Missing the pathological expansion in Huntington disease: de novo c. 51C >G variant on the expanded allele causing intrafamilial allele dropout

2020 ◽  
Author(s):  
Stefania Magri ◽  
Lorenzo Nanetti ◽  
Alessia Mongelli ◽  
Elena Rizzo ◽  
Franco Taroni ◽  
...  
Keyword(s):  
Huntington Disease ◽  
De Novo ◽  
Allele Dropout ◽  
Expanded Allele

Removing the bad apples: a simple bioinformatic method to improve loci-recovery in de novo RADseq data for non-model organisms

2020 ◽  
Author(s):  
José Cerca ◽  
Marius F. Maurstad ◽  
Nicolas Rochette ◽  
Angel Rivera-Colón ◽  
Niraj Rayamajhi ◽  
...  
Keyword(s):  
Missing Data ◽  
Restriction Site ◽  
De Novo ◽  
Model Organisms ◽  
Library Preparation ◽  
Allele Dropout ◽  
Bioinformatic Tools ◽  
Restriction Sites ◽  
Genomic Markers ◽  
Wet Lab

The restriction site-associated DNA (RADseq) family of protocols involves digesting DNA and sequencing the region flanking the cut site, thus providing a cost and time efficient way for obtaining thousands of genomic markers. However, when working with non-model taxa with few genomic resources, optimization of RADseq wet-lab and bioinformatic tools may be challenging, often resulting in allele dropout – that is when a given RADseq locus is not sequenced in one or more individuals resulting in missing data. Additionally, as datasets include divergent taxa, rates of dropout will increase since restriction sites may be lost due to mutation. Mitigating the impacts of allele dropout is crucial, as missing data may lead to incorrect inferences in population genetics and phylogenetics. Here, we demonstrate a simple pipeline for the optimization of RADseq datasets which involves reducing and analysing datasets at a population or species level. By running the software Stacks at this level, we were able to reliably identify and remove individuals with high levels of missing data (bad apples) likely stemming from artefacts in library preparation, DNA quality or sequencing artefacts. Removal of the bad apples generally led to an increase of loci and decrease of missing data in the final datasets, thus improving the biological interpretability of the data.

scholarly journals De novo Huntington disease caused by 26-44 CAG repeat expansion on a low-risk haplotype

Neurology ◽  
2013 ◽  
Vol 81 (12) ◽  
pp. 1099-1100 ◽  
Author(s):  
G. Houge ◽  
O. Bruland ◽  
I. Bjornevoll ◽  
M. R. Hayden ◽  
A. Semaka
Keyword(s):  
Huntington Disease ◽  
De Novo ◽  
Repeat Expansion ◽  
Low Risk ◽  
Cag Repeat ◽  
Risk Haplotype ◽  
Cag Repeat Expansion

scholarly journals Estimating the probability of de novo HD cases from transmissions of expanded penetrant CAG alleles in the Huntington disease gene from male carriers of high normal alleles (27-35 CAG)

2009 ◽  
Vol 149A (7) ◽  
pp. 1375-1381 ◽  
Author(s):  
Audrey E. Hendricks ◽  
Jeanne C. Latourelle ◽  
Kathryn L. Lunetta ◽  
L. Adrienne Cupples ◽  
Vanessa Wheeler ◽  
...  
Keyword(s):  
Huntington Disease ◽  
Disease Gene ◽  
De Novo ◽  
Huntington Disease Gene ◽  
Male Carriers

The Morphology of the Rat Kidney Following Folic Acid Administration

1970 ◽  
Vol 28 ◽  
pp. 200-201
Author(s):  
Aline Byrnes ◽  
Elsa E. Ramos ◽  
Minoru Suzuki ◽  
E.D. Mayfield
Keyword(s):  
Folic Acid ◽  
De Novo ◽  
Specific Activity ◽  
Rat Kidney ◽  
Present Report ◽  
Intracellular Localization ◽  
Male Rats ◽  
Renal Hypertrophy ◽  
Electron Microscopic ◽  
Biochemical Alterations

Renal hypertrophy was induced in 100 g male rats by the injection of 250 mg folic acid (FA) dissolved in 0.3 M NaHCO3/kg body weight (i.v.). Preliminary studies of the biochemical alterations in ribonucleic acid (RNA) metabolism of the renal tissue have been reported recently (1). They are: RNA content and concentration, orotic acid-c14 incorporation into RNA and acid soluble nucleotide pool, intracellular localization of the newly synthesized RNA, and the specific activity of enzymes of the de novo pyrimidine biosynthesis pathway. The present report describes the light and electron microscopic observations in these animals. For light microscopy, kidney slices were fixed in formalin, embedded, sectioned, and stained with H & E and PAS.

Early ossicle growth in the regenerating disc of a brittle star

1994 ◽  
Vol 52 ◽  
pp. 364-365
Author(s):  
M. Shlepr ◽  
R. L. Turner
Keyword(s):  
Cell Membrane ◽  
Light Microscopy ◽  
De Novo ◽  
Current Model ◽  
Syncytium Formation ◽  
Brittle Star ◽  
Intracellular Location ◽  
Limited Volume ◽  
Tissue Calcification

Calcification in the echinoderms occurs within a limited-volume cavity enclosed by cytoplasmic extensions of the mineral depositing cells, the sclerocytes. The current model of this process maintains that the sheath formed from these cytoplasmic extensions is syncytial. Prior studies indicate that syncytium formation might be dependent on sclerocyte density and not required for calcification. This model further envisions that ossicles formed de novo nucleate and grow intracellularly until the ossicle effectively outgrows the vacuole. Continued ossicle growth occurs within the sheath but external to the cell membrane. The initial intracellular location has been confirmed only for elements of the echinoid tooth.The regenerating aboral disc integument of ophiophragmus filograneus was used to test the current echinoderm calcification model. This tissue is free of calcite fragments, thus avoiding questions of cellular engulfment, and ossicles are formed de novo. The tissue calcification pattern was followed by light microscopy in both living and fixed preparations.

Arabidopsis 4-COUMAROYL-COA LIGASE 8 contributes to the biosynthesis of the benzenoid ring of coenzyme Q in peroxisomes

2019 ◽  
Vol 476 (22) ◽  
pp. 3521-3532
Author(s):  
Eric Soubeyrand ◽  
Megan Kelly ◽  
Shea A. Keene ◽  
Ann C. Bernert ◽  
Scott Latimer ◽  
...  
Keyword(s):  
Oxidative Metabolism ◽  
Time Course ◽  
Reverse Genetics ◽  
De Novo ◽  
Coenzyme Q ◽  
Control Level ◽  
Wild Type ◽  
Fluorescent Reporters ◽  
Coa Ligase ◽  
Peroxisomal Targeting

Plants have evolved the ability to derive the benzenoid moiety of the respiratory cofactor and antioxidant, ubiquinone (coenzyme Q), either from the β-oxidative metabolism of p-coumarate or from the peroxidative cleavage of kaempferol. Here, isotopic feeding assays, gene co-expression analysis and reverse genetics identified Arabidopsis 4-COUMARATE-COA LIGASE 8 (4-CL8; At5g38120) as a contributor to the β-oxidation of p-coumarate for ubiquinone biosynthesis. The enzyme is part of the same clade (V) of acyl-activating enzymes than At4g19010, a p-coumarate CoA ligase known to play a central role in the conversion of p-coumarate into 4-hydroxybenzoate. A 4-cl8 T-DNA knockout displayed a 20% decrease in ubiquinone content compared with wild-type plants, while 4-CL8 overexpression boosted ubiquinone content up to 150% of the control level. Similarly, the isotopic enrichment of ubiquinone's ring was decreased by 28% in the 4-cl8 knockout as compared with wild-type controls when Phe-[Ring-13C6] was fed to the plants. This metabolic blockage could be bypassed via the exogenous supply of 4-hydroxybenzoate, the product of p-coumarate β-oxidation. Arabidopsis 4-CL8 displays a canonical peroxisomal targeting sequence type 1, and confocal microscopy experiments using fused fluorescent reporters demonstrated that this enzyme is imported into peroxisomes. Time course feeding assays using Phe-[Ring-13C6] in a series of Arabidopsis single and double knockouts blocked in the β-oxidative metabolism of p-coumarate (4-cl8; at4g19010; at4g19010 × 4-cl8), flavonol biosynthesis (flavanone-3-hydroxylase), or both (at4g19010 × flavanone-3-hydroxylase) indicated that continuous high light treatments (500 µE m−2 s−1; 24 h) markedly stimulated the de novo biosynthesis of ubiquinone independently of kaempferol catabolism.

Mo1845 ASSOCIATION OF COMPLICATED DIVERTICULITIS WITH SUBSEQUENT DE NOVO INFLAMMATORY BOWEL DISEASE

2020 ◽  
Vol 158 (6) ◽  
pp. S-947
Author(s):  
Asad Ur Rahman ◽  
Ishtiaq Hussain ◽  
Badar Hasan ◽  
Kanwarpreet Tandon ◽  
Fernando Castro
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
De Novo ◽  
Complicated Diverticulitis ◽  
Inflammatory Bowel

1195: De-Novo Detrusor Underactivity Following Laparoscopic Radical Prostatectomy

2007 ◽  
Vol 177 (4S) ◽  
pp. 394-394
Author(s):  
Yoshihisa Matsukawa ◽  
Yoko Yoshikawa ◽  
Tomonori Komatsu ◽  
Yasushi Yoshino ◽  
Ryohei Hattori ◽  
...  
Keyword(s):  
Radical Prostatectomy ◽  
De Novo ◽  
Laparoscopic Radical Prostatectomy ◽  
Detrusor Underactivity

1949: Six Month Randomized Study Comparing Cyclosporine Microemulsion with C2 Monitoring and Tacrolimus in De Novo Kidney Transplantation

2004 ◽  
Vol 171 (4S) ◽  
pp. 515-515
Author(s):  
Felipe G. Balbontin ◽  
Bryce Kiberd ◽  
Philip Belitsky ◽  
Dharm Singh ◽  
Albert Fraser ◽  
...  
Keyword(s):  
Kidney Transplantation ◽  
De Novo ◽  
Randomized Study ◽  
C2 Monitoring ◽  
Cyclosporine Microemulsion
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