keyword
MENU ▼
Read by QxMD icon Read
search

R loop

keyword
https://www.readbyqxmd.com/read/29351845/a-precise-cdk-activity-threshold-determines-passage-through-the-restriction-point
#1
Clayton Schwarz, Amy Johnson, Mardo Kõivomägi, Evgeny Zatulovskiy, Carolyn J Kravitz, Andreas Doncic, Jan M Skotheim
At the restriction point (R), mammalian cells irreversibly commit to divide. R has been viewed as a point in G1 that is passed when growth factor signaling initiates a positive feedback loop of Cdk activity. However, recent studies have cast doubt on this model by claiming R occurs prior to positive feedback activation in G1 or even before completion of the previous cell cycle. Here we reconcile these results and show that whereas many commonly used cell lines do not exhibit a G1 R, primary fibroblasts have a G1 R that is defined by a precise Cdk activity threshold and the activation of cell-cycle-dependent transcription...
January 18, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29351033/closing-the-loop-on-centralization-of-cleft-care-in-the-united-kingdom
#2
Andrew R Ness, Andrew R Wills, Andrea Waylen, Jackie Smallridge, Amanda J Hall, Debbie Sell, Jonathan R Sandy
OBJECTIVE: We highlight a major study that investigated the impact of reconfigured cleft care in the United Kingdom some 15 years after centralization. We argue that centralization as an intervention has a major impact on outcomes. SETTING: Audit clinics held in Cleft Centers in the United Kingdom. PATIENTS, PARTICIPANTS: Five-year-olds born between April 1, 2005, and March 31, 2007, with nonsyndromic unilateral cleft lip and palate. INTERVENTIONS: Centralization of cleft care...
February 2018: Cleft Palate-craniofacial Journal
https://www.readbyqxmd.com/read/29350681/aav-9-mediated-phosphatase-1-inhibitor-1-overexpression-improves-cardiac-contractility-in-unchallenged-mice-but-is-deleterious-in-pressure-overload
#3
D M Schwab, L Tilemann, R Bauer, M Heckmann, A Jungmann, M Wagner, J Burgis, C Vettel, H A Katus, A El-Armouche, O J Müller
The downregulation of β-adrenergic receptors (β-AR) and decreased cAMP-dependent protein kinase activity in failing hearts results in decreased phosphorylation and inactivation of phosphatase-inhibitor-1 (I-1), a distal amplifier element of β-adrenergic signaling, leading to increased protein phosphatase 1 activity and dephosphorylation of key phosphoproteins, including phospholamban. Downregulated and hypophosphorylated I-1 likely contributes to β-AR desensitization; therefore its modulation is a promising approach in heart failure treatment...
January 19, 2018: Gene Therapy
https://www.readbyqxmd.com/read/29350254/sacubitril-valsartan-for-heart-failure-with-reduced-left-ventricular-ejection-fraction-a%C3%A2-retrospective-cohort-study
#4
R De Vecchis, C Ariano, G Di Biase, M Noutsias
BACKGROUND: The combination drug sacubitril/valsartan was reported to be superior to enalapril in reducing all-cause death, cardiovascular mortality, and heart failure (HF) hospitalizations in patients with cardiac insufficiency and reduced left ventricular ejection fraction (HFREF) with NYHA class II-IV. METHODS: Our retrospective cohort study aimed to assess the effects of sacubitril/valsartan in addition to a beta-blocker and mineral receptor antagonist (MRA) in a group of HFREF patients with NYHA class II-III HF vs...
January 19, 2018: Herz
https://www.readbyqxmd.com/read/29348367/a-pathway-for-mitotic-chromosome-formation
#5
Johan H Gibcus, Kumiko Samejima, Anton Goloborodko, Itaru Samejima, Natalia Naumova, Johannes Nuebler, Masato T Kanemaki, Linfeng Xie, James R Paulson, William C Earnshaw, Leonid A Mirny, Job Dekker
Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations. We show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner and arrays of consecutive 60 kb loops are formed. During prometaphase ~80 kb inner loops are nested within ~400 kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central spiral-staircase condensin scaffold...
January 18, 2018: Science
https://www.readbyqxmd.com/read/29347657/mapping-of-the-bak-tang-and-wiesenfeld-sandpile-model-on-a-two-dimensional-ising-correlated-percolation-lattice-to-the-two-dimensional-self-avoiding-random-walk
#6
J Cheraghalizadeh, M N Najafi, H Dashti-Naserabadi, H Mohammadzadeh
The self-organized criticality on the random fractal networks has many motivations, like the movement pattern of fluid in the porous media. In addition to the randomness, introducing correlation between the neighboring portions of the porous media has some nontrivial effects. In this paper, we consider the Ising-like interactions between the active sites as the simplest method to bring correlations in the porous media, and we investigate the statistics of the BTW model in it. These correlations are controlled by the artificial "temperature" T and the sign of the Ising coupling...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346769/switching-on-depression-and-potentiation-in-the-cerebellum
#7
Andrew R Gallimore, Taegon Kim, Keiko Tanaka-Yamamoto, Erik De Schutter
Long-term depression (LTD) and long-term potentiation (LTP) in the cerebellum are important for motor learning. However, the signaling mechanisms controlling whether LTD or LTP is induced in response to synaptic stimulation remain obscure. Using a unified model of LTD and LTP at the cerebellar parallel fiber-Purkinje cell (PF-PC) synapse, we delineate the coordinated pre- and postsynaptic signaling that determines the direction of plasticity. We show that LTP is the default response to PF stimulation above a well-defined frequency threshold...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346393/computational-study-of-hiv-gp120-as-a-target-for-polyanionic-entry-inhibitors-exploiting-the-v3-loop-region
#8
Louis R Hollingsworth, Anne M Brown, Richard D Gandour, David R Bevan
Multiple approaches are being utilized to develop therapeutics to treat HIV infection. One approach is designed to inhibit entry of HIV into host cells, with a target being the viral envelope glycoprotein, gp120. Polyanionic compounds have been shown to be effective in inhibiting HIV entry, with a mechanism involving electrostatic interactions with the V3 loop of gp120 being proposed. In this study, we applied computational methods to elucidate molecular interactions between the repeat unit of the precisely alternating polyanion, Poly(4,4'-stilbenedicarboxylate-alt-maleic acid) (DCSti-alt-MA) and the V3 loop of gp120 from strains of HIV against which these polyanions were previously tested (IIIb, BaL, 92UG037, JR-CSF) as well as two strains for which gp120 crystal structures are available (YU2, 2B4C)...
2018: PloS One
https://www.readbyqxmd.com/read/29344285/long-noncoding-rna-h19-derived-mir-675-regulates-cell-proliferation-by-down-regulating-e2f-1-in-human-pancreatic-ductal-adenocarcinoma
#9
Ling Ma, Xiaodong Tian, Huahu Guo, Zhengkui Zhang, Chong Du, Feng Wang, Xuehai Xie, Hongqiao Gao, Yan Zhuang, Marko Kornmann, Hong Gao, Yinmo Yang
The long noncoding RNA (lncRNA) H19 has been proven to be overexpressed in human pancreatic ductal adenocarcinoma (PDAC). H19-induced PDAC cell proliferation is cell cycle-dependent by modulating E2F-1. However, the mechanism of how H19 regulates E2F-1 remains unclear. In this study, we investigated the expression of miR-675 in PDAC tumours and cells, the biological function of miR-675 in PDAC cell proliferation and the possible relationship among H19, miR-675 and E2F-1. As a transcript of the first exon of H19, the level of miR-675 was negatively correlated with H19 expression in microdissected PDAC tissues (r=-0...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29341686/nonequilibrium-chromosome-looping-via-molecular-slip-links
#10
C A Brackley, J Johnson, D Michieletto, A N Morozov, M Nicodemi, P R Cook, D Marenduzzo
We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site...
September 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29339412/the-sequence-specific-peptide-binding-activity-of-the-protein-sulfide-isomerase-agr2-directs-its-stable-binding-to-the-oncogenic-receptor-epcam
#11
M Aiman Mohtar, Lenka Hernychova, Robert O'Neill, Melanie Lawrence, Euan Murray, Borek Vojtesek, Ted R Hupp
AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a specific peptide motif (TTIYY). A synthetic TTIYY-containing peptide column was used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131-135 (VDPSL)...
January 16, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29335561/sub-%C3%A3-ngstr%C3%A3-m-cryo-em-structure-of-a-prion-protofibril-reveals-a-polar-clasp
#12
Marcus Gallagher-Jones, Calina Glynn, David R Boyer, Michael W Martynowycz, Evelyn Hernandez, Jennifer Miao, Chih-Te Zee, Irina V Novikova, Lukasz Goldschmidt, Heather T McFarlane, Gustavo F Helguera, James E Evans, Michael R Sawaya, Duilio Cascio, David S Eisenberg, Tamir Gonen, Jose A Rodriguez
The atomic structure of the infectious, protease-resistant, β-sheet-rich and fibrillar mammalian prion remains unknown. Through the cryo-EM method MicroED, we reveal the sub-ångström-resolution structure of a protofibril formed by a wild-type segment from the β2-α2 loop of the bank vole prion protein. The structure of this protofibril reveals a stabilizing network of hydrogen bonds that link polar zippers within a sheet, producing motifs we have named 'polar clasps'.
January 15, 2018: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29335461/pixelated-spatial-gene-expression-analysis-from-tissue
#13
A Ganguli, A Ornob, N Spegazzini, Y Liu, G Damhorst, T Ghonge, B Thornton, C J Konopka, W Dobrucki, S E Clare, R Bhargava, A M Smith, F Kosari, R Bashir
Here, we present a technique that performs on-chip picoliter real-time reverse transcriptase loop mediated isothermal amplification (RT-LAMP) reactions on a histological tissue section without any analyte purification while preserving the native spatial location of the nucleic acid molecules. We demonstrate this method by amplifying TOP2A messenger RNA (mRNA) in a prostate cancer xenograft with 100 µm spatial resolution and by visualizing the variation in threshold time of amplification across the tissue...
January 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29334377/detecting-hierarchical-genome-folding-with-network-modularity
#14
Heidi K Norton, Daniel J Emerson, Harvey Huang, Jesi Kim, Katelyn R Titus, Shi Gu, Danielle S Bassett, Jennifer E Phillips-Cremins
Mammalian genomes are folded in a hierarchy of compartments, topologically associating domains (TADs), subTADs and looping interactions. Here, we describe 3DNetMod, a graph theory-based method for sensitive and accurate detection of chromatin domains across length scales in Hi-C data. We identify nested, partially overlapping TADs and subTADs genome wide by optimizing network modularity and varying a single resolution parameter. 3DNetMod can be applied broadly to understand genome reconfiguration in development and disease...
January 15, 2018: Nature Methods
https://www.readbyqxmd.com/read/29333595/implanted-closed-loop-gastric-electrical-stimulation-clges-system-with-sensor-based-feedback-safely-limits-weight-regain-at-24%C3%A2-months
#15
S Morales-Conde, I Alarcón Del Agua, L Busetto, F Favretti, M Anselmino, G M Rovera, M Socas-Macias, A Barranco-Moreno, R Province-Azalde, A J Torres
BACKGROUND: Weight regain following bariatric surgery is not uncommon. Safe, effective weight loss treatment up to 1 year has been reported with the closed-loop gastric electrical stimulation (CLGES) system. Continuous recording of eating and activity behavior by onboard sensors is one of the novel features of this closed-loop electrical stimulation therapy, and may provide improved long-term weight maintenance by enhancing aftercare. METHODS: Four centers participating in a 12-month prospective multicenter randomized study monitored all implanted participants (n = 47) up to 24 months after laparoscopic implantation of a CLGES system...
January 15, 2018: Obesity Surgery
https://www.readbyqxmd.com/read/29331357/differentiation-of-inflammatory-from-fibrotic-ileal-strictures-among-patients-with-crohn-s-disease-based-on-visual-analysis-feasibility-study-combining-conventional-b-mode-ultrasound-contrast-enhanced-ultrasound-and-strain-elastography
#16
Emilio Quaia, Antonio Giulio Gennari, Maria Assunta Cova, Edwin J R van Beek
The aim of this pilot study was to assess prospectively the feasibility of conventional B-mode ultrasound (US) and contrast-enhanced ultrasound (CEUS) combined with real-time strain elastography (SE) in the differentiation of inflammatory from fibrotic ileal strictures among patients with Crohn's disease (CD) based on visual analysis. Twenty non-consecutive patients (15 male and 5 female; mean age ± standard deviation, 40.2 ± 10.22 y) with CD and stricture of the terminal ileal loop were scanned by conventional B-mode US and CEUS and, subsequently, by real-time SE...
January 10, 2018: Ultrasound in Medicine & Biology
https://www.readbyqxmd.com/read/29327083/r-loops-targets-for-nuclease-cleavage-and-repeat-instability
#17
REVIEW
Catherine H Freudenreich
R-loops form when transcribed RNA remains bound to its DNA template to form a stable RNA:DNA hybrid. Stable R-loops form when the RNA is purine-rich, and are further stabilized by DNA secondary structures on the non-template strand. Interestingly, many expandable and disease-causing repeat sequences form stable R-loops, and R-loops can contribute to repeat instability. Repeat expansions are responsible for multiple neurodegenerative diseases, including Huntington's disease, myotonic dystrophy, and several types of ataxias...
January 11, 2018: Current Genetics
https://www.readbyqxmd.com/read/29323933/cardioventilatory-control-in-preterm-born-children-and-the-risk-of-obstructive-sleep-apnea
#18
Keren Armoni Domany, Md Monir Hossain, Leonardo Nava-Guerra, Michael C Khoo, Keith McConnell, John L Carroll, Yuanfang Xu, Mark DiFrancesco, Raouf S Amin
Rationale The contribution of ventilatory control to the pathogenesis of obstructive sleep apnea (OSA) in preterm born children is unknown. Objectives To characterize phenotypes of ventilatory control that are associated with the presence of OSA in preterm born children during early childhood. Methods Preterm and term born children without comorbid conditions were enrolled. They were categorized into OSA group and non-OSA group based on polysomnography. Measurements Loop gain, controller gain and plant gain, reflecting ventilatory instability, chemoreceptor sensitivity and blood gas response to a change in ventilation, respectively, were estimated from spontaneous sighs identified during polysomnography...
January 11, 2018: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/29320733/dna-unwinding-is-the-primary-determinant-of-crispr-cas9-activity
#19
Shanzhong Gong, Helen Hong Yu, Kenneth A Johnson, David W Taylor
Bacterial adaptive immunity utilizes RNA-guided surveillance complexes comprising Cas proteins together with CRISPR RNAs (crRNAs) to target foreign nucleic acids for destruction. Cas9, a type II CRISPR-Cas effector complex, can be programed with a single-guide RNA that base pairs with the target strand of dsDNA, displacing the non-target strand to create an R-loop, where the HNH and the RuvC nuclease domains cleave opposing strands. While many structural and biochemical studies have shed light on the mechanism of Cas9 cleavage, a clear unifying model has yet to emerge...
January 9, 2018: Cell Reports
https://www.readbyqxmd.com/read/29311615/hoxc5-and-mir-615-3p-target-newly-evolved-genomic-regions-to-repress-htert-and-inhibit-tumorigenesis
#20
TingDong Yan, Wen Fong Ooi, Aditi Qamra, Alice Cheung, DongLiang Ma, Gopinath Meenakshi Sundaram, Chang Xu, Manjie Xing, LaiFong Poon, Jing Wang, Yan Ping Loh, Jess Hui Jie Ho, Joscelyn Jun Quan Ng, Muhammad Khairul Ramlee, Luay Aswad, Steve G Rozen, Sujoy Ghosh, Frederic A Bard, Prabha Sampath, Vinay Tergaonkar, James O J Davies, Jim R Hughes, Eyleen Goh, Xuezhi Bi, Melissa Jane Fullwood, Patrick Tan, Shang Li
The repression of telomerase activity during cellular differentiation promotes replicative aging and functions as a physiological barrier for tumorigenesis in long-lived mammals, including humans. However, the underlying mechanisms remain largely unclear. Here we describe how miR-615-3p represses hTERT expression. mir-615-3p is located in an intron of the HOXC5 gene, a member of the highly conserved homeobox family of transcription factors controlling embryogenesis and development. Unexpectedly, we found that HoxC5 also represses hTERT expression by disrupting the long-range interaction between hTERT promoter and its distal enhancer...
January 8, 2018: Nature Communications
keyword
keyword
42368
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"