Temporal order of RNase IIIb and loss-of-function mutations during development determines phenotype in pleuropulmonary blastoma / DICER1 syndrome: a unique variant of the two-hit t... by Mark Brenneman, Amanda Field, Jiandong Yang, Gretchen Williams, Leslie Doros, Christopher Rossi, Kris Ann Schultz, Avi Rosenberg, Jennifer Ivanovich, Joyce Turner, Heather Gordish-Dressman, Douglas Stewart, Weiying Yu, Anne Harris, Peter Schoettler, Paul Goodfellow, Louis Dehner, Yoav Messinger, D. Ashley Hill

“…The genetics of DICER1-associated tumorigenesis are unusual in that tumors typically bear neomorphic missense mutations at one of five specific “hotspot” codons within the RNase IIIb domain of DICER 1, combined with complete loss of function (LOF) in the other allele. …”
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Case report: Successful outcome of treatment using rituximab in an adult patient with refractory minimal change disease and β-thalassemia complicating autoimmune hemolytic anemia by Jing Zhuang, Zhigang Zhao, Changrong Zhang, Xue Song, Chen Lu, Xuefei Tian, Hong Jiang

“…The β-thalassemia minor was caused by heterozygosity for a 4-base deletion mutation [codons 41/42 (−TTCT) BETA0] of the β-globin gene. …”
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Molecular Characterization of Choroideremia-Associated Deletions Reveals an Unexpected Regulation of <i>CHM</i> Gene Transcription by Tiziana Fioretti, Valentina Di Iorio, Barbara Lombardo, Francesca De Falco, Armando Cevenini, Fabio Cattaneo, Francesco Testa, Lucio Pastore, Francesca Simonelli, Gabriella Esposito

“…Small nucleotide variants leading to premature termination codons (PTCs) are a major cause of CHM, but about 20% of patients has <i>CHM</i> gene deletions. …”
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Global genetic diversity and evolutionary patterns among Potato leafroll virus populations by Tahir Farooq, Muhammad Dilshad Hussain, Muhammad Taimoor Shakeel, Hasan Riaz, Ummara Waheed, Maria Siddique, Irum Shahzadi, Muhammad Naveed Aslam, Yafei Tang, Xiaoman She, Zifu He

“…Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. …”
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Patterns of Somatic Variants in Colorectal Adenoma and Carcinoma Tissue and Matched Plasma Samples from the Hungarian Oncogenome Program by Alexandra Kalmár, Orsolya Galamb, Gitta Szabó, Orsolya Pipek, Anna Medgyes-Horváth, Barbara K. Barták, Zsófia B. Nagy, Krisztina A. Szigeti, Sára Zsigrai, István Csabai, Péter Igaz, Béla Molnár, István Takács

“…Variants in <i>KRAS</i> codons 12 (AD: 8/27, CRC: 11/51 (0.216)) and 13 (CRC: 3/51 (0.06)) were the most frequent in our sample set, with G12V (5/27) dominance in ADs and G12D (5/51 (0.098)) in CRCs. …”
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Improving spinosad production by tuning expressions of the forosamine methyltransferase and the forosaminyl transferase to reduce undesired less active byproducts in the heterologo... by Xiaochen Li, Ruofei Guo, Ji Luan, Jun Fu, Youming Zhang, Hailong Wang

“…Because the spinosad native producer is difficult to genetically manipulate, we previously changed promoters, ribosome binding sites and start codons of 23 spinosad biosynthetic genes to construct an artificial gene cluster which resulted in a 328-fold yield improvement in the heterologous host Streptomyces albus J1074 compared with the native gene cluster. …”
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A novel mutation in GTPBP3 causes combined oxidative phosphorylation deficiency 23 by affecting pre-mRNA splicing by Yanjun Wang, Juan He, Fangling Dong, Weihua Shou, Xingxing Feng, Ya Yang, Cuifen Li, Jingjing Wang, Bin Li, Shufang Xiao

“…The minigene assay proved that the novel mutation resulted in two aberrant transcripts that created premature termination codons. Conclusions: The clinical manifestations, brain imaging change, mitochondrial metabolism disturbances and the detection and validation of the GTPBP3 mutations expand the profile of COXPD23 and the pathogenic mutation spectrum. …”
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Compound heterozygous mutations in GRM6 causing complete Schubert-Bornschein type congenital stationary night blindness by Dong'e Bai, Ruru Guo, Dandan Huang, Jian Ji, Wei Liu

“…Several bioinformatics prediction programs revealed the mutations were “Damaging” or “Disease Causing” and conservation analysis showed both the codons Gly51 and Val243 were highly conserved among species, suggesting the changes were pathogenic. …”
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Comparative and phylogenetic analysis of complete chloroplast genomes from seven Neocinnamomum taxa (Lauraceae) by Zhengying Cao, Zhengying Cao, Linyi Yang, Yaxuan Xin, Yaxuan Xin, Wenbin Xu, Qishao Li, Qishao Li, Haorong Zhang, Haorong Zhang, Yuxiang Tu, Yuxiang Tu, Yu Song, Peiyao Xin, Peiyao Xin

“…The chloroplast genome contained a total of 31 preferred codons. Three highly variable regions, trnN-GUU-ndhF, petA-psbJ, and ccsA-ndhD, were identified with Pi values &gt; 0.004. …”
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Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach by Muhammad Tahir ul Qamar, Zeeshan Shokat, Iqra Muneer, Usman Ali Ashfaq, Hamna Javed, Farooq Anwar, Amna Bari, Barira Zahid, Nazamid Saari

“…The computationally mediated immune response of MEV demonstrated increased interferon-γ production, a significant abundance of immunoglobulin and activation of macrophages which are essential for immune-response against RSV. Moreover, MEV codons were optimized and in silico cloning was performed, to ensure its increased expression. …”
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Structure and evolution of the squamate major histocompatibility complex as revealed by two Anolis lizard genomes by Daren C. Card, Daren C. Card, Andrew G. Van Camp, Andrew G. Van Camp, Trenten Santonastaso, Michael I. Jensen-Seaman, Nicola M. Anthony, Scott V. Edwards, Scott V. Edwards

“…Signals of diversifying selection in each anole species was evident across codons of mhc1, many of which appear functionally relevant given known structures of this protein from the green anole, chicken, and human. …”
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Molecular Evolution of the Bactericidal/Permeability-Increasing Protein (BPIFA1) Regulating the Innate Immune Responses in Mammals by Hafiz Ishfaq Ahmad, Faheem Ahmed Khan, Musarrat Abbas Khan, Safdar Imran, Rana Waseem Akhtar, Nuruliarizki Shinta Pandupuspitasari, Windu Negara, Jinping Chen

“…We performed probability tests comparing various models based on dN/dS ratios to recognize specific codons under positive selection pressure. We identified positively selected sites in the LBP-BPI domain of BPIFA1 proteins in the mammalian genome, including a lipid-binding domain with a very high degree of selectivity for DPPC. …”
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The clinical spectrum of SMA‐PME and in vitro normalization of its cellular ceramide profile by Michelle M. Lee, Graeme S. V. McDowell, Darryl C. De Vivo, Daniel Friedman, Samuel F. Berkovic, Maria Spanou, Argirios Dinopoulos, Katheryn Grand, Pedro A. Sanchez‐Lara, Michelle Allen‐Sharpley, Jodi Warman‐Chardon, Alexander Solyom, Thierry Levade, Edward H. Schuchman, Steffany A. L. Bennett, David A. Dyment, Toni S. Pearson

“…Five of six patients carried at least one of the recurrent SMA‐PME variants observed in two specific codons of ASAH1. A review of 30 total cases revealed that patients who were homozygous for the most common c.125C > T variant presented in the first decade of life with limb‐girdle weakness as the initial symptom. …”
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Purriato is a conserved small open reading frame gene that interacts with the CASA pathway to regulate muscle homeostasis and epithelial tissue growth in Drosophila by Jose I. Pueyo, Jorge Salazar, Carolina Grincho, Jimena Berni, Benjamin P. Towler, Benjamin P. Towler, Sarah F. Newbury

“…Recent advances in proteogenomic techniques and bioinformatic pipelines have permitted the detection of thousands of translated small Open Reading Frames (smORFs), which contain less than 100 codons, in eukaryotic genomes. Hundreds of these actively translated smORFs display conserved sequence, structure and evolutionary signatures indicating that the translated peptides could fulfil important biological roles. …”
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Case report: A novel heterozygous synonymous variant in deep exon region of NIPBL gene generating a non-canonical splice donor in a patient with cornelia de lange syndrome by Meizhen Shi, Meizhen Shi, Yuying Liang, Bobo Xie, Bobo Xie, Xianda Wei, Xianda Wei, Haiyang Zheng, Haiyang Zheng, Chunrong Gui, Chunrong Gui, Rong Huang, Rong Huang, Xin Fan, Xin Fan, Chuan Li, Chuan Li, Xiaojiao Wei, Yunting Ma, Shaoke Chen, Shaoke Chen, Yujun Chen, Yujun Chen, Baoheng Gui, Baoheng Gui

“…A loss of 137 bp at the 3′ end of NIPBL exon 40 was detected, which potentially altered the open reading frame by inserting multiple premature termination codons. Quantitative real-time PCR analysis showed that the ratio of the transcription level of the full-length transcript to that of the altered short transcript in the patient was 5:1, instead of 1:1. …”
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Influence of Microsatellite Instability and KRAS and BRAF Mutations on Lymph Node Harvest in Stage I–III Colon Cancers by Marianne Berg, Marianne Guriby, Oddmund Nordgård, Bjørn S. Nedrebø, Terje C. Ahlquist, Rune Smaaland, Satu Oltedal, Jon Arne Søreide, Hartwig Kørner, Ragnhild A. Lothe, Kjetil Søreide

“…The presence of MSI, KRAS mutations in codons 12 and 13, and BRAFV600E mutations was analyzed. …”
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<em>APOB</em> CRISPR-Cas9 Engineering in Hypobetalipoproteinemia: A Promising Tool for Functional Studies of Novel Variants by Xavier Vanhoye, Alexandre Janin, Amandine Caillaud, Antoine Rimbert, Fabienne Venet, Morgane Gossez, Wieneke Dijk, Oriane Marmontel, Séverine Nony, Charlotte Chatelain, Christine Durand, Pierre Lindenbaum, Jennifer Rieusset, Bertrand Cariou, Philippe Moulin, Mathilde Di Filippo

“…Familial hypobetalipoproteinemia (FHBL) is mostly caused by premature termination codons in the <i>APOB</i> gene, a condition associated with fatty liver and steatohepatitis. …”
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Intron Retention: What that means for the biologist by Ruby Dhar, Arun Kumar, Subhradip Karmakar

“…The retained introns may contain premature stop codons or regulatory elements that can influence gene expression and protein function. …”
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Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery by Stothard Paul, Choi Jung-Woo, Basu Urmila, Sumner-Thomson Jennifer M, Meng Yan, Liao Xiaoping, Moore Stephen S

“…Several SNPs predicted to create or remove stop codons were also found. A comparison between the sequencing SNPs and genotyping results from the BovineHD high-density genotyping chip indicates a detection rate of 91% for homozygous SNPs and 81% for heterozygous SNPs. …”
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Comparative bioinformatics and experimental analysis of the intergenic regulatory regions of Bacillus cereus hbl and nhe enterotoxin operons and the impact of CodY on virulence het... by Maria-Elisabeth eBöhm, Viktoria Magdalena Krey, Nadja eJessberger, Elrike eFrenzel, Siegfried eScherer

“…By determining transcription start sites, unusually long 5’ untranslated regions (5’UTRs) upstream of the nhe and hbl start codons were identified, which are not present upstream of cytK-1 and cytK-2. …”
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