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https://www.readbyqxmd.com/read/29103173/a-role-for-the-mutagenic-dna-self-catalyzed-depurination-mechanism-in-the-evolution-of-7sl-derived-rnas
#1
Maxwell P Gold, Jacques R Fresco
The Alu element, the most prevalent SINE (short interspersed element) in the human genome, is one of the many RNA-encoding genes that evolved from the 7SL RNA gene. During analysis of the evolution of 7SL-derived RNAs, two distinct evolutionary intermediates capable of self-catalyzed DNA depurination (SDP) were identified. These SDP sequences spontaneously create apurinic sites that can result in increased mutagenesis due to their error-prone repair. This DNA self-depurination mechanism has been shown both in vitro and in vivo to lead to substitution and short frameshift mutations at a frequency that far exceeds their occurrence due to random errors in DNA replication...
October 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/29100349/alu-hypomethylation-and-mgmt-hypermethylation-in-serum-as-biomarkers-of-glioma
#2
Mingjie Gong, Wei Shi, Jing Qi, Guoping Shao, Zhenghua Shi, Junxiang Wang, Jian Chen, Rongtao Chu
In order to improve prognosis of glioma patients, better tools are required for early diagnosis and treatment. Serum cell-free DNA methylation levels of Alu, MGMT, P16, RASSF1A from 124 glioma patients and 58 healthy controls were detected by the bisulfite sequencing. The median methylation level of Alu was 46.15% (IQR, 36.57%-54.00%) and 60.85% (IQR, 57.23%-65.68%) in glioma patients and healthy controls respectively. The median methylation level of MGMT in glioma samples was 64.65% (IQR, 54.87%-74.37%) compared to 38...
September 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/29047728/narrowband-transparent-absorbers-based-on-ellipsoidal-nanoparticles
#3
Alessio Monti, Andrea Alù, Alessandro Toscano, Filiberto Bilotti
In this paper, we propose the design of an optical device that is able to selectively absorb impinging light in a desired frequency range while being almost completely transparent outside this range. The proposed absorber is a variant of the optical Salisbury screen we recently proposed [Opt. Lett.41, 3383 (2016)OPLEDP0146-959210.1364/OL.41.003383] but, differently from this earlier version, is transparent for any electromagnetic wave whose frequency is outside the absorption spectrum. Such an absorber also exhibits excellent performance in terms of angular bandwidth and may find application in all scenarios where narrowband absorption is required, such as for light filters or digital sensors...
September 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/29043294/integrating-networks-and-comparative-genomics-reveals-retroelement-proliferation-dynamics-in-hominid-genomes
#4
Orr Levy, Binyamin A Knisbacher, Erez Y Levanon, Shlomo Havlin
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29038571/highly-sensitive-and-specific-alu-based-quantification-of-human-cells-among-rodent-cells
#5
Kodai Funakoshi, Mozhdeh Bagheri, Ming Zhou, Ryoji Suzuki, Hiroshi Abe, Hideo Akashi
Alu elements are primate-specific short interspersed elements (SINEs), over 1 million copies of which are present in the human genome; thus, Alu elements are useful targets for detecting human cells. However, previous Alu-based techniques for detecting human genomic DNA do not reach the theoretical limits of sensitivity and specificity. In this study, we developed a highly sensitive and specific Alu-based real-time PCR method for discriminating human cells from rodent cells, using a primer and probe set carefully designed to avoid possible cross-reactions with rodent genomes...
October 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29029327/the-exonization-and-functionalization-of-an-alu-j-element-in-the-protein-coding-region-of-glycoprotein-hormone-alpha-gene-represent-a-novel-mechanism-to-the-evolution-of-hemochorial-placentation-in-primates
#6
Haidi Chen, Li Chen, Yune Wu, Hao Shen, Guang Yang, Cheng Deng
Alu elements contribute considerably to gene regulation and genome evolution in primates. The generation of new exons from Alu elements has been found in various human genes, and the regulatory function of the Alu exon has been investigated in many studies. However, the functionalization of Alu elements in protein coding regions remains unknown. Here, we reported that an Alu-J element exonized in the glycoprotein hormone alpha (GPHA) gene and encoded an additional N-terminal peptide (Alu-J encoding peptide) of the mature GPHA peptide, leading to a splicing variant of Alu-GPHA in anthropoid primates approximately 35 million years ago...
September 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29023671/genetics-in-pulmonary-arterial-hypertension-in-a-large-homogeneous-japanese-population
#7
REVIEW
Shinobu Gamou, Masaharu Kataoka, Yuki Aimi, Tomohiro Chiba, Yuichi Momose, Sarasa Isobe, Tomomi Hirayama, Hideaki Yoshino, Keiichi Fukuda, Toru Satoh
Pulmonary arterial hypertension (PAH) is a rare but serious disease with a grave prognosis. Bone morphogenetic protein type 2 receptor (BMPR2) gene is a strong pathogenic factor for PAH. As a collaborative team from Kyorin University and Keio University in Japan, we have analyzed the BMPR2 gene in 356 probands and more than 50 family members, including secondary patients. Importantly, the study population is a racially, ethnically, and socially homogeneous population. In PAH patients, there is a high incidence of unique mutations in BMPR2, and several mutations are frequently observed in the Japanese population, suggesting that these common and recurring mutations may be highly pathogenic or have high penetrance, explaining why they are found frequently throughout the world...
October 10, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29020232/staging-classification-of-aortic-stenosis-based-on-the-extent-of-cardiac-damage
#8
Philippe Généreux, Philippe Pibarot, Björn Redfors, Michael J Mack, Raj R Makkar, Wael A Jaber, Lars G Svensson, Samir Kapadia, E Murat Tuzcu, Vinod H Thourani, Vasilis Babaliaros, Howard C Herrmann, Wilson Y Szeto, David J Cohen, Brian R Lindman, Thomas McAndrew, Maria C Alu, Pamela S Douglas, Rebecca T Hahn, Susheel K Kodali, Craig R Smith, D Craig Miller, John G Webb, Martin B Leon
Aims: In patients with aortic stenosis (AS), risk stratification for aortic valve replacement (AVR) relies mainly on valve-related factors, symptoms and co-morbidities. We sought to evaluate the prognostic impact of a newly-defined staging classification characterizing the extent of extravalvular (extra-aortic valve) cardiac damage among patients with severe AS undergoing AVR. Methods and results: Patients with severe AS from the PARTNER 2 trials were pooled and classified according to the presence or absence of cardiac damage as detected by echocardiography prior to AVR: no extravalvular cardiac damage (Stage 0), left ventricular damage (Stage 1), left atrial or mitral valve damage (Stage 2), pulmonary vasculature or tricuspid valve damage (Stage 3), or right ventricular damage (Stage 4)...
July 21, 2017: European Heart Journal
https://www.readbyqxmd.com/read/29016854/absence-of-rnase-h2-triggers-generation-of-immunogenic-micronuclei-removed-by-autophagy
#9
Kareen Bartsch, Katharina Knittler, Christopher Borowski, Sönke Rudnik, Markus Damme, Konrad Aden, Martina E Spehlmann, Norbert Frey, Paul Saftig, Athena Chalaris, Björn Rabe
Hypomorphic mutations in the DNA repair enzyme RNase H2 cause the neuroinflammatory autoimmune disorder Aicardi-Goutières syndrome (AGS). Endogenous nucleic acids are believed to accumulate in patient cells and instigate pathogenic type I interferon expression. However, the underlying nucleic acid species amassing in the absence of RNase H2 has not been established yet. Here, we report that murine RNase H2 knockout cells accumulated cytosolic DNA aggregates virtually indistinguishable from micronuclei. RNase H2-dependent micronuclei were surrounded by nuclear lamina and most of them contained damaged DNA...
October 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28993934/successful-nuclear-dna-profiling-of-rootless-hair-shafts-a-novel-approach
#10
Kelly S Grisedale, Gina M Murphy, Hiromi Brown, Mark R Wilson, Sudhir K Sinha
Historically, rootless hair shaft samples submitted to a forensic laboratory for DNA analysis are reserved for mitochondrial DNA (mtDNA) analysis due to the presence of highly degraded as well as insufficient amounts of nuclear DNA. Although mtDNA has been very successful in obtaining results from rootless hair, this system has its limitations, namely, it is a lineage marker that cannot differentiate between maternally related genotypes. Given the high incidence of hairs as forensic evidence, there is a need for the use of a nuclear DNA test system capable of producing reliable results for hair shaft forensic evidence...
October 9, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28991230/alu-rna-accumulation-induces-epithelial-to-mesenchymal-transition-by-modulating-mir-566-and-is-associated-with-cancer-progression
#11
F Di Ruocco, V Basso, M Rivoire, P Mehlen, J Ambati, S De Falco, V Tarallo
Alu sequences are the most abundant short interspersed repeated elements in the human genome. Here we show that in a cell culture model of colorectal cancer (CRC) progression, we observe accumulation of Alu RNA that is associated with reduced DICER1 levels. Alu RNA induces epithelial-to-mesenchymal transition (EMT) by acting as a molecular sponge of miR-566. Moreover, Alu RNA accumulates as consequence of DICER1 deficit in colorectal, ovarian, renal and breast cancer cell lines. Interestingly, Alu RNA knockdown prevents DICER1 depletion-induced EMT despite global microRNA (miRNA) downregulation...
October 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28989020/development-of-a-novel-amorphous-agomelatine-formulation-with-improved-storage-stability-and-enhanced-bioavailability
#12
Panagiotis Barmpalexis, Agni Grypioti, Elisavet Vardaka, Anna Karagianni, Kyriakos Kachrimanis
The present work describes the development of a novel formulation of amorphous agomelatine (AGM) that exhibits enhanced in vitro dissolution rate and bioavailability, as well as improved storage stability. Agomelatine was loaded on a mixture of microcrystalline cellulose with a high specific surface area excipient, namely colloidal silicon dioxide, employing a wet granulation method and the resultant AGM granules were subsequently formulated into immediate release film-coated tablets. Modulated differential scanning calorimetry (MT-DSC), hot-state light microscopy, powder X-Ray diffraction (PXRD), attenuated total reflection ATR-FTIR and micro-Raman spectroscopy revealed that the API existed primarily in the amorphous state within the prepared formulations, with some crystals of polymorph I also present...
October 5, 2017: Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28986530/synchronized-conductivity-modulation-to-realize-broadband-lossless-magnetic-free-non-reciprocity
#13
Tolga Dinc, Mykhailo Tymchenko, Aravind Nagulu, Dimitrios Sounas, Andrea Alu, Harish Krishnaswamy
Recent research has explored the spatiotemporal modulation of permittivity to break Lorentz reciprocity in a manner compatible with integrated-circuit fabrication. However, permittivity modulation is inherently weak and accompanied by loss due to carrier injection, particularly at higher frequencies, resulting in large insertion loss, size, and/or narrow operation bandwidths. Here, we show that the presence of absorption in an integrated electronic circuit may be counter-intuitively used to our advantage to realize a new generation of magnet-free non-reciprocal components...
October 6, 2017: Nature Communications
https://www.readbyqxmd.com/read/28984711/genomic-organization-of-tbk1-copy-number-variations-in-glaucoma-patients
#14
Adam P DeLuca, L M Alward Wallace, Jeffrey Liebmann, Robert Ritch, Kazuhide Kawase, Young H Kwon, Alan L Robin, Edwin M Stone, Todd E Scheetz, John H Fingert
BACKGROUND: Approximately 1% of normal tension glaucoma cases are caused by TANK binding kinase 1 (TBK1) gene duplications and triplications. However, the precise borders and orientation of these TBK1 gene copy number variations (CNVs) on chromosome 12 are unknown. METHODS: We determined the exact borders of TBK1 CNVs and the orientation of duplicated or triplicated DNA segments in five NTG patients with different TBK1 mutations using whole genome sequencing. RESULTS: Tandemly duplicated chromosome segments spanning the TBK1 gene were detected in four NTG patients, each with unique borders...
September 3, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/28973520/longitudinal-hemodynamics-of-transcatheter-and-surgical-aortic-valves-in-the-partner-trial
#15
Pamela S Douglas, Martin B Leon, Michael J Mack, Lars G Svensson, John G Webb, Rebecca T Hahn, Philippe Pibarot, Neil J Weissman, D Craig Miller, Samir Kapadia, Howard C Herrmann, Susheel K Kodali, Raj R Makkar, Vinod H Thourani, Stamatios Lerakis, Ashley M Lowry, Jeevanantham Rajeswaran, Matthew T Finn, Maria C Alu, Craig R Smith, Eugene H Blackstone
Importance: Use of transcatheter aortic valve replacement (TAVR) for severe aortic stenosis is growing rapidly. However, to our knowledge, the durability of these prostheses is incompletely defined. Objective: To determine the midterm hemodynamic performance of balloon-expandable transcatheter heart valves. Design, Setting, and Participants: In this study, we analyzed core laboratory-generated data from echocardiograms of all patients enrolled in the Placement of Aortic Transcatheter Valves (PARTNER) 1 Trial with successful TAVR or surgical AVR (SAVR) obtained preimplantation and at 7 days, 1 and 6 months, and 1, 2, 3, 4, and 5 years postimplantation...
November 1, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/28973091/association-of-paravalvular-regurgitation-with-1-year-outcomes-after-transcatheter-aortic-valve-replacement-with-the-sapien-3-valve
#16
Philippe Pibarot, Rebecca T Hahn, Neil J Weissman, Marie Arsenault, Jonathan Beaudoin, Mathieu Bernier, Abdellaziz Dahou, Omar K Khalique, Federico M Asch, Oumhani Toubal, Jonathon Leipsic, Philipp Blanke, Feifan Zhang, Rupa Parvataneni, Maria Alu, Howard Herrmann, Raj Makkar, Michael Mack, Richard Smalling, Martin Leon, Vinod H Thourani, Susheel Kodali
Importance: Moderate/severe and even mild paravalvular regurgitation (PVR) are associated with increased mortality following transcatheter aortic valve replacement (TAVR) with first and second generations of transcatheter valves. Objective: To examine the incidence, evolution, and effect on 1-year outcomes of PVR following TAVR with a third-generation balloon-expandable transcatheter heart valve. Design, Setting, and Participants: Prespecified analysis of PVR in the Placement of Aortic Transcatheter Valves (PARTNER) II SAPIEN 3 trial, conducted between October 1, 2013, and September 3, 2014...
November 1, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/28965946/d-allulose-a-stereoisomer-of-d-fructose-extends-caenorhabditis-elegans-lifespan-through-a-dietary-restriction-mechanism-a-new-candidate-dietary-restriction-mimetic
#17
Tomoya Shintani, Hirofumi Sakoguchi, Akihide Yoshihara, Ken Izumori, Masashi Sato
Dietary restriction (DR) is an effective intervention known to increase lifespan in a wide variety of organisms. DR also delays the onset of aging-associated diseases. DR mimetics, compounds that can mimic the effects of DR, have been intensively explored. d-Allulose (d-Alu), the C3-epimer of d-fructose, is a rare sugar that has various health benefits, including anti-hyperglycemia and anti-obesity effects. Here, we report that d-Alu increased the lifespan of Caenorhabditis elegans both under monoxenic and axenic culture conditions...
December 2, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28957465/alu-insertion-polymorphisms-as-evidence-for-population-structure-in-baboons
#18
Cody J Steely, Jerilyn A Walker, Vallmer E Jordan, Thomas O Beckstrom, Cullen L McDaniel, Corey P St Romain, Emily C Bennett, Arianna Robichaux, Brooke N Clement, Muthuswamy Raveendran, Kim C Worley, Jane Phillips-Conroy, Clifford J Jolly, Jeff Rogers, Miriam K Konkel, Mark A Batzer
Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for unusually long distances, is not readily documented by direct field observation. In this pilot study, we investigate the possibility of retrieving baboon population structure in yellow (Papio cynocephalus) and kinda (Papio kindae) baboons from the distribution of variation in a genome-wide set of 494 Alu insertion polymorphisms, made available via the recently completed Baboon Genome Analysis Consortium...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28957461/evolution-of-alu-subfamily-structure-in-the-saimiri-lineage-of-new-world-monkeys
#19
Jasmine N Baker, Jerilyn A Walker, John A Vanchiere, Kacie R Phillippe, Corey P St Romain, Paulina Gonzalez-Quiroga, Michael W Denham, Jackson R Mierl, Miriam K Konkel, Mark A Batzer
Squirrel monkeys, Saimiri, are commonly found in zoological parks and used in biomedical research. S. boliviensis is the most common species for research; however, there is little information about genome evolution within this primate lineage. Here, we reconstruct the Alu element sequence amplification and evolution in the genus Saimiri at the time of divergence within the family Cebidae lineage. Alu elements are the most successful SINE (Short Interspersed Element) in primates. Here, we report 46 Saimiri lineage specific Alu subfamilies...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28951006/genetic-portrait-of-jewish-populations-based-on-three-sets-of-x-chromosome-markers-indels-alu-insertions-and-strs
#20
J F Ferragut, K Bentayebi, R Pereira, J A Castro, A Amorim, C Ramon, A Picornell
Population genetic data for 53 X-chromosome markers (32 X-indels, 9 X-Alu insertions and 12 X-STRs) are reported for five populations with Jewish ancestry (Sephardim, North African Jews, Middle Eastern Jews, Ashkenazim, and Chuetas) and Majorca, as the host population of Chuetas. Genetic distances between these populations demonstrated significant differences, except between Sephardic and North African Jews, with the Chuetas as the most differentiated group, in accordance with the particular demographic history of this population...
September 18, 2017: Forensic Science International. Genetics
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