Comparison of the mitochondrial genomes of three geographical strains of Apis laboriosa indicates high genetic diversity in the black giant honeybee (Hymenoptera: Apidae) by Xiang‐You Tang, Yu‐Xin Yao, Yao‐Hui Li, Hua‐Li Song, Rui Luo, Peng Shi, Ze‐Yang Zhou, Jin‐Shan Xu

“…Three mitochondrial genomes all harbor 37 common genes and present the same AT bias and the frequency of codon usage. However, the fragments including COX1, SSUrRNA, LSUrRNA, and the AT‐rich region of the mitochondrial genome from Shangri‐La region demonstrate distinctive insertions and deletions compared to those from Chongqing and Nepal regions. …”
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The complete mitochondrial genome of Hyotissa sinensis (Bivalvia, Ostreoidea) indicates the genetic diversity within Gryphaeidae by Fengping Li, Hongyue Liu, Xin Heng, Yu Zhang, Mingfu Fan, Shunshun Wang, Chunsheng Liu, Zhifeng Gu, Aimin Wang, Yi Yang

“…The nucleotide composition and codon usage preference of H. sinensis mtDNA is similar to that of H. hyotis within the same genus. …”
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Neuronal transcription of autism gene PTCHD1 is regulated by a conserved downstream enhancer sequence by Stephen F. Pastore, Tahir Muhammad, Cassandra Stan, Paul W. Frankland, Paul A. Hamel, John B. Vincent

“…Using a pairwise comparison of chromatin accessibility between mouse forebrain and liver tissues, a candidate regulatory region, ~ 9.1 kbp downstream of the Ptchd1 stop codon was defined. This region harbours two ENCODE-predicted enhancer cis-regulatory elements. …”
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Novel Allele of <i>FAD2-1A</i> from an EMS-Induced Mutant Soybean Line (PE529) Produces Elevated Levels of Oleic Acid in Soybean Oil by Hyun Jo, Changwan Woo, Nabachwa Norah, Jong Tae Song, Jeong-Dong Lee

“…The single nucleotide polymorphism (SNP) in PE529 also induced the conversion from tryptophan to a premature stop codon at position 293 in the amino acid sequence (W293STOP). …”
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Diagnosis, Phenotype, and Molecular Genetics of Congenital Analbuminemia by Lorenzo Minchiotti, Gianluca Caridi, Monica Campagnoli, Francesca Lugani, Monica Galliano, Ulrich Kragh-Hansen

“…These include a variant in the start codon, frame-shift/insertions, frame-shift/deletions, nonsense variants, and variants affecting splicing. …”
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<i>Drosophila</i> as a Model of Unconventional Translation in Spinocerebellar Ataxia Type 3 by Sean L. Johnson, Matthew V. Prifti, Alyson Sujkowski, Kozeta Libohova, Jessica R. Blount, Luke Hong, Wei-Ling Tsou, Sokol V. Todi

“…RAN translation occurs around long nucleotide repeats that form hairpin loops, allowing for translation initiation in the absence of a start codon that results in potentially toxic, poly-amino acid repeat-containing proteins. …”
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The Performance of the Abbott Real Time MTB RIF/INH Compared to the MTBDRplus V2 for the Identification of MDR-TB Among Isolates by David A, Singh L, Da Silva P, Scott L, Stevens W

“…Of the 10 discordant results, where sequencing was used as the reference method, the RT MTB RIF/INH assays misclassified six resistance isolates, while the LPA misclassified seven.Discussion: Overall, the RT MTB RIF/INH demonstrated good agreement with the LPA, and a better correlation with sequencing on discrepant isolates specifically with mutations occurring in codon 511 of the rpoB gene. The RT MTB RIF/INH therefore can be used to complement existing laboratory algorithms determining Rif and INH resistance profiles, with less emphasis on manual laboratory processing.Keywords: molecular diagnostics, tuberculosis, line-probe assay…”
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MPEPE, a predictive approach to improve protein expression in E. coli based on deep learning by Zundan Ding, Feifei Guan, Guoshun Xu, Yuchen Wang, Yaru Yan, Wei Zhang, Ningfeng Wu, Bin Yao, Huoqing Huang, Tamir Tuller, Jian Tian

“…Therefore, the study provides foundational insights into the relationship between specific amino acid usage, codon usage, and protein expression, and is essential for research and industrial applications.…”
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Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History by Semmannan Kalaiyarasu, Niranjan Mishra, Saravanan Subramaniam, Dashprakash Moorthy, Shashi Bhusan Sudhakar, Vijendra Pal Singh, Aniket Sanyal

“…Additionally, 21.8% of the ORF codon sites were found under strong episodic diversifying selection, providing first evidence of negative selection in HoBiPeV evolution. …”
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Extreme plastomes in holoparasitic Balanophoraceae are not the norm by Woorin Kim, Thea Lautenschläger, Jay F. Bolin, Mathew Rees, Albertina Nzuzi, Renchao Zhou, Stefan Wanke, Matthias Jost

“…Its protein-coding genes show a more biased codon usage compared to Sarcophyte, with an accumulation of in-frame TAG stop codons. …”
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Complete Sequence of pABTJ2, A Plasmid from Acinetobacter baumannii MDR-TJ, Carrying Many Phage-like Elements by He Huang, Yan Dong, Zhi-Liang Yang, Hao Luo, Xi Zhang, Feng Gao

“…The tRNA gene is specific for asparagine codon GTT, which may be a small chromosomal sequence picked up through incorrect excision during plasmid formation. …”
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Species-Specific Duplication and Adaptive Evolution of a Candidate Sex Pheromone Receptor Gene in Weather Loach by Lei Zhong, Weimin Wang, Xiaojuan Cao

“…<i>Ma_or114-1b</i> has base insertions that delayed the stop codon, causing the protein sequence length to be extended by 8 amino acids. …”
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DNA Vaccine-Encoded Flagellin Can Be Used as an Adjuvant Scaffold to Augment HIV-1 gp41 Membrane Proximal External Region Immunogenicity by Lara Ajamian, Luca Melnychuk, Patrick Jean-Pierre, Gerasimos J. Zaharatos

“…Using plasmid DNA vector-based expression in mammalian cells, we demonstrate robust expression of codon-optimized full length and hypervariable region-deleted constructs of Salmonella enterica subsp. enterica serovar Typhi flagellin (FliC). …”
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A novel canine model for Duchenne muscular dystrophy (DMD): single nucleotide deletion in DMD gene exon 20 by Sara Mata López, James J. Hammond, Madison B. Rigsby, Cynthia J. Balog-Alvarez, Joe N. Kornegay, Peter P. Nghiem

“…Whole genome sequencing, polymerase chain reaction, and Sanger sequencing revealed a frameshift, single nucleotide deletion in canine DMD exon 20, position 27,626,466 (c.2841delT mRNA), resulting in a stop codon six nucleotides downstream. Semen was archived for future line perpetuation. …”
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A novel mutation deep within intron 7 of the GBA gene causes Gaucher disease by Anna Malekkou, Ioanna Sevastou, Gavriella Mavrikiou, Theodoros Georgiou, Lluisa Vilageliu, Marina Moraitou, Helen Michelakakis, Chrystalla Prokopiou, Anthi Drousiotou

“…This mutation creates a new donor splice site leading to aberrant splicing and resulting in the insertion of the first 239nt of intron 7 as a pseudoexon in the mRNA, creating a premature stop codon. Conclusion This study expands the mutation spectrum of GD and highlights the importance of RNA sequencing for the molecular diagnosis of patients bearing mutations in nonexonic regions.…”
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Purification and Characterization of Double-Stranded Nucleic Acid-Dependent ATPase Activities of Tagged Dicer-Related Helicase 1 and its Short Isoform in <i>Caenorhabditis elegans<... by Taishi Kobayashi, Takuro Murakami, Yuu Hirose, Toshihiko Eki

“…We investigated expressions and purifications of a codon-optimized DRH-1 with four different N-terminal tags, identifying poly-histidine (His)-small ubiquitin-like modifier (SUMO) as a suitable tag for DRH-1 preparation. …”
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Comparative analysis of medicinal plants Scutellaria baicalensis and common adulterants based on chloroplast genome sequencing by Zhen Li, Baozhong Duan, Zhongyu Zhou, Hui Fang, Meihua Yang, Conglong Xia, Ying Zhou, Jing Wang

“…Furthermore, the nine species exhibited high conservation from aspects of the genome structure, codon usage, repeat sequences, and gene content. …”
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Genomic epidemiology of SARS-CoV-2 from Uttar Pradesh, India by Gauri Misra, Ashrat Manzoor, Meenu Chopra, Archana Upadhyay, Amit Katiyar, Brij Bhushan, Anup Anvikar

“…We have also identified three escape variants in the S gene at codon position 19 (T19I/R), 484 (E484A/Q), and 681 (P681R/H) during the fourth and fifth waves in India. …”
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Clinical and Genetic Characteristics of the Heidenhain Variant of Creutzfeldt–Jakob Disease by Yu Kong, Zhongyun Chen, Jing Zhang, Xue Wang, Liyong Wu

“…The most common mutation was V210I (4/9), and all patients (9/9) had methionine homozygosity (MM) at codon 129. Only 25% of cases had a family history of the disease. …”
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X-linked recessive ichthyosis in 8 Tunisian patients: awareness of misdiagnosis due to the technical trap of the STS pseudogene by Hamza Chouk, Sarra Saad, Sarra Dimassi, Nadia Ghariani Fetoui, Ayda Bennour, Rima Gammoudi, Haifa Elmabrouk, Ali Saad, Mohamed Denguezli, Dorra H’mida

“…Results Direct Sanger sequencing of the STS gene showed the same deletion of 13 base pairs within the exon 4 in all patients resulting in a premature stop codon. However, all patients’ mothers were not carriers of this variant and no common haplotype flanking STS gene was shared between affected patients. …”
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