The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants by Carolina Campos, Sergi Colomer-Castell, Damir Garcia-Cehic, Josep Gregori, Cristina Andrés, Maria Piñana, Alejandra González-Sánchez, Blanca Borràs, Oleguer Parés-Badell, Caroline Melanie Adombi, Marta Ibañez-Lligoña, Juliana Esperalba, Maria Gema Codina, Ariadna Rando-Segura, Narcis Saubí, Juan Ignacio Esteban, Francisco Rodriguez-Frías, Tomàs Pumarola, Andrés Antón, Josep Quer

“…In March 2020 we performed a study in clinical samples, where we found that a portion of genomes in the SARS-CoV-2 viral population accumulated deletions immediately before the S1/S2 cleavage site (furin-like cleavage site, PRRAR/S) of the spike gene, generating a frameshift and appearance of a premature stop codon. The main aim of this study was to determine the frequency of defective deletions in prevalent variants from the first to sixth pandemic waves in our setting and discuss whether the differences observed might support epidemiological proposals. …”
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Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern by Ben Katowa, Annie Kalonda, Benjamin Mubemba, Japhet Matoba, Doreen Mainza Shempela, Jay Sikalima, Boniface Kabungo, Katendi Changula, Simbarashe Chitanga, Mpanga Kasonde, Otridah Kapona, Nathan Kapata, Kunda Musonda, Mwaka Monze, John Tembo, Matthew Bates, Alimuddin Zumla, Catherine G. Sutcliffe, Masahiro Kajihara, Junya Yamagishi, Ayato Takada, Hirofumi Sawa, Roma Chilengi, Victor Mukonka, Walter Muleya, Edgar Simulundu

“…Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. …”
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A multi-epitope vaccine GILE against Echinococcus Multilocularis infection in mice by Pei Zhou, Pei Zhou, Zhen Zhou, Meiduo Huayu, Lei Wang, Lin Feng, Lin Feng, Yang Xiao, Yang Xiao, Yao Dai, Yao Dai, Mingyuan Xin, Feng Tang, Runle Li, Runle Li

“…IntroductionThe objective of this study is to construct a multi-epitope vaccine GILE containing B-cell and T-cell epitopes against Echinococcus Multilocularis (E. multilocularis) infection based on the dominant epitopes of E. multilocularis EMY162, LAP, and GLUT1.MethodsThe structure and hydrophobicity of GILE were predicted by SWISSMODEL, pyMOL, SOPMA and VMD, and its sequence was optimized by Optimum™ Codon. The GILE gene was inserted into pCzn1 and transformed into Escherichia coli Arctic express competent cells. …”
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Case report: Extending the spectrum of clinical and molecular findings in FOXC1 haploinsufficiency syndrome by Alexandra Garza Flores, Alexandra Garza Flores, Ida Nordgren, Maria Pettersson, Maria Pettersson, Dora Dias-Santagata, Daniel Nilsson, Daniel Nilsson, Anna Hammarsjö, Anna Hammarsjö, Anna Lindstrand, Anna Lindstrand, Dominyka Batkovskyte, Janey Wiggs, David S. Walton, Paula Goldenberg, Jesper Eisfeldt, Jesper Eisfeldt, Angela E. Lin, Ralph S. Lachman, Ralph S. Lachman, Ralph S. Lachman, Gen Nishimura, Gen Nishimura, Giedre Grigelioniene, Giedre Grigelioniene, Giedre Grigelioniene

“…Patient 2 had a heterozygous single nucleotide deletion, resulting in a frameshift and a premature stop codon in FOXC1 (NM_001453.3): c.467del, p.(Pro156Argfs*25). …”
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Genomic characterization of SARS-CoV-2 in Egypt: insights into spike protein thermodynamic stability by Deena Jalal, Omar Samir, Mariam G. Elzayat, Hend E. El-Shqanqery, Aya A. Diab, Lamiaa ElKaialy, Aya M. Mohammed, Donia Hamdy, Islam K. Matar, Islam K. Matar, Khaled Amer, Mostafa Elnakib, Wael Hassan, Tarek Mansour, Tarek Mansour, Sonia Soliman, Sonia Soliman, Reem Hassan, Reem Hassan, Ghada M. Al-Toukhy, Mahmoud Hammad, Mahmoud Hammad, Ibrahim Abdo, Ahmed A. Sayed, Ahmed A. Sayed

“…Mutation analysis shows SNPs, stop codon mutation gain, and deletion/insertion mutations, with distinct patterns of mutations governed by Nextclade or WHO variant. …”
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A Nonsense Variant in <i>CCDC65</i> Gene Causes Respiratory Failure Associated with Increased Lamb Mortality in French Lacaune Dairy Sheep by Maxime Ben Braiek, Carole Moreno-Romieux, Charlotte Allain, Philippe Bardou, Arnaud Bordes, Frédéric Debat, Cord Drögemüller, Florence Plisson-Petit, David Portes, Julien Sarry, Némuel Tadi, Florent Woloszyn, Stéphane Fabre

“…After variant calling and filtering against the variants of 86 non-carrier rams, we have identified a single nucleotide variant (SNV) in the two LDHH6 carriers whose variant allele induced a premature stop codon (p.Glu111*) in the <i>Coiled-Coil Domain Containing 65</i> (<i>CCDC65</i>) gene. …”
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基于组合优化策略在毕赤酵母中高效表达 杜邦嗜热菌脂肪酶High-efficient expression of Thermomyces dupontii lipase in Pichia pastoris based on combinatorial optimization strategy... by 汪步青1，陈洲1，王亚森1，许向阳2，高晓冬1，藤田盛久1，李子杰1WANG Buqing1, CHEN Zhou1, WANG Yasen1, XU Xiangyang2, GAO Xiaodong1, FUJITA Morihisa1, LI Zijie1

“…Firstly, a Pichia pastoris prefered codon optimized LIP1 gene was constructed, and the recombinant strain with higher LIP1 gene copy numbers was screened through high-concentration G418 plates and BMMY-rhodamine B qualitative plates. …”
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A case report: New-onset refractory status epilepticus in a patient with FASTKD2-related mitochondrial disease by Alexandra Astner-Rohracher, Alexandra Astner-Rohracher, Matthias Mauritz, Matthias Mauritz, Markus Leitinger, Markus Leitinger, Fabio Rossini, Fabio Rossini, Gudrun Kalss, Gudrun Kalss, Caroline Neuray, Elisabeth Retter, Saskia B. Wortmann, Saskia B. Wortmann, Melanie T. Achleitner, Johannes A. Mayr, Eugen Trinka, Eugen Trinka, Eugen Trinka, Eugen Trinka

“…(Arg358Ter);(Arg358Ter)] in FASTKD2 (NM_001136193), resulting in a premature termination codon in the protein-coding region and loss of function of FASTKD2. …”
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Identification of positively selected genes in Mycobacterium tuberculosis from southern Xinjiang Uygur autonomous region of China by Lele Deng, Lele Deng, Quan Wang, Haican Liu, Yi Jiang, Miao Xu, Yu Xiang, Yu Xiang, Ting Yang, Shuliu Yang, Shuliu Yang, Di Yan, Machao Li, Lili Zhao, Xiuqin Zhao, Kanglin Wan, Guangxue He, Xiaokaiti Mijiti, Guilian Li

“…There was a codon in Rv0336 under positive selection in L3 strains but not in L2 and L4 strains. …”
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METTL1 promotes neuroblastoma development through m7G tRNA modification and selective oncogenic gene translation by Ying Huang, Jieyi Ma, Cuiyun Yang, Paijia Wei, Minghui Yang, Hui Han, Hua Dong Chen, Tianfang Yue, Shu Xiao, Xuanyu Chen, Zuoqing Li, Yanlai Tang, Jiesi Luo, Shuibin Lin, Libin Huang

“…Further analysis revealed these genes contained higher frequency of codons decoded by m7G-modified tRNAs and were enriched in oncogenic pathways. …”
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Whole‐exome sequencing identifies a donor splice‐site variant in SMPX that causes rare X‐linked congenital deafness by Yuan Lv, Jia Gu, Hao Qiu, Huan Li, Zhitao Zhang, Shaowei Yin, Yan Mao, Lingyin Kong, Bo Liang, Hongkun Jiang, Caixia Liu

“…The variant generated a novel frameshift variant, creating a premature termination codon (PTC) upstream of a newly formed splice site (p.Met45Glyfs*16). …”
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PRIMEIRO RELATO DE CASO DE FAMILIA BRASILEIRA COM HEMOGLOBINAS VARIANTES RARAS: HB MAPUTO E HB OKAYAMA by EA Santos, RS Carvalho, LW Serrão

“…Segundo banco de dados de genes variantes da Globina (https://globin.bx.psu.edu/), as Hb Maputo e G Copenhagen apresentam mutação no mesmo códon, a mutação observada foi correspondente à Hb Maputo. …”
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Unraveling the Pathobiological Role of the Fungal KEOPS Complex in Cryptococcus neoformans by Yeseul Choi, Eunji Jeong, Dong-Gi Lee, Jae-Hyung Jin, Yee-Seul So, Seong-Ryong Yu, Kyung-Jo Lee, Yoonjie Ha, Chi-Jan Lin, Ying-Lien Chen, Jun Bae Park, Hyun-Soo Cho, Anna F. Averette, Joseph Heitman, Kyu-Ho Lee, Kangseok Lee, Yong-Sun Bahn

“…Supporting its pleiotropic roles, the CnKEOPS complex not only played conserved roles in t6A modification of ANN codon-recognizing tRNAs but also acted as a major transcriptional regulator, thus controlling hundreds of genes involved in various cellular processes, particularly ergosterol biosynthesis. …”
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Spastic paraplegia preceding PSEN1‐related familial Alzheimer's disease by Viorica Chelban, Marianthi Breza, Maria Szaruga, Jana Vandrovcova, David Murphy, Chia‐Ju Lee, Sondos Alikhwan, Thomas Bourinaris, George Vavougios, Muhammad Ilyas, Sobia Ahsan Halim, Ahmed Al‐Harrasi, Chrisoula Kartanou, Coras Ronald, Ingmar Blumcke, Athanasia Alexoudi, Stylianos Gatzonis, Leonidas Stefanis, Georgia Karadima, Nicholas W. Wood, Lucía Chávez‐Gutiérrez, John Hardy, Henry Houlden, Georgios Koutsis

“…We found that PSEN1 cases manifesting initially as SP have a later age of onset, are associated with mutations located beyond codon 200, and showed larger diffuse, cored plaques, amyloid‐ring arteries, and severe CAA. …”
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Capsular Polysaccharide Is Essential for the Virulence of the Antimicrobial-Resistant Pathogen Enterobacter hormaechei by Amelia St. John, Andrew I. Perault, Sabrina I. Giacometti, Alexis G. Sommerfield, Ashley L. DuMont, Keenan A. Lacey, Xuhui Zheng, Julia Sproch, Chris Petzold, Kristen Dancel-Manning, Sandra Gonzalez, Medini Annavajhala, Colleen Beckford, Nathalie Zeitouni, Feng-Xia Liang, Harm van Bakel, Bo Shopsin, Anne-Catrin Uhlemann, Alejandro Pironti, Victor J. Torres

“…Comparative genomics between the serum-sensitive NR3055 strain and the isolated serum-resistant clones revealed a premature stop codon in the wzy gene of the capsular polysaccharide biosynthesis locus of NR3055. …”
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Thirteen complete chloroplast genomes of the costaceae family: insights into genome structure, selective pressure and phylogenetic relationships by Dong-Mei Li, Yan-Gu Pan, Hai-Lin Liu, Bo Yu, Dan Huang, Gen-Fa Zhu

“…The gene orders, gene contents, amino acid frequencies and codon usage within Costaceae were highly conservative, but several variations in intron loss, long repeats, simple sequence repeats (SSRs) and gene expansion on the IR/SC boundaries were also found among these 13 genomes. …”
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RGA1 regulates grain size, rice quality and seed germination in the small and round grain mutant srg5 by Xia Yang, Jun Lu, Wu-Jian Shi, Yu-Hao Chen, Jia-Wen Yu, Sai-Hua Chen, Dong-Sheng Zhao, Li-Chun Huang, Xiao-Lei Fan, Chang-Quan Zhang, Lin Zhang, Qiao-Quan Liu, Qian-Feng Li

“…A SNP at the splice site of the first intron disrupted the normal splicing of the RGA1 transcript precursor, resulting in a premature stop codon. Additional linkage analysis confirmed that the target gene causing the srg5 mutant phenotype was RGA1. …”
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<i>Populus euphratica GLABRA3</i> Binds <i>PLDδ</i> Promoters to Enhance Salt Tolerance by Ying Zhang, Kexin Yin, Jun Yao, Ziyan Zhao, Zhe Liu, Caixia Yan, Yanli Zhang, Jian Liu, Jing Li, Nan Zhao, Rui Zhao, Xiaoyang Zhou, Shaoliang Chen

“…We isolated a 1138 bp promoter fragment upstream of the translation initiation codon of <i>PePLDδ</i>. A promoter–reporter construct, <i>PePLDδ-pro</i>::GUS, was introduced into Arabidopsis plants (<i>Arabidopsis thaliana</i>) to demonstrate the NaCl-induced <i>PePLDδ</i> promoter activity in root and leaf tissues. …”
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Clinical and biochemical effects of omega-3 fatty acid supplementation on patients with homozygous sickle cell disease by Daak, Ahmed A.

“…Sickle Cell Disease (SCD) is a group of autosomal recessive genetic blood disorders due to a mutation in the sixth codon of the β goblin gene. The resultant haemoglobin S (HbS) polymerises under low oxygen tension causes rigid, sickled red blood cells. …”
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Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity by Turcot, V, Lu, Y, Highland, HM, Schurmann, C, Justice, AE, Fine, RS, Bradfield, JP, Esko, T, Giri, A, Graff, M, Guo, X, Hendricks, AE, Karaderi, T, Lempradl, A, Locke, AE, Mahajan, A, Marouli, E, Sivapalaratnam, S, Young, KL, Alfred, T, Feitosa, MF, Masca, NGD, Manning, AK, Medina-Gomez, C, Mudgal, P, Ng, MCY, Reiner, AP, Vedantam, S, Willems, SM, Winkler, TW, Abecasis, G, Aben, KK, Alam, DS, Alharthi, SE, Allison, M, Amouyel, P, Asselbergs, FW, Auer, PL, Balkau, B, Bang, LE, Barroso, I, Bastarache, L, Benn, M, Bergmann, S, Bielak, LF, Blüher, M, Boehnke, M, Boeing, H, Boerwinkle, E, Böger, CA, Bork-Jensen, J, Bots, ML, Bottinger, EP, Bowden, DW, Brandslund, I, Breen, G, Brilliant, MH, Broer, L, Brumat, M, Burt, AA, Butterworth, AS, Campbell, PT, Cappellani, S, Carey, DJ, Catamo, E, Caulfield, MJ, Chambers, JC, Chasman, DI, Chen, Y-DI, Chowdhury, R, Christensen, C, Chu, AY, Cocca, M, Collins, FS, Cook, JP, Corley, J, Galbany, J, Cox, AJ, Crosslin, DS, Cuellar-Partida, G, D'Eustacchio, A, Danesh, J, Davies, G, Bakker, PIW, Groot, MCH, Mutsert, R, Deary, IJ, Dedoussis, G, Demerath, EW, Heijer, M, Hollander, AI, Ruijter, HM, Dennis, JG, Denny, JC, Angelantonio, E, Drenos, F, Du, M, Dubé, M-P, Dunning, AM, Easton, DF, Edwards, TL, Ellinghaus, D, Ellinor, PT, Elliott, P, Evangelou, E, Farmaki, A-E, Farooqi, IS, Faul, JD, Fauser, S, Feng, S, Ferrannini, E, Ferrieres, J, Florez, JC, Ford, I, Fornage, M, Franco, OH, Franke, A, Franks, PW, Friedrich, N, Frikke-Schmidt, R, Galesloot, TE, Gan, W, Gandin, I, Gasparini, P, Gibson, J, Giedraitis, V, Gjesing, AP, Gordon-Larsen, P, Gorski, M, Grabe, H-J, Grant, SFA, Grarup, N, Griffiths, HL, Grove, ML, Gudnason, V, Gustafsson, S, Haessler, J, Hakonarson, H, Hammerschlag, AR, Hansen, T, Harris, KM, Harris, TB, Hattersley, AT, Have, CT, Hayward, C, He, L, Heard-Costa, NL, Heath, AC, Heid, IM, Helgeland, Ø, Hernesniemi, J, Hewitt, AW, Holmen, OL, Hovingh, GK, Howson, JMM, Hu, Y, Huang, PL, Huffman, JE, Ikram, MA, Ingelsson, E, Jackson, AU, Jansson, J-H, Jarvik, GP, Jensen, GB, Jia, Y, Johansson, S, Jørgensen, ME, Jørgensen, T, Jukema, JW, Kahali, B, Kahn, RS, Kähönen, M, Kamstrup, PR, Kanoni, S, Kaprio, J, Karaleftheri, M, Kardia, SLR, Karpe, F, Kathiresan, S, Kee, F, Kiemeney, LA, Kim, E, Kitajima, H, Komulainen, P, Kooner, JS, Kooperberg, C, Korhonen, T, Kovacs, P, Kuivaniemi, H, Kutalik, Z, Kuulasmaa, K, Kuusisto, J, Laakso, M, Lakka, TA, Lamparter, D, Lange, EM, Lange, LA, Langenberg, C, Larson, EB, Lee, NR, Lehtimäki, T, Lewis, CE, Li, H, Li, J, Li-Gao, R, Lin, H, Lin, K-H, Lin, L-A, Lin, X, Lind, L, Lindström, J, Linneberg, A, Liu, C-T, Liu, DJ, Liu, Y, Lo, KS, Lophatananon, A, Lotery, AJ, Loukola, A, Luan, J, Lubitz, SA, Lyytikäinen, L-P, Männistö, S, Marenne, G, Mazul, AL, McCarthy, MI, McKean-Cowdin, R, Medland, SE, Meidtner, K, Milani, L, Mistry, V, Mitchell, P, Mohlke, KL, Moilanen, L, Moitry, M, Montgomery, GW, Mook-Kanamori, DO, Moore, C, Mori, TA, Morris, AD, Morris, AP, Müller-Nurasyid, M, Munroe, PB, Nalls, MA, Narisu, N, Nelson, CP, Neville, M, Nielsen, SF, Nikus, K, Njølstad, PR, Nordestgaard, BG, Nyholt, DR, O'Connel, JR, O'Donoghue, ML, Loohuis, LM, Ophoff, RA, Owen, KR, Packard, CJ, Padmanabhan, S, Palmer, CNA, Palmer, ND, Pasterkamp, G, Patel, AP, Pattie, A, Pedersen, O, Peissig, PL, Peloso, GM, Pennell, CE, Perola, M, Perry, JA, Perry, JRB, Pers, TH, Person, TN, Peters, A, Petersen, ERB, Peyser, PA, Pirie, A, Polasek, O, Polderman, TJ, Puolijoki, H, Raitakari, OT, Rasheed, A, Rauramaa, R, Reilly, DF, Renström, F, Rheinberger, M, Ridker, PM, Rioux, JD, Rivas, MA, Roberts, DJ, Robertson, NR, Robino, A, Rolandsson, O, Rudan, I, Ruth, KS, Saleheen, D, Salomaa, V, Samani, NJ, Sapkota, Y, Sattar, N, Schoen, RE, Schreiner, PJ, Schulze, MB, Scott, RA, Segura-Lepe, MP, Shah, SH, Sheu, WH-H, Sim, X, Slater, AJ, Small, KS, Smith, AV, Southam, L, Spector, TD, Speliotes, EK, Starr, JM, Stefansson, K, Steinthorsdottir, V, Stirrups, KE, Strauch, K, Stringham, HM, Stumvoll, M, Sun, L, Surendran, P, Swift, AJ, Tada, H, Tansey, KE, Tardif, J-C, Taylor, KD, Teumer, A, Thompson, DJ, Thorleifsson, G, Thorsteinsdottir, U, Thuesen, BH, Tönjes, A, Tromp, G, Trompet, S, Tsafantakis, E, Tuomilehto, J, Tybjaerg-Hansen, A, Tyrer, JP, Uher, R, Uitterlinden, AG, Uusitupa, M, Laan, SW, Duijn, CM, Leeuwen, N, van Setten, J, Vanhala, M, Varbo, A, Varga, TV, Varma, R, Edwards, DR, Vermeulen, SH, Veronesi, G, Vestergaard, H, Vitart, V, Vogt, TF, Völker, U, Vuckovic, D, Wagenknecht, LE, Walker, M, Wallentin, L, Wang, F, Wang, CA, Wang, S, Wang, Y, Ware, EB, Wareham, NJ, Warren, HR, Waterworth, DM, Wessel, J, White, HD, Willer, CJ, Wilson, JG, Witte, DR, Wood, AR, Wu, Y, Yaghootkar, H, Yao, J, Yao, P, Yerges-Armstrong, LM, Young, R, Zeggini, E, Zhan, X, Zhang, W, Zhao, JH, Zhao, W, Zhou, W, Zondervan, KT, Rotter, JI, Pospisilik, JA, Rivadeneira, F, Borecki, IB, Deloukas, P, Frayling, TM, Lettre, G, North, KE, Lindgren, CM, Hirschhorn, JN, Loos, RJF

“…The effect sizes of rare variants are ~10 times larger than those of common variants, with the largest effect observed in carriers of an MC4R mutation introducing a stop codon (p.Tyr35Ter, MAF = 0.01%), who weighed ~7 kg more than non-carriers. …”