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PDBe-KB
PDBe-KB consortium
Mar 11, 2021
The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional...
Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control.
Miguel L Soares, Carol A Edwards, Frances L Dearden, Sacri R Ferrón, Scott Curran, Jennifer A Corish, Rebecca C Rancourt, Sarah E Allen, Marika Charalambous, Malcolm A Ferguson-Smith, Willem Rens, David J Adams, Anne C Ferguson-Smith
Mar 28, 2018
Approximately half the mammalian genome is composed of repetitive sequences, and accumulating evidence suggests that some may have an impact on genome function. Here, we characterized a large array class of repeats of...
Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome.
Peter D Fields, Gus Waneka, Matthew Naish, Michael C Schatz, Ian R Henderson, Daniel B Sloan
May 21, 2022
Intracellular transfers of mitochondrial DNA continue to shape nuclear genomes. Chromosome 2 of the model plant Arabidopsis thaliana contains one of the largest known nuclear insertions of mitochondrial DNA (numts). Estimated at...
Direct observation of the gene organization of the complement C4 and 21-hydroxylase loci by pulsed field gel electrophoresis.
Pulsed field gel electrophoresis and enzymes that cut genomic DNA infrequently have been used to define large RFLPs at the human C4 loci. With the enzymes BssH II or Sac II, and C4 or 21-hydroxylase DNA probes, it has been...
Identification of novel epithelial ovarian cancer loci in women of African ancestry.
Ani Manichaikul, Lauren C Peres, Xin-Qun Wang, Mollie E Barnard, Deanna Chyn, Xin Sheng, Zhaohui Du, Jonathan Tyrer, Joseph Dennis, Ann G Schwartz, Michele L Cote, Edward Peters, Patricia G Moorman, Melissa Bondy, Jill S Barnholtz-Sloan, Paul Terry, Anthony J Alberg, Elisa V Bandera, Ellen Funkhouser, Anna H Wu, Celeste Leigh Pearce, Malcom Pike, Veronica Wendy Setiawan, Christopher A Haiman, African American Breast Cancer Consortium (AABC), African Ancestry Prostate Cancer Consortium (AAPC), Julie R Palmer, Loic Lemarchand, Lynne R Wilkens, Andrew Berchuck, Jennifer A Doherty, Francesmary Modugno, Roberta Ness, Kirsten Moysich, Beth Y Karlan, Alice S Whittemore, Valerie McGuire, Weiva Sieh, Kate Lawrenson, Simon Gayther, Thomas A Sellers, Paul Pharoah, Joellen M Schildkraut, African American Cancer Epidemiology Study (AACES) and the Ovarian Cancer Association Consortium (OCAC)
Aug 20, 2019
Women of African ancestry have lower incidence of epithelial ovarian cancer (EOC) yet worse survival compared to women of European ancestry. We conducted a genome-wide association study in African ancestry women with 755 EOC...
African ancestry eQTLs Gene Expression Genome wide association study ovarian cancer Black or African American Aldo-Keto Reductase Family 1 Member C3 Antigens Neoplasm Black People Breast Neoplasms Carcinoma Ovarian Epithelial Female Follistatin Genetic Predisposition to Disease Genome-Wide Association Study Humans Neoplasm Proteins Polymorphism Single Nucleotide United States White People
Mobilization of giant piggyBac transposons in the mouse genome.
Meng Amy Li, Daniel J Turner, Zemin Ning, Kosuke Yusa, Qi Liang, Sabine Eckert, Lena Rad, Tomas W Fitzgerald, Nancy L Craig, Allan Bradley
Oct 14, 2020
The development of technologies that allow the stable delivery of large genomic DNA fragments in mammalian systems is important for genetic studies as well as for applications in gene therapy. DNA transposons have emerged as...
BedMachine v3
M Morlighem, CN Williams, E Rignot, L An, JE Arndt, JL Bamber, G Catania, N Chauché, JA Dowdeswell, B Dorschel, I Fenty, K Hogan, I Howat, A Hubbard, M Jakobsson, TM Jordan, KK Kjeldsen, R Millan, L Mayer, J Mouginot, BPY Noël, C O'Cofaigh, S Palmer, S Rysgaard, H Seroussi, MJ Siegert, P Slabon, F Straneo, MR van den Broeke, W Weinrebe, M Wood, KB Zinglersen
Jan 24, 2018
Greenland's bed topography is a primary control on ice flow, grounding line migration, calving dynamics, and subglacial drainage. Moreover, fjord bathymetry regulates the penetration of warm Atlantic water (AW) that rapidly...
The Effects of Fasting or Ketogenic Diet on Endurance Exercise Performance and Metabolism in Female Mice
The promotion of ketone body (KB) metabolism via ketosis has been suggested as a strategy to increase exercise performance. However, studies in humans and animals have yielded inconsistent results. The purpose of the current...
nutritional ketosis Lipid Metabolism ketone body metabolism Glycogen Triglycerides Exercise Physiology
Published by: Ursinus College
Identification of Post-Transcriptional Modulators of Breast Cancer Transcription Factor Activity Using MINDy
We have recently identified transcription factors (TFs) that are key drivers of breast cancer risk. To better understand the pathways or sub-networks in which these TFs mediate their function we sought to identify upstream...
A single mitochondrial DNA deletion accurately detects significant prostate cancer in men in the PSA 'grey zone'.
Jennifer Creed, Laurence Klotz, Andrew Harbottle, Andrea Maggrah, Brian Reguly, Anne George, Vincent Gnanapragasm
Mar 23, 2018
PURPOSE: To determine the clinical performance of a blood-based test for clinically significant (CS) prostate cancer (PCa) (grade group ≥ 2) intended for use in men with prostate serum antigen levels in the 'grey zone'...
biomarker DNA deletion Diagnostic accuracy Mitochondrial DNA Multi-parametric magnetic resonance imaging Plasma prostate cancer Real-time PCR Aged Base Sequence Biopsy DNA Mitochondrial Humans Image-guided biopsy Kallikreins Male Middle Aged Prostate Prostate-specific antigen Prostatectomy Prostatic Neoplasms RNA Ribosomal 18S ROC Curve Sensitivity and Specificity Sequence Deletion
The Effect of Immunosuppressive Agents on the Induction of Nuclear Factors that Bind to Sites on the Interleukin 2 Promoter
Cyclosporin A (CSA), FK506, and glucocorticosteroids all inhibit the production of lymphokines by decreasing lymphokine gene expression. Previous experiments have defined six different sites that may contribute to the...
Published by: Rockefeller University
Linear mtDNA fragments and unusual mtDNA rearrangements associated with pathological deficiency of MGME1 exonuclease.
Thomas J Nicholls, Gábor Zsurka, Viktoriya Peeva, Susanne Schöler, Roman J Szczesny, Dominik Cysewski, Aurelio Reyes, Cornelia Kornblum, Monica Sciacco, Maurizio Moggio, Andrzej Dziembowski, Wolfram S Kunz, Michal Minczuk
Nov 13, 2017
MGME1, also known as Ddk1 or C20orf72, is a mitochondrial exonuclease found to be involved in the processing of mitochondrial DNA (mtDNA) during replication. Here, we present detailed insights on the role of MGME1 in mtDNA...
Identification of phenotype-specific networks from paired gene expression-cell shape imaging data
Charlie George Barker, Eirini Petsalaki, Girolamo Giudice, Julia Sero, Emmanuel Nsa Ekpenyong, Chris Bakal, Evangelia Petsalaki
Apr 01, 2022
The morphology of breast cancer cells is often used as an indicator of tumor severity and prognosis. Additionally, morphology can be used to identify more fine-grained, molecular developments within a cancer cell, such as...
The transcription factors Egr1 and Egr2 have opposing influences on adipocyte differentiation.
The zinc finger-containing transcription factors Egr1 (Krox24) and Egr2 (Krox20) have been implicated in the proliferation and differentiation of many cell types. Egr2 has earlier been shown to play a positive role in adipocyte...
1-Methyl-3-isobutylxanthine 3T3-L1 Cells Adipocytes Animals CCAAT-Enhancer-Binding Protein-alpha CCAAT-Enhancer-Binding Protein-beta Cell Differentiation Cell Line Early Growth Response Protein 1 Early Growth Response Protein 2 Gene Knockdown Techniques Mice PPAR gamma Phosphorylation RNA Interference
A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana.
Reuben W Nowell, Ben Elsworth, Vicencio Oostra, Bas J Zwaan, Christopher W Wheat, Marjo Saastamoinen, Ilik J Saccheri, Arjen E Van't Hof, Bethany R Wasik, Heidi Connahs, Muhammad L Aslam, Sujai Kumar, Richard J Challis, Antónia Monteiro, Paul M Brakefield, Mark Blaxter
Feb 08, 2019
The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a...
The orphan G protein-coupled receptor GPR139 is activated by the peptides
AC Nøhr, MA Shehata, AS Hauser, V Isberg, J Mokrosinski, KB Andersen, IS Farooqi, DS Pedersen, DE Gloriam, H Bräuner-Osborne
Feb 22, 2017
Antisense Activity across the Nesp Promoter is Required for Nespas-Mediated Silencing in the Imprinted Gnas Cluster.
Charlotte J Tibbit, Christine M Williamson, Stuti Mehta, Simon T Ball, Mita Chotalia, Wade T Nottingham, Sally A Eaton, Mohamed M Quwailid, Lydia Teboul, Gavin Kelsey, Jo Peters
Jun 24, 2019
Macro long non-coding RNAs (lncRNAs) play major roles in gene silencing in inprinted gene clusters. Within the imprinted Gnas cluster, the paternally expressed Nespas lncRNA downregulates its sense counterpart Nesp. To explore...
Exploration of signals of positive selection derived from genotype-based human genome scans using re-sequencing data.
Min Hu, Qasim Ayub, José Afonso Guerra-Assunção, Quan Long, Zemin Ning, Ni Huang, Irene Gallego Romero, Lira Mamanova, Pelin Akan, Xin Liu, Alison J Coffey, Daniel J Turner, Harold Swerdlow, John Burton, Michael A Quail, Donald F Conrad, Anton J Enright, Chris Tyler-Smith, Yali Xue
Jan 23, 2018
We have investigated whether regions of the genome showing signs of positive selection in scans based on haplotype structure also show evidence of positive selection when sequence-based tests are applied, whether the target of...
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