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Cellular Biology

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https://www.readbyqxmd.com/read/28930980/immunostaining-for-dna-modifications-computational-analysis-of-confocal-images
#1
Ashley H Ramsawhook, Lara C Lewis, Maria Eleftheriou, Abdulkadir Abakir, Paulina Durczak, Robert Markus, Seema Rajani, Nicholas R F Hannan, Beth Coyle, Alexey Ruzov
For several decades, 5-methylcytosine (5mC) has been thought to be the only DNA modification with a functional significance in metazoans. The discovery of enzymatic oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) as well as detection of N6-methyladenine (6mA) in the DNA of multicellular organisms provided additional degrees of complexity to the epigenetic research. According to a growing body of experimental evidence, these novel DNA modifications may play specific roles in different cellular and developmental processes...
September 7, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28930614/inter-species-functional-interactome-of-nuclear-steroid-receptors-r1
#2
Styliani A Geronikolou, Athanasia Pavlopoulou, Christina Kanaka-Gantenbein, George Chrousos
Steroids exert their actions by binding to the glucocorticoid, mineralocorticoid, androgen, estrogen and progesterone classes of receptors. Despite an exponential increase in our knowledge of steroid receptors, their interactions with other molecules, subcellular location and functions still need further elucidation. To unravel the mechanism(s) of action of the steroid hormones, as well as the function of their cognate nuclear receptors, an interaction network was created (henceforth referred to as "R1 Interactome")- illustrating that robust interactions have been preserved in rodents, frog, zebra fish and drosophila...
January 1, 2018: Frontiers in Bioscience (Elite Edition)
https://www.readbyqxmd.com/read/28930553/fetal-nucleic-acids-in-maternal-plasma-from-biology-to-clinical-translation
#3
Neha Bunkar, Arpit Bhargava, Koel Chaudhury, Radhey Shyam Sharma, Nirmal Kumar Lohiya, Pradyumna Kumar Mishra
Exposure to environmental contaminants during the critical window of pregnancy results in deregulation of highly coordinated genetic and epigenetic mechanisms involved in prenatal growth. Such disturbances significantly alter the fetal programming, and lead to various developmental disorders immediately, over the lifetime, or transgenerationally. During the process of placental development, fetal nucleic acids enter maternal plasma as a result of necrotic, apoptotic, and inflammatory mechanisms. These nucleic acids reflect normal or abnormal ongoing cellular changes during prenatal fetal development...
January 1, 2018: Frontiers in Bioscience (Landmark Edition)
https://www.readbyqxmd.com/read/28930451/a-biomimetic-stress-sensitive-hydrogel-controlled-by-dna-nanoswitches
#4
Swapneel R Deshpande, Roel Hammink, Frank H T Nelissen, Alan E Rowan, Hans A Heus
One of the most intriguing and important aspects of biological supramolecular materials is its ability to adapt macroscopic properties in response to environmental cues for controlling cellular processes. Recently, bulk matrix stiffness, in particular stress sensitivity, has been established as a key mechanical cue in cellular function and development. However, stress-stiffening capacity and the ability to control and exploit this key characteristic is relatively new to the field of biomimetic materials. In this work, DNA-responsive hydrogels, composed of semiflexible PIC polymers equipped with DNA cross-linkers, were engineered to create mimics of natural biopolymer networks that capture these essential elastic properties and can be controlled by external stimuli...
September 20, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28930429/mapping-protein-targets-of-bioactive-small-molecules-using-lipid-based-chemical-proteomics
#5
Kenneth M Lum, Yoshiaki Sato, Brittney A Beyer, Warren C Plaisted, Justin L Anglin, Luke L Lairson, Benjamin F Cravatt
Lipids play critical roles in cell biology, often through direct interactions with proteins. We recently described the use of photoreactive lipid probes combined with quantitative mass spectrometry to globally map lipid-protein interactions, and the effects of drugs on these interactions, in cells. Here, we investigate the broader potential of lipid-based chemical proteomic probes for determining the cellular targets of biologically active small molecules, including natural product derivatives and repurposed drugs of ill-defined mechanisms...
September 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#6
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P Telles, Gabriela Vaz Meirelles, Rosane Minghim
BACKGROUND: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929804/fluorinated-nucleosides-as-an-important-class-of-anticancer-and-antiviral-agents
#7
Alessandra Cavaliere, Katrin C Probst, Andrew D Westwell, Magdalena Slusarczyk
Fluorine-containing nucleoside analogs (NAs) represent a significant class of the US FDA-approved chemotherapeutics widely used in the clinic. The incorporation of fluorine into drug-like agents modulates lipophilic, electronic and steric parameters, thus influencing pharmacodynamic and pharmacokinetic properties of drugs. Fluorine can block oxidative metabolism of drugs and the formation of undesired metabolites by changing H-bonding interactions. In this review, we focus our attention on chemical fluorination reagents and methods used in the NAs field, including positron emission tomography radiochemistry...
September 20, 2017: Future Medicinal Chemistry
https://www.readbyqxmd.com/read/28929768/protein-corona-analysis-of-silver-nanoparticles-links-to-their-cellular-effects
#8
Sabine Juling, Alicia Niedzwiecka, Linda Böhmert, Dajana Lichtenstein, Soeren Selve, Albert Braeuning, Andreas F Thünemann, Eberhard Krause, Alfonso Lampen
The breadth of applications of nanoparticles and the access to food-associated consumer products containing nano-sized materials lead to oral human exposure to such particles. In biological fluids nanoparticles dynamically interact with biomolecules and form a protein corona. Knowledge about the protein corona is of great interest for understanding the molecular effects of particles as well as their fate inside the human body. We used a mass spectrometry-based toxicoproteomics approach to elucidate mechanisms of toxicity of silver nanoparticles and to comprehensively characterize the protein corona formed around silver nanoparticles in Caco-2 human intestinal epithelial cells...
September 20, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28929304/embryonic-body-culturing-in-an-all-glass-microfluidic-device-with-laser-processed-4%C3%A2-%C3%AE-m-thick-ultra-thin-glass-sheet-filter
#9
Y Yalikun, N Tanaka, Y Hosokawa, T Iino, Y Tanaka
In this paper, we report the development and demonstration of a method to fabricate an all-glass microfluidic cell culturing device without circulation flow. On-chip microfluidic cell culturing is an indispensable technique for cellular replacement therapies and experimental cell biology. Polydimethylsiloxane (PDMS) have become a popular material for fabricating microfluidic cell culture devices because it is a transparent, biocompatible, deformable, easy-to-mold, and gas-permeable. However, PDMS is also a chemically and physically unstable material...
September 19, 2017: Biomedical Microdevices
https://www.readbyqxmd.com/read/28928907/adipose-derived-stromal-cell-in-regenerative-medicine-a-review
#10
REVIEW
Reza Tabatabaei Qomi, Mohsen Sheykhhasan
The application of appropriate cell origin for utilizing in regenerative medicine is the major issue. Various kinds of stem cells have been used for the tissue engineering and regenerative medicine. Such as, several stromal cells have been employed as treat option for regenerative medicine. For example, human bone marrow-derived stromal cells and adipose-derived stromal cells (ADSCs) are used in cell-based therapy. Data relating to the stem cell therapy and processes associated with ADSC has developed remarkably in the past 10 years...
August 26, 2017: World Journal of Stem Cells
https://www.readbyqxmd.com/read/28928904/depletion-of-the-third-complement-component-ameliorates-age-dependent-oxidative-stress-and-positively-modulates-autophagic-activity-in-aged-retinas-in-a-mouse-model
#11
Dorota Rogińska, Miłosz P Kawa, Ewa Pius-Sadowska, Renata Lejkowska, Karolina Łuczkowska, Barbara Wiszniewska, Kai Kaarniranta, Jussi J Paterno, Christian A Schmidt, Bogusław Machaliński, Anna Machalińska
The aim of the study was to investigate the influence of complement component C3 global depletion on the biological structure and function of the aged retina. In vivo morphology (OCT), electrophysiological function (ERG), and the expression of selected oxidative stress-, apoptosis-, and autophagy-related proteins were assessed in retinas of 12-month-old C3-deficient and WT mice. Moreover, global gene expression in retinas was analyzed by RNA arrays. We found that the absence of active C3 was associated with (1) alleviation of the age-dependent decrease in retinal thickness and gradual deterioration of retinal bioelectrical function, (2) significantly higher levels of antioxidant enzymes (catalase and glutathione reductase) and the antiapoptotic survivin and Mcl-1/Bak dimer, (3) lower expression of the cellular oxidative stress marker-4HNE-and decreased activity of proapoptotic caspase-3, (4) ameliorated retinal autophagic activity with localization of ubiquitinated protein conjugates commonly along the retinal pigment epithelium (RPE) layer, and (5) significantly increased expression of several gene sets associated with maintenance of the physiological functions of the neural retina...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/28928868/villi-specific-gene-expression-reveals-novel-prognostic-biomarkers-in-multiple-human-cancers
#12
Botao Zhang, Lin Feng, Honglin Guo, Hongxia Li, Yuanjing Wang, Kaitai Zhang, Xuexin Yu, Shujun Cheng
Despite many striking connections, the biological similarities between embryonic development and tumorigenesis have not been well explored. Development of the placental villi is a crucial process involving many cellular activities, including immunity, proliferation, and cell adhesion. In this study, we designed a strategy to identify the gene expression pattern of villi development and to explore the corresponding features in tumors. We discovered villi-specific genes that are highly expressed in the villus as opposed to the mature placenta and then measured the expression levels of these genes in tumors...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28928844/inhibitory-effects-of-low-intensity-pulsed-ultrasound-sonication-on-the-proliferation-of-osteosarcoma-cells
#13
Toshihiro Matsuo, Keiji Sato, Takuya Matsui, Shigeyuki Sawada, Yoshitaka Muramatsu, Katsuhisa Kawanami, Masataka Deie
To date, there is limited data on the biological effects of low-intensity pulsed ultrasound (LIPUS) on primary malignant bone tumors. The purpose of the present study was to investigate the antitumor effects of LIPUS on osteosarcoma cells. The effects of LIPUS on cell viability, induction of apoptosis, mitochondrial membrane potential and intracellular signaling molecules in the LM8 osteosarcoma cell line were investigated. LIPUS inhibited cell viability (P=0.0022) and mitochondrial membrane potential (P=0...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28928806/alterations-in-iqgap1-expression-and-localization-in-colorectal-carcinoma-and-liver-metastases-following-oxaliplatin-based-chemotherapy
#14
Deborah Rotoli, Manuel Morales, María Del Carmen Maeso, María Del Pino García, Ricardo Gutierrez, Francisco Valladares, Julio Ávila, Lucio Díaz-Flores, Ali Mobasheri, Pablo Martín-Vasallo
IQGAP1 is a scaffolding protein that serves a key role in cell dynamics by integrating internal and external stimuli to distinct signal outputs. Previous studies have identified several genes that are significantly up- or downregulated in the peripheral white cells (PWCs) of patients with colorectal adenocarcinoma (CRC), who underwent oxaliplatin-based chemotherapy (CT). In addition, screening studies have reported that IQ-motif containing GTPase activating protein 1 (IQGAP1) transcriptional expression levels varied from 'off' to 'on' following oxaliplatin CT...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28928672/micrornas-clustered-within-the-14q32-locus-are-associated-with-endothelial-damage-and-microparticle-secretion-in-bicuspid-aortic-valve-disease
#15
Neus Martínez-Micaelo, Raúl Beltrán-Debón, Gerard Aragonés, Marta Faiges, Josep M Alegret
Background: We previously described that PECAM(+) circulating endothelial microparticles (EMPs) are elevated in bicuspid aortic valve (BAV) disease as a manifestation of endothelial damage. In this study, we hypothesized that this endothelial damage, is functionally related to the secretion of a specific pattern of EMP-associated miRNAs. Methods: We used a bioinformatics approach to correlate the PECAM(+) EMP levels with the miRNA expression profile in plasma in healthy individuals and BAV patients (n = 36)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28928631/glaucoma-biological-trabecular-and-neuroretinal-pathology-with-perspectives-of-therapy-innovation-and-preventive-diagnosis
#16
REVIEW
Raffaele Nuzzi, Federico Tridico
Glaucoma is a common degenerative disease affecting retinal ganglion cells (RGC) and optic nerve axons, with progressive and chronic course. It is one of the most important reasons of social blindness in industrialized countries. Glaucoma can lead to the development of irreversible visual field loss, if not treated. Diagnosis may be difficult due to lack of symptoms in early stages of disease. In many cases, when patients arrive at clinical evaluation, a severe neuronal damage may have already occurred. In recent years, newer perspective in glaucoma treatment have emerged...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28928428/phosphorylation-of-suppressor-of-hairless-impedes-its-dna-binding-activity
#17
Anja C Nagel, Jasmin S Auer, Adriana Schulz, Jens Pfannstiel, Zhenyu Yuan, Courtney E Collins, Rhett A Kovall, Anette Preiss
Notch signalling activity governs cellular differentiation in higher metazoa, where Notch signals are transduced by the transcription factor CSL, called Suppressor of Hairless [Su(H)] in Drosophila. Su(H) operates as molecular switch on Notch target genes: within activator complexes, including intracellular Notch, or within repressor complexes, including the antagonist Hairless. Mass spectrometry identified phosphorylation on Serine 269 in Su(H), potentially serving as a point of cross-regulation by other signalling pathways...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928399/a-ring-polymer-model-shows-how-macromolecular-crowding-controls-chromosome-arm-organization-in-escherichia-coli
#18
Chanil Jeon, Youngkyun Jung, Bae-Yeun Ha
Macromolecular crowding influences various cellular processes such as macromolecular association and transcription, and is a key determinant of chromosome organization in bacteria. The entropy of crowders favors compaction of long chain molecules such as chromosomes. To what extent is the circular bacterial chromosome, often viewed as consisting of "two arms", organized entropically by crowding? Using computer simulations, we examine how a ring polymer is organized in a crowded and cylindrically-confined space, as a coarse-grained bacterial chromosome...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928279/metabolism-in-time-and-space-exploring-the-frontier-of-developmental-biology
#19
REVIEW
Alena Krejci, Jason M Tennessen
Despite the fact that metabolic studies played a prominent role in the early history of developmental biology research, the field of developmental metabolism was largely ignored following the advent of modern molecular biology. Metabolism, however, has recently re-emerged as a focal point of biomedical studies and, as a result, developmental biologists are once again exploring the chemical and energetic forces that shape growth, development and maturation. In May 2017, a diverse group of scientists assembled at the EMBO/EMBL Symposium 'Metabolism in Time and Space' to discuss how metabolism influences cellular and developmental processes...
September 15, 2017: Development
https://www.readbyqxmd.com/read/28927933/azopolymer-photopatterning-for-directional-control-of-angiogenesis
#20
Chiara Fedele, Maria De Gregorio, Paolo A Netti, Silvia Cavalli, Chiara Attanasio
Understanding cellular behavior in response to microenvironmental stimuli is central to tissue engineering. An increasing number of reports emphasize the high sensitivity of cells to the physical characteristics of the surrounding milieu and in particular, topographical cues. In this work, we investigated the influence of dynamic topographic signal presentation on sprout formation and the possibility to obtain a space-time control over sprouting directionality without growth factors, in order to investigate the contribution of just topography in the angiogenic process...
September 16, 2017: Acta Biomaterialia
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