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1. Linker Domains: Why ABC Transporters ‘Live in Fragments no Longer’

Author:
Ford, Robert C.; Marshall-Sabey, Dominic; Schuetz, John
Source:
Trends in biochemical sciences 2020 v.45 no.2 pp. 137-148
ISSN:
0968-0004
Subject:
mutation,   etc   ; ABC transporters; humans;     Show all 3 Subjects
Abstract:
... ATP-binding cassette (ABC) transporters are membrane proteins present in all kingdoms of life. We have considered the disordered region that connects the N- and C-terminal halves in many eukaryotic ABC transporters, allowing all four consensus functional domains to be linked. The recent availability of structures of ABC transporters containing linker regions has allowed us to identify the start an ...
DOI:
10.1016/j.tibs.2019.11.004
PubMed:
31839525
PubMed Central:
PMC7219603

2. Acquired ‘Phase Separation’ Underlies Aberrant Cell Fate Control?

Author:
Gao, Yifei; Li, Pilong
Source:
Trends in biochemical sciences 2020 v.45 no.6 pp. 457-458
ISSN:
0968-0004
Subject:
mutation,   etc   ; chromatin; condensates; epigenetics; gene expression; phenotype;     Show all 6 Subjects
Abstract:
... Chromatin readers are important intermediaries linking epigenetic information and biological phenotypes. Many diseases are caused by mutations in epigenetic readers. Recently, a study by Wan et al. uncovered that cancer-associated mutations promote self-association of eleven-nineteen-leukemia protein (ENL), leading to abnormal condensates, elevated gene expression, and impaired cell fate determina ...
DOI:
10.1016/j.tibs.2020.02.007

3. Interference of the acid stress on the expression of llsX by Listeria monocytogenes pathogenic island 3 (LIPI-3) variants

Author:
Tavares, Rafaela de Melo; Silva, Danilo Augusto Lopes da; Camargo, Anderson Carlos; Yamatogi, Ricardo Seiti; Nero, Luís Augusto
Source:
Food research international 2020 v.132 pp. 109063
ISSN:
0963-9969
Subject:
mutation,   etc   ; Listeria monocytogenes; pathogenicity islands; virulence;     Show all 4 Subjects
Abstract:
... Listeria monocytogenes harbor different virulence factors, with a highly heterogeneous distribution between distinct lineages and serotypes. The Listeria Pathogenicity Island 3 (LIPI-3), mainly described in lineage I, encodes for Listeriolysin S (LLS), a virulence factor expressed by L. monocytogenes in the gastrointestinal tract during in vivo infections. The aim of this study was to carry out a ...
DOI:
10.1016/j.foodres.2020.109063

4. Highly Parallel Profiling of Cas9 Variant Specificity

Author:
Schmid-Burgk, Jonathan L.; Gao, Linyi; Li, David; Gardner, Zachary; Strecker, Jonathan; Lash, Blake; Zhang, Feng
Source:
Molecular cell 2020 v.78 no.4 pp. 794-800.e8
ISSN:
1097-2765
Subject:
frameshift mutation,   etc   ; DNA damage; gene editing; nucleases;     Show all 4 Subjects
Abstract:
... Determining the off-target cleavage profile of programmable nucleases is an important consideration for any genome editing experiment, and a number of Cas9 variants have been reported that improve specificity. We describe here tagmentation-based tag integration site sequencing (TTISS), an efficient, scalable method for analyzing double-strand breaks (DSBs) that we apply in parallel to eight Cas9 v ...
DOI:
10.1016/j.molcel.2020.02.023

5. Parameter estimation of PEM fuel cells employing the hybrid grey wolf optimization method

Author:
Miao, Di; Chen, Wei; Zhao, Wei; Demsas, Tekle
Source:
Energy 2020 v.193 pp. 116616
ISSN:
0360-5442
Subject:
mutation,   etc   ; algorithms; fuel cells; models; system optimization;     Show all 5 Subjects
Abstract:
... Scheming and creating a precise model of fuel cell systems is essential to simulate, control, manage, and obtain the optimized parameters accurately in the case of Proton Exchange Membrane Fuel Cell. To get the optimal parameters of the Proton Exchange Membrane Fuel Cell, in this work, a new optimization method, which is called Hybrid Grey Wolf Optimizer, is presented. Hybrid Grey wolf optimizer i ...
DOI:
10.1016/j.energy.2019.116616

6. Plasmid‐chromosome cross‐talks

Author:
Vial, Ludovic; Hommais, Florence
Source:
Environmental microbiology 2020 v.22 no.2 pp. 540-556
ISSN:
1462-2912
Subject:
mutation,   etc   ; chromosomes; gene expression; plasmids; transcription factors;     Show all 5 Subjects
Abstract:
... Plasmids can be acquired by recipient bacteria at a significant cost while conferring them advantageous traits. To counterbalance the costs of plasmid carriage, both plasmids and host bacteria have developed a tight regulatory network that may involve a cross‐talk between the chromosome and the plasmids. Although plasmid regulation by chromosomal regulators is generally well known, chromosome regu ...
DOI:
10.1111/1462-2920.14880

7. Predicting CRISPR/Cas9-Induced Mutations for Precise Genome Editing

Author:
Molla, Kutubuddin A.; Yang, Yinong
Source:
Trends in biotechnology 2020 v.38 no.2 pp. 136-141
ISSN:
0167-7799
Subject:
mutation,   etc   ; artificial intelligence; gene editing; genome; prediction;     Show all 5 Subjects
Abstract:
... SpCas9 creates blunt end cuts in the genome and generates random and unpredictable mutations through error-prone repair systems. However, a growing body of recent evidence points instead to Cas9-induced staggered end generation, nonrandomness of mutations, and the predictability of editing outcomes using machine learning models. ...
DOI:
10.1016/j.tibtech.2019.08.002

8. The Short-Term Economical Operation Problem for Hydropower Station Using Chaotic Normal Cloud Model Based Discrete Shuffled Frog Leaping Algorithm

Author:
Yang, Zhe; Yang, Kan; Su, Lyuwen; Hu, Hu
Source:
Water resources management 2020 v.34 no.3 pp. 905-927
ISSN:
0920-4741
Subject:
mutation,   etc   ; algorithms; frogs; hydrology; models; water power;     Show all 6 Subjects
Abstract:
... The short-term economical operation (STEO) in hydropower station is nonlinear mixed integer problem, satisfying complex hydrologic constraints simultaneously. In this paper, we decomposed STEO into unit commitment (UC) and economical load dispatch (ELD) sub-problems. In terms of premature convergence and inefficient search performance of conventional shuffled frog leaping algorithm (SFLA), we prop ...
DOI:
10.1007/s11269-019-02435-0

9. A Therapy for Most with Cystic Fibrosis

Author:
Bear, Christine E.
Source:
Cell 2020 v.180 no.2 pp. 211
ISSN:
0092-8674
Subject:
mutation,   etc   ; cystic fibrosis; drugs; homozygosity; patients; therapeutics;     Show all 6 Subjects
Abstract:
... TRIKAFTA is the third drug approved by the FDA that rescues defects caused by the major mutation F508del. It is superior to its predecessors that were approved for patients who are homozygous for F508del because TRIKAFTA is also effective in CF patients who harbor only one copy of this mutation. ...
DOI:
10.1016/j.cell.2019.12.032

10. Temperature Unmasks Allosteric Propensity in a Thermophilic Malate Dehydrogenase via Dewetting and Collapse

Author:
Katava, M.; Marchi, M.; Madern, D.; Sztucki, M.; Maccarini, M.; Sterpone, F.
Source:
TheJournal of physical chemistry 2020 v.124 no.6 pp. 1001-1008
ISSN:
1520-5207
Subject:
mutation,   etc   ; malate dehydrogenase; molecular dynamics; temperature;     Show all 4 Subjects
Abstract:
... In this work, we combine experiments and molecular simulations to unveil the hidden allosteric propensity of a thermophilic malate dehydrogenase protein (MDH). We provide evidence that, at its working temperature, the nonallosteric MDH takes a compact structure because of internal dewetting and reorganizes the active state toward functional conformations similar to its homologous allosteric LDHs. ...
DOI:
10.1021/acs.jpcb.9b10776

11. TBX1 is required for normal stria vascularis and semicircular canal development

Author:
Tian, Cong; Johnson, Kenneth R.
Source:
Developmental biology 2020 v.457 no.1 pp. 91-103
ISSN:
0012-1606
Subject:
missense mutation,   etc   ; inner ear; mice; mutants; proteins;     Show all 5 Subjects
Abstract:
... Little is known about the role of TBX1 in post-otocyst stages of inner ear development. Here, we report on mice with a missense mutation of Tbx1 that are viable with fully developed but abnormally formed inner ears. Mutant mice are deaf due to an undeveloped stria vascularis and show vestibular dysfunction associated with abnormal semicircular canal formation. We show that TBX1 is expressed in end ...
DOI:
10.1016/j.ydbio.2019.09.013

12. The secondary KIT mutation p.Ala510Val in a cutaneous mast cell tumour carrying the activating mutation p.Asn508Ile confers resistance to masitinib in dogs

Author:
Gentilini, Fabio; Turba, Maria Elena; Dally, Claire; Takanosu, Masamine; Kurita, Sena; Bonkobara, Makoto
Source:
BMC veterinary research 2020 v.16 no.1 pp. 64
ISSN:
1746-6148
Subject:
gain-of-function mutation; missense mutation; somatic mutation,   etc   ; aggression; carcinogenesis; dogs; enzyme inhibitors; exons; mast cells; metastasis; neoplasms; pets; phenotype; prognosis; receptor protein-tyrosine kinase; screening; transfection; vinblastine;     Show all 18 Subjects
Abstract:
... BACKGROUND: Gain-of-function mutations in KIT are driver events of oncogenesis in mast cell tumours (MCTs) affecting companion animals. Somatic mutations of KIT determine the constitutive activation of the tyrosine kinase receptor leading to a worse prognosis and a shorter survival time than MCTs harbouring wild-type KIT. However, canine MCTs carrying KIT somatic mutations generally respond well t ...
DOI:
10.1186/s12917-020-02284-9
PubMed:
32075643
PubMed Central:
PMC7029481

13. 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
PubMed:
30791923
PubMed Central:
PMC6383211

14. Identifying Epistasis in Cancer Genomes: A Delicate Affair

Author:
van de Haar, Joris; Canisius, Sander; Yu, Michael K.; Voest, Emile E.; Wessels, Lodewyk F.A.; Ideker, Trey
Source:
Cell 2019 v.177 no.6 pp. 1375-1383
ISSN:
0092-8674
Subject:
mutation,   etc   ; epistasis; genes; neoplasms;     Show all 4 Subjects
Abstract:
... Recent studies of the tumor genome seek to identify cancer pathways as groups of genes in which mutations are epistatic with one another or, specifically, “mutually exclusive.” Here, we show that most mutations are mutually exclusive not due to pathway structure but to interactions with disease subtype and tumor mutation load. In particular, many cancer driver genes are mutated preferentially in t ...
DOI:
10.1016/j.cell.2019.05.005
PubMed:
31150618
PubMed Central:
PMC6816465

15. Modeling of Mutational Events in the Evolution of Viruses

Author:
Ali, Akhtar; Melcher, Ulrich
Source:
Viruses 2019 v.11 no.5
ISSN:
1999-4915
Subject:
mutation,   etc   ; models; phylogeny; viruses;     Show all 4 Subjects
Abstract:
... Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated—with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause sho ...
DOI:
10.3390/v11050418
PubMed:
31060293
PubMed Central:
PMC6563203

16. 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
PubMed:
30888641
PubMed Central:
PMC6828417

17. 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

18. Whole-genome sequencing of prostate cancer reveals novel mutation-driven processes and molecular subgroups

Author:
Liang, Caixia; Niu, Lijuan; Xiao, Zejun; Zheng, Cuiling; Shen, Yinchen; Shi, Yuankai; Han, Xiaohong
Source:
Life sciences 2020 v.254 pp. 117218
ISSN:
0024-3205
Subject:
mutation,   etc   ; genes; genomics; men; patients; prostatic neoplasms; sequence analysis;     Show all 7 Subjects
Abstract:
... Prostate cancer (PCa) is the second most frequently diagnosed cancer in men. However, its genetic characteristics in the Chinese population have not been extensively profiled. Here we screened 27 Chinese patients and preformed whole-genome sequencing to dissect their genomic patterns. We found that 18.5% (5/27) tumors harbored non-protein coding mutations on FOXA1. Besides, novel focal amplificati ...
DOI:
10.1016/j.lfs.2019.117218

19. Algicidal activity recovery by a Li-doped up-conversion material converting visible light into UV

Author:
Sun, Pengfei; Zhao, Jingyu; Tang, Jun; Li, Lin; Wong, Po Keung; Song, Lirong; Wu, Yonghong
Source:
The Science of the total environment 2020 v.720 pp. 137596
ISSN:
0048-9697
Subject:
mutation,   etc   ; Citrobacter; algicides; bacteria; light; metabolism; secretion; wavelengths;     Show all 8 Subjects
Abstract:
... Citrobacter sp. R1, a highly efficient algicidal bacterium, undergoes a serious degeneration after long-term preservation. Here, we prepared a Li-doped up-conversion material ([Y₂SiO₅; Li (1%)]) to recover the degenerated Strain R1. As a result, the [Y₂SiO₅; Li (1%)] successfully enhanced the maximum algicidal activity of Strain R1 from 43.2 ± 1.2 to 72.5 ± 1.3%. In terms of recovery mechanisms, 1 ...
DOI:
10.1016/j.scitotenv.2020.137596

20. rec-Y3H screening allows the detection of simultaneous RNA-protein interface mutations

Author:
Garriga-Canut, Mireia; Yang, Jae-Seong; Preusser, Friedrich; Speroni, Silvia; Gili, Maria; Maurer, Sebastian P.
Source:
Methods 2020 v.178 pp. 19-32
ISSN:
1046-2023
Subject:
mutation,   etc   ; RNA; RNA-binding proteins; amino acid sequences; genes; screening;     Show all 6 Subjects
Abstract:
... Understanding which proteins and RNAs directly interact is crucial for revealing cellular mechanisms of gene regulation. Efficient methods allowing to detect RNA-protein interactions and dissect the underlying molecular origin for RNA-binding protein (RBP) specificity are in high demand. The recently developed recombination-Y3H screening (rec-Y3H) enabled many-by-many detection of interactions bet ...
DOI:
10.1016/j.ymeth.2019.09.002