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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. 17-17
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. 76-76
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. 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

10. 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

11. 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

12. 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

13. 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

14. Molecular characterization of α- and β-thalassemia in the Yulin region of Southern China

Author:
He, Sheng; Li, Jihui; Li, Dong Ming; Yi, Shang; Lu, Xiongcai; Luo, Yudi; Liang, Yi; Feng, Chunfeng; Chen, Biyan; Zheng, Chenguang; Qiu, Xiaoxia
Source:
Gene 2018 v.655 pp. 61-64
ISSN:
0378-1119
Subject:
mutation,   etc   ; genetic analysis; genotype; thalassemia; China;     Show all 5 Subjects
Abstract:
... Thalassemia is one of the most common hereditary blood disorders. Epidemiological data regarding the prevalence and distribution of mutations is important for planning a thalassemia control program. To reveal the prevalence of thalassemia and mutation spectrum in the Yulin region of southern China, we screened 130,318 individuals from Yulin region by hematological and genetic analysis. Totally, 24 ...
DOI:
10.1016/j.gene.2018.02.058

15. The Cancer Mutation D83V Induces an α-Helix to β-Strand Conformation Switch in MEF2B

Author:
Lei, Xiao; Kou, Yi; Fu, Yang; Rajashekar, Niroop; Shi, Haoran; Wu, Fang; Xu, Jiang; Luo, Yibing; Chen, Lin
Source:
Journal of molecular biology 2018 v.430 pp. 1157-1172
ISSN:
0022-2836
Subject:
somatic mutation,   etc   ; neoplasm cells; non-Hodgkin lymphoma;     Show all 3 Subjects
Abstract:
... MEF2B is a major target of somatic mutations in non-Hodgkin lymphoma. Most of these mutations are non-synonymous substitutions of surface residues in the MADS-box/MEF2 domain. Among them, D83V is the most frequent mutation found in tumor cells. The link between this hotspot mutation and cancer is not well understood. Here we show that the D83V mutation induces a dramatic α-helix to β-strand switch ...
DOI:
10.1016/j.jmb.2018.02.012

16. A new twist in the coil: functions of the coiled-coil domain of structural maintenance of chromosome (SMC) proteins

Author:
Matityahu, Avi; Onn, Itay
Source:
Current genetics 2018 v.64 no.1 pp. 109-116
ISSN:
0172-8083
Subject:
mutation,   etc   ; adenosinetriphosphatase; chromosomes; genome; humans; proteins;     Show all 6 Subjects
Abstract:
... The higher-order organization of chromosomes ensures their stability and functionality. However, the molecular mechanism by which higher order structure is established is poorly understood. Dissecting the activity of the relevant proteins provides information essential for achieving a comprehensive understanding of chromosome structure. Proteins of the structural maintenance of chromosome (SMC) fa ...
DOI:
10.1007/s00294-017-0735-2

17. Best available science still supports an ancient common origin of Devils Hole and Devils Hole pupfish

Author:
Sağlam, İsmail K.; Baumsteiger, Jason; Smith, Matt J.; Linares‐Casenave, Javier; Nichols, Andrew L.; O'Rourke, Sean M.; Miller, Michael R.
Source:
Molecular ecology 2018 v.27 no.4 pp. 839-842
ISSN:
0962-1083
Subject:
mutation,   etc   ; Cyprinodon diabolis; data collection; genomics; models;     Show all 5 Subjects
Abstract:
... The age of DHP and how pupfish colonized Devils Hole have always been a topic of interest. Recently, two different publications (Martin, Crawford, Turner, & Simons, & Sağlam et al.,) tackled this issue using genomic data sets and demographic models but came to widely different conclusions. In their comment, Martin and Höhne () argue that our results (Sağlam et al.,) were misleading because we used ...
DOI:
10.1111/mec.14502

18. Engineering the Delivery System for CRISPR-Based Genome Editing

Author:
Glass, Zachary; Lee, Matthew; Li, Yamin; Xu, Qiaobing
Source:
Trends in biotechnology 2018 v.36 pp. 173-185
ISSN:
0167-7799
Subject:
mutation,   etc   ; bioengineering; gene editing; gene targeting; therapeutics;     Show all 5 Subjects
Abstract:
... Clustered regularly interspaced short palindromic repeat-CRISPR-associated protein (CRISPR-Cas) systems, found in nature as microbial adaptive immune systems, have been repurposed into an important tool in biological engineering and genome editing, providing a programmable platform for precision gene targeting. These tools have immense promise as therapeutics that could potentially correct disease ...
DOI:
10.1016/j.tibtech.2017.11.006

19. Characterizing interaction forces between actin and proteins of the tropomodulin family reveals the presence of the N-terminal actin-binding site in leiomodin

Author:
Arslan, Baran; Colpan, Mert; Gray, Kevin T.; Abu-Lail, Nehal I.; Kostyukova, Alla S.
Source:
Archives of biochemistry and biophysics 2018 v.638 pp. 18-26
ISSN:
0003-9861
Subject:
mutation,   etc   ; actin; atomic force microscopy; polymerization;     Show all 4 Subjects
Abstract:
... Tropomodulin family of proteins includes several isoforms of tropomodulins (Tmod) and leiomodins (Lmod). These proteins can sequester actin monomers or nucleate actin polymerization. Although it is known that their actin-binding properties are isoform-dependent, knowledge on how they vary in strengths of interactions with G-actin is missing. While it is confirmed in many studies that Tmods have tw ...
DOI:
10.1016/j.abb.2017.12.005

20. The trouble with collective nouns for genome editing

Author:
Wells, Sara; Joly, Jean Stéphane
Source:
Mammalian genome 2017 v.28 no.7-8 pp. 365-366
ISSN:
0938-8990
Subject:
mutation,   etc   ; gene editing; scientists;     Show all 3 Subjects
Abstract:
... We should start as we mean to go on and try to avoid the confusion most of us experience when bombarded with acronyms with overstated significations. You will be familiar with the situation, you are in a seminar or a meeting and someone who has been using a set of acronyms for years, includes them in sentence after sentence that has you lost because you don’t know what some or most of them stand f ...
DOI:
10.1007/s00335-017-9707-6