Charged Amino Acids Contribute to ZorO Toxicity by Bikash Bogati, Selene F. H. Shore, Thomas D. Nipper, Oana Stoiculescu, Elizabeth M. Fozo

“…Though these charged residues are hypothesized to be critical for the toxic effects of the protein, they have not been studied broadly across different type I toxins. Herein, we mutated codons encoding charged residues in the type I toxin <i>zorO</i>, from the <i>zor-orz</i> toxin-antitoxin system, to determine their impacts on growth inhibition, membrane depolarization, ATP depletion, and the localization of this small protein. …”
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APOBEC3G mRNA expression in exposed seronegative and early stage HIV infected individuals decreases with removal of exposure and with disease progression by Reyes-Terán Gustavo, Torres Klintsy J, Hernández-Juan Ramón, Ormsby Christopher E, Vázquez-Pérez Joel A

“…Out of 8 LVLs, 3 had hypermutations, and 4 had premature stop codons only in viral <it>vif</it>.</p> <p>Conclusion</p> <p>The results suggest that exposure to HIV may trigger APOBEC3G expression in PBMCs, in the absence of infection. …”
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Cancer cells possess different isotopic enrichment: Isotopic induced functionalizations of normal DNA mutations leading to cancer by Reginald B. Little, Maiya Snowton, Orit Uziel

“…This replacement may subsequently modulate DNA and telomere codons resulting in transformation of normal cells to cancer cells (in 15 N depletion in telomeres dependent manner). …”
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Antiretroviral resistance and genetic diversity of human immunodeficiency virus type 1 isolates from the Federal District, Central Brazil by Daniela M Cerqueira, Regina MS Amorim, Ruiter R Silva, Geni NL Camara, Marcelo M Brígido, Cláudia RF Martins

“…The entire viral protease and codons 19 to 234 of the reverse transcriptase gene from 45 HIV-1 isolates were amplified and sequenced for subtyping and genotyping. …”
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Somatic <it>VHL </it>gene alterations in MEN2-associated medullary thyroid carcinoma by Pacak Karel, Zhuang Zhengping, Libutti Steven K, Tannapfel Andrea, Vortmeyer Alexander O, Brouwers Frederieke M, Koch Christian A, Neumann Hartmut PH, Paschke Ralf

“…</p> <p>Methods</p> <p>We analyzed 6 MTCs and 1 C-cell hyperplasia (CCH) specimen from 7 patients with MEN2A and <it>RET </it>germline mutations in codons 609, 618, 620, or 634, using microdissection, microsatellite analysis, phosphorimage densitometry, and <it>VHL </it>mutation analysis.…”
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Identification of a Novel C-Terminal Truncated WT1 Isoform with Antagonistic Effects against Major WT1 Isoforms. by Naoya Tatsumi, Nozomi Hojo, Hiroyuki Sakamoto, Rena Inaba, Nahoko Moriguchi, Keiko Matsuno, Mari Fukuda, Akihide Matsumura, Seiji Hayashi, Soyoko Morimoto, Jun Nakata, Fumihiro Fujiki, Sumiyuki Nishida, Hiroko Nakajima, Akihiro Tsuboi, Yoshihiro Oka, Naoki Hosen, Haruo Sugiyama, Yusuke Oji

“…The insertion of exon 4a resulted in the introduction of premature translational stop codons in the reading frame in exon 4a and production of C-terminal truncated WT1 proteins lacking zinc finger DNA-binding domain. …”
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Distinctive mitochondrial genome of Calanoid copepod <it>Calanus sinicus </it>with multiple large non-coding regions and reshuffled gene order: Useful molecular markers for phyloge... by Chaolun Li, Song Sun, Minxiao Wang, Xin Shen

“…Further particularities in the mitogenome of <it>C. sinicus </it>include low A + T-content, symmetrical nucleotide composition between strands, abbreviated stop codons for several PCGs and extended lengths of the genes <it>atp6 </it>and <it>atp8 </it>relative to other copepods. …”
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Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca by Zhao, Dehua, Voigt, Christopher A., Temme, Karsten

“…First, all noncoding DNA, regulatory proteins, and nonessential genes are removed. The codons of essential genes are changed to create a DNA sequence as divergent as possible from the wild-type (WT) gene. …”
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Characterization of hepatitis C virus resistance to grazoprevir reveals complex patterns of mutations following on-treatment breakthrough that are not observed at relapse by Bonsall, D, Black, S, Howe, A, Chase, R, Ingravallo, P, Pak, I, Brown, A, Smith, D, Bowden, R, Barnes, E

“…Significant viral sequence divergence (up to 5.9% codons) was observed across whole genomes in association with the acquisition and reversion of RASs. …”

Nonlinear mixed-effects modelling of in vitro drug susceptibility and molecular correlates of multidrug resistant Plasmodium falciparum by Simpson, J, Jamsen, K, Anderson, T, Zaloumis, S, Nair, S, Woodrow, C, White, N, Nosten, F, Price, R

“…In contrast pfmdr1 mutation at codons 86 or 1042 were associated with an increase in chloroquine EC50 (44–48%). …”

Multi-center evaluation of the fully automated PCR-based Idylla™ KRAS mutation assay for rapid KRAS mutation status determination on formalin-fixed paraffin-embedded tissue of huma... by Solassol, J, Vendrell, J, Märkl, B, Haas, C, Bellosillo, B, Montagut, C, Smith, M, O'Sullivan, B, D'Haene, N, Le Mercier, M, Grauslund, M, Melchior, L, Burt, E, Cotter, F, Stieber, D, Schmitt, F, Schmitt, F, Motta, V, Lauricella, C, Colling, R, Soilleux, E, Fassan, M, Mescoli, C, Collin, C, Pagès, J, Sillekens, P

“…This test enables qualitative detection of 21 mutations in codons 12, 13, 59, 61, 117, and 146 of the <em>KRAS</em> oncogene being clinically relevant according to the latest clinical guidelines. …”

Temporal trends in prevalence of Plasmodium falciparum drug resistance alleles over two decades of changing antimalarial policy in coastal Kenya. by Okombo, J, Kamau, A, Marsh, K, Sutherland, C, Ochola-Oyier, L

“…To assess temporal trends of established genotypes associated with tolerance to clinically important antimalarials used in Kenya over the last two decades, we sequenced a region of the pfcrt locus encompassing codons 72-76 of the Plasmodium falciparum chloroquine resistance transporter, full-length pfmdr1 - encoding multi-drug resistance protein, P-glycoprotein homolog (Pgh1) and pfdhfr encoding dihydrofolate reductase, in 485 archived Plasmodium falciparum positive blood samples collected in coastal Kenya at four different time points between 1995 and 2013. …”

Biological, immunological and functional properties of two novel multi-variant chimeric recombinant proteins of CSP antigens for vaccine development against Plasmodium vivax infect... by Shabani, S, Zakeri, S, Salmanian, A, Amani, J, Mehrizi, A, Snounou, G, Nosten, F, Andolina, C, Mourtazavi, Y, Djadid, N

“…DNA encoding the selected chimeras (named CS127 and CS712) were synthetically constructed based on E. coli codons, then cloned and expressed. Mouse monoclonal antibodies (mAbs; anti-Pv-210-CDC and -Pv-247-CDC), recognized the chimeric antigens in ELISA, indicating correct conformation and accessibility of the B-cell epitopes. …”

HLA-associated polymorphisms in the HIV-2 capsid highlight key differences between HIV-1 and HIV-2 immune adaptation by de Silva, T, Leligdowicz, A, Carlson, J, Garcia-Knight, M, Onyango, C, Miller, N, Yindom, L, Hué, S, Jaye, A, Dong, T, Cotten, M, Rowland-Jones, S

“…</p><p><b>Results:</b> We identified greater purifying selection and less sites under positive selective pressure in HIV-2 compared to HIV-1. Five HIV-2 codons with <i>HLA</i>-associated polymorphisms were detected all within or around known or predicted CTL epitopes. …”

Interactions between residues in staphylococcal alpha-hemolysin revealed by reversion mutagenesis. by Panchal, R, Bayley, H

“…The analysis of 22 revertants revealed new codons clustered predominantly in three distinct regions of the H35N gene. …”

Performance of two commercially available sequence-based HIV-1 genotyping systems for the detection of drug resistance against HIV type 1 group M subtypes. by Beddows, S, Galpin, S, Kazmi, S, Ashraf, A, Johargy, A, Frater, A, White, N, Braganza, R, Clarke, J, McClure, M, Weber, J

“…Discrepancies were found between the consensus sequences reported by each system for each sample (mean difference 1.0%; range 0.0-3.2%), but these appeared to be random and did not affect interpretation of the major resistance codons. In addition, both systems were able to amplify template RNA from low copy viral load plasma samples (10(2)-10(3) RNA copies/ml) taken from a random selection of patient samples encompassing subtypes A-C. …”

Single-Frame, Multiple-Frame and Framing Motifs in Genes by Christian J. Michel

“…The constraints studied are: initiation and stop codons, periodic codons <inline-formula> <math display="inline"> <semantics> <mrow> <mrow> <mo>{</mo> <mrow> <mi>A</mi> <mi>A</mi> <mi>A</mi> <mo>,</mo> <mi>C</mi> <mi>C</mi> <mi>C</mi> <mo>,</mo> <mi>G</mi> <mi>G</mi> <mi>G</mi> <mo>,</mo> <mi>T</mi> <mi>T</mi> <mi>T</mi> </mrow> <mo>}</mo> </mrow> </mrow> </semantics> </math> </inline-formula>, antiparallel complementarity and parallel complementarity. …”
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(Phospho)proteomic Profiling of Microsatellite Unstable CRC Cells Reveals Alterations in Nuclear Signaling and Cholesterol Metabolism Caused by Frameshift Mutation of NMD Regulator... by Malwina Michalak, Eva-Maria Katzenmaier, Nina Roeckel, Stefan M. Woerner, Vera Fuchs, Uwe Warnken, Yan P. Yuan, Peer Bork, Gabriele Neu-Yilik, Andreas Kulozik, Magnus von Knebel Doeberitz, Matthias Kloor, Jürgen Kopitz, Johannes Gebert

“…When coding mononucleotide repeats (cMNRs) are affected, tumors accumulate frameshift mutations and premature termination codons (PTC) potentially leading to truncated proteins. …”
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Truncated FRMD7 proteins in congenital Nystagmus: novel frameshift mutations and proteasomal pathway implications by Yuqing Su, Juntao Zhang, Jiahui Gao, Guoqing Ding, Heng Jiang, Yang Liu, Yulei Li, Guohua Yang

“…A predominant occurrence of shift code mutations was observed in exons 11 and 12, possibly associated with the localization of premature termination codons (PTCs), leading to the generation of deleterious truncated proteins. …”
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Detection Analysis and Study of Genomic Region Variability of JCPyV, BKPyV, MCPyV, HPyV6, HPyV7 and QPyV in the Urine and Plasma of HIV-1-Infected Patients by Sara Passerini, Carla Prezioso, Annalisa Prota, Giulia Babini, Luigi Coppola, Alessandra Lodi, Anna Chiara Epifani, Loredana Sarmati, Massimo Andreoni, Ugo Moens, Valeria Pietropaolo, Marco Ciotti

“…LT did not show mutations causing stop codons, and LT transcripts were expressed in MCPyV positive samples. …”
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