A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals by Mag Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Ward, Lucas D., Jungreis, Irwin, Rasmussen, Matthew D., Kellis, Manolis

“…These elements reveal a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons. …”
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Dengue Virus Type 3 Adaptive Changes during Epidemics in Sao Jose de Rio Preto, Brazil, 2006–2007 by Villabona-Arenas, Christian Julian, Mondini, Adriano, Bosch, Irene, Schimitt, Diane, Calzavara-Silva, Carlos E., de A Zanotto, Paolo M., Nogueira, Mauricio Lacerda

“…By inferring the evolutionary history on a local-scale and estimating rates of synonymous (dS) and nonsynonimous (dN) substitutions, we have documented at least two different introductions of DENV-3 into the city and detected 10 polymorphic codon sites under significant positive selection (dN/dS > 1) and 8 under significant purifying selection (dN/dS < 1). …”
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Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing by Arribere, Joshua Alexander, Gilbert, Wendy

“…We also identified hundreds of genes with very short TLs, and demonstrated that short TLs were associated with poor translation initiation at the annotated start codon and increased initiation at downstream AUGs. …”
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YoeB-ribosome structure: a canonical RNase that requires the ribosome for its specific activity by Tang, Kai, Wang, Meitian, Feng, Shu, Chen, Yun, Kamada, Katsuhiko, Wang, Han, Gao, Yong-Gui

“…In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3′–phosphate at the newly formed 3′ end. …”
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Loss of the habenula intrinsic neuromodulator Kisspeptin1 affects learning in larval zebrafish by Lupton, Charlotte, Sengupta, Mohini, Cheng, Ruey-Kuang, Chia, Joanne, Thirumalai, Vatsala, Jesuthasan, Suresh

“…Mutants, which have a stop codon upstream of the active Kisspeptin1 peptide, have a deficiency in learning to avoid a shock that is predicted by light. …”
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Activating point mutations in cyclin-dependent kinase 4 are not seen in sporadic pituitary adenomas, insulinomas or Leydig cell tumours. by Vax, V, Bibi, R, Diaz-Cano, S, Gueorguiev, M, Kola, B, Borboli, N, Bressac-de Paillerets, B, Walker, G, Dedov, I, Grossman, AB, Korbonits, M

“…Dominant activating mutations affecting codon 24 of the CDK4 gene (replacement of Arg24 by Cys or His) render CDK4 insensitive to p16(INK4) inhibition and are responsible for melanoma susceptibility in some kindreds. …”

Inherited IL-12p40 deficiency: genetic, immunologic, and clinical features of 49 patients from 30 kindreds. by Prando, C, Samarina, A, Bustamante, J, Boisson-Dupuis, S, Cobat, A, Picard, C, AlSum, Z, Al-Jumaah, S, Al-Hajjar, S, Frayha, H, Alangari, A, Al-Mousa, H, Mobaireek, K, Ben-Mustapha, I, Adimi, P, Feinberg, J, de Suremain, M, Jannière, L, Filipe-Santos, O, Mansouri, N, Stephan, J, Nallusamy, R, Kumararatne, D, Bloorsaz, MR, Ben-Ali, M

“…There are only 9 different mutant alleles of the IL12B gene: 2 small insertions, 3 small deletions, 2 splice site mutations, and 1 large deletion, each causing a frameshift and leading to a premature stop codon, and 1 nonsense mutation. Four of these 9 variants are recurrent, affecting 25 of the 30 reported kindreds, due to founder effects in specific countries. …”

Loss-of-function mutations in RAB18 cause Warburg micro syndrome. by Bem, D, Yoshimura, S, Nunes-Bastos, R, Bond, F, Kurian, M, Rahman, F, Handley, M, Hadzhiev, Y, Masood, I, Straatman-Iwanowska, A, Cullinane, A, McNeill, A, Pasha, S, Kirby, G, Foster, K, Ahmed, Z, Morton, J, Williams, D, Graham, J, Dobyns, W, Burglen, L, Ainsworth, JR, Gissen, P, Müller, F, Maher, E

“…A single family whose members were compound heterozygotes for an anti-termination mutation of the stop codon c.619T &gt; C (p.X207QextX20) and an inframe arginine deletion c.277_279 del (p.Arg93 del) were identified after direct gene sequencing and multiplex ligation-dependent probe amplification (MLPA) of a further 58 families. …”

Dihydrofolate-reductase mutations in Plasmodium knowlesi appear unrelated to selective drug pressure from putative human-to-human transmission in Sabah, Malaysia by Grigg, MJ, Barber, BE, Marfurt, J, Imwong, M, William, T, Bird, E, Piera, KA, Aziz, A, Boonyuen, U, Drakeley, CJ, Cox, J, White, NJ, Cheng, Q, Yeo, TW, Auburn, S, Anstey, NM

“…</p> <p><strong>Results</strong> Fourteen non-synonymous mutations were detected, with the most common being at codon T91P (10.2%) and R34L (10.0%), resulting in 21 different genotypes, including the wild-type, 14 single mutants, and six double mutants. …”

Apoplastic effectors secreted by two unrelated eukaryotic plant pathogens target the tomato defense protease Rcr3. by Song, J, Win, J, Tian, M, Schornack, S, Kaschani, F, Ilyas, M, van der Hoorn, R, Kamoun, S

“…We also found that the rcr3-3 mutant of tomato that carries a premature stop codon in the Rcr3 gene exhibits enhanced susceptibility to P. infestans, suggesting a role for Rcr3(pim) in defense. …”

Culture-adapted Plasmodium falciparum isolates from UK travellers: in vitro drug sensitivity, clonality and drug resistance markers by van Schalkwyk, D, Burrow, R, Henriques, G, Gadalla, N, Beshir, K, Hasford, C, Wright, S, Ding, X, Chiodini, P, Sutherland, C

“…Two lines displayed high chloroquine IC50 estimates, and carried the CVIET haplotype at codons 72–76, whereas the remaining five lines carried the CVMNK haplotype and were sensitive in vitro. …”

APOBEC3G induces a hypermutation gradient: purifying selection at multiple steps during HIV-1 replication results in levels of G-to-A mutations that are high in DNA, intermediate i... by Russell, R, Moore, M, Hu, W, Pathak, V

“…Additionally, genomes containing start codon mutations and early termination codons within gag were isolated from the vRNA. …”

Envisioning the development of a CRISPR-Cas mediated base editing strategy for a patient with a novel pathogenic CRB1 single nucleotide variant by Bellingrath, J-S, McClements, ME, Shanks, M, Clouston, P, Fischer, MD, MacLaren, RE

“…While a base editing strategy for c.2885T>A would encompass a CRISPR-pass mediated “read-through” of the premature stop codon, the resulting missense changes were predicted to be “possibly damaging” in in-silico analysis. …”

Thalassaemia in Sri Lanka: implications for the future health burden of Asian populations. Sri Lanka Thalassaemia Study Group. by de Silva, S, Fisher, C, Premawardhena, A, Lamabadusuriya, S, Peto, T, Perera, G, Old, J, Clegg, J, Olivieri, N, Weatherall, D

“…The third common mutation, codon 26 (G--&gt;A), which produces HbE, interacts with one or other of these mutations to produce HbE/beta thalassaemia; this comprises 13.0-30.9% of cases in the main centres. …”

The Plasmodium falciparum Rh5 invasion protein complex reveals an excess of rare variant mutations by Ndwiga, L, Osoti, V, Ochwedo, KO, Wamae, K, Bejon, P, Rayner, JC, Githinji, G, Ochola-Oyier, LI

“…Collectively, 12 high frequency SNPs (> 5%) were identified: four in Rh5 codon 147, 148, 203 and 429, two in p113 at codons 7 and 267 and six in Ripr codons 190, 259, 524, 985, 1003 and 1039. …”

Site-directed mutagenesis of newcastle disease VIRUS V protein in virus pathogenicity by Tham, May Ling

“…As a result, the stop codon was substituted with other amino acids and the V protein was no longer truncated. …”
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The complete genome sequence of EC1-UPM, a novel N4-like bacteriophage that infects Escherichia coli O78:K80 by Gan, Han Ming, Sieo, Chin Chin, Gee, Shirley Hoon Tang, Omar, Abdul Rahman, Ho, Yin Wan

“…The complete genome sequence of bacteriophage EC1-UPM was analysed and compared with other closely related N4-like phage groups to assess their genetic similarities and differences.Bacteriophage EC1-UPM displays a very similar codon usage profile with its host and does not contain any tRNA gene. …”

Interaction of recombinant Gallus gallus SEPT5 and brain proteins of H5N1-avian influenza virus-infected chickens by Khairat, Jasmine Elanie, Balasubramaniam, Vinod R. M. T., Othman, Iekhsan, Omar, Abdul Rahman, Syed Hassan, Sharifah

“…Results from this study suggest that the codon-optimized SEPT5 gene can be efficiently expressed in the E. coli bacterial system producing authentic SEPT5 protein, thus, enabling multiple host’s proteins to interact with the SEPT5 protein.…”
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Identifying common mutations in colorectal cancer using a 7-gene panel by next generation sequencing by Chai, Boon Lee, Yip, Wai Kien, Mohd Dusa, Noraini, Mohtarrudin, Norhafizah, Seow, Heng Fong

“…Conclusion: Mutations in KRAS codon 12 and 13, BRAF and PIK3CAwhich predict resistance to anti-EGFR therapies and three TP53 mutations were found. …”
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Mutant allele-specific CRISPR disruption in DYT1 dystonia fibroblasts restores cell function by Cruz, Lilian, Bence, György, Cheah, Pike See, Kleinstiver, Benjamin P., Eimer, William A., Garcia, Sara P., Sharma, Nutan, Ozelius, Laurie J., Cristopher, Bragg D., Joung, Keith J., Norberto de Souza, Osmar, Macedo Timmers, Luis Fernando Saraiva, Breakefield, Xandra O.

“…Selective targeting of the DYT1 allele was highly efficient with most common non-homologous end joining (NHEJ) edits, leading to a predicted premature stop codon with loss of the torsinA C terminus (delta 302–332 aa). …”
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