SGCD Homozygous Nonsense Mutation (p.Arg97∗) Causing Limb-Girdle Muscular Dystrophy Type 2F (LGMD2F) in a Consanguineous Family, a Case Report by Muhammad Younus, Muhammad Younus, Farooq Ahmad, Erum Malik, Muhammad Bilal, Mehran Kausar, Mehran Kausar, Safdar Abbas, Shabnam Shaheen, Mohib Ullah Kakar, Majid Alfadhel, Majid Alfadhel, Muhammad Umair, Muhammad Umair

“…Direct targeted next generation sequencing was performed for the single affected individual (VI-1) followed by Sanger sequencing.Results: Targeted next generation sequencing revealed a novel homozygous nonsense mutation (c.289C>T; p.Arg97∗) in the exon 3 of the delta-sarcoglycan (SGCD) gene, that introduces a premature stop codon (TCA), resulting in a nonsense mediated decay or a truncated protein product.Discussion and Conclusion: This is the first report of LGMD2F caused by an SGCD variant in a Pakistani population. …”
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Genome-Wide Identification, Classification, Expression and Duplication Analysis of bZIP Family Genes in <i>Juglans regia</i> L. by Zhongrong Zhang, Shaowen Quan, Jianxin Niu, Caihua Guo, Chao Kang, Jinming Liu, Xing Yuan

“…The 88 <i>JrbZIP</i> genes were involved in DNA binding and nucleus and RNA biosynthetic processes of three ontological categories, molecular functions, cellular components and biological processes. The codon preference analysis showed that the bZIP gene family has a stronger bias for AGA, AGG, UUG, GCU, GUU, and UCU than other codons. …”
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New variant of PRDM16 gene nucleotide sequence in a family with various phenotypic manifestations of the non-compacted myocardium by R. P. Myasnikov, A. A. Bukaeva, O. V. Kulikova, A. I. Ershova, A. V. Petukhova, E. D. Zotova, A. N. Meshkov, E. A. Mershina, A. V. Kiseleva, M. G. Divashuk, P. S. Pilyus, M. S. Kharlap, V. M. Mikova, S. N. Koretsky, L. A. Gandaeva, V. E. Sinitsyn, E.. N. Basargina, S. A. Boytsov, E. A. Snigir, A. I. Akinshina, D. A. Kashtanova, V. V. Makarov, V. S. Yudin, O. M. Drapkina

“…As a result of a molecular genetics tests, a previously undescribed single nucleotide deletion in the PRDM16 gene was revealed in all family members with the LVNC phenotype, leading to a frameshift mutation in exon 9 and the formation of a premature termination codon. This gene encodes a transcription factor responsible for after-birth suppressing the expression of genes involved in prenatal and postnatal development. …”
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Evolutionary changes in transcription factor coding sequence quantitatively alter sensory organ development and function by Simon Weinberger, Matthew P Topping, Jiekun Yan, Annelies Claeys, Natalie De Geest, Duru Ozbay, Talah Hassan, Xiaoli He, Joerg T Albert, Bassem A Hassan, Ariane Ramaekers

“…This proneural potency gradient correlated directly with ATH protein stability, including in response to Notch signaling, independently of mRNA levels or codon usage. This establishes a distinct and ancient function for ATHs and demonstrates that coding sequence evolution can underlie quantitative variation in sensory development and function.…”
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The association between EPCR gene p.Ser219Gly polymorphism and venous thromboembolism risk: a case–control study, meta-analysis, and a reproducibility study by Dóra Pituk, Tünde Miklós, Ágota Schlammadinger, Katalin Rázsó, Zsuzsanna Bereczky

“…BackgroundThe rs867186 single-nucleotide polymorphism in the PROCR gene (g.6936A &gt; G, c.4600A &gt; G) results in a serine-to-glycine substitution at codon 219 of endothelial protein C receptor (EPCR). …”
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Characterization and expression of fungal defensin in Escherichia coli and its antifungal mechanism by RNA-seq analysis by Yu-Pei Chen, Yu-Pei Chen, Yu-Pei Chen, Yingying Li, Yingying Li, Fangfang Chen, Fangfang Chen, Hongtan Wu, Hongtan Wu, Shudi Zhang, Shudi Zhang

“…The fungal defensin as an antifungal protein can widely inhibit fungi.MethodsIn this study, eight antifungal genes from different filamentous fungi were optimized by synonymous codon bias and heterologously expressed in Escherichia coli.Results and discussionOnly the antifungal protein (AFP) from Aspergillus giganteus was produced, whereas the AFP from its mutation of the chitin-binding domain could not be expressed, thereby suggesting the importance of the motif for protein folding. …”
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Pathogenic evaluation of synonymous COL4A5 variants in X‐linked Alport syndrome using a minigene assay by Tomoko Horinouchi, Tomohiko Yamamura, Shogo Minamikawa, China Nagano, Nana Sakakibara, Koichi Nakanishi, Yuko Shima, Naoya Morisada, Shinya Ishiko, Yuya Aoto, Hiroaki Nagase, Hiroki Takeda, Rini Rossanti, Shingo Ishimori, Hiroshi Kaito, Masafumi Matsuo, Kazumoto Iijima, Kandai Nozu

“…Methods In this study, we conducted in vitro splicing analysis using a hybrid minigene assay and specimens from three XLAS patients with synonymous variants causing aberrant splicing, including previously reported pathogenic mutations in the same codon. The variants were c.876 A>T (p.Gly292=), c.2358 A>G (p.Pro786=), and c.3906 A>G (p.Gln1302=). …”
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Correlation of <i>gyr</i> Mutations with the Minimum Inhibitory Concentrations of Fluoroquinolones among Multidrug-Resistant <i>Mycobacterium tuberculosis</i> Isolates in Banglades... by Mohammad Khaja Mafij Uddin, Md. Fahim Ather, Rumana Nasrin, Tanjina Rahman, A. S. M. Iftekhairul Islam, S. M. Mazidur Rahman, Shahriar Ahmed, Sayera Banu

“…In conclusion, the substitutions of codon A90V and D94G in the <i>gyr</i> genes were mostly responsible for the FQs’ resistance among <i>Mtb</i> isolates in Bangladesh. …”
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Correction of Fanconi Anemia Mutations Using Digital Genome Engineering by Christopher J. Sipe, Mitchell G. Kluesner, Samuel P. Bingea, Walker S. Lahr, Aneesha A. Andrew, Minjing Wang, Anthony P. DeFeo, Timothy L. Hinkel, Kanut Laoharawee, John E. Wagner, Margaret L. MacMillan, Gregory M. Vercellotti, Jakub Tolar, Mark J. Osborn, R. Scott McIvor, Beau R. Webber, Branden S. Moriarity

“…These genetic corrections or conservative codon substitution strategies lead to phenotypic rescue as illustrated by a resistance to the alkylating crosslinking agent Mitomycin C (MMC). …”
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Efficiency of Recombinant CRISPR/rCas9-Mediated miRNA Gene Editing in Rice by Pil Joong Chung, Hoyong Chung, Nuri Oh, Joohee Choi, Seung Woon Bang, Se Eun Jung, Harin Jung, Jae Sung Shim, Ju-Kon Kim

“…For the further functional investigation of the miRNAs, we applied recombinant codon-optimized Cas9 (rCas9) for rice with single-guide RNAs specifically targeting mature miRNA sequences or sites required for the biogenesis of mature miRNA. …”
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Complete sequence and comparative analysis of the mitochondrial genome of the rare and endangered Clematis acerifolia, the first clematis mitogenome to provide new insights into th... by Dan Liu, Dan Liu, Kai Qu, Yangchen Yuan, Yangchen Yuan, Zhiheng Zhao, Ying Chen, Biao Han, Wei Li, Yousry A. El-Kassaby, Yangyang Yin, Xiaoman Xie, Boqiang Tong, Hongshan Liu

“…Further, our C. acerifolia mitogenome characteristics investigation included GC contents, codon usage, repeats and synteny analysis. Overall, our results are expected to provide fundamental information for C. acerifolia mitogenome evolution and confirm the validity of mitochondrial analysis in determining the phylogenetic positioning of Clematis plants.…”
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Molecular characterization and identification of SNPs in ATP1A1 isoform of sodium-phosphate adenosine triphosphatase across diverse breeds of riverine buffaloes (Bubalus bubalis) a... by RAMNEEK KAUR, MONIKA SODHI, ANKITA SHARMA, VIJAY LAKSHMI SHARMA, PREETI VERMA, SHELESH KUMAR SWAMI, RANJIT S KATARIA, MANOJ K SINGH, PARVESH K, MANISHI MUKESH

“…Base calling was performed with Phred and contig assembly was done via Phrap/Cross_match/Swat tool available in the suite Codon code Aligner v. 3.5.1. The results revealed a total of 26 variations in exons 18–21 of ATP1A1 gene in riverine buffalo. …”
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Rare variants in the GABAA receptor subunit ε identified in patients with a wide spectrum of epileptic phenotypes by Fenja Markus, Chloé Angelini, Aurelien Trimouille, Gabrielle Rudolf, Gaetan Lesca, Cyril Goizet, Eulalie Lasseaux, Benoit Arveiler, Marjon vanSlegtenhorst, Alice S. Brooks, Rami Abou Jamra, Georg‐Christoph Korenke, John Neidhardt, Marta Owczarek‐Lipska

“…Results We identified four hemizygous sequence variants in the GABAA receptor subunit ε gene (GABRE), including one nonsense (NM_004961.3: c.399C>A, p.Tyr133*), two missense variants (NM_004961.3: c.664G>A, p.Glu222Lys; NM_004961.3: c.1045G>A, p.Val349Ile), and one variant affecting the translation initiation codon (NM_004961.3: c.1A>G, p.Met1?) in four unrelated families. …”
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Transcript Regulation of the Recoded Archaeal α-<span style="font-variant: small-caps">l</span>-Fucosidase In Vivo by Federica De Lise, Roberta Iacono, Andrea Strazzulli, Rosa Giglio, Nicola Curci, Luisa Maurelli, Rosario Avino, Antonio Carandente, Stefano Caliro, Alessandra Tortora, Fabio Lorenzini, Paola Di Donato, Marco Moracci, Beatrice Cobucci-Ponzano

“…In <i>Archaea</i>, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for −1 programmed frameshifting that allow the expression of a fully functional α-<span style="font-variant: small-caps;">l</span>-fucosidase in the crenarchaeon <i>Saccharolobus solfataricus</i>, in which several functional interrupted genes have been identified. …”
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Evolutionary and phylogenetic analyses of 11 Cerasus species based on the complete chloroplast genome by Tian Wan, Bai-xue Qiao, Jing Zhou, Ke-sen Shao, Liu-yi Pan, Feng An, Xu-sheng He, Tao Liu, Ping-ke Li, Yu-liang Cai

“…During cp plastome evolution, the codon profile has been strongly biased toward the use of A/T at the third base, and leucine and isoleucine codons appear the most frequently. …”
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Whole-genome analysis of monozygotic Brazilian twins discordant for type 1 narcolepsy: a case report by João H. C. Campos, Ana C. R. Aguilar, Fernando Antoneli, Giselle Truzzi, Marcelo R. S. Briones, Renata C. Ferreira, Fernando M. S. Coelho

“…The unaffected twin has significantly more frameshift mutations as compared to the affected twin (108 versus 75) and mutations that affect stop codons (61 versus 5 in stop gain, 26 versus 2 in start lost). …”
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Case Report: Longitudinal monitoring of clonal evolution by circulating tumor DNA for resistance to anti-EGFR antibody in a case of metastatic colorectal cancer by Tamotsu Sagawa, Yasushi Sato, Masahiro Hirakawa, Kyoko Hamaguchi, Fumito Tamura, Hiroyuki Nagashima, Koshi Fujikawa, Koichi Okamoto, Yutaka Kawano, Masahiro Sogabe, Hiroshi Miyamoto, Tetsuji Takayama

“…The RAS status changed from wild type to mutant type, back to wild type, and again to mutant type (NRAS/KRAS codon 61) during the course of treatment.ConclusionIn this report, tracking of ctDNA allowed us to describe clonal evolution in a case in which we observed genomic alterations in KRAS and NRAS in a patient who acquired resistance to anti-EGFR antibody drugs during treatment. …”
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Zebrafish Tric-b is required for skeletal development and bone cells differentiation by Francesca Tonelli, Laura Leoni, Valentina Daponte, Roberta Gioia, Silvia Cotti, Imke A. K. Fiedler, Daria Larianova, Andy Willaert, Paul J. Coucke, Simona Villani, Björn Busse, Roberta Besio, Antonio Rossi, P. Eckhard Witten, Antonella Forlino

“…Two zebrafish mutants for tmem38b were generated by CRISPR/Cas9, one carrying an out of frame mutation introducing a premature stop codon (tmem38b-/-) and one with an in frame deletion that removes the highly conserved KEV domain (tmem38bΔ120-7/Δ120-7). …”
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Genetic Diversity of Listeria monocytogenes Isolated From Three Commercial Tree Fruit Packinghouses and Evidence of Persistent and Transient Contamination by Yi Chen, Tobin Simonetti, Kari Peter, Qing Jin, Eric Brown, Luke F. LaBorde, Dumitru Macarisin

“…Only 1 isolate in the three facilities contained a premature stop codon in virulence gene inlA. Fourteen samples yielded 2–3 clones per sample, demonstrating the importance of choosing appropriate methodologies and selecting a sufficient number of isolates per sample for studying L. monocytogenes diversity. …”
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Differential Expression of Proteins in an Atypical Presentation of Autoimmune Lymphoproliferative Syndrome by Dulce María Delgadillo, Adriana Ivonne Céspedes-Cruz, Emmanuel Ríos-Castro, María Guadalupe Rodríguez Maldonado, Mariel López-Nogueda, Miguel Márquez-Gutiérrez, Rocío Villalobos-Manzo, Lorena Ramírez-Reyes, Misael Domínguez-Fuentes, José Tapia-Ramírez

“…A mutation resulting in an in-frame premature stop codon and protein truncation was detected in the <i>Fas</i> gene from patient 2. …”
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