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1. Fragile DNA contributes to repeated evolution

Author:
Kratochwil, Claudius F.; Meyer, Axel
Source:
Genome biology 2019 v.20 no.1 pp. 39
ISSN:
1474-760X
Subject:
mutation,   etc   ; DNA; evolution; genomics;     Show all 4 Subjects
Abstract:
... Sequence features that affect DNA fragility might facilitate fast, repeated evolution by elevating mutation rates at genomic hotspots. ...
DOI:
10.1186/s13059-019-1655-x

2. Correction to: Splicing mutations in human genetic disorders: examples, detection, and confirmation

Author:
Abramowicz, Anna; Gos, Monika
Source:
Journal of applied genetics 2019 v.60 no.2 pp. 231
ISSN:
1234-1983
Subject:
mutation,   etc   ; genetic disorders; humans;     Show all 3 Subjects
Abstract:
... The original version on this paper contained an error. The first names and last names of Anna Abramowicz and Monika Gos are inadvertently interchanged and are incorrectly displayed in indexing sites. The correct names are presented above. ...
DOI:
10.1007/s13353-019-00493-z

3. Evolving Inversions

Author:
Faria, Rui; Johannesson, Kerstin; Butlin, Roger K.; Westram, Anja M.
Source:
Trends in ecology & evolution 2019 v.34 no.3 pp. 239-248
ISSN:
0169-5347
Subject:
mutation,   etc   ; genes; models;     Show all 3 Subjects
Abstract:
... Empirical data suggest that inversions in many species contain genes important for intraspecific divergence and speciation, yet mechanisms of evolution remain unclear. While genes inside an inversion are tightly linked, inversions are not static but evolve separately from the rest of the genome by new mutations, recombination within arrangements, and gene flux between arrangements. Inversion polym ...
DOI:
10.1016/j.tree.2018.12.005

4. Human Antibody Bispecifics through Phage Display Selection

Author:
Luthra, Ansha; Langley, David B.; Schofield, Peter; Jackson, Jennifer; Abdelatti, Mahmoud; Rouet, Romain; Nevoltris, Damien; Mazigi, Ohan; Crossett, Ben; Christie, Mary; Christ, Daniel
Source:
Biochemistry 2019 v.58 no.13 pp. 1701-1704
ISSN:
1520-4995
Subject:
mutation,   etc   ; antibodies; humans; peptide libraries;     Show all 4 Subjects
Abstract:
... We developed a repertoire approach to generate human antibody bispecifics. Using phage display selection of antibody heavy chains in the presence of a competitor light chain and providing a cognate light chain with an affinity handle, we identified mutations that prevent heavy/light chain mispairing. The strategy allows for the selection of human antibody chains that autonomously assemble into bis ...
DOI:
10.1021/acs.biochem.9b00037

5. Emergent structure in a stochastic model of ecological evolution

Author:
Roach, Ty N.F.; Nulton, James; Sibani, Paolo; Rohwer, Forest; Salamon, Peter
Source:
Ecological modelling 2019 v.401 pp. 129-133
ISSN:
0304-3800
Subject:
mutation,   etc   ; ecology; entropy; mathematical models; stochastic processes;     Show all 5 Subjects
Abstract:
... Nonequilibrium thermodynamic theory has much to offer in explaining ecological and evolutionary processes. Formalizing biological processes in terms of thermodynamic parameters reveals that the generation of natural organization and complexity is an emergent property of entropy in systems maintained far from equilibrium. Understanding the interplay between thermodynamics, ecology and evolution pro ...
DOI:
10.1016/j.ecolmodel.2019.03.004

6. Interactions in the ESCRT-III network of the yeast Saccharomyces cerevisiae

Author:
Brune, Thomas; Kunze-Schumacher, Heike; Kölling, Ralf
Source:
Current genetics 2019 v.65 no.2 pp. 607-619
ISSN:
0172-8083
Subject:
mutation,   etc   ; Saccharomyces cerevisiae; phenotype; prediction; proteins; yeasts;     Show all 6 Subjects
Abstract:
... Here, we examine the genetic interactions between ESCRT-III mutations in the yeast Saccharomyces cerevisiae. From the obtained interaction network, we make predictions about alternative ESCRT-III complexes. By the successful generation of an octuple deletion strain using the CRISPR/Cas9 technique, we demonstrate for the first time that ESCRT-III activity as a whole is not essential for the life of ...
DOI:
10.1007/s00294-018-0915-8

7. π-π stacking interaction is a key factor for the stability of GH11 xylanases at low pH

Author:
Ge, Hui-Hua; Qiu, Yue; Yi, Zhi-Wei; Zeng, Run-Ying; Zhang, Guang-Ya
Source:
International journal of biological macromolecules 2019 v.124 pp. 895-902
ISSN:
0141-8130
Subject:
mutation,   etc   ; amino acids; engineering; equations; pH; xylanases;     Show all 6 Subjects
Abstract:
... Acidic xylanases possess the unique features necessary for the tolerance of acidic environments, which may have great potentials for industrial purposes. However, factors controlling the pH-dependent stability of xylanases are only partially known. Here we proposed a residue interaction networks based method to analyze the differences of residue interactions between 6 pairs of experimentally verif ...
DOI:
10.1016/j.ijbiomac.2018.11.282

8. “Saddle-shaped” dose-survival effect, is it a general and valuable phenomenon in microbes in response to heavy ion beam irradiation?

Author:
Guo, Xiaopeng; Zhang, Miaomiao; Gao, Yue; Li, Wenjian; Lu, Dong
Source:
Annals of microbiology 2019 v.69 no.3 pp. 221-232
ISSN:
1590-4261
Subject:
mutation,   etc   ; bibliometric analysis; breeding; irradiation; microorganisms; mutants;     Show all 6 Subjects
Abstract:
... We aimed to verify the “saddle-shaped” dose-survival effect of microbes in response to heavy ion beam irradiation (HI), and further determine the radiation parameter that affects saddle shape formation, and the relationship between the saddle region and the positive mutation rate. A bibliometric analysis was performed based on literature containing the dose-survival effect of microbes in response ...
DOI:
10.1007/s13213-019-1442-7

9. “Top” or “bottom” switches of a cyclohexanone monooxygenase controlling the enantioselectivity of the sandwiched substrate

Author:
Hu, Yujing; Wang, Jie; Cen, Yixin; Zheng, He; Huang, Meilan; Lin, Xianfu; Wu, Qi
Source:
Chemical communications 2019 v.55 no.15 pp. 2198-2201
ISSN:
1364-548X
Subject:
mutation,   etc   ; cyclohexanones; enantioselectivity; enzymes; lactones; oxidation;     Show all 6 Subjects
Abstract:
... Single mutation at the switch residues F432 (F432I/L) or L435 (L435A/G) efficiently reversed the inherent enantiopreference of WT CHMOAcᵢₙₑₜₒ in the Baeyer–Villiger oxidation of various 4-phenyl-cyclohexanone derivatives and 4-alkyl-cyclohexanones, producing a series of substituted lactones with inversed configuration (up to 99% ee and 99% conversion). ...
DOI:
10.1039/c8cc09951k

10. Mosaicism in CRISPR/Cas9-mediated genome editing

Author:
Mehravar, Maryam; Shirazi, Abolfazl; Nazari, Mahboobeh; Banan, Mehdi
Source:
Developmental biology 2019 v.445 no.2 pp. 156-162
ISSN:
0012-1606
Subject:
mutation,   etc   ; animals; gene editing; genotyping; germ cells;     Show all 5 Subjects
Abstract:
... The CRISPR/Cas9 system is a rapid, simple, and often extremely efficient gene editing method. This method has been used in a variety of organisms and cell types over the past several years. However, using this technology for generating gene-edited animals involves a number of obstacles. One such obstacle is mosaicism, which is common in founder animals. This is especially the case when the CRISPR/ ...
DOI:
10.1016/j.ydbio.2018.10.008

11. A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions

Author:
Cheung, Rocky; Insigne, Kimberly D.; Yao, David; Burghard, Christina P.; Wang, Jeffrey; Hsiao, Yun-Hua E.; Jones, Eric M.; Goodman, Daniel B.; Xiao, Xinshu; Kosuri, Sriram
Source:
Molecular cell 2019 v.73 no.1 pp. 183-194.e8
ISSN:
1097-2765
Subject:
mutation,   etc   ; exons; genetic variation; humans; introns;     Show all 5 Subjects
Abstract:
... Mutations that lead to splicing defects can have severe consequences on gene function and cause disease. Here, we explore how human genetic variation affects exon recognition by developing a multiplexed functional assay of splicing using Sort-seq (MFASS). We assayed 27,733 variants in the Exome Aggregation Consortium (ExAC) within or adjacent to 2,198 human exons in the MFASS minigene reporter and ...
DOI:
10.1016/j.molcel.2018.10.037

12. Temporal evolution of Acinetobacter baumannii ST107 clone: conversion of blaOXA-143 into blaOXA-231 coupled with mobilization of ISAba1 upstream occAB1

Author:
Rodrigues-Costa, Fernanda; Cayô, Rodrigo; Matos, Adriana Pereira; Girardello, Raquel; Martins, Willames M.B.S.; Carrara-Marroni, Floristher Elaine; Gales, Ana Cristina
Source:
Research in microbiology 2019 v.170 no.1 pp. 53-59
ISSN:
0923-2508
Subject:
mutation,   etc   ; Acinetobacter baumannii; carbapenems; transcription (genetics);     Show all 4 Subjects
Abstract:
... Nine carbapenem-resistant Acinetobacter baumannii isolates carrying blaOXA-231 and an ISAba1 upstream occAB1 were evaluated. They were clonally related and belonged to ST107. An OXA-143-producing A. baumannii ST107 strain (Ac-148) that did not possess ISAba1 upstream occAB1 was included in the analysis. Reduction in the expression of occAB1 and a 4-fold increase of carbapenem MICs were observed fo ...
DOI:
10.1016/j.resmic.2018.07.001

13. Effects of molecular crowding on a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers

Author:
Rahman, Md Motiar; Matsumura, Shigeyoshi; Ikawa, Yoshiya
Source:
Biochemical and biophysical research communications 2018 v.507 no.1-4 pp. 136-141
ISSN:
0006-291X
Subject:
mutation,   etc   ; assays; ribozymes;     Show all 3 Subjects
Abstract:
... In the RNA world, enrichment of self-replicating RNAs would have been beneficial to their survival, amplification, and evolution. Self-assembly of RNAs may be a strategy by which they enrich themselves. We examined the effects of molecular crowding on the activity of a bimolecular group I ribozyme and its derivative that self-assembles to form ribozyme oligomers. In a comparative activity assay us ...
DOI:
10.1016/j.bbrc.2018.10.188

14. Novel c.C2254T (p.Q752*) mutation in ZFYVE26 (SPG15) gene in a patient with hereditary spastic paraparesis

Author:
Vinci, Mirella; Fichera, Marco; Musumeci, Sebastiano Antonino; Cali, Francesco; Vitello, Girolamo Aurelio
Source:
Journal of genetics 2018 v.97 no.5 pp. 1469-1472
ISSN:
0022-1333
Subject:
mutation,   etc   ; genes; patients;     Show all 3 Subjects
Abstract:
... Hereditary spastic paraplegias are clinically and genetically heterogeneous degenerative disorders, and pathological variants in the autosomal recessive ZFYVE26 gene are considered as very rare causes. We describe a novel mutation in ZFYVE26 gene found in a patient with autosomal recessive spastic paraplegias. The use of a ‘target-gene’ approach allowed us to expand the clinical spectrum associate ...
DOI:
10.1007/s12041-018-1038-1

15. Do GWAS and studies of heterozygotes for NPC1 and/or NPC2 explain why NPC disease cases are so rare?

Author:
Erickson, Robert P.
Source:
Journal of applied genetics 2018 v.59 no.4 pp. 441-447
ISSN:
1234-1983
Subject:
mutation,   etc   ; alleles; heterozygosity;     Show all 3 Subjects
Abstract:
... Early onset Niemann-Pick C diseases are extremely rare, especially Niemann-Pick C2. Perhaps unusually for autosomal recessive diseases, heterozygotes for mutations in NPC1 manifest many biological variations. NPC2 deficiency has large effects on fertility. These features of NPC1 and NPC2 are reviewed in regard to possible negative selection for heterozygotes carrying null and hypomorphic alleles. ...
DOI:
10.1007/s13353-018-0465-2

16. Cancer Mutations in SPOP Put a Stop to Its Inter-compartmental Hops

Author:
Riley, Julia F.; Dao, Thuy P.; Castañeda, Carlos A.
Source:
Molecular cell 2018 v.72 no.1 pp. 1-3
ISSN:
1097-2765
Subject:
mutation,   etc   ; neoplasms; separation; ubiquitination;     Show all 4 Subjects
Abstract:
... In this issue of Molecular Cell, Bouchard et al. (2018) identify liquid-liquid phase separation as a mechanism for substrate-triggered localization of SPOP and ubiquitination machinery to different nuclear bodies and describe how cancer mutations disrupt this process. ...
DOI:
10.1016/j.molcel.2018.09.025

17. Self-Digestion for Lifespan Extension: Enhanced Autophagy Delays Aging

Author:
Arensman, Michael D.; Eng, Christina H.
Source:
Molecular cell 2018 v.71 no.4 pp. 485-486
ISSN:
1097-2765
Subject:
mutation,   etc   ; autophagy; longevity; mammals;     Show all 4 Subjects
Abstract:
... By systemically boosting autophagy with a knockin mutation that prevents binding of beclin 1 to BCL2, Fernández et al. (2018) demonstrate that enhanced autophagy prolongs lifespan in mammals. ...
DOI:
10.1016/j.molcel.2018.08.002

18. 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

19. 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

20. Effects of mismatches distant from the target position on gene correction with a 5′-tailed duplex

Author:
Suzuki, Tetsuya; Yanai, Yuri; Nishigaki, Natsuki; Nakatsu, Yoshimichi; Tsuzuki, Teruhisa; Kamiya, Hiroyuki
Source:
Journal of bioscience and bioengineering 2018 v.125 no.5 pp. 619-623
ISSN:
1389-1723
Subject:
mutation,   etc   ; DNA; genes;     Show all 3 Subjects
Abstract:
... The introduction of a 5′-tailed duplex (5′-TD) fragment into cells corrects a base-substitution mutation in a target DNA. We previously reported that the gene correction efficiency was improved when a frameshift type of second mismatch was present ∼330 bases distant from the target position, between the target DNA and the 5′-TD fragment. In this study, the effects of the second mismatches on the g ...
DOI:
10.1016/j.jbiosc.2017.12.017