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https://www.readbyqxmd.com/read/28324612/quantitative-image-analysis-of-single-molecule-mrna-dynamics-in-living-cells
#1
José Rino, Ana C de Jesus, Maria Carmo-Fonseca
Single mRNA molecules can be imaged in living cells by a method that consists in genetically inserting binding sites for a bacteriophage protein in the gene of interest. The resulting reporter transgene is then integrated in the genome of cells that express the phage protein fused to a fluorescent tag. Upon transcription, binding of the fluorescent protein to its target sequence makes the RNA visible. With this approach it is possible to track, in real time, the life cycle of a precursor mRNA at the site of transcription in the nucleus and transport of mature mRNA to the cytoplasm...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324506/induction-of-site-specific-oxidative-damage-at-telomeres-by-killerred-fused-shelretin-proteins
#2
Rong Tan, Li Lan
Chronic oxidative stress is the major endogenous metabolic stress and contributes directly to telomere shortening and senescence. Understanding the dysfunction of telomeres under oxidative stress will greatly facilitate healthy aging and advance the treatment of aging-related diseases. Here, we describe the KR-TEL (KillerRed induced DNA damage at telomeres) system that induces site-specific oxidative damage at telomeres. We have developed the KR-TEL system by fusing killerred with the shelterin component TRF1 (KR-TRF1) or other shelterin proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324494/analysis-of-average-telomere-length-in-human-telomeric-protein-knockout-cells-generated-by-crispr-cas9
#3
Jun Xu, Zhou Songyang, Dan Liu, Hyeung Kim
Telomeres play an important role in ensuring the integrity of the genome. Telomere shortening can lead to loss of genetic information and trigger DNA damage responses. Cultured mammalian cells have served as critical model systems for studying the function of telomere binding proteins and telomerase. Tremendous heterogeneity can be observed both between species and within a single cell population. Recent advances in genome editing (such as the development of the CRISPR/Cas9 platform) have further enabled researchers to carry out loss-of-function analysis of how disrupting key players in telomere maintenance affects telomere length regulation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28323831/genetic-assessment-of-age-associated-alzheimer-disease-risk-development-and-validation-of-a-polygenic-hazard-score
#4
Rahul S Desikan, Chun Chieh Fan, Yunpeng Wang, Andrew J Schork, Howard J Cabral, L Adrienne Cupples, Wesley K Thompson, Lilah Besser, Walter A Kukull, Dominic Holland, Chi-Hua Chen, James B Brewer, David S Karow, Karolina Kauppi, Aree Witoelar, Celeste M Karch, Luke W Bonham, Jennifer S Yokoyama, Howard J Rosen, Bruce L Miller, William P Dillon, David M Wilson, Christopher P Hess, Margaret Pericak-Vance, Jonathan L Haines, Lindsay A Farrer, Richard Mayeux, John Hardy, Alison M Goate, Bradley T Hyman, Gerard D Schellenberg, Linda K McEvoy, Ole A Andreassen, Anders M Dale
BACKGROUND: Identifying individuals at risk for developing Alzheimer disease (AD) is of utmost importance. Although genetic studies have identified AD-associated SNPs in APOE and other genes, genetic information has not been integrated into an epidemiological framework for risk prediction. METHODS AND FINDINGS: Using genotype data from 17,008 AD cases and 37,154 controls from the International Genomics of Alzheimer's Project (IGAP Stage 1), we identified AD-associated SNPs (at p < 10-5)...
March 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28319850/methylation-of-hpa-axis-related-genes-in-men-with-hypersexual-disorder
#5
Jussi Jokinen, Adrian E Boström, Andreas Chatzittofis, Diana M Ciuculete, Katarina Görts Öberg, John N Flanagan, Stefan Arver, Helgi B Schiöth
Hypersexual Disorder (HD) defined as non-paraphilic sexual desire disorder with components of compulsivity, impulsivity and behavioral addiction, and proposed as a diagnosis in the DSM 5, shares some overlapping features with substance use disorder including common neurotransmitter systems and dysregulated hypothalamic-pituitary-adrenal (HPA) axis function. In this study, comprising 67 HD male patients and 39 male healthy volunteers, we aimed to identify HPA-axis coupled CpG-sites, in which modifications of the epigenetic profile are associated with hypersexuality...
March 10, 2017: Psychoneuroendocrinology
https://www.readbyqxmd.com/read/28319194/genome-wide-analysis-of-brain-and-gonad-transcripts-reveals-changes-of-key-sex-reversal-related-genes-expression-and-signaling-pathways-in-three-stages-of-monopterus-albus
#6
Wei Chi, Yu Gao, Qing Hu, Wei Guo, Dapeng Li
BACKGROUND: The natural sex reversal severely affects the sex ratio and thus decreases the productivity of the rice field eel (Monopterus albus). How to understand and manipulate this process is one of the major issues for the rice field eel stocking. So far the genomics and transcriptomics data available for this species are still scarce. Here we provide a comprehensive study of transcriptomes of brain and gonad tissue in three sex stages (female, intersex and male) from the rice field eel to investigate changes in transcriptional level during the sex reversal process...
2017: PloS One
https://www.readbyqxmd.com/read/28318141/zika-virus-induced-cellular-remodeling
#7
Evan D Rossignol, Kristen N Peters, John H Connor, Esther Bullitt
Zika virus (ZIKV) has been associated with morbidities such as Guillain-Barré, infant microcephaly, and ocular disease. The spread of this positive-sense, single-stranded RNA virus and its growing public health threat underscore gaps in our understanding of basic ZIKV virology. To advance knowledge of the virus replication cycle within mammalian cells, we use serial section three-dimensional electron tomography to demonstrate the widespread remodeling of intracellular membranes upon infection with ZIKV. We report extensive structural rearrangements of the endoplasmic reticulum and reveal stages of the ZIKV viral replication cycle...
March 20, 2017: Cellular Microbiology
https://www.readbyqxmd.com/read/28317934/dek-is-required-for-homologous-recombination-repair-of-dna-breaks
#8
Eric A Smith, Boris Gole, Nicholas A Willis, Rebeca Soria, Linda M Starnes, Eric F Krumpelbeck, Anil G Jegga, Abdullah M Ali, Haihong Guo, Amom R Meetei, Paul R Andreassen, Ferdinand Kappes, Lisa M Privette Vinnedge, Jeremy A Daniel, Ralph Scully, Lisa Wiesmüller, Susanne I Wells
DEK is a highly conserved chromatin-bound protein whose upregulation across cancer types correlates with genotoxic therapy resistance. Loss of DEK induces genome instability and sensitizes cells to DNA double strand breaks (DSBs), suggesting defects in DNA repair. While these DEK-deficiency phenotypes were thought to arise from a moderate attenuation of non-homologous end joining (NHEJ) repair, the role of DEK in DNA repair remains incompletely understood. We present new evidence demonstrating the observed decrease in NHEJ is insufficient to impact immunoglobulin class switching in DEK knockout mice...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317860/gene-delivery-to-nile-tilapia-cells-for-transgenesis-and-the-role-of-pi3k-c2%C3%AE-in-angiogenesis
#9
Fernanda Maria Policarpo Tonelli, Samyra Maria Dos Santos Nassif Lacerda, Marcela Santos Procópio, Breno Luiz Sales Lemos, Luiz Renato de França, Rodrigo Ribeiro Resende
Microinjection is commonly performed to achieve fish transgenesis; however, due to difficulties associated with this technique, new strategies are being developed. Here we evaluate the potential of lentiviral particles to genetically modify Nile tilapia cells to achieve transgenesis using three different approaches: spermatogonial stem cell (SSC) genetic modification and transplantation (SC), in vivo transduction of gametes (GT), and fertilised egg transduction (ET). The SC protocol using larvae generates animals with sustained production of modified sperm (80% of animals with 77% maximum sperm fluorescence [MSF]), but is a time-consuming protocol (sexual maturity in Nile tilapia is achieved at 6 months of age)...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317760/antibacterial-activity-of-phenyllactic-acid-against-listeria-monocytogenes-and-escherichia-coli-by-dual-mechanisms
#10
Yawei Ning, Aihong Yan, Kun Yang, Zhixin Wang, Xingfeng Li, Yingmin Jia
Phenyllactic acid (PLA), a phenolic acid phytochemical, is considered to be a promising candidate for use as a chemical preservative due to its broad antimicrobial activity. The antibacterial target of PLA has rarely been reported, thus investigations were performed to elucidate the antibacterial mechanism of PLA against Listeria monocytogenes and Escherichia coli. Flow cytometry analysis stained with propidium iodide (PI) demonstrated that PLA could damage the membrane integrity of L. monocytogenes, while it could not disrupt that of E...
August 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28317293/a-new-location-to-split-cre-recombinase-for-protein-fragment-complementation
#11
Maryam Rajaee, David W Ow
We have previously described a recombinase-mediated gene stacking system in which the Cre recombinase is used to remove lox-site flanked DNA no longer needed after each round of Bxb1 integrase-mediated site-specific integration. The Cre recombinase can be conveniently introduced by hybridization with a cre-expressing plant. However, maintaining an efficient cre-expressing line over many generations can be a problem, as high production of this DNA binding protein might interfere with normal chromosome activities...
March 19, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28317029/listeriomics-an-interactive-web-platform-for-systems-biology-of-listeria
#12
Christophe Bécavin, Mikael Koutero, Nicolas Tchitchek, Franck Cerutti, Pierre Lechat, Nicolas Maillet, Claire Hoede, Hélène Chiapello, Christine Gaspin, Pascale Cossart
As for many model organisms, the amount of Listeria omics data produced has recently increased exponentially. There are now >80 published complete Listeria genomes, around 350 different transcriptomic data sets, and 25 proteomic data sets available. The analysis of these data sets through a systems biology approach and the generation of tools for biologists to browse these various data are a challenge for bioinformaticians. We have developed a web-based platform, named Listeriomics, that integrates different tools for omics data analyses, i...
March 2017: MSystems
https://www.readbyqxmd.com/read/28316892/from-big-data-to-diagnosis-and-prognosis-gene-expression-signatures-in-liver-hepatocellular-carcinoma
#13
Hong Yang, Xin Zhang, Xiao-Yong Cai, Dong-Yue Wen, Zhi-Hua Ye, Liang Liang, Lu Zhang, Han-Lin Wang, Gang Chen, Zhen-Bo Feng
BACKGROUND: Liver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in. METHODS: Big data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes...
2017: PeerJ
https://www.readbyqxmd.com/read/28315825/effects-of-florida-red-tides-on-histone-variant-expression-and-dna-methylation-in-the-eastern-oyster-crassostrea-virginica
#14
Rodrigo Gonzalez-Romero, Victoria Suarez-Ulloa, Javier Rodriguez-Casariego, Daniel Garcia-Souto, Gabriel Diaz, Abraham Smith, Juan Jose Pasantes, Gary Rand, Jose M Eirin-Lopez
Massive algal proliferations known as Harmful Algal Blooms (HABs) represent one of the most important threats to coastal areas. Among them, the so-called Florida Red Tides (FRTs, caused by blooms of the dinoflagellate Karenia brevis and associated brevetoxins) are particularly detrimental in the southeastern U.S., causing high mortality rates and annual losses in excess of $40 million. The ability of marine organisms to cope with environmental stressors (including those produced during HABs) is influenced by genetic and epigenetic mechanisms, the latter resulting in phenotypic changes caused by heritable modifications in gene expression, without involving changes in the genetic (DNA) sequence...
March 7, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28315775/assessment-of-histone-tail-modifications-and-transcriptional-profiling-during-colon-cancer-progression-reveals-a-global-decrease-in-h3k4me3-activity
#15
Karen Triff, Mathew W McLean, Kranti Konganti, Jiahui Pang, Evelyn Callaway, Beiyan Zhou, Ivan Ivanov, Robert S Chapkin
During colon cancer, epigenetic alterations contribute to the dysregulation of major cellular functions and signaling pathways. Modifications in chromatin signatures such as H3K4me3 and H3K9ac, which are associated with transcriptionally active genes, can lead to genomic instability and perturb the expression of gene sets associated with oncogenic processes. In order to further elucidate early pre-tumorigenic epigenetic molecular events driving CRC, we integrated diverse, genome-wide, epigenetic inputs (by high throughput sequencing of RNA, H3K4me3, and H3K9ac) and compared differentially expressed transcripts (DE) and enriched regions (DER) in an in-vivo rat colon cancer progression model...
March 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28315703/molecular-endocrinology-of-vitamin-d-on-the-epigenome-level
#16
REVIEW
Carsten Carlberg
The molecular endocrinology of vitamin D is based on the facts that i) its metabolite 1α,25-dihydroxyvitamin D3 (1,25(OH)2D3) is the high affinity ligand of the nuclear receptor vitamin D receptor (VDR) and ii) the transcription factor VDR is the unique target of 1,25(OH)2D3 in the nucleus. Short-term alterations of the epigenome are primarily changes in the post-translational modification status of nucleosome-forming histone proteins, the consequences of which are i) a local increase or decrease in chromatin accessibility and ii) the activation or repression of gene transcription...
March 15, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28314780/non-coding-rnas-the-dark-side-of-nuclear-mitochondrial-communication
#17
REVIEW
Roberto Vendramin, Jean-Christophe Marine, Eleonora Leucci
Mitochondria are critical hubs for the integration of several key metabolic processes implicated in cell growth and survival. They originated from bacterial ancestors through endosymbiosis, following the transfer of more than 90% of their endosymbiont genome to the host cell nucleus. Over time, a mutually beneficial symbiotic relationship has been established, which relies on continuous and elaborate signaling mechanisms between this life-essential organelle and its host. The ability of mitochondria to signal their functional state and trigger compensatory and adaptive cellular responses has long been recognized, but the underlying molecular mechanisms involved have remained poorly understood...
March 17, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28314779/an-atr-dependent-function-for-the-ddx19-rna-helicase-in-nuclear-r-loop-metabolism
#18
Dana Hodroj, Bénédicte Recolin, Kamar Serhal, Susan Martinez, Nikolay Tsanov, Raghida Abou Merhi, Domenico Maiorano
Coordination between transcription and replication is crucial in the maintenance of genome integrity. Disturbance of these processes leads to accumulation of aberrant DNA:RNA hybrids (R-loops) that, if unresolved, generate DNA damage and genomic instability. Here we report a novel, unexpected role for the nucleopore-associated mRNA export factor Ddx19 in removing nuclear R-loops formed upon replication stress or DNA damage. We show, in live cells, that Ddx19 transiently relocalizes from the nucleopore to the nucleus upon DNA damage, in an ATR/Chk1-dependent manner, and that Ddx19 nuclear relocalization is required to clear R-loops...
March 17, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28314775/insights-into-rad3-kinase-recruitment-from-the-crystal-structure-of-the-dna-damage-checkpoint-protein-rad26
#19
Kasper Røjkjær Andersen
Metabolic products and environmental factors constantly damage DNA. To protect against these insults and maintain genome integrity, cells have evolved mechanisms to repair DNA lesions. One such mechanism involves Rad3, a master kinase coordinating the DNA damage response. Rad26 is a functional subunit of the Rad3-Rad26 complex and responsible for bringing the kinase to sites of DNA damage. Here, I present the crystal structure of Rad26 and identify the elements important for recruiting Rad3. The structure suggests that Rad26 is a dimer with a conserved interface in the N-terminal part of the protein...
March 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28306242/excision-repair-initiated-enzyme-assisted-bicyclic-cascade-signal-amplification-for-ultrasensitive-detection-of-uracil-dna-glycosylase
#20
Li-Juan Wang, Ming Ren, Qianyi Zhang, Bo Tang, Chun-Yang Zhang
Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification...
March 17, 2017: Analytical Chemistry
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