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Ciyu Yang, Angela G Arnold, Magan Trottier, Yukio Sonoda, Nadeem R Abu-Rustum, Oliver Zivanovic, Mark E Robson, Zsofia K Stadler, Michael F Walsh, David M Hyman, Kenneth Offit, Liying Zhang
PURPOSE: Mutations in PALB2 have been associated with a predisposition to breast and pancreatic cancers. This study aims to characterize a novel PALB2 exon 13 duplication in a hereditary breast and ovarian cancer family. METHODS: The PALB2 exon 13 duplication in this family was evaluated using Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT™) and confirmed by multiplex ligation-dependent probe amplification (MLPA)...
October 18, 2016: Breast Cancer Research and Treatment
Olympia Gianfrancesco, Vivien J Bubb, John P Quinn
Many facets of human behaviour are likely to have developed in part due to evolutionary changes in the regulation of neuropeptide and other brain-related genes. This has allowed species-specific expression patterns and unique epigenetic modulation in response to our environment, regulating response not only at the molecular level, but also contributing to differences in behaviour between individuals. As such, genetic variants or epigenetic changes that may alter neuropeptide gene expression are predicted to play a role in behavioural conditions and psychiatric illness...
October 11, 2016: Neuropeptides
Songmi Kim, Chun-Sung Cho, Kyudong Han, Jungnam Lee
Transposable elements are one of major sources to cause genomic instability through various mechanisms including de novo insertion, insertion-mediated genomic deletion, and recombination-associated genomic deletion. Among them is Alu element which is the most abundant element, composing ~10% of the human genome. The element emerged in the primate genome 65 million years ago and has since propagated successfully in the human and non-human primate genomes. Alu element is a non-autonomous retrotransposon and therefore retrotransposed using L1-enzyme machinery...
September 2016: Genomics & Informatics
Amandine Ketele, Tamás Kiss, Beáta E Jády
Mammalian cells express hundreds of intron-encoded box H/ACA RNAs which fold into a common hairpin-hinge-hairpin-tail structure, interact with four evolutionarily conserved proteins, dyskerin, Nop10, Nhp2 and Gar1, and function mainly in RNA pseudouridylation. The human telomerase H/ACA RNA (hTR) directs telomeric DNA synthesis and it carries a 5'-terminal domain encompassing the telomeric template sequence. The primary hTR transcript is synthesized from an independent gene by RNA polymerase II and undergoes 3' end processing controlled by the 3'-terminal H/ACA domain...
October 11, 2016: RNA Biology
Jürgen Schmitz, Angela Noll, Carsten A Raabe, Gennady Churakov, Reinhard Voss, Martin Kiefmann, Timofey Rozhdestvensky, Jürgen Brosius, Robert Baertsch, Hiram Clawson, Christian Roos, Aleksey Zimin, Patrick Minx, Michael J Montague, Richard K Wilson, Wesley C Warren
Tarsiers are phylogenetically located between the most basal strepsirrhines and the most derived anthropoid primates. While they share morphological features with both groups, they also possess uncommon primate characteristics, rendering their evolutionary history somewhat obscure. To investigate the molecular basis of such attributes, we present here a new genome assembly of the Philippine tarsier (Tarsius syrichta), and provide extended analyses of the genome and detailed history of transposable element insertion events...
October 6, 2016: Nature Communications
Jongbum Kim, Sajid Choudhury, Clayton DeVault, Yang Zhao, Alexander V Kildishev, Vladimir M Shalaev, Andrea Alu, Alexandra Boltasseva
Conventional plasmonic materials, namely noble metals, hamper the realization of practical plasmonic devices due to their intrinsic limitations, such as lack of capabilities to tune in real-time their optical properties, failure to assimilate with CMOS-standards, and severe degradation at elevated temperatures. Transparent conducting oxides (TCOs) is a promising alternative as plasmonic material throughout the near- and mid-infrared wavelengths. In addition to compatibility with established silicon-based fabrication procedures, TCOs provide great flexibility in the design and optimization of plasmonic devices since their intrinsic optical properties can be tailored and dynamically tuned...
October 5, 2016: ACS Nano
Emma Bondy-Chorney, Tara E Crawford Parks, Aymeric Ravel-Chapuis, Bernard J Jasmin, Jocelyn Côté
In a recent issue of PLOS Genetics, we reported that the double-stranded RNA-binding protein, Staufen1, functions as a disease modifier in the neuromuscular disorder Myotonic Dystrophy Type I (DM1). In this work, we demonstrated that Staufen1 regulates the alternative splicing of exon 11 of the human Insulin Receptor, a highly studied missplicing event in DM1, through Alu elements located in an intronic region. Furthermore, we found that Staufen1 overexpression regulates numerous alternative splicing events, potentially resulting in both positive and negative effects in DM1...
2016: Rare Diseases
Shanshan Hu, Xiaolin Wang, Ge Shan
Noncoding RNAs, mobile elements, and alternative splicing are all critical for the regulation of gene expression. Here we show that a conserved noncoding RNA acquires a new function due to the insertion of a mobile element. We identified a noncoding RNA, termed 5S-OT, which is transcribed from 5S rDNA loci in eukaryotes including fission yeast and mammals. 5S-OT plays a cis role in regulating the transcription of 5S rRNA in mice and humans. In the anthropoidea suborder of primates, an antisense Alu element has been inserted at the 5S-OT locus...
October 3, 2016: Nature Structural & Molecular Biology
Lahiru S Wijedasa, Jyrki Jauhiainen, Mari Könönen, Maija Lampela, Harri Vasander, Marie-Claire LeBlanc, Stephanie Evers, Thomas E L Smith, Catherine M Yule, Helena Varkkey, Massimo Lupascu, Faizal Parish, Ian Singleton, Gopalasamy R Clements, Sheema Abdul Aziz, Mark E Harrison, Susan Cheyne, Gusti Z Anshari, Erik Meijaard, Jenny E Goldstein, Susan Waldron, Kristell Hergoualc'h, René Dommain, Steve Frolking, Christopher D Evans, Mary Rose C Posa, Paul H Glaser, Nyoman Suryadiputra, Reza Lubis, Truly Santika, Rory Padfield, Sofyan Kurnianto, Panut Hadisiswoyo, Teck Wyn Lim, Susan E Page, Vincent Gauci, Peter J van der Meer, Helen Buckland, Fabien Garnier, Marshall K Samuel, Liza Nuriati Lim Kim Choo, Patrick O'Reilly, Matthew Warren, Surin Suksuwan, Elham Sumarga, Anuj Jain, William F Laurance, John Couwenberg, Hans Joosten, Ronald Vernimmen, Aljosja Hooijer, Chris Malins, Mark A Cochrane, Balu Perumal, Florian Siegert, Kelvin S-H Peh, Louis-Pierre Comeau, Louis Verchot, Charles F Harvey, Alex Cobb, Zeehan Jaafar, Henk Wösten, Solichin Manuri, Moritz Müller, Wim Giesen, Jacob Phelps, Ding Li Yong, Marcel Silvius, Béatrice M M Wedeux, Alison Hoyt, Mitsuru Osaki, Hirano Takashi, Hidenori Takahashi, Takashi S Kohyama, Akira Haraguchi, Nunung P Nugroho, David A Coomes, Le Phat Quoi, Alue Dohong, Haris Gunawan, David L A Gaveau, Andreas Langner, Felix K S Lim, David P Edwards, Xingli Giam, Guido van der Werf, Rachel Carmenta, Caspar C Verwer, Luke Gibson, Laure Grandois, Laura Linda Bozena Graham, Jhanson Regalino, Serge A Wich, Jack Rieley, Nicholas Kettridge, Chloe Brown, Romain Pirard, Sam Moore, B Ripoll Capilla, Uwe Ballhorn, Hua Chew Ho, Agata Hoscilo, Sandra Lohberger, Theodore A Evans, Nina Yulianti, Grace Blackham, Onrizal, Simon Husson, Daniel Murdiyarso, Sunita Pangala, Lydia E S Cole, Luca Tacconi, Hendrik Segah, Prayoto Tonoto, Janice S H Lee, Gerald Schmilewski, Stephan Wulffraat, Erianto Indra Putra, Megan E Cattau, R S Clymo, Ross Morrison, Aazani Mujahid, Jukka Miettinen, Soo Chin Liew, Samu Valpola, David Wilson, Laura D'Arcy, Michiel Gerding, Siti Sundari, Sara A Thornton, Barbara Kalisz, Stephen J Chapman, Ahmad Suhaizi Mat Su, Imam Basuki, Masayuki Itoh, Carl Traeholt, Sean Sloan, Alexander K Sayok, Roxane Andersen
The first International Peat Congress (IPC) held in the tropics - in Kuching (Malaysia) - brought together over 1000 international peatland scientists and industrial partners from across the world ("International Peat Congress with over 1000 participants!," 2016). The congress covered all aspects of peatland ecosystems and their management, with a strong focus on the environmental, societal and economic challenges associated with contemporary large-scale agricultural conversion of tropical peat. This article is protected by copyright...
September 27, 2016: Global Change Biology
Zhou Qihui, Zhu Biao
Latent reservoir (LR) of HIV is the cells (such as CD4(+)T cell) where HIV is able to hide. These cellular reservoirs are located throughout the body, including the spleen, lymph nodes, gastrointestinal lymphoid tissues, and become the major obstacle to cure HIV infection. To truly cure patients, a new strategy "shock and kill" was put forward by scientists, which is to shock HIV-infected cells out of hidden reservoirs in the body and then kill them. Quantitatively evaluating the size of long-lived LR is essential to this strategy...
May 25, 2016: Zhejiang da Xue Xue Bao. Yi Xue Ban, Journal of Zhejiang University. Medical Sciences
Wesley K Utomo, Vincent T Janmaat, Auke P Verhaar, Jérôme Cros, Philippe Lévy, Philippe Ruszniewski, Mirella S Vredenbregt-van den Berg, Guido Jenster, Marco J Bruno, Henri Braat, Gwenny M Fuhler, Maikel P Peppelenbosch
Identification of pancreatic cysts with malignant potential is important to prevent pancreatic cancer development. Integrity of cell free DNA (cfDNA) has been described as tumor biomarker, but its potential for pancreatic cancer is unclear. While normal apoptotic cells release uniformly truncated DNA, malignant tissues release long fragments of cell free DNA (cfDNA). We measured 247 base pair (bp) and 115 bp DNA fragments of ALU repeats by qPCR in serum from healthy controls and pancreatic cancer patients, and in cyst fluid from pancreatic cyst patients...
2016: American Journal of Cancer Research
Aleks Schein, Silvia Zucchelli, Sakari Kauppinen, Stefano Gustincich, Piero Carninci
Mammalian genomes encode numerous natural antisense long noncoding RNAs (lncRNAs) that regulate gene expression. Recently, an antisense lncRNA to mouse Ubiquitin carboxyl-terminal hydrolase L1 (Uchl1) was reported to increase UCHL1 protein synthesis, representing a new functional class of lncRNAs, designated as SINEUPs, for SINE element-containing translation UP-regulators. Here, we show that an antisense lncRNA to the human protein phosphatase 1 regulatory subunit 12A (PPP1R12A), named as R12A-AS1, which overlaps with the 5' UTR and first coding exon of the PPP1R12A mRNA, functions as a SINEUP, increasing PPP1R12A protein translation in human cells...
2016: Scientific Reports
Thomas J Meyer, Ulrike Held, Kimberly A Nevonen, Sabine Klawitter, Thomas Pirzer, Lucia Carbone, Gerald G Schumann
LAVA ( L: INE- A: lu- V: NTR- A: lu-like) elements comprise a family of non-autonomous, composite, non-LTR retrotransposons specific to gibbons and may have played a role in the evolution of this lineage. A full-length LAVA element consists of portions of repeats found in most primate genomes: CT-rich, Alu-like, and VNTR regions from the SVA retrotransposon, and portions of the AluSz and L1ME5 elements. To evaluate whether the gibbon genome currently harbors functional LAVA elements capable of mobilization by the endogenous LINE-1 (L1) protein machinery and which LAVA components are important for retrotransposition, we established a trans-mobilization assay in HeLa cells...
September 15, 2016: Genome Biology and Evolution
Amal Fawzy, Karima M Sweify, Hany M El-Fayoumy, Nagwa Nofal
BACKGROUND: Prostate cancer (PC) is the most common cancer affecting men, it accounts for 29% of all male cancer and 11% of all male cancer related death. DNA is normally released from an apoptotic source which generates small fragments of cell-free DNA, whereas cancer patients have cell-free circulating DNA that originated from necrosis, autophagy, or mitotic catastrophe, which produce large fragments. AIM OF WORK: Differentiate the cell free DNA levels (cfDNA) and its integrity in prostate cancer patients and control group composed of benign prostate hyperplasia (BPH) and healthy persons...
September 12, 2016: Journal of the Egyptian National Cancer Institute
Ramesh Reddy, Ngoc M P Nguyen, Guillaume Sarrabay, Maryam Rezaei, Mayra C G Rivas, Aysenur Kavasoglu, Hakan Berkil, Alaa Elshafey, Ebtesam Abdalla, Kristin P Nunez, Hélène Dreyfus, Merviel Philippe, Zahra Hadipour, Asude Durmaz, Erin E Eaton, Brittany Schubert, Volkan Ulker, Fatemeh Hadipour, Isabelle Touitou, Majid Fardaei, Rima Slim
No abstract text is available yet for this article.
October 2016: European Journal of Human Genetics: EJHG
M Farhat, P Y Chen, S Guenneau, H Bağcı, K N Salama, A Alù
A new cloaking mechanism, which makes enclosed objects invisible to diffusive photon density waves, is proposed. First, diffusive scattering from a basic core-shell geometry, which represents the cloaked structure, is studied. The conditions of scattering cancellation in a quasi-static scattering regime are derived. These allow for tailoring the diffusivity constant of the shell enclosing the object so that the fields scattered from the shell and the object cancel each other. This means that the photon flow outside the cloak behaves as if the cloaked object were not present...
August 2016: Proceedings. Mathematical, Physical, and Engineering Sciences
Shuichi Shimma, Henri-Obadja Kumada, Hisanori Taniguchi, Alu Konno, Ikuko Yao, Kyoji Furuta, Tadashi Matsuda, Seiji Ito
No abstract text is available yet for this article.
November 2016: Analytical and Bioanalytical Chemistry
Hannah Happ, Eric Weh, Deborah Costakos, Linda M Reis, Elena V Semina
BACKGROUND: Congenital cataracts affect 3-6 per 10,000 live births and represent one of the leading causes of blindness in children. Congenital cataracts have a strong genetic component with high heterogeneity and variability. CASE PRESENTATION: Analysis of whole exome sequencing data in a patient affected with congenital cataracts identified a pathogenic deletion which was further defined by other techniques. A ~98-kb homozygous deletion of 6p24.3 involving the first three exons (two non-coding and one coding) of GCNT2 isoform A, the first exon (coding) of GCNT2 isoform B, and part of the intergenic region between GCNT2 and TFAP2A was identified in the patient and her brother while both parents were found to be heterozygous carriers of the deletion...
2016: BMC Medical Genetics
Manuella Bouttier, David Laperriere, Babak Memari, Joseph Mangiapane, Amanda Fiore, Eric Mitchell, Mark Verway, Marcel A Behr, Robert Sladek, Luis B Barreiro, Sylvie Mader, John H White
To understand the epigenetic regulation of transcriptional response of macrophages during early-stage M. tuberculosis (Mtb) infection, we performed ChIPseq analysis of H3K4 monomethylation (H3K4me1), a marker of poised or active enhancers. De novo H3K4me1 peaks in infected cells were associated with genes implicated in host defenses and apoptosis. Our analysis revealed that 40% of de novo regions contained human/primate-specific Alu transposable elements, enriched in the AluJ and S subtypes. These contained several transcription factor binding sites, including those for members of the MEF2 and ATF families, and LXR and RAR nuclear receptors, all of which have been implicated in macrophage differentiation, survival, and responses to stress and infection...
September 6, 2016: Nucleic Acids Research
Smrithi Rajendiran, Lee D Gibbs, Timothy Van Treuren, David L Klinkebiel, Jamboor K Vishwanatha
Migration and invasion enhancer 1 (MIEN1) is a novel gene involved in prostate cancer progression by enhancing prostate cancer cell migration and invasion. DNA methylation, an important epigenetic regulation, is one of the most widely altered mechanisms in prostate cancer. This phenomenon frames the basis to study the DNA methylation patterns in the promoter region of MIEN1. Bisulfite pyrosequencing demonstrates the MIEN1 promoter contains a short interspersed nuclear Alu element (SINE Alu) repeat sequence...
August 29, 2016: Oncotarget
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