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https://www.readbyqxmd.com/read/29330773/mechanistic-regulation-of-epithelial-to-mesenchymal-transition-through-ras-signaling-pathway-and-therapeutic-implications-in-human-cancer
#1
REVIEW
Kiran Tripathi, Minal Garg
RAS effector signaling instead of being simple, unidirectional and linear cascade, is actually recognized as highly complex and dynamic signaling network. RAF-MEK-ERK cascade, being at the center of complex signaling network, links to multiple scaffold proteins through feed forward and feedback mechanisms and dynamically regulate tumor initiation and progression. Three isoforms of Ras harbor mutations in a cell and tissue specific manner. Besides mutations, their epigenetic silencing also attributes them to exhibit oncogenic activities...
January 12, 2018: Journal of Cell Communication and Signaling
https://www.readbyqxmd.com/read/29330297/characterization-and-evidence-of-the-mir-888-cluster-as-a-novel-cancer-network-in-prostate
#2
Tsuyoshi Hasegawa, Garrison Glavich, Mary Pahuski, Aleena M Short, Oliver John Semmes, Lifang Yang, Vitold Galkin, Richard R Drake, Aurora Esquela-Kerscher
Prostate cancer afflicts 1 in 7 men and is the second leading cause of male cancer-related deaths in the United States. MicroRNAs (miRNAs), an extensive class of ~22 nucleotide non-coding RNAs, are often aberrantly expressed in tissues and fluids from prostate cancer patients but the mechanism of how specific miRNAs regulate prostate tumorigenesis and metastasis are poorly understood. Here, miR-888 was identified as a novel prostate factor that promotes proliferation and migration. miR-888 resides within a genomic cluster of 7 miRNA genes (mir-892c, mir-890, mir-888, mir-892a, mir-892b, mir-891b, mir-891a) on human chromosome Xq27...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29328463/construction-and-investigation-of-lncrna-associated-cerna-regulatory-network-in-papillary-thyroid-cancer
#3
Yangjing Zhao, Hui Wang, Chengjiang Wu, Meina Yan, Haojie Wu, Jingzhe Wang, Xinxin Yang, Qixiang Shao
Increasing evidence has experimentally proved the competitive endogenous RNA (ceRNA) hypothesis that long non-coding RNA (lncRNA) can affect the expression of RNA targets by competitively combining microRNA (miRNA) via miRNA response elements. However, an extensive ceRNA network of thyroid carcinoma in a large cohort has not been evaluated. We analyzed the RNAseq and miRNAseq data of 348 cases of primary papillary thyroid cancer (PTC) patients with clinical information downloaded from The Cancer Genome Atlas (TCGA) project to search for potential biomarkers or therapeutic targets...
January 10, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29327437/intra-species-variation-in-a-widely-distributed-tree-species-regulates-the-responses-of-soil-microbiome-to-different-temperature-regimes
#4
Cui-Jing Zhang, Manuel Delgado-Baquerizo, John E Drake, Peter B Reich, Mark G Tjoelker, David T Tissue, Jun-Tao Wang, Ji-Zheng He, Brajesh K Singh
Plant characteristics in different provenances within a single species may vary in response to climate change, which might alter soil microbial communities and ecosystem functions. We conducted a glasshouse experiment and grew seedlings of three provenances (temperate, subtropical and tropical origins) of a tree species (i.e. Eucalyptus tereticornis) at different growth temperatures (18, 21.5, 25, 28.5, 32 and 35.5°C) for 54 days. At the end of the experiment, bacterial and fungal community composition, diversity and abundance were characterized...
January 12, 2018: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29325627/epigenetic-mechanisms-underlying-nervous-system-diseases
#5
Irfan A Qureshi, Mark F Mehler
Epigenetic mechanisms act as control systems for modulating genomic structure and activity in response to evolving profiles of cell-extrinsic, cell-cell, and cell-intrinsic signals. These dynamic processes are responsible for mediating cell- and tissue-specific gene expression and function and gene-gene and gene-environmental interactions. The major epigenetic mechanisms include DNA methylation and hydroxymethylation; histone protein posttranslational modifications, nucleosome remodeling/repositioning, and higher-order chromatin reorganization; noncoding RNA regulation; and RNA editing...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29323241/integrative-approach-using-liver-and-duodenum-rna-seq-data-identifies-candidate-genes-and-pathways-associated-with-feed-efficiency-in-pigs
#6
Yuliaxis Ramayo-Caldas, Maria Ballester, Juan Pablo Sánchez, Olga González-Rodríguez, Manuel Revilla, Henry Reyer, Klaus Wimmers, David Torrallardona, Raquel Quintanilla
This study aims identifying candidate genes and pathways associated with feed efficiency (FE) in pigs. Liver and duodenum transcriptomes of 37 gilts showing high and low residual feed intake (RFI) were analysed by RNA-Seq. Gene expression data was explored through differential expression (DE) and weighted gene co-expression network analyses. DE analysis revealed 55 and 112 differentially regulated genes in liver and duodenum tissues, respectively. Clustering genes according to their connectivity resulted in 23 (liver) and 25 (duodenum) modules of genes with a co-expression pattern...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322794/integrated-analysis-of-the-rna-seq-data-of-liver-hepatocellular-carcinoma
#7
H Xue, L Luo, Y T Yao, L L Wei, S P Deng, X L Huang
The present study aimed to explore the genetic changes involved in the liver hepatocellular carcinoma (HCC) development. The RNA-Seq data of 212 HCC tissue samples and 50 normal tissue samples were downloaded using TCGA-Assembler. A total of 4 subgroups were obtained, and 4167, 6279, 5379, and 2548 DEGs were screened in group 1, group 2, group 3, and group 4, respectively. Enrichment analysis found that cell cycle, metabolism, and translation related terms were the most significantly changed functions and pathways...
2018: Neoplasma
https://www.readbyqxmd.com/read/29320577/genome-wide-profiling-of-the-piwi-interacting-rna-mrna-regulatory-networks-in-epithelial-ovarian-cancers
#8
Garima Singh, Jyoti Roy, Pratiti Rout, Bibekanand Mallick
PIWI-interacting (piRNAs), ~23-36 nucleotide-long small non-coding RNAs (sncRNAs), earlier believed to be germline-specific, have now been identified in somatic cells, including cancer cells. These sncRNAs impact critical biological processes by fine-tuning gene expression at post-transcriptional and epigenetic levels. The expression of piRNAs in ovarian cancer, the most lethal gynecologic cancer is largely uncharted. In this study, we investigated the expression of PIWILs by qRT-PCR and western blotting and then identified piRNA transcriptomes in tissues of normal ovary and two most prevalent epithelial ovarian cancer subtypes, serous and endometrioid by small RNA sequencing...
2018: PloS One
https://www.readbyqxmd.com/read/29316363/exploiting-advanced-hydrogel-technologies-to-address-key-challenges-in-regenerative-medicine
#9
REVIEW
Daniel A Foyt, Michael D A Norman, Tracy T L Yu, Eileen Gentleman
Regenerative medicine aims to tackle a panoply of challenges from repairing focal damage to articular cartilage to preventing pathological tissue remodeling after myocardial infarction. Hydrogels are water-swollen networks formed from synthetic or naturally derived polymers and are emerging as important tools to address these challenges. Recent advances in hydrogel chemistries are enabling researchers to create hydrogels that can act as 3D ex vivo tissue models, allowing them to explore fundamental questions in cell biology by replicating tissues' dynamic and nonlinear physical properties...
January 9, 2018: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/29315226/unfolding-role-of-a-danger-molecule-adenosine-signaling-in-modulation-of-microbial-infection-and-host-cell-response
#10
REVIEW
Jaden S Lee, Özlem Yilmaz
Ectonucleotidases CD39 and CD73, specific nucleotide metabolizing enzymes located on the surface of the host, can convert a pro-inflammatory environment driven by a danger molecule extracellular-ATP to an adenosine-mediated anti-inflammatory milieu. Accordingly, CD39/CD73 signaling have has strongly implicated in modulating the intensity, duration, and composition of purinergic danger signals delivered to host. Recent studies have eluted potential roles for CD39 and CD73 in selective triggering of a variety of host immune cells and molecules in the presence of pathogenic microorganisms or microbial virulence molecules...
January 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29314616/3d-extrusion-bioprinting-of-single-and-double-network-hydrogels-containing-dynamic-covalent-crosslinks
#11
Leo L Wang, Christopher B Highley, Yi-Cheun Yeh, Jonathan H Galarraga, Selen Uman, Jason A Burdick
The fabrication of three-dimensional (3D) scaffolds is indispensable to tissue engineering and 3D printing is emerging as an important approach towards this. Hydrogels are often used as inks in extrusion-based 3D printing, including with encapsulated cells; however, numerous challenging requirements exist, including appropriate viscosity, the ability to stabilize after extrusion, and cytocompatibility. Here, we present a shear-thinning and self-healing hydrogel crosslinked through dynamic covalent chemistry for 3D bioprinting...
January 3, 2018: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/29313052/a-deep-learning-approach-to-digitally-stain-optical-coherence-tomography-images-of-the-optic-nerve-head
#12
Sripad Krishna Devalla, Khai Sing Chin, Jean-Martial Mari, Tin A Tun, Nicholas G Strouthidis, Tin Aung, Alexandre H Thiéry, Michaël J A Girard
Purpose: To develop a deep learning approach to digitally stain optical coherence tomography (OCT) images of the optic nerve head (ONH). Methods: A horizontal B-scan was acquired through the center of the ONH using OCT (Spectralis) for one eye of each of 100 subjects (40 healthy and 60 glaucoma). All images were enhanced using adaptive compensation. A custom deep learning network was then designed and trained with the compensated images to digitally stain (i.e., highlight) six tissue layers of the ONH...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29312749/circular-rnas-in-thoracic-diseases
#13
REVIEW
Fan Yang, Ping Zhu, Jintao Guo, Xiang Liu, Sheng Wang, Guoxin Wang, Wen Liu, Shupeng Wang, Nan Ge
Circular RNAs (circRNAs) are a class of noncoding RNAs with continuous, covalently closed circular structures. Investigators have shown previously that circRNAs are regulators of gene expression in mammals. These tissue-specific transcripts are produced primarily by exonic or intronic sequences of housekeeping genes. Several biosynthetic models have been proposed for circRNAs, and consensus is lacking. CircRNAs are widely expressed in the cytoplasm and highly conserved, what is more, unlike other noncoding RNAs, circRNAs are relatively stable...
December 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/29311672/ephb3-signaling-induces-cortical-endothelial-cell-death-and-disrupts-the-blood-brain-barrier-after-traumatic-brain-injury
#14
Poincyane Assis-Nascimento, Yanina Tsenkina, Daniel J Liebl
Damage to the cerebrovascular network is a major contributor to dysfunction in patients suffering from traumatic brain injury (TBI). Vessels are composed of lumen-forming endothelial cells that associate closely with both glial and neuronal units to establish a functional blood-brain barrier (BBB). Under normal physiological conditions, these vascular units play important roles in central nervous system (CNS) homeostasis by delivering oxygen and nutrients while filtering out molecules and cells that could be harmful; however, after TBI this system is disrupted...
January 8, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29311280/an-algu-regulated-antisense-transcript-encoded-within-the-pseudomonas-syringae-fleq-gene-has-a-positive-effect-on-motility
#15
Eric Markel, Hollie Dalenberg, Caroline L Monteil, Boris A Vinatzer, Bryan Swingle
Production of bacterial flagella is controlled by a multi-tiered regulatory system that coordinates expression of 40-50 subunits and ordered assembly of these elaborate structures. Flagellar expression is environmentally controlled, presumably to optimize the benefits and liabilities of having these organelles with cell growth and survival. We recently reported a global survey of AlgU-dependent regulation and binding in Pseudomonas syringae pv. tomato DC3000 that included evidence for strong down-regulation of many flagellar and chemotaxis motility genes...
January 8, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29310798/mechanotransduction-in-blood-and-lymphatic-vascular-development-and-disease
#16
Sofia Urner, Molly Kelly-Goss, Shayn M Peirce, Eckhard Lammert
The blood and lymphatic vasculatures are hierarchical networks of vessels, which constantly transport fluids and, therefore, are exposed to a variety of mechanical forces. Considering the role of mechanotransduction is key for fully understanding how these vascular systems develop, function, and how vascular pathologies evolve. During embryonic development, for example, initiation of blood flow is essential for early vascular remodeling, and increased interstitial fluid pressure as well as initiation of lymph flow is needed for proper development and maturation of the lymphatic vasculature...
2018: Advances in Pharmacology
https://www.readbyqxmd.com/read/29309507/segreg-a-database-for-human-specifically-expressed-genes-and-their-regulations-in-cancer-and-normal-tissue
#17
Qin Tang, Qiong Zhang, Yao Lv, Ya-Ru Miao, An-Yuan Guo
Human specifically expressed genes (SEGs) usually serve as potential biomarkers for disease diagnosis and treatment. However, the regulation underlying their specific expression remains to be revealed. In this study, we constructed SEG regulation database (SEGreg; available at http://bioinfo.life.hust.edu.cn/SEGreg) for showing SEGs and their transcription factors (TFs) and microRNA (miRNA) regulations under different physiological conditions, which include normal tissue, cancer tissue and cell line. In total, SEGreg collected 6387, 1451, 4506 and 5320 SEGs from expression profiles of 34 cancer types and 55 tissues of The Cancer Genome Atlas, Cancer Cell Line Encyclopedia, Human Body Map and Genotype-Tissue Expression databases/projects, respectively...
January 3, 2018: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29308830/starling-forces-drive-intracranial-water-exchange-during-normal-and-pathological-states
#18
Andreas A Linninger, Colin Xu, Kevin Tangen, Grant Hartung
AIM: To quantify the exchange of water between cerebral compartments, specifically blood, tissue, perivascular pathways, and cerebrospinal fluid-filled spaces, on the basis of experimental data and to propose a dynamic global model of water flux through the entire brain to elucidate functionally relevant fluid exchange phenomena. METHODS: The mechanistic computer model to predict brain water shifts is discretized by cerebral compartments into nodes. Water and species flux is calculated between these nodes across a network of arcs driven by Hagen-Poiseuille flow (blood), Darcy flow (interstitial fluid transport), and Starling's Law (transmembrane fluid exchange)...
December 31, 2017: Croatian Medical Journal
https://www.readbyqxmd.com/read/29307754/physical-constraints-in-cell-fate-specification-a-case-in-point-microgravity-and-phenotypes-differentiation
#19
REVIEW
Maria Grazia Masiello, Roberto Verna, Alessandra Cucina, Mariano Bizzarri
Data obtained by studying mammalian cells in absence of gravity strongly support the notion that cell fate specification cannot be understood according to the current molecular model. A paradigmatic case in point is provided by studying cell populations growing in absence of gravity. When the physical constraint (gravity) is 'experimentally removed', cells spontaneously allocate into two morphologically different phenotypes. Such phenomenon is likely enacted by the intrinsic stochasticity, which, in turn, is successively 'canalized' by a specific gene regulatory network...
January 4, 2018: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29305255/comparative-analysis-of-gene-expression-in-maternal-peripheral-blood-and-monocytes-during-spontaneous-preterm-labor
#20
Alison G Paquette, Oksana Shynlova, Mark Kibschull, Nathan D Price, Stephen J Lye
BACKGROUND: Preterm birth is the leading cause of newborn death worldwide, and is associated with significant cognitive and physiological challenges in later life. There is a pressing need to define the mechanisms that initiate spontaneous preterm labor , and for development of novel clinical biomarkers to identify high-risk pregnancies. Most preterm birth studies utilize fetal tissues, and there is limited understanding of the transcriptional changes that occur in mothers undergoing spontaneous preterm labor...
January 2, 2018: American Journal of Obstetrics and Gynecology
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