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https://read.qxmd.com/read/30781586/cvm6a-a-visualization-and-exploration-database-for-m%C3%A2-as-in-cell-lines
#1
Yujing Han, Jing Feng, Linjian Xia, Xin Dong, Xinyang Zhang, Shihan Zhang, Yuqi Miao, Qidi Xu, Shan Xiao, Zhixiang Zuo, Laixin Xia, Chunjiang He
N6-methyladenosine (m⁶A) has been identified in various biological processes and plays important regulatory functions in diverse cells. However, there is still no visualization database for exploring global m⁶A patterns across cell lines. Here we collected all available MeRIP-Seq and m⁶A-CLIP-Seq datasets from public databases and identified 340,950 and 179,201 m⁶A peaks dependent on 23 human and eight mouse cell lines respectively. Those m⁶A peaks were further classified into mRNA and lncRNA groups...
February 17, 2019: Cells
https://read.qxmd.com/read/30781504/a-novel-mva-based-hiv-vaccine-candidate-mva-gp145-gpn-co-expressing-clade-c-membrane-bound-trimeric-gp145-env-and-gag-induced-virus-like-particles-vlps-triggered-broad-and-multifunctional-hiv-1-specific-t-cell-and-antibody-responses
#2
Beatriz Perdiguero, Cristina Sánchez-Corzo, Carlos Oscar S Sorzano, Lidia Saiz, Pilar Mediavilla, Mariano Esteban, Carmen Elena Gómez
The development of an effective Human Immunodeficiency Virus (HIV) vaccine that is able to stimulate both the humoral and cellular HIV-1-specific immune responses remains a major priority challenge. In this study, we described the generation and preclinical evaluation of single and double modified vaccinia virus Ankara (MVA)-based candidates expressing the HIV-1 clade C membrane-bound gp145(ZM96) trimeric protein and/or the Gag(ZM96)-Pol-Nef(CN54) (GPN) polyprotein that was processed to form Gag-induced virus-like particles (VLPs)...
February 16, 2019: Viruses
https://read.qxmd.com/read/30780127/quinaldic-acid-induces-changes-in-the-expression-of-p53-tumor-suppressor-both-on-protein-and-gene-level-in-colon-cancer-ls180-cells
#3
Ewa Langner, Witold Jeleniewicz, Waldemar A Turski, Tomasz Plech
BACKGROUND: Origin, synthesis and activity of quinaldic acid (QA), proposed derivative of kynurenic acid, have been poorly studied to date. Previously, we have demonstrated the antiproliferative effect of QA in a colon cancer model in vitro. The goal of present study was to verify QA activity to modify the expression of p53 tumor suppressor in colon cancer cells, and to relate it to its cancer cell growth inhibiting activity in vitro. METHODS: LS180 colon cancer cells possessing the wild type form of p53 were used in the study...
October 30, 2018: Pharmacological Reports: PR
https://read.qxmd.com/read/30779743/dynein-promotes-sustained-axonal-growth-and-schwann-cell-remodeling-early-during-peripheral-nerve-regeneration
#4
Melissa Ducommun Priest, Maria F Navarro, Juliane Bremer, Michael Granato
Following injury, axons of the peripheral nervous system have retained the capacity for regeneration. While it is well established that injury signals require molecular motors for their transport from the injury site to the nucleus, whether kinesin and dynein motors play additional roles in peripheral nerve regeneration is not well understood. Here we use genetic mutants of motor proteins in a zebrafish peripheral nerve regeneration model to visualize and define in vivo roles for kinesin and dynein. We find that both kinesin-1 and dynein are required for zebrafish peripheral nerve regeneration...
February 19, 2019: PLoS Genetics
https://read.qxmd.com/read/30779484/-the-israeli-inherited-retinal-diseases-consortium-iirdc-clinical-genetic-mapping-and-future-perspectives
#5
Dror Sharon, Tamar Ben-Yosef, Eran Pras, Nitza Goldenberg-Cohen, Libe Gradstein, Noam Shomron, Ohad Birk, Miriam Ehrenberg, Jaime Levy, Eedy Mezer, Shiri Soudry, Ygal Rotenstreich, Hadas Newman, Rina Leibu, Eyal Banin, Ido Perlman
INTRODUCTION: The sense of vision is highly important for humans and its loss markedly affects function and quality of life. Many inherited retinal diseases (IRDs) cause visual loss due to dysfunction or progressive degeneration of photoreceptor cells. These diseases show clinical and genetic heterogeneity. AIMS: The Israeli IRD consortium (IIRDC) was established with the goal of performing clinical and genetic mapping of IRDs in the Israeli population. METHODS: Clinical evaluation is carried out at electroretinography (ERG) centers and ophthalmology departments, where the patients undergo a comprehensive eye exam, including testing of visual acuity, refractive error, imaging techniques and ERG tests...
February 2019: Harefuah
https://read.qxmd.com/read/30779038/fish-and-fiction-in-lymphoma-research
#6
Maciej Giefing, Reiner Siebert
Fluorescence in situ hybridization (FISH) is a powerful and robust technique allowing the visualization of target sequences like genes in interphase nuclei. It is widely used in routine diagnostics to identify cancer-specific aberrations including lymphoma-associated translocations or gene copy number changes in single tumor cells. By combining FISH with immunophenotyping-a technique called fluorescence immunophenotyping and interphase cytogenetic as a tool for investigation of neoplasia (FICTION)-it is moreover possible to identify a cell population of interest...
2019: Methods in Molecular Biology
https://read.qxmd.com/read/30778173/de-novo-variants-in-hk1-associated-with-neurodevelopmental-abnormalities-and-visual-impairment
#7
Volkan Okur, Megan T Cho, Richard van Wijk, Brigitte van Oirschot, Jonathan Picker, Stephanie A Coury, Dorothy Grange, Linda Manwaring, Ian Krantz, Colleen Clark Muraresku, Peter J Hulick, Holley May, Eric Pierce, Emily Place, Kinga Bujakowska, Aida Telegrafi, Ganka Douglas, Kristin G Monaghan, Amber Begtrup, Ashley Wilson, Kyle Retterer, Kwame Anyane-Yeboa, Wendy K Chung
Hexokinase 1 (HK1) phosphorylates glucose to glucose-6-phosphate, the first rate-limiting step in glycolysis. Homozygous and heterozygous variants in HK1 have been shown to cause autosomal recessive non-spherocytic hemolytic anemia, autosomal recessive Russe type hereditary motor and sensory neuropathy, and autosomal dominant retinitis pigmentosa (adRP). We report seven patients from six unrelated families with a neurodevelopmental disorder associated with developmental delay, intellectual disability, structural brain abnormality, and visual impairments in whom we identified four novel, de novo missense variants in the N-terminal half of HK1...
February 18, 2019: European Journal of Human Genetics: EJHG
https://read.qxmd.com/read/30778082/the-effect-of-robertsonian-translocations-on-the-intranuclear-positioning-of-nors-nucleolar-organizing-regions-in-human-sperm-cells
#8
Ewa Wiland, Marta Olszewska, Nataliya Huleyuk, Vyacheslav B Chernykh, Maciej Kurpisz
Only a few studies have described sperm chromosome intranuclear positioning changes in men with reproductive failure and an incorrect somatic karyotype. We studied the influence of Robertsonian translocations on the acrocentric chromosome positioning in human sperm cells. The basis of the analysis was the localization of NORs (nucleolar organizing regions) in sperm nuclei from three Robertsonian translocation carriers, namely, rob(13;22), rob(13;15) and rob(13;14), with a known meiotic segregation pattern. All three carriers presented with a similar percentage of genetically normal sperm cells (i...
February 18, 2019: Scientific Reports
https://read.qxmd.com/read/30777950/three-dimensional-digital-visualization-of-phacoemulsification-and-intraocular-lens-implantation
#9
Zhuyun Qian, Hongxia Wang, Hua Fan, Dong Lin, Wensheng Li
Purpose: To evaluate the feasibility and safety of heads-up three-dimensional (3D) vision system for phacoemulsification and intraocular lens (IOL) implantation surgery. Methods: In this prospective, randomized controlled study, 20 eyes with age-related cataract received phacoemulsification and IOL implantation and were randomly divided into "heads-up" 3D vision group and conventional surgery group. Ocular and surgical parameters such as surgery time, pre and postoperative best-corrected visual acuity (BCVA), and corneal endothelial cells density were recorded and statistically analyzed...
March 2019: Indian Journal of Ophthalmology
https://read.qxmd.com/read/30777743/biomineralization-synthesis-of-cobalt-nanozyme-in-sp94-ferritin-nanocage-for-prognostic-diagnosis-of-hepatocellular-carcinoma
#10
Bing Jiang, Liang Yan, Jianlin Zhang, Meng Zhou, Guizhi Shi, Xiuyun Tian, Kelong Fan, Chunyi Hao, Xiyun Yan
Nanomaterials with intrinsic enzyme-like activities (nanozymes), have emerged as promising agents for cancer theranostics strategies. However, size controllable synthesis of nanozymes and their targeting modifications are still challenging. Here, we report a monodispersed ferritin-based cobalt nanozyme (HccFn(Co3O4)) that specifically targets and visualizes clinical hepatocellular carcinoma (HCC) tissues. The cobalt nanozyme is biomimetically synthesized within the protein shell of HCC targeted ferritin (HccFn) nanocage, which is enabled by the display of HCC cell-specific peptide SP94 on the surface of ferritin through genetic engineering approach...
February 19, 2019: ACS Applied Materials & Interfaces
https://read.qxmd.com/read/30777430/an-aptamer-based-near-infrared-fluorescence-nanoprobe-for-detecting-and-imaging-of-pln-micropeptide-in-cardiomyocytes
#11
Renhui Zhan, Xiaofeng Li, Wenfei Guo, Xiaojun Liu, Zhi-Xian Liu, Kehua Xu, Bo Tang
A growing body of evidence indicates that micropeptides encoded by long noncoding RNAs (lncRNAs) act independently or as regulators of larger proteins in fundamental biological processes, especially in the maintenance of cellular homeostasis. However, due to their small size and low intracellular expression, visual monitoring of micropeptides in living cells is still a challenge. In this work, we have designed and synthesized an aptamer-based near-infrared fluorescence nanoprobe for fluorescence imaging of phospholamban (PLN), which is an intracellular micropeptide that affects calcium homeostasis, and is closely associated with human heart failure in clinic...
February 19, 2019: ACS Sensors
https://read.qxmd.com/read/30777183/analysis-of-immune-response-in-the-sea-urchin-larva
#12
Katherine M Buckley, Nicholas W Schuh, Andreas Heyland, Jonathan P Rast
Sea urchin larvae deploy a complex immune system in the context of relatively simple morphology. Several types of phagocytic or granular immune cells respond rapidly to microbes and microbial components within the body cavity. Many of these cells also respond to microbial disturbances in the gut lumen. In the course of immune response, hundreds of genes are up- and downregulated, many of which have homologs involved in immunity in other species. Thus, the larval sea urchin provides an experimentally advantageous model for investigating the response to immune challenge at the level of cell behavior and gene regulatory networks...
2019: Methods in Cell Biology
https://read.qxmd.com/read/30777010/statistical-assessment-and-visualization-of-synergies-for-large-scale-sparse-drug-combination-datasets
#13
Arnaud Amzallag, Sridhar Ramaswamy, Cyril H Benes
BACKGROUND: Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to screen large numbers of drug pairs, but complicates statistical assessment of synergy. Furthermore, since the number of pairwise combinations grows with the square of the number of drugs, exploration of large screens necessitates advanced visualization tools...
February 18, 2019: BMC Bioinformatics
https://read.qxmd.com/read/30775994/elevation-of-ps262-tau-and-demethylated-pp2a-in-retina-occurs-earlier-than-in-hippocampus-during-hyperhomocysteinemia
#14
Jing Guo, Cheng Xu, Shaozhou Ni, Shujuan Zhang, Qihang Li, Peng Zeng, Guilin Pi, Enjie Liu, Dong-Sheng Sun, Yanchao Liu, Zhouyi Wang, Haote Chen, Ying Yang, Jian-Zhi Wang
Hyperhomocysteinemia is an independent risk factor of Alzheimer's disease (AD), which is not diagnosed for many years before onset due to lack of peripherally detectable early biomarkers. Visual dysfunction is prevalent in AD patients and correlates with the severity of cognitive defects. Importantly, alterations in eyes can be non-invasively detected. To search for early biomarkers in eyes from high risk factors of AD, we injected homocysteine (Hcy) into the rats via vena caudalis for 3, 7, and 14 days, respectively, and characterized the chronological order of the AD-like pathologies appearing in retina and the hippocampus during the progression of hyperhomocysteinemia, and their correlations with cognitive impairment...
February 11, 2019: Journal of Alzheimer's Disease: JAD
https://read.qxmd.com/read/30775090/novel-window-for-cancer-nanotheranostics-non-invasive-ocular-assessments-of-tumor-growth-and-nanotherapeutic-treatment-efficacy-in-vivo
#15
Mayank Goswami, Xinlei Wang, Pengfei Zhang, Wenwu Xiao, Sarah J Karlen, Yuanpei Li, Robert J Zawadzki, Marie E Burns, Kit S Lam, Edward N Pugh
In cancer research there is a fundamental need for animal models that allow the in vivo longitudinal visualization and quantification of tumor development, nanotherapeutic delivery, the tumor microenvironment including blood vessels, macrophages, fibroblasts, immune cells, and extracellular matrix, and the tissue response to treatment. To address this need, we developed a novel mouse ocular xenograft model. Green fluorescent protein (GFP) expressing human glioblastoma cells (between 500 and 10,000) were implanted into the subretinal space of immunodeficient mice (56 eyes)...
January 1, 2019: Biomedical Optics Express
https://read.qxmd.com/read/30775085/multiscale-x-ray-phase-contrast-tomography-in-a-mouse-model-of-transient-focal-cerebral-ischemia
#16
Mareike Töpperwien, Thorsten R Doeppner, Bozena Zechmeister, Mathias Bähr, Tim Salditt
Cerebral ischemia is associated with a lack of oxygen and high-energy phosphates within the brain tissue, leading to irreversible cell injury. Visualizing these cellular injuries has long been a focus of experimental stroke research with application of immunohistochemistry as one of the standard approaches. It is, however, a destructive imaging technique with non-isotropic resolution, as only the two-dimensional tissue structure of a thin brain section is visualized using optical microscopy and specific stainings...
January 1, 2019: Biomedical Optics Express
https://read.qxmd.com/read/30775083/cellular-scale-evaluation-of-induced-photoreceptor-degeneration-in-the-living-primate-eye
#17
Sarah Walters, Christina Schwarz, Robin Sharma, Ethan A Rossi, William S Fischer, David A DiLoreto, Jennifer Strazzeri, Dasha Nelidova, Botond Roska, Jennifer J Hunter, David R Williams, William H Merigan
Progress is needed in developing animal models of photoreceptor degeneration and evaluating such models with longitudinal, noninvasive techniques. We employ confocal scanning laser ophthalmoscopy, optical coherence tomography (OCT) and high-resolution retinal imaging to noninvasively observe the retina of non-human primates with induced photoreceptor degeneration. Photoreceptors were imaged at the single-cell scale in three modalities of adaptive optics scanning light ophthalmoscopy: traditional confocal reflectance, indicative of waveguiding; a non-confocal offset aperture technique visualizing scattered light; and two-photon excited fluorescence, the time-varying signal of which, at 730 nm excitation, is representative of visual cycle function...
January 1, 2019: Biomedical Optics Express
https://read.qxmd.com/read/30775081/fast-volumetric-live-cell-imaging-using-high-resolution-light-field-microscopy
#18
Haoyu Li, Changliang Guo, Deborah Kim-Holzapfel, Weiyi Li, Yelena Altshuller, Bryce Schroeder, Wenhao Liu, Yizhi Meng, Jarrod B French, Ken-Ichi Takamaru, Michael A Frohman, Shu Jia
Visualizing diverse anatomical and functional traits that span many spatial scales with high spatio-temporal resolution provides insights into the fundamentals of living organisms. Light-field microscopy (LFM) has recently emerged as a scanning-free, scalable method that allows for high-speed, volumetric functional brain imaging. Given those promising applications at the tissue level, at its other extreme, this highly-scalable approach holds great potential for observing structures and dynamics in single-cell specimens...
January 1, 2019: Biomedical Optics Express
https://read.qxmd.com/read/30774135/probing-the-structure-and-dynamics-of-nucleosomes-using-atomic-force-microscopy-imaging
#19
Micah P Stumme-Diers, Tommy Stormberg, Zhiqiang Sun, Yuri L Lyubchenko
Chromatin, which is a long chain of nucleosome subunits, is a dynamic system that allows for such critical processes as DNA replication and transcription to take place in eukaryotic cells. The dynamics of nucleosomes provides access to the DNA by replication and transcription machineries, and critically contributes to the molecular mechanisms underlying chromatin functions. Single-molecule studies such as atomic force microscopy (AFM) imaging have contributed significantly to our current understanding of the role of nucleosome structure and dynamics...
January 31, 2019: Journal of Visualized Experiments: JoVE
https://read.qxmd.com/read/30774126/using-in-vitro-and-in-cell-shape-to-investigate-small-molecule-induced-pre-mrna-structural-changes
#20
Jingxin Wang, John Hammond, Kristen A Johnson
In the process of drug development of RNA-targeting small molecules, elucidating the structural changes upon their interactions with target RNA sequences is desired. We herein provide a detailed in vitro and in-cell selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) protocol to study the RNA structural change in the presence of an experimental drug for spinal muscular atrophy (SMA), survival of motor neuron (SMN)-C2, and in exon 7 of the pre-mRNA of the SMN2 gene. In in vitro SHAPE, an RNA sequence of 140 nucleotides containing SMN2 exon 7 is transcribed by T7 RNA polymerase, folded in the presence of SMN-C2, and subsequently modified by a mild 2'-OH acylation reagent, 2-methylnicotinic acid imidazolide (NAI)...
January 30, 2019: Journal of Visualized Experiments: JoVE
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