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Cody J Steely, Jasmine N Baker, Jerilyn A Walker, Charles D Loupe, Mark A Batzer
Background: Alu elements are primate-specific retroposons that mobilize using the enzymatic machinery of L1 s. The recently completed baboon genome project found that the mobilization rate of Alu elements is higher than in the genome of any other primate studied thus far. However, the Alu subfamily structure present in and specific to baboons had not been examined yet. Results: Here we report 129 Alu subfamilies that are propagating in the genome of the olive baboon, with 127 of these subfamilies being new and specific to the baboon lineage...
2018: Mobile DNA
Siyuan Dai, Mykhailo Tymchenko, Yafang Yang, Qiong Ma, Marta Pita-Vidal, Kenji Watanabe, Takashi Taniguchi, Pablo Jarillo-Herrero, Michael M Fogler, Andrea Alù, Dimitri N Basov
Hexagonal boron nitride (hBN) is a natural hyperbolic material that supports both volume-confined hyperbolic polaritons and sidewall-confined hyperbolic surface polaritons (HSPs). In this work, efficient excitation, control, and steering of HSPs are demonstrated in hBN through engineering the geometry and orientation of hBN sidewalls. By combining infrared nanoimaging and numerical simulations, the reflection, transmission, and scattering of HSPs are investigated at the hBN corners with various apex angles...
March 13, 2018: Advanced Materials
Selma Maacha, Simon Saule
Metastases is largely responsible for the mortality among cancer patients. Metastasis formation is a complex multistep process, which results from the propagation of cancer cells from the primary tumor to distant sites of the body. Research on cancer metastasis aims to understand the mechanisms involved in the spread of cancer cells through the development of in vivo assays that assess cell invasion. Here we describe the use of the chick chorioallantoic membrane to evaluate cancer cell invasiveness in vivo...
2018: Methods in Molecular Biology
Ke Chen, Yuxuan Wang, Jie Sun
The Alu-element plays important roles in mediating alternative splicing, RNA editing and translation regulation. However, the distribution and function of the Alu-element are never analysed at the transcriptome level. This study presents a statistical analysis of the Alu-element on human transcriptome. We found that mRNAs and lncRNAs share the same sequence form for the Alu-element. The Alu-element covers 5.8% of the coding transcripts and 17.1% of the coding genes for mRNAs, and covers 9.3% of the transcripts and 13...
March 7, 2018: Biochemical and Biophysical Research Communications
Maxim A Gorlach, Xiang Ni, Daria A Smirnova, Dmitry Korobkin, Dmitry Zhirihin, Alexey P Slobozhanyuk, Pavel A Belov, Andrea Alù, Alexander B Khanikaev
Topological phase transitions in condensed matter systems give rise to exotic states of matter such as topological insulators, superconductors, and superfluids. Photonic topological systems open a whole new realm of research and technological opportunities, exhibiting a number of important distinctions from their condensed matter counterparts. Photonic modes can leak into free space, which makes it possible to probe topological photonic phases by spectroscopic means via Fano resonances. Based on this idea, we develop a technique to retrieve the topological properties of all-dielectric metasurfaces from the measured far-field scattering characteristics...
March 2, 2018: Nature Communications
Eitan Lavi, Liran Carmel
In mammals, transposable elements are largely silenced, but under fortuitous circumstances may be co-opted to play a functional role. Here, we show that when Alu elements are inserted within or nearby genes in sense orientation, they may contribute to the transcriptome diversity by forming new cleavage and polyadenylation sites. We mapped these new gene ends in human onto the Alu sequence and identified three hotspots of cleavage and polyadenylation site formation. Interestingly, the native Alu sequence does not contain any canonical polyadenylation signal...
March 1, 2018: RNA Biology
Thorsten Frenzel, Jordana Siekmann, Carsten Grohmann, Ursula Valentiner, Rüdiger Schmitz, Kristoffer Riecken, Boris Fehse, Udo Schumacher, Tobias Lange, Andreas Krüll
PURPOSE: To investigated the influence of radiation therapy (RT), surgery (OP), radio-chemotherapy (RChT), or chemotherapy (ChT) on small cell lung cancer metastases in 2 xenograft models. METHODS AND MATERIALS: A total of 1 × 106 human small cell lung cancer cells (OH1, H69) were subcutaneously injected into severe combined immunodeficiency mice to form a local primary tumor node at the lower trunk. Radiation therapy, OP, RChT, or ChT were started after development of palpable tumors...
March 15, 2018: International Journal of Radiation Oncology, Biology, Physics
Ioana Visan
No abstract text is available yet for this article.
February 23, 2018: Nature Immunology
Tatsiana Aneichyk, William T Hendriks, Rachita Yadav, David Shin, Dadi Gao, Christine A Vaine, Ryan L Collins, Aloysius Domingo, Benjamin Currall, Alexei Stortchevoi, Trisha Multhaupt-Buell, Ellen B Penney, Lilian Cruz, Jyotsna Dhakal, Harrison Brand, Carrie Hanscom, Caroline Antolik, Marisela Dy, Ashok Ragavendran, Jason Underwood, Stuart Cantsilieris, Katherine M Munson, Evan E Eichler, Patrick Acuña, Criscely Go, R Dominic G Jamora, Raymond L Rosales, Deanna M Church, Stephen R Williams, Sarah Garcia, Christine Klein, Ulrich Müller, Kirk C Wilhelmsen, H T Marc Timmers, Yechiam Sapir, Brian J Wainger, Daniel Henderson, Naoto Ito, Neil Weisenfeld, David Jaffe, Nutan Sharma, Xandra O Breakefield, Laurie J Ozelius, D Cristopher Bragg, Michael E Talkowski
X-linked Dystonia-Parkinsonism (XDP) is a Mendelian neurodegenerative disease that is endemic to the Philippines and is associated with a founder haplotype. We integrated multiple genome and transcriptome assembly technologies to narrow the causal mutation to the TAF1 locus, which included a SINE-VNTR-Alu (SVA) retrotransposition into intron 32 of the gene. Transcriptome analyses identified decreased expression of the canonical cTAF1 transcript among XDP probands, and de novo assembly across multiple pluripotent stem-cell-derived neuronal lineages discovered aberrant TAF1 transcription that involved alternative splicing and intron retention (IR) in proximity to the SVA that was anti-correlated with overall TAF1 expression...
February 22, 2018: Cell
Yoav Lubelsky, Igor Ulitsky
Long noncoding RNAs (lncRNAs) are emerging as key players in multiple cellular pathways1 , but their modes of action and how those are dictated by sequence remain unclear. lncRNAs tend to be enriched in the nuclear fraction, whereas most mRNAs are overtly cytoplasmic2 , although several studies have found that hundreds of mRNAs in various cell types are retained in the nucleus3,4 . It is thus conceivable that some mechanisms that promote nuclear enrichment are shared between lncRNAs and mRNAs. In order to identify elements that can force nuclear localization in lncRNAs and mRNAs we screened libraries of short fragments tiled across nuclear RNAs, which were cloned into the untranslated regions of an efficiently exported mRNA...
January 24, 2018: Nature
Peter A Larsen, Kelsie E Hunnicutt, Roxanne J Larsen, Anne D Yoder, Ann M Saunders
Alu elements are a highly successful family of primate-specific retrotransposons that have fundamentally shaped primate evolution, including the evolution of our own species. Alus play critical roles in the formation of neurological networks and the epigenetic regulation of biochemical processes throughout the central nervous system (CNS), and thus are hypothesized to have contributed to the origin of human cognition. Despite the benefits that Alus provide, deleterious Alu activity is associated with a number of neurological and neurodegenerative disorders...
February 19, 2018: Chromosome Research
Maurizio Cardelli
Endogenous retroelements, transposons that mobilize through RNA intermediates, include some of the most abundant repetitive sequences of the human genome, such as Alu and LINE-1 sequences, and human endogenous retroviruses. Recent discoveries demonstrate that these mobile genetic elements not only act as intragenomic parasites, but also exert regulatory roles in living cells. The risk of genomic instability represented by endogenous retroelements is normally counteracted by a series of epigenetic control mechanisms which include, among the most important, CpG DNA methylation...
February 16, 2018: Mechanisms of Ageing and Development
Marilia Rita Pinzone, Una O'Doherty
The identification of the most appropriate marker to measure reservoir size has been a great challenge for the HIV field. Quantitative viral outgrowth assay (QVOA), the reference standard to quantify the amount of replication-competent virus, has several limitations, as it is laborious, expensive, and unable to robustly reactivate every single integrated provirus. PCR-based assays have been developed as an easier, cheaper and less error-prone alternative to QVOA, but also have limitations. Historically, measuring integrated HIV DNA has provided insights about how reservoirs are formed and maintained...
February 17, 2018: Retrovirology
Jasmine N Baker, Jerilyn A Walker, Michael W Denham, Charles D Loupe, Mark A Batzer
Background: The evolution of Alu elements has been ongoing in primate lineages and Alu insertion polymorphisms are widely used in phylogenetic and population genetics studies. Alu subfamilies in the squirrel monkey ( Saimiri ), a New World Monkey (NWM), were recently reported. Squirrel monkeys are commonly used in biomedical research and often require species identification. The purpose of this study was two-fold: 1) Perform locus-specific PCR analyses on recently integrated Alu insertions in Saimiri to determine their amplification dynamics, and 2) Identify a subset of Alu insertion polymorphisms with species informative allele frequency distributions between the Saimiri sciureus and Saimiri boliviensis groups...
2018: Mobile DNA
Francesco Di Virgilio, Anna L Giuliani, Valentina Vultaggio-Poma, Simonetta Falzoni, Alba C Sarti
The P2X7 receptor (P2X7R) is a ligand-gated plasma membrane ion channel belonging to the P2X receptor subfamily activated by extracellular nucleotides. General consensus holds that the physiological (and maybe the only) agonist is ATP. However, scattered evidence generated over the last several years suggests that ATP might not be the only agonist, especially at inflammatory sites. Solid data show that NAD + covalently modifies the P2X7R of mouse T lymphocytes, thus lowering the ATP threshold for activation...
2018: Frontiers in Pharmacology
Mónica Loreto Acevedo, Francisco García-de Gracia, Camila Miranda-Cárdenas, Ricardo Soto-Rifo, Francisco Aguayo, Oscar León
Self-inactivating VSVG-pseudotyped murine leukemia virus (SIN-VSVG-MLV) has been widely used to generate stable cell lines and produce gene delivery vectors. Despite the broad cellular tropism of the VSVG-pseudotyped MLV, we observed differential viral transduction efficiency depending on the host cell type used. In order to determine the mechanism underlying these differences, we used a GFP-expressing SIN-VSVG-MLV and analyzed the major steps of viral transduction in different cell lines including human epithelial, T-lymphocytes, monocytes and murine fibroblast cells...
February 6, 2018: Journal of Virological Methods
Adriana Roithová, Klára Klimešová, Josef Pánek, Cindy L Will, Reinhard Lührmann, David Stanek, Cyrille Girard
Cajal bodies (CBs) are nuclear non-membrane bound organelles where small nuclear ribonucleoprotein particles (snRNPs) undergo their final maturation and quality control before they are released to the nucleoplasm. However, the molecular mechanism how immature snRNPs are targeted and retained in CBs has yet to be described. Here, we microinjected and expressed various snRNA deletion mutants as well as chimeric 7SK, Alu or bacterial SRP non-coding RNAs and provide evidence that Sm and SMN binding sites are necessary and sufficient for CB localization of snRNAs...
February 5, 2018: Nucleic Acids Research
Raffaella Liccardo, Marina De Rosa, Giovanni Battista Rossi, Gabriele Rigler, Paola Izzo, Francesca Duraturo
Lynch syndrome (LS) is associated with germ-line mutations in the DNA mismatch repair (MMR) genes, mainly MLH1, MSH2, MSH6, and PMS2. Most of genetic variants in the MMR genes predisposing to LS are point mutations, small deletions and insertions but large genomic rearrangements in the MMR genes also predisposing to Lynch syndrome. In this study, we report a novel, large rearrangement of the MSH2 gene, manifested by a duplication spanning a 14,846-bps region from intron 7 through intron 9. The breakpoints of this rearrangement were characterized by sequencing...
February 2018: Cancer Genetics
Rong Zhang, Wangyang Pu, Shuyun Zhang, Li Chen, Weipei Zhu, Li Xiao, Chungen Xing, Kai Li
CA125 amounts have a large overlap in ovarian cancer and benign diseases. We conducted a retrospective cohort trial to assess the clinical value of circulating cell-free DNA concentration and integrity index for the diagnosis of ovarian cancer. A total of 150 patients were recruited. Plasma samples of 24 ovarian cancer patients, 12 benign ovarian cysts, and 12 healthy controls were assessed. By amplifying short ALU-115 repeat and long ALU-219 fragments, circulating cell-free DNA concentrations and integrity index were measured...
2018: PloS One
Sadeem Ahmad, Xin Mu, Fei Yang, Emily Greenwald, Ji Woo Park, Etai Jacob, Cheng-Zhong Zhang, Sun Hur
Aberrant activation of innate immune receptors can cause a spectrum of immune disorders, such as Aicardi-Goutières syndrome (AGS). One such receptor is MDA5, a viral dsRNA sensor that induces antiviral immune response. Using a newly developed RNase-protection/RNA-seq approach, we demonstrate here that constitutive activation of MDA5 in AGS results from the loss of tolerance to cellular dsRNAs formed by Alu retroelements. While wild-type MDA5 cannot efficiently recognize Alu-dsRNAs because of its limited filament formation on imperfect duplexes, AGS variants of MDA5 display reduced sensitivity to duplex structural irregularities, assembling signaling-competent filaments on Alu-dsRNAs...
January 8, 2018: Cell
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