for the development of primary hypertension, and examine the downstream signaling pathway, which mediates the effect of the miRNA. Reverse transcription‑quantitative polymerase chain reaction analysis was performed to identify which miRNA may be involved in the pathogenesis of hypertension. In silico analysis and a luciferase assay were used to validate the target of the selected miRNA, and miRNA mimics and small interfering (si)RNA of the target were transfected into smooth muscle cells to examine its effect on the biological activity of the cells...
January 16, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098759/reactive-oxygen-species-generated-by-nadph-oxidases-promote-radicle-protrusion-and-root-elongation-during-rice-seed-germination
#14
Wen-Yan Li, Bing-Xian Chen, Zhong-Jian Chen, Yin-Tao Gao, Zhuang Chen, Jun Liu
Seed germination is a complicated biological process that requires regulation through various enzymatic and non-enzymatic mechanisms. Although it has been recognized that reactive oxygen species (ROS) regulate radicle emergence and root elongation in a non-enzymatic manner during dicot seed germination, the role of ROS in monocot seed germination remains unknown. NADPH oxidases (NOXs) are the major ROS producers in plants; however, whether and how NOXs regulate rice seed germination through ROS generation remains unclear...
January 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28098434/method-for-the-unique-identification-of-hyperelastic-material-properties-using-full-field-measures-application-to-the-passive-myocardium-material-response
#15
Luigi E Perotti, Aditya V Ponnaluri, Shankarjee Krishnamoorthi, Daniel Balzani, Daniel B Ennis, William S Klug
Quantitative measurement of the material properties (e.g., stiffness) of biological tissues is poised to become a powerful diagnostic tool. There are currently several methods in the literature to estimating material stiffness and we extend this work by formulating a framework that leads to uniquely identified material properties. We design an approach to work with full field displacement data - i.e., we assume the displacement field due to the applied forces is known both on the boundaries and also within the interior of the body of interest - and seek stiffness parameters that lead to balanced internal and external forces in a model...
January 18, 2017: International Journal for Numerical Methods in Biomedical Engineering
https://www.readbyqxmd.com/read/28098306/effective-viscosity-and-dynamics-of-spreading-epithelia-a-solvable-model
#16
C Blanch-Mercader, R Vincent, E Bazellières, X Serra-Picamal, X Trepat, J Casademunt
Collective cell migration in spreading epithelia in controlled environments has become a landmark in our current understanding of fundamental biophysical processes in development, regeneration, wound healing or cancer. Epithelial monolayers are treated as thin layers of a viscous fluid that exert active traction forces on the substrate. The model is exactly solvable and shows a broad range of applicabilities for the quantitative analysis and interpretation of force microscopy data of monolayers from a variety of experiments and cell lines...
January 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/28097810/physicochemical-and-biological-evaluation-of-a-cinnamamide-derivative-r-s-2e-1-3-hydroxypiperidin-1-yl-3-phenylprop-2-en-1-one-km-608-for-nervous-system-disorders
#17
Agnieszka Gunia-Krzyżak, Ewa Żesławska, Florence Bareyre, Wojciech Nitek, Anna M Waszkielewicz, Henryk Marona
A cinnamamide scaffold has been successfully incorporated in several compounds possessing desirable pharmacological activities in central and peripheral nervous system such as anticonvulsant, antidepressant, neuroprotective, analgesic, anti-inflammatory, muscle relaxant, and sedative/hypnotic properties. R,S-(2E)-1-(3-hydroxypiperidin-1-yl)-3-phenylprop-2-en-1-one (KM-608), a cinnamamide derivative, was synthesized, its chemical structure was confirmed by means of spectroscopy and crystallography, additionally thermal analysis showed that it exists in one crystalline form...
January 18, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28097324/molecular-based-recursive-partitioning-analysis-model-for-glioblastoma-in-the-temozolomide-era-a-correlative-analysis-based-on-nrg-oncology-rtog-0525
#18
Erica Hlavin Bell, Stephanie L Pugh, Joseph P McElroy, Mark R Gilbert, Minesh Mehta, Alexander C Klimowicz, Anthony Magliocco, Markus Bredel, Pierre Robe, Anca-L Grosu, Roger Stupp, Walter Curran, Aline P Becker, Andrea L Salavaggione, Jill S Barnholtz-Sloan, Kenneth Aldape, Deborah T Blumenthal, Paul D Brown, Jon Glass, Luis Souhami, R Jeffrey Lee, David Brachman, John Flickinger, Minhee Won, Arnab Chakravarti
Importance: There is a need for a more refined, molecularly based classification model for glioblastoma (GBM) in the temozolomide era. Objective: To refine the existing clinically based recursive partitioning analysis (RPA) model by incorporating molecular variables. Design, Setting, and Participants: NRG Oncology RTOG 0525 specimens (n = 452) were analyzed for protein biomarkers representing key pathways in GBM by a quantitative molecular microscopy-based approach with semiquantitative immunohistochemical validation...
January 12, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/28097161/effects-of-extremely-low-frequency-electromagnetic-field-on-expression-levels-of-some-antioxidant-genes-in-human-mcf-7-cells
#19
Hamideh Mahmoudinasab, Fatemeh Sanie-Jahromi, Mostafa Saadat
In the past three decades, study on the biological effects of extremely low-frequency electromagnetic fields (ELF-EMFs) has been of interest to scientists. Although the exact mechanism of its effect is not fully understood, free radical processes has been proposed as a possible mechanism. This study was designed to evaluate the effect of 50-Hz EMFs on the mRNA levels of seven antioxidant genes (CAT, SOD1, SOD2, GSTO1, GSTM3, MSGT1, and MSGT3) in human MCF-7 cells. The EMF exposure patterns were: 1) 5 min field-on/5 min filed-off, 2) 15 min field-on/15 min field-off, 3) 30 min field-on continuously...
June 2016: Molecular Biology Research Communications
https://www.readbyqxmd.com/read/28097087/identification-of-the-vascular-endothelial-growth-factor-signalling-pathway-by-quantitative-proteomic-analysis-of-rat-condylar-cartilage
#20
Liting Jiang, Yinyin Xie, Li Wei, Qi Zhou, Xing Shen, Xinquan Jiang, Yiming Gao
Angiogenesis mediated by vascular endothelial growth factor (VEGF) is known to play an important role in regulating cartilage remodelling and endochondral ossification. However, the details of how VEGF signalling mechanisms affect condyle remodelling in response to alterations in functional loading remains unclear. To explore this, eighty 16-day-old male SD rats were divided into two equal groups which were fed either a soft/powdery diet or a hard diet for 4 weeks; the stiffness of the diet results in alteration of mastication force and hence temporomandibular joint (TMJ) development...
January 2017: FEBS Open Bio
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