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https://www.readbyqxmd.com/read/28346922/epigenetics-in-gastrointestinal-health-and-disease-spotlight-on-dna-methylation-in-the-intestinal-epithelium
#1
Matthias Zilbauer, Judith Kraiczy
Epigenetics can be defined as stable, potentially heritable changes in cellular phenotype caused by mechanisms other than alterations in the underlying DNA sequence. DNA methylation is amongst the most intensely studied epigenetic mechanisms and has been shown to play a major role in regulating fundamental aspects of cell biology including cellular differentiation, organ development, and cell type-specific gene expression. Importantly, it is becoming increasingly clear that epigenetic mechanisms operate at the interface between the genetic code and our environment and are able to mediate environmental changes into stable phenotypic alterations...
2017: Nestlé Nutrition Institute Workshop Series
https://www.readbyqxmd.com/read/28344971/how-to-train-a-cell-cutting-edge-molecular-tools
#2
REVIEW
Jakub Czapiński, Michał Kiełbus, Joanna Kałafut, Michał Kos, Andrzej Stepulak, Adolfo Rivero-Müller
In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs...
2017: Frontiers in Chemistry
https://www.readbyqxmd.com/read/28343999/a-genome-wide-analysis-of-human-pluripotent-stem-cell-derived-endothelial-cells-in-2d-or-3d-culture
#3
Jue Zhang, Michael P Schwartz, Zhonggang Hou, Yongsheng Bai, Hamisha Ardalani, Scott Swanson, John Steill, Victor Ruotti, Angela Elwell, Bao Kim Nguyen, Jennifer Bolin, Ron Stewart, James A Thomson, William L Murphy
A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type...
March 10, 2017: Stem Cell Reports
https://www.readbyqxmd.com/read/28340565/u-par-expression-in-cancer-associated-fibroblast-new-acquisitions-in-multiple-myeloma-progression
#4
S Ciavarella, A Laurenzana, S De Summa, B Pilato, A Chillà, R Lacalamita, C Minoia, F Margheri, A Iacobazzi, A Rana, F Merchionne, G Fibbi, M Del Rosso, A Guarini, S Tommasi, S Serratì
BACKGROUND: Multiple Myeloma (MM) is a B-cell malignancy in which clonal plasma cells progressively expand within the bone marrow (BM) as effect of complex interactions with extracellular matrix and a number of microenvironmental cells. Among these, cancer-associated fibroblasts (CAF) mediate crucial reciprocal signals with MM cells and are associated to aggressive disease and poor prognosis. A large body of evidence emphasizes the role of the urokinase plasminogen activator (u-PA) and its receptor u-PAR in potentiating the invasion capacity of tumor plasma cells, but little is known about their role in the biology of MM CAF...
March 24, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28339466/in-silico-search-for-modifier-genes-associated-with-pancreatic-and-liver-disease-in-cystic-fibrosis
#5
Pascal Trouvé, Emmanuelle Génin, Claude Férec
Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes...
2017: PloS One
https://www.readbyqxmd.com/read/28332571/profiling-protein-expression-in-circulating-tumour-cells-using-microfluidic-western-blotting
#6
Elly Sinkala, Elodie Sollier-Christen, Corinne Renier, Elisabet Rosàs-Canyelles, James Che, Kyra Heirich, Todd A Duncombe, Julea Vlassakis, Kevin A Yamauchi, Haiyan Huang, Stefanie S Jeffrey, Amy E Herr
Circulating tumour cells (CTCs) are rare tumour cells found in the circulatory system of certain cancer patients. The clinical and functional significance of CTCs is still under investigation. Protein profiling of CTCs would complement the recent advances in enumeration, transcriptomic and genomic characterization of these rare cells and help define their characteristics. Here we describe a microfluidic western blot for an eight-plex protein panel for individual CTCs derived from estrogen receptor-positive (ER+) breast cancer patients...
March 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28322874/reconstructing-the-genotype-to-fitness-map-for-the-bacterial-chemotaxis-network-and-its-emergent-behavioural-phenotypes
#7
Alberto Nakauma, G Sander van Doorn
The signal-transduction network responsible for chemotaxis in Escherichia coli has been characterised in extraordinary detail. Yet, relatively little is known about eco-evolutionary aspects of chemotaxis, such as how the network has been shaped by selection and to what extent natural populations may fine-tune their chemotactic behaviour to the ecological conditions. To address these questions, we here develop an evolutionary-systems-biology model of the chemotaxis network of E. coli, which we apply to estimate the resource accumulation rate (here used as a proxy for fitness) of wildtype and a large number of potential mutant genotypes...
March 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28320399/vasculogenic-mimicry-signaling-revisited-focus-on-non-vascular-ve-cadherin
#8
REVIEW
Daniel Delgado-Bellido, Santiago Serrano-Saenz, Mónica Fernández-Cortés, F Javier Oliver
Vasculogenic mimicry (VM) is a blood supply system independent of endothelial vessels in tumor cells from different origins. It reflects the plasticity of aggressive tumor cells that express vascular cell markers and line tumor vasculature. The presence of VM is associated with a high tumor grade, short survival, invasion and metastasis. Endothelial cells (ECs) express various members of the cadherin superfamily, in particular vascular endothelial (VE-) cadherin, which is the main adhesion receptor of endothelial adherent junctions...
March 21, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28317484/redox-systems-antioxidants-and-sarcopenia
#9
Bertrand Fougère, Gabor Abellan van Kan, Bruno Vellas, Matteo Cesari
According to the free-radical theory of aging, oxidative stress is a key contributor to the onset of age-related conditions by inducing structural and functional alterations in several cellular components. Although innate defenses exist for limiting the occurrence of such detrimental effects, their ability to counteract the continuous and large production of reactive oxygen species becomes increasingly inefficient with aging. In this context, interventions aimed at preserving the homeostatic balance between oxidant production and antioxidant protection may be beneficial on the pathophysiological modifications and clinical manifestations featuring the aging process...
March 17, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28306354/bronchiectasis-phenotyping-a-complex-disease
#10
James D Chalmers
Bronchiectasis is a long-neglected disease currently experiencing a surge in interest. It is a highly complex condition with numerous aetiologies, co-morbidities and a heterogeneous disease presentation and clinical course. The past few years have seen major advances in our understanding of the disease, primarily through large real-life cohort studies. The main outcomes of interest in bronchiectasis are symptoms, exacerbations, treatment response, disease progression and death. We are now more able to identify clearly the radiological, clinical, microbiological and inflammatory contributors to these outcomes...
March 15, 2017: COPD
https://www.readbyqxmd.com/read/28304149/predicting-brain-structure-in-population-based-samples-with-biologically-informed-genetic-scores-for-schizophrenia
#11
Sandra Van der Auwera, Katharina Wittfeld, Elena Shumskaya, Janita Bralten, Marcel P Zwiers, A Marten H Onnink, Niccolo Usberti, Johannes Hertel, Henry Völzke, Uwe Völker, Norbert Hosten, Barbara Franke, Hans J Grabe
Schizophrenia is associated with brain structural abnormalities including gray and white matter volume reductions. Whether these alterations are caused by genetic risk variants for schizophrenia is unclear. Previous attempts to detect associations between polygenic factors for schizophrenia and structural brain phenotypes in healthy subjects have been negative or remain non-replicated. In this study, we used genetic risk scores that were based on the accumulated effect of selected risk variants for schizophrenia belonging to specific biological systems like synaptic function, neurodevelopment, calcium signaling, and glutamatergic neurotransmission...
April 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28303788/dynamics-and-robustness-of-the-cardiac-progenitor-cell-induced-pluripotent-stem-cell-network-during-cell-phenotypes-transition
#12
Yuangen Yao, Chengzhang Ma, Haiyou Deng, Quan Liu, Wei Cao, Rong Gui, Tianquan Feng, Ming Yi
Robustness is a fundamental characteristic of biological systems since all living systems need to adapt to internal or external perturbations, unpredictable environments, stochastic events and unreliable components, and so on. A long-term challenge in systems biology is to reveal the origin of robustness underlying molecular regulator network. In this study, a simple Boolean model is used to investigate the global dynamic properties and robustness of cardiac progenitor cell (CPC) induced pluripotent stem cell network that governs reprogramming and directed differentiation process...
February 2017: IET Systems Biology
https://www.readbyqxmd.com/read/28301138/a-secretion-amplification-role-for-salmonella-enterica-translocon-protein-sipd
#13
Anum Azam Glasgow, Han Teng Wong, Danielle Tullman-Ercek
The bacterial type III secretion system (T3SS) is an important target for enabling high-titer production of proteins of biotechnological interest as well as for synthetic biology applications that rely on protein delivery to host cells. The T3SS forms a membrane-embedded needle complex that is capped by the translocon proteins and extends into the extracellular space. The needle tip complex in Salmonella enterica consists of three translocon proteins: SipB, SipC, and SipD. It is known that knocking out sipD disrupts T3SS regulation to cause constitutive secretion of native proteins...
March 16, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28300644/the-connective-tissue-phenotype-of-glaucomatous-cupping-in-the-monkey-eye-clinical-and-research-implications
#14
REVIEW
Hongli Yang, Juan Reynaud, Howard Lockwood, Galen Williams, Christy Hardin, Luke Reyes, Cheri Stowell, Stuart K Gardiner, Claude F Burgoyne
In a series of previous publications we have proposed a framework for conceptualizing the optic nerve head (ONH) as a biomechanical structure. That framework proposes important roles for intraocular pressure (IOP), IOP-related stress and strain, cerebrospinal fluid pressure (CSFp), systemic and ocular determinants of blood flow, inflammation, auto-immunity, genetics, and other non-IOP related risk factors in the physiology of ONH aging and the pathophysiology of glaucomatous damage to the ONH. The present report summarizes 20 years of technique development and study results pertinent to the characterization of ONH connective tissue deformation and remodeling in the unilateral monkey experimental glaucoma (EG) model...
March 12, 2017: Progress in Retinal and Eye Research
https://www.readbyqxmd.com/read/28299960/molecular-dissection-of-the-response-of-the-rice-systemic-acquired-resistance-deficient-1-sard1-gene-to-different-types-of-ionizing-radiation
#15
In Jung Jung, Jung Eun Hwang, Sung Min Han, Dong Sub Kim, Joon-Woo Ahn, Hong-Il Choi, Soon-Jae Kwon, Si-Yong Kang, Jin-Baek Kim
PURPOSE: Exposure to ionizing radiation induces plant defenses by regulating the expression of response genes. The systemic acquired resistance deficient 1 (SARD1) is a key gene in plant defense response. In this study, the function of Oryza sativa SARD1 (OsSARD1) was investigated after exposure of seeds/plants to ionizing radiation, jasmonic acid (JA) or salicylic acid (SA). MATERIALS AND METHODS: Rice seeds exposed to two types of ionizing radiations (gamma ray [GR] and ion beam [IB]) were analyzed by quantitative reverse transcription PCR (qRT-PCR) to identify the genes that are altered in response to ionizing radiation...
March 16, 2017: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/28297929/flexible-dynamics-of-two-quorum-sensing-coupled-repressilators
#16
Edward H Hellen, Evgeny Volkov
Genetic oscillators play important roles in cell life regulation. The regulatory efficiency usually depends strongly on the emergence of stable collective dynamic modes, which requires designing the interactions between genetic networks. We investigate the dynamics of two identical synthetic genetic repressilators coupled by an additional plasmid which implements quorum sensing (QS) in each network thereby supporting global coupling. In a basic genetic ring oscillator network in which three genes inhibit each other in unidirectional manner, QS stimulates the transcriptional activity of chosen genes providing for competition between inhibitory and stimulatory activities localized in those genes...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28297570/human-lung-spheroids-as-in-vitro-niches-of-lung-progenitor-cells-with-distinctive-paracrine-and-plasticity-properties
#17
Isotta Chimenti, Francesca Pagano, Francesco Angelini, Camilla Siciliano, Giorgio Mangino, Vittorio Picchio, Elena De Falco, Mariangela Peruzzi, Roberto Carnevale, Mohsen Ibrahim, Giuseppe Biondi-Zoccai, Elisa Messina, Giacomo Frati
Basic and translational research on lung biology has discovered multiple progenitor cell types, specialized or facultative, responsible for turnover, renewal, and repair. Isolation of populations of resident lung progenitor cells (LPCs) has been described by multiple protocols, and some have been successfully applied to healthy human lung tissue. We aimed at understanding how different cell culture conditions may affect, in vitro, the phenotype of LPCs to create an ideal niche-like microenvironment. The influence of different substrates (i...
March 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28294608/an-engineered-split-tet2-enzyme-for-inducible-epigenetic-remodeling
#18
Minjung Lee, Jia Li, Yi Liang, Guolin Ma, Jixiang Zhang, Lian He, Yuliang Liu, Qian Li, Minyong Li, Deqiang Sun, Yubin Zhou, Yun Huang
The Ten-eleven translocation (TET) family of 5-methylcytosine (5mC) dioxygenases catalyze the conversion of 5mC into 5-hydroxymethylcytosine (5hmC) and further oxidized species to promote active DNA demethylation. Here we engineered a split-TET2 enzyme to enable temporal control of 5mC oxidation and subsequent remodeling of epigenetic states in mammalian cells. We further demonstrate the use of this chemically-inducible system to dissect the correlation between DNA hydroxymethylation and chromatin accessibility in the mammalian genome...
March 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28294393/the-new-msc-mscs-as-pericytes-are-sentinels-and-gatekeepers
#19
REVIEW
Arnold I Caplan
Human Mesenchymal Stem Cells, hMSCs, were first named over 25 years ago with the "stem cell" nomenclature derived from the fact that we and others could cause these cells to differentiate into a number of different mesodermal phenotypes in cell culture. The capacity to form skeletal tissue in vitro encouraged the use of hMSCs for the fabrication of tissue engineered skeletal repair tissue with subsequent transplantation to in vivo sites. With the current realization that MSCs are derived from perivascular cells, pericytes, and the immunomodulatory and trophic capabilities of MSCs in both in vitro and in vivo test systems, a complete re-evaluation of the role and functions of MSCs in the body was required...
March 15, 2017: Journal of Orthopaedic Research: Official Publication of the Orthopaedic Research Society
https://www.readbyqxmd.com/read/28289374/discovery-of-compounds-that-positively-modulate-the-high-affinity-choline-transporter
#20
Parul Choudhary, Emma J Armstrong, Csilla C Jorgensen, Mary Piotrowski, Maria Barthmes, Rubben Torella, Sarah E Johnston, Yuya Maruyama, John S Janiszewski, R Ian Storer, Sarah E Skerratt, Caroline L Benn
Cholinergic hypofunction is associated with decreased attention and cognitive deficits in the central nervous system in addition to compromised motor function. Consequently, stimulation of cholinergic neurotransmission is a rational therapeutic approach for the potential treatment of a variety of neurological conditions. High affinity choline uptake (HACU) into acetylcholine (ACh)-synthesizing neurons is critically mediated by the sodium- and pH-dependent high-affinity choline transporter (CHT, encoded by the SLC5A7 gene)...
2017: Frontiers in Molecular Neuroscience
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