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1. Detecting Rare Mutations and DNA Damage with Sequencing-Based Methods

Author:
Sloan, Daniel B.; Broz, Amanda K.; Sharbrough, Joel; Wu, Zhiqiang
Source:
Trends in biotechnology 2018 v.36 pp. 729-740
ISSN:
0167-7799
Subject:
mutation,   etc   ; DNA damage; tissues;     Show all 3 Subjects
Abstract:
... There is a great need in biomedical and genetic research to detect DNA damage and de novo mutations, but doing so is inherently challenging because of the rarity of these events. The enormous capacity of current DNA sequencing technologies has opened the door for quantifying sequence variants present at low frequencies in vivo, such as within cancerous tissues. However, these sequencing technologi ...
DOI:
10.1016/j.tibtech.2018.02.009

2. Phosphorylation alters Bim‐mediated Mcl‐1 stabilization and priming

Author:
Conage‐Pough, Jason E.; Boise, Lawrence H.
Source:
TheFEBS journal 2018 v.285 no.14 pp. 2626-2640
ISSN:
1742-464X
Subject:
mutation,   etc   ; apoptosis; phosphorylation; proteins;     Show all 4 Subjects
Abstract:
... Mcl‐1 is a highly labile protein, subject to extensive post‐translational regulation. This distinguishes Mcl‐1 from other antiapoptotic proteins and necessitates further study to better understand how interactions with proapoptotic Bcl‐2 proteins affect its regulation. One such protein, Bim, is known to stabilize Mcl‐1, and Bim phosphorylation has been associated with increased Mcl‐1 binding. Cons ...
DOI:
10.1111/febs.14505

3. Interactions between BTB domain of CP190 and two adjacent regions in Su(Hw) are required for the insulator complex formation

Author:
Melnikova, Larisa; Kostyuchenko, Margarita; Molodina, Varvara; Parshikov, Alexander; Georgiev, Pavel; Golovnin, Anton
Source:
Chromosoma 2018 v.127 no.1 pp. 59-71
ISSN:
0009-5915
Subject:
mutation,   etc   ; Drosophila; chromatin; genomics;     Show all 4 Subjects
Abstract:
... The best-studied Drosophila insulator complex consists of two BTB-containing proteins, the Mod(mdg4)-67.2 isoform and CP190, which are recruited cooperatively to chromatin through interactions with the DNA-binding architectural protein Su(Hw). While Mod(mdg4)-67.2 interacts only with Su(Hw), CP190 interacts with many other architectural proteins. In spite of the fact that CP190 is critical for the ...
DOI:
10.1007/s00412-017-0645-6

4. Solving Mendelian Mysteries: The Non-coding Genome May Hold the Key

Author:
Valente, Enza Maria; Bhatia, Kailash P.
Source:
Cell 2018 v.172 pp. 889-891
ISSN:
0092-8674
Subject:
mutation,   etc   ; genes; genomics; transcriptomics;     Show all 4 Subjects
Abstract:
... Despite revolutionary advances in sequencing approaches, many mendelian disorders have remained unexplained. In this issue of Cell, Aneichyk et al. combine genomic and cell-type-specific transcriptomic data to causally link a non-coding mutation in the ubiquitous TAF1 gene to X-linked dystonia-parkinsonism. ...
DOI:
10.1016/j.cell.2018.02.022

5. Correction to: A statistical framework for analyzing deep mutational scanning data

Author:
Rubin, Alan F.; Gelman, Hannah; Lucas, Nathan; Bajjalieh, Sandra M.; Papenfuss, Anthony T.; Speed, Terence P.; Fowler, Douglas M.
Source:
Genome biology 2018 v.19 no.1 pp. 17
ISSN:
1474-760X
Subject:
mutation,   etc   ; human genetics; models; variance;     Show all 4 Subjects
Abstract:
... CORRECTION: After publication of our article [1] it was brought to our attention that a line of code was missing from our program to combine the within-replicate variance and between-replicate variance. This led to an overestimation of the standard errors calculated using the Enrich2 random-effects model. ...
DOI:
10.1186/s13059-018-1391-7

6. Corneal Dystrophy Mutations Drive Pathogenesis by Targeting TGFBIp Stability and Solubility in a Latent Amyloid-forming Domain

Author:
Stenvang, Marcel; Schafer, Nicholas P.; Malmos, Kirsten Gade; Pérez, Adriana-Michelle Wolf; Niembro, Olatz; Sormanni, Pietro; Basaiawmoit, Rajiv Vaid; Christiansen, Gunna; Andreasen, Maria; Otzen, Daniel E.
Source:
Journal of molecular biology 2018 v.430 pp. 1116-1140
ISSN:
0022-2836
Subject:
mutation,   etc   ; bioinformatics; cornea; pathogenesis; solubility;     Show all 5 Subjects
Abstract:
... Numerous mutations in the corneal protein TGFBIp lead to opaque extracellular deposits and corneal dystrophies (CDs). Here we elucidate the molecular origins underlying TGFBIp's mutation-induced increase in aggregation propensity through comprehensive biophysical and bioinformatic analyses of mutations associated with every major subtype of TGFBIp-linked CDs including lattice corneal dystrophy (LC ...
DOI:
10.1016/j.jmb.2018.03.001

7. Correction to: Inheritance of the narrow leaf mutation in traditional Japanese evergreen azaleas

Author:
Tasaki, Keisuke; Nakatsuka, Akira; Cheon, Kyeong-Seong; Kobayashi, Nobuo
Source:
Euphytica 2018 v.214 no.4 pp. 76
ISSN:
0014-2336
Subject:
mutation,   etc   ; Rhododendron; leaves; plant breeding;     Show all 4 Subjects
Abstract:
... This article has been published with an erroneous version of Table 2. Please find the correct Table 2 in this document. ...
DOI:
10.1007/s10681-018-2130-6

8. Cooperative Interactions of Three Hotspot Heparin Binding Residues Are Critical for Allosteric Activation of Antithrombin by Heparin

Author:
Richard, Benjamin; Swanson, Richard; Izaguirre, Gonzalo; Olson, Steven T.
Source:
Biochemistry 2018 v.57 no.15 pp. 2211-2226
ISSN:
1520-4995
Subject:
mutation,   etc   ; anticoagulants; energy; heparin; sulfates;     Show all 5 Subjects
Abstract:
... Heparin allosterically activates the anticoagulant serpin, antithrombin, by binding through a sequence-specific pentasaccharide and inducing activating conformational changes in the protein. Three basic residues of antithrombin, Lys114, Lys125, and Arg129, have been shown to be hotspots for binding the pentasaccharide, but the molecular basis for such hotspot binding has been unclear. To determine ...
DOI:
10.1021/acs.biochem.8b00216

9. Rapid, real-time chemiluminescent detection of DNA mutation based on digital microfluidics and pyrosequencing

Author:
Zou, Fenxiang; Ruan, Qingyu; Lin, Xiaoye; Zhang, Mingxia; Song, Yanling; Zhou, Leiji; Zhu, Zhi; Lin, Shuichao; Wang, Wei; Yang, Chaoyong James
Source:
Biosensors & bioelectronics 2019 v.126 pp. 551-557
ISSN:
0956-5663
Subject:
mutation,   etc   ; DNA; automation; bioluminescence; biosensors; genes; genetic testing; microfluidic technology; mutants; sequence analysis; sex determination analysis;     Show all 11 Subjects
Abstract:
... To explore genome mutation meaningfully, it is in urgent need to develop an automated and inexpensive platform for DNA mutation analysis. Digital microfluidics is a powerful platform for a broad range of applications due to the advantages of high automatization and low reagent consumption. Pyrosequencing enables DNA sequencing based on non-electrophoresis bioluminescence, which is suitable for rap ...
DOI:
10.1016/j.bios.2018.09.092

10. Tebuconazole induces triazole-resistance in Aspergillus fumigatus in liquid medium and soil

Author:
Cui, Ning; He, Yiwen; Yao, Shijie; Zhang, Hongchao; Ren, Jingbei; Fang, Hua; Yu, Yunlong
Source:
The Science of the total environment 2019 v.648 pp. 1237-1243
ISSN:
0048-9697
Subject:
mutation,   etc   ; Aspergillus fumigatus; agricultural soils; aspergillosis; genes; liquids; morbidity; mortality; patients; plant protection; tebuconazole; triazoles;     Show all 12 Subjects
Abstract:
... Aspergillus fumigatus is the mainly leading cause of invasive aspergillosis associated with significant morbidity and mortality in immunocompromised patients. However, triazole resistance in A. fumigatus has increased dramatically throughout the world nowadays. The emergence of triazole resistance has aroused growing concern. This research was conducted to assess if the resistance in A. fumigatus ...
DOI:
10.1016/j.scitotenv.2018.08.247

11. Multiplex navigation of global regulatory networks (MINR) in yeast for improved ethanol tolerance and production

Author:
Liu, Rongming; Liang, Liya; Choudhury, Alaksh; Garst, Andrew D.; Eckert, Carrie A.; Oh, Eun Joong; Winkler, James; Gill, Ryan T.
Source:
Metabolic engineering 2019 v.51 pp. 50-58
ISSN:
1096-7176
Subject:
mutation,   etc   ; diploidy; ethanol; gene expression; glucose tolerance; mutants; phenotype; regulator genes; synthetic biology; yeasts;     Show all 10 Subjects
Abstract:
... Multiplex navigation of global regulatory networks (MINR) is an approach for combinatorially reprogramming gene expression to manipulate complex phenotypes. We designed, constructed, and mapped MINR libraries containing 43,020 specific mutations in 25 regulatory genes expected to perturb the yeast regulatory network. We selected growth competition experiments for library mutants conferring increas ...
DOI:
10.1016/j.ymben.2018.07.007

12. Analysis of phage resistance in Staphylococcus aureus SA003 reveals different binding mechanisms for the closely related Twort-like phages ɸSA012 and ɸSA039

Author:
Azam, Aa Haeruman; Hoshiga, Fumiya; Takeuchi, Ippei; Miyanaga, Kazuhiko; Tanji, Yasunori
Source:
Applied microbiology and biotechnology 2018 v.102 no.20 pp. 8963-8977
ISSN:
0175-7598
Subject:
missense mutation; nonsense mutation; point mutation,   etc   ; DNA; Staphylococcus aureus; adsorption; alleles; bacteriophages; coevolution; phenotypic plasticity; proteins; tail; teichoic acids;     Show all 13 Subjects
Abstract:
... We have previously generated strains of Staphylococcus aureus SA003 resistant to its specific phage ɸSA012 through a long-term coevolution experiment. However, the DNA mutations responsible for the phenotypic change of phage resistance are unknown. Whole-genome analysis revealed eight genes that acquired mutations: six point mutations (five missense mutations and one nonsense mutation) and two del ...
DOI:
10.1007/s00253-018-9269-x

13. Investigation of the hydraulic properties of deep fractured rocks around underground excavations using high-pressure injection tests

Author:
Huang, Zhen; Li, Xiaozhao; Li, Shijie; Zhao, Kui; Zhang, Rui
Source:
Engineering geology 2018 v.245 pp. 180-191
ISSN:
0013-7952
Subject:
mutation,   etc   ; dewatering; engineering; groundwater; models; permeability; rocks;     Show all 7 Subjects
Abstract:
... Groundwater inrush during excavation is one of the greatest challenges in modern underground engineering. The characteristics of groundwater inrush induced by high-pressure water in fractured rocks are poorly understood, and the risk assessment of water inrush hazard associated with deep geological conditions remains to be improved. Here, we present an in situ high-pressure fluid injection experim ...
DOI:
10.1016/j.enggeo.2018.07.020

14. Frequent ploidy changes in growing yeast cultures

Author:
Harari, Yaniv; Ram, Yoav; Kupiec, Martin
Source:
Current genetics 2018 v.64 no.5 pp. 1001-1004
ISSN:
0172-8083
Subject:
mutation,   etc   ; chromosomes; endopolyploidy; genomics; neoplasms; yeasts;     Show all 6 Subjects
Abstract:
... Ploidy is considered a very stable cellular characteristic. Although rare, changes in ploidy play important roles in the acquisition of long-term adaptations. Since these duplications allow the subsequent loss of individual chromosomes and accumulation of mutations, changes in ploidy can also cause genomic instability, and have been found to promote cancer. Despite the importance of the subject, m ...
DOI:
10.1007/s00294-018-0823-y

15. Genome editing of pufferfish saxitoxin- and tetrodotoxin-binding protein type 2 in Takifugu rubripes

Author:
Kato-Unoki, Yoko; Takai, Yuki; Kinoshita, Masato; Mochizuki, Toshitaka; Tatsuno, Ryohei; Shimasaki, Yohei; Oshima, Yuji
Source:
Toxicon 2018 v.153 pp. 58-61
ISSN:
0041-0101
Subject:
frameshift mutation,   etc   ; RNA; Takifugu rubripes; gene editing;     Show all 4 Subjects
Abstract:
... The pufferfish saxitoxin- and tetrodotoxin-binding protein 2 (PSTBP2), which is involved in toxin accumulation, was knocked out in Takifugu rubripes embryos by using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 genome-editing technology. Treating the embryos with one of two single-guide RNA (sgRNA) resulted in mutation rates of 57.1% and 62.5%, res ...
DOI:
10.1016/j.toxicon.2018.08.001

16. Investigating the role of loop 131–140 in activity and thermal stability of chondroitinase ABC I

Author:
Kheirollahi, Asma; Khajeh, Khosro; Golestani, Abolfazl
Source:
International journal of biological macromolecules 2018 v.116 pp. 811-816
ISSN:
0141-8130
Subject:
mutation,   etc   ; catalytic activity; mutants; proline; thermal stability;     Show all 5 Subjects
Abstract:
... Previously, we attempted to improve the thermostability of chondroitinase ABC I by substituting proline in flexible sites and successfully obtained a mutant; E138P, with increased thermostability (Kheirollahi et al., 2017). In this study, we focused on the role of Glu138 in activity and stability of the enzyme using its further mutation to Ala, Lys, and Asp. Moreover, we coupled the two mutations ...
DOI:
10.1016/j.ijbiomac.2018.05.094

17. Aligner-mediated cleavage-triggered exponential amplification for sensitive detection of nucleic acids

Author:
Wu, Wanghua; Fan, Hongliang; Lian, Xiang; Zhou, Jianguang; Zhang, Tao
Source:
Talanta 2018 v.185 pp. 141-145
ISSN:
0039-9140
Subject:
mutation,   etc   ; DNA; blood serum; detection limit; humans;     Show all 5 Subjects
Abstract:
... Exponential amplification reaction (EXPAR), as a simple and high sensitive method, holds great promise in nucleic acids detection. One major challenge in EXPAR is the generation of trigger DNA with a definite 3′-end, which now relies on fingerprinting technology. However, the requirement of different endonucleases for varying target sequences and two head-to-head recognition sites in double strand ...
DOI:
10.1016/j.talanta.2018.03.067

18. Correction to: Identification of novel mutations in FFPE lung adenocarcinomas using DEPArray sorting technology and next-generation sequencing

Author:
Lee, Ji Won; Shin, Jong-Yeon; Seo, Jeong-Sun
Source:
Journal of applied genetics 2018 v.59 no.3 pp. 279-280
ISSN:
1234-1983
Subject:
mutation,   etc   ; adenocarcinoma; high-throughput nucleotide sequencing; lungs;     Show all 4 Subjects
Abstract:
... In the original article, part of Table 1 headings and entries were missing. The correct Table is as shown below. The original article has been corrected. ...
DOI:
10.1007/s13353-018-0442-9

19. The LRRK2 signalling system

Author:
Price, Alice; Manzoni, Claudia; Cookson, Mark R.; Lewis, Patrick A.
Source:
Cell and tissue research 2018 v.373 no.1 pp. 39-50
ISSN:
0302-766X
Subject:
mutation,   etc   ; Parkinson disease; genes; risk; signal transduction;     Show all 5 Subjects
Abstract:
... The LRRK2 gene is a major contributor to genetic risk for Parkinson’s disease and understanding the biology of the leucine-rich repeat kinase 2 (LRRK2, the protein product of this gene) is an important goal in Parkinson’s research. LRRK2 is a multi-domain, multi-activity enzyme and has been implicated in a wide range of signalling events within the cell. Because of the complexities of the signal t ...
DOI:
10.1007/s00441-017-2759-9

20. Redefining Molecular Amphipathicity in Reversing the “Coffee-Ring Effect”: Implications for Single Base Mutation Detection

Author:
Huang, Chi; Wang, Jie; Lv, Xiaobo; Liu, Liu; Liang, Ling; Hu, Wei; Luo, Changliang; Wang, Fubing; Yuan, Quan
Source:
Langmuir 2018 v.34 no.23 pp. 6777-6783
ISSN:
1520-5827
Subject:
mutation,   etc   ; DNA; drying; hydrophilicity; hydrophobicity; surface tension;     Show all 6 Subjects
Abstract:
... The “coffee ring effect” is a natural phenomenon wherein sessile drops leave ring-shaped structures on the solid surfaces upon drying. It drives a nonuniform deposition of suspended compounds on the substrates, which adversely affects many processes, including surface-assisted biosensing and molecular self-assembly. In this study, we describe how the coffee ring effect can be eliminated by control ...
DOI:
10.1021/acs.langmuir.8b01248