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Cellular Biology

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https://www.readbyqxmd.com/read/28735484/microsphere-based-assessment-of-dna-methylation-for-aml-prognosis
#1
Gerald B W Wertheim, Marlise R Luskin, Martin Carroll, Stephen R Master
Epigenetic dysregulation, including aberrant methylation of cytosine residues in DNA, is a hallmark of cancer and clearly results in oncogenic cellular alterations such as transcriptional attenuation of tumor suppressors and genomic instability. A number of studies have examined DNA methylation alterations in patients with acute myeloid leukemia (AML) and have shown that analysis of multilocus methylation patterns can identify biologically distinct AML subclasses and can predict patient prognosis. In order to utilize the prognostic capability of methylation analysis in a clinical setting, we have developed a microsphere-based HpaII tiny fragment enrichment by ligation-mediated PCR (xMELP) assay to interrogate the methylation state of genomic multiple loci along with a random forest-based classification algorithm that correlates DNA methylation status with patient prognosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735473/low-concentration-bpaf-and-bpf-induced-cell-biological-effects-are-mediated-by-ros-in-mcf-7-breast-cancer-cells
#2
Bingli Lei, Su Sun, Jie Xu, Chenglian Feng, Yingxin Yu, Gang Xu, Minghong Wu, Wei Peng
Reactive oxygen species (ROS) induced by bisphenol A (BPA) have been implicated in cellular oxidative damage and carcinogenesis. It is not known whether the potential alternatives of BPA, bisphenol AF (BPAF), and bisphenol F (BPF) can also induce ROS involved in mediating biological responses. This study evaluated the toxicity of BPAF and BPF on cell proliferation, DNA damage, intracellular calcium homeostasis, and ROS generation in MCF-7 human breast cancer cells. The results showed that BPAF at 0.001-1 μM and BPF at 0...
July 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28735414/bone-mechanobiology-in-mice-toward-single-cell-in-vivo-mechanomics
#3
Ariane Scheuren, Esther Wehrle, Felicitas Flohr, Ralph Müller
Mechanically driven bone (re)modeling is a multiscale process mediated through complex interactions between multiple cell types and their microenvironments. However, the underlying mechanisms of how cells respond to mechanical signals are still unclear and are at the focus of the field of bone mechanobiology. Traditionally, this complex process has been addressed by reducing the system to single scales and cell types. It is only recently that more integrative approaches have been established to study bone mechanobiology across multiple scales in which mechanical load at the organ level is related to molecular responses at the cellular level...
July 22, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28735230/granulometry-microbial-composition-and-biological-activity-of-dusts-collected-in-french-dairy-farms
#4
Hugo Pfister, Claudie Morzadec, Pierre Le Cann, Laurent Madec, Valérie Lecureur, Martine Chouvet, Stéphane Jouneau, Laurent Vernhet
BACKGROUND: Dairy working increases the prevalence of lower airway respiratory diseases, especially COPD and asthma. Epidemiological studies have reported that chronic inhalation of organic dusts released during specific daily tasks could represent a major risk factor for development of these pathologies in dairy workers. Knowledge on size, nature and biological activity of such organic dusts remain however limited. OBJECTIVE: To compare size distribution, microbial composition and cellular effects of dusts liberated by the spreading of straw bedding in five French dairy farms located in Brittany...
July 20, 2017: Environmental Research
https://www.readbyqxmd.com/read/28735187/progress-in-targeting-the-bcl-2-family-of-proteins
#5
REVIEW
Thomas P Garner, Andrea Lopez, Denis E Reyna, Adam Z Spitz, Evripidis Gavathiotis
The network of protein-protein interactions among the BCL-2 protein family plays a critical role in regulating cellular commitment to mitochondrial apoptosis. Anti-apoptotic BCL-2 proteins are considered promising targets for drug discovery and exciting clinical progress has stimulated intense investigations in the broader family. Here, we discuss recent developments in small molecules targeting anti-apoptotic proteins and alternative approaches to targeting BCL-2 family interactions. These studies advance our understanding of the role of BCL-2 family proteins in physiology and disease, providing unique tools for dissecting these functions...
July 20, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28735108/structural-biology-outside-the-box-inside-the-cell
#6
REVIEW
Jürgen M Plitzko, Benjamin Schuler, Philipp Selenko
Recent developments in cellular cryo-electron tomography, in-cell single-molecule Förster resonance energy transfer-spectroscopy, nuclear magnetic resonance-spectroscopy and electron paramagnetic resonance-spectroscopy delivered unprecedented insights into the inner workings of cells. Here, we review complementary aspects of these methods and provide an outlook toward joint applications in the future.
July 20, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28735096/lipid-droplet-functions-beyond-energy-storage
#7
REVIEW
Michael A Welte, Alex P Gould
Lipid droplets are cytoplasmic organelles that store neutral lipids and are critically important for energy metabolism. Their function in energy storage is firmly established and increasingly well characterized. However, emerging evidence indicates that lipid droplets also play important and diverse roles in the cellular handling of lipids and proteins that may not be directly related to energy homeostasis. Lipid handling roles of droplets include the storage of hydrophobic vitamin and signaling precursors, and the management of endoplasmic reticulum and oxidative stress...
July 19, 2017: Biochimica et Biophysica Acta
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
#8
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/28734934/analysis-of-rna-protein-interactions-in-vertebrate-embryos-using-uv-crosslinking-approaches
#9
Vladimir Despic, Mario Dejung, Falk Butter, Karla M Neugebauer
A decade ago, we believed that at least 300 RNA binding proteins (RBPs) were encoded in our genomes based on annotations of known or predicted RNA binding domains. Deciphering the roles of those RBPs in regulated gene expression was a vast frontier awaiting exploration. Since then, the field has developed a number of key tools that navigate the landscape of cellular RNA. These rely principally on UV crosslinking to create covalent bonds between RBPs and target RNAs in vivo, revealing not only target identities but also local binding sites upon RNA-Seq...
July 19, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28734476/quantifying-the-interaction-between-egfr-dimers-and-grb2-in-live-cells
#10
Nuala Del Piccolo, Kalina Hristova
Adaptor proteins are a class of cytoplasmic proteins that bind to phosphorylated residues in receptor tyrosine kinases and trigger signaling cascades that control critically important cellular processes, such as cell survival, growth, differentiation, and motility. Here, we seek to characterize the interaction between epidermal growth factor receptor (EGFR) and the cytoplasmic adaptor protein growth factor receptor-bound protein 2 (Grb2) in a cellular context. To do so, we explore the utility of a highly biologically relevant model system, mammalian cells under reversible osmotic stress, and a recently introduced Förster resonance energy transfer microscopy method, fully quantified spectral imaging...
July 19, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28734132/high-dimensional-single-cell-mapping-of-cerium-distribution-in-the-lung-immune-microenvironment-of-an-active-smoker
#11
Adeeb H Rahman, Yonit Lavin, Soma Kobayashi, Andrew Leader, Miriam Merad
BACKGROUND: Mass cytometry leverages inductively coupled mass spectrometry to perform high dimensional single cell analyses using antibodies tagged with rare earth isotopes that are considered to be largely absent in biological samples. We have recently noted an unusual exception to this rule while analyzing tissue samples from patients undergoing surgical resection for early stage lung cancer, and here we present a detailed cytometric characterization of cerium in a clinical patient sample...
July 22, 2017: Cytometry. Part B, Clinical Cytometry
https://www.readbyqxmd.com/read/28733924/cellular-mechanosensitivity-to-substrate-stiffness-decreases-with-increasing-dissimilarity-to-cell-stiffness
#12
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/28733914/molecular-and-functional-analysis-of-monoclonal-antibodies-in-support-of-biologics-development
#13
REVIEW
Xin Wang, Zhiqiang An, Wenxin Luo, Ningshao Xia, Qinjian Zhao
Monoclonal antibody (mAb)-based therapeutics are playing an increasingly important role in the treatment or prevention of many important diseases such as cancers, autoimmune disorders, and infectious diseases. Multi-domain mAbs are far more complex than small molecule drugs with intrinsic heterogeneities. The critical quality attributes of a given mAb, including structure, post-translational modifications, and functions at biomolecular and cellular levels, need to be defined and profiled in details during the developmental phases of a biologics...
July 21, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28733904/polyamines-therapeutic-perspectives-in-oxidative-stress-and-inflammatory-diseases
#14
REVIEW
Tarique Hussain, Bie Tan, Wenkai Ren, Najma Rahu, Rahim Dad, Dildar Hussain Kalhoro, Yulong Yin
Polyamines are naturally occurring aliphatic compounds, particularly essential elements for biological functions. These compounds play a central role in regulating molecular pathways which are responsible for cellular proliferation, growth, and differentiation. Importantly, excessive polyamine catabolism can lead to a prominent source of oxidative stress which increases inflammatory response and thought to be involved in several diseases including stroke, renal failure, neurological disease, liver disease, and even cancer...
July 21, 2017: Amino Acids
https://www.readbyqxmd.com/read/28733901/current-knowledge-on-exosome-biogenesis-and-release
#15
REVIEW
Nina Pettersen Hessvik, Alicia Llorente
Exosomes are nanosized membrane vesicles released by fusion of an organelle of the endocytic pathway, the multivesicular body, with the plasma membrane. This process was discovered more than 30 years ago, and during these years, exosomes have gone from being considered as cellular waste disposal to mediate a novel mechanism of cell-to-cell communication. The exponential interest in exosomes experienced during recent years is due to their important roles in health and disease and to their potential clinical application in therapy and diagnosis...
July 21, 2017: Cellular and Molecular Life Sciences: CMLS
https://www.readbyqxmd.com/read/28733351/multi-cellular-transcriptional-analysis-of-mammalian-heart-regeneration
#16
Gregory A Quaife-Ryan, Choon Boon Sim, Mark Ziemann, Antony Kaspi, Haloom Rafehi, Mirana Ramialison, Assam El-Osta, James E Hudson, Enzo R Porrello
Background -The inability of the adult mammalian heart to regenerate following injury represents a major barrier in cardiovascular medicine. In contrast, the neonatal mammalian heart retains a transient capacity for regeneration, which is lost shortly after birth. Defining the molecular mechanisms that govern regenerative capacity in the neonatal period remains a central goal in cardiac biology. Here, we assemble a transcriptomic framework of multiple cardiac cell populations during postnatal development and following injury, which enables comparative analyses of the regenerative (neonatal) versus non-regenerative (adult) state for the first time...
July 21, 2017: Circulation
https://www.readbyqxmd.com/read/28733120/employing-decomposable-partially-observable-markov-decision-processes-to-control-gene-regulatory-networks
#17
Utku Erdogdu, Faruk Polat, Reda Alhajj
OBJECTIVE: Formulate the induction and control of gene regulatory networks (GRNs) from gene expression data using Partially Observable Markov Decision Processes (POMDPs). METHODS AND MATERIAL: Different approaches exist to model GRNs; they are mostly simulated as mathematical models that represent relationships between genes. Actually, it has been realized that biological functions at the cellular level are controlled by genes; thus, by controlling the behavior of genes, it is possible to regulate these biological functions...
July 18, 2017: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/28733090/intravital-multiphoton-microscopy-as-a-tool-for-studying-renal-physiology-and-pathophysiology
#18
Ruben M Sandoval, Bruce A Molitoris
The kidney is a complex and dynamic organ with over 40 cell types, and tremendous structural and functional diversity. Intravital multi-photon microscopy, development of fluorescent probes and innovative software, have rapidly advanced the study of intracellular and intercellular processes within the kidney. Researchers can quantify the distribution, behavior, and dynamic interactions of up to four labeled chemical probes and proteins simultaneously and repeatedly in four dimensions (time), with subcellular resolution in near real time...
July 18, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28732943/encompassment-of-benzyl-isothiocyanate-in-cyclodextrin-using-ultrasonication-methodology-to-enhance-its-stability-for-biological-applications
#19
Shivani Uppal, Khushwinder Kaur, Rajendra Kumar, Nakshdeep Kaur Kahlon, Rachna Singh, S K Mehta
The use of methodical and innovative sonication method has been explored for the fabrication of inclusion complex of Benzyl Isothiocyanate, a potential anticancer and -antimicrobial agent. The advancement involved investigation of inclusion behaviour, characterisation and an in-depth study of thermal and UV stability of Benzyl Isothiocyanate with cyclodextrins; β-CD and hp-β-CD. The sonication driven encompassment in cyclodextrins helped to overcome the hindrance of low solubility and high volatility. Investigations of physical and thermodynamic parameters using UV-visible spectroscopy, FTIR, XRD, TGA etc confirmed stability of inclusion complexes...
November 2017: Ultrasonics Sonochemistry
https://www.readbyqxmd.com/read/28732343/an-ultrasensitive-electrochemical-biosensor-for-polynucleotide-kinase-assay-based-on-gold-nanoparticle-mediated-lambda-exonuclease-cleavage-induced-signal-amplification
#20
Lin Cui, Yueying Li, Mengfei Lu, Bo Tang, Chun-Yang Zhang
Polynucleotide kinase (PNK) plays an essential role in cellular nucleic acid metabolism and the cellular response to DNA damage. However, conventional methods for PNK assay suffer from low sensitivity and involve multiple steps. Herein, we develop a simply electrochemical method for sensitive detection of PNK activity on the basis of Au nanoparticle (AuNP)-mediated lambda exonuclease cleavage-induced signal amplification. We use [Ru(NH3)6](3+) as the electrochemically active indicator and design two DNA strands (i...
July 13, 2017: Biosensors & Bioelectronics
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