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1. Comparative Analysis of Within-Host Mutation Patterns and Diversity of Hepatitis C Virus Subtypes 1a, 1b, and 3a

Author:
Tisthammer, Kaho H.; Dong, Weiyan; Joy, Jeffrey B.; Pennings, Pleuni S.
Source:
Viruses 2021 v.13 no.3
ISSN:
1999-4915
Subject:
mutation; mutation rate,   etc   ; Hepatitis C virus; genetic variation; genomics; humans;     Show all 6 Subjects
Abstract:
... Understanding within-host evolution is critical for predicting viral evolutionary outcomes, yet such studies are currently lacking due to difficulty involving human subjects. Hepatitis C virus (HCV) is an RNA virus with high mutation rates. Its complex evolutionary dynamics and extensive genetic diversity are demonstrated in over 67 known subtypes. In this study, we analyzed within-host mutation f ...
DOI:
10.3390/v13030511

2. Mutational effects of Pannexin 1 R217H depend on the carboxyl-terminus

Author:
Purohit, Rutambhara; Bera, Amal Kanti
Source:
Biochemical and biophysical research communications 2021 v.548 pp. 143-147
ISSN:
0006-291X
Subject:
mutation,   etc   ; cell death; pannexins; research;     Show all 4 Subjects
Abstract:
... Pannexin 1 (Panx1) has been implicated in a plethora of physiological and pathophysiological processes. It is one of the major ATP release channels in many cell types. Extracellular ATP, activates purinergic P2X and P2Y receptors, triggering several signaling cascades. A disease-associated mutation, Arg-217-His (R217H) in the 3rd transmembrane domain of Panx1 attenuates channel functions through a ...
DOI:
10.1016/j.bbrc.2021.02.060

3. An Engineered Arginine Residue of Unusual pH-Sensitive Reactivity Facilitates Site-Selective Antibody Conjugation

Author:
Nilchan, Napon; Alburger, James M.; Roush, William R.; Rader, Christoph
Source:
Biochemistry 2021 v.60 no.14 pp. 1080-1087
ISSN:
1520-4995
Subject:
mutation,   etc   ; arginine; lysine; monoclonal antibodies;     Show all 4 Subjects
Abstract:
... Monoclonal antibody h38C2 is a humanized catalytic antibody that has been used to generate various immunoconjugate species such as chemically programmed antibodies, antibody–drug conjugates, and antibody–siRNA conjugates. Highly efficient and specific conjugation of h38C2 occurs at its uniquely reactive lysine (Lys) residue buried inside the antibody’s catalytic pocket. We recently reported the ra ...
DOI:
10.1021/acs.biochem.0c00955

4. Precise identification of an RNA methyltransferase's substrate modification site

Author:
Xiang, Siying; Gao, Minsong; Cao, Jie; Shu, Xiao; Cheng, Mohan; Wang, Fengqin; Deng, Ting; Liu, Jianzhao
Source:
Chemical communications 2021 v.57 no.20 pp. 2499-2502
ISSN:
1364-548X
Subject:
mutation,   etc   ; RNA; humans; methylation; methyltransferases;     Show all 5 Subjects
Abstract:
... Here we report a simple and nonradioactive biochemical assay which is capable of accurately determining the substrate methylation sites of human RNA N⁶-methyladenosine methyltransferases METTL3/METTL14 and METTL16. This method employs enzyme-assisted chemical labelling of a specific base in an RNA substrate with the assistance of an allyl-substituted methyltransferase cofactor, and enables precise ...
DOI:
10.1039/d0cc08260k

5. Testing tumors from different anatomic sites for clonal relatedness using somatic mutation data

Author:
Ostrovnaya, Irina; Mauguen, Audrey; Seshan, Venkatraman E.; Begg, Colin B.
Source:
Biometrics 2021 v.77 no.1 pp. 283-292
ISSN:
0006-341X
Subject:
somatic mutation,   etc   ; metastasis; neoplasms; patients;     Show all 4 Subjects
Abstract:
... A common task for the cancer pathologist is to determine, in a patient suffering from cancer, whether a new tumor in a distinct anatomic site from the primary is an independent occurrence of cancer or a metastasis. As mutational profiling of tumors becomes more widespread in routine clinical practice, this diagnostic task can be greatly enhanced by comparing mutational profiles of the tumors to de ...
DOI:
10.1111/biom.13256

6. The isolated La-module of LARP1 mediates 3’ poly(A) protection and mRNA stabilization, dependent on its intrinsic PAM2 binding to PABPC1

Author:
Mattijssen, Sandy; Kozlov, Guennadi; Gaidamakov, Sergei; Ranjan, Amitabh; Fonseca, Bruno D.; Gehring, Kalle; Maraia, Richard J.
Source:
RNA biology 2021 v.18 no.2 pp. 275-289
ISSN:
1555-8584
Subject:
point mutation,   etc   ; metabolism; protein domains;     Show all 3 Subjects
Abstract:
... The protein domain arrangement known as the La-module, comprised of a La motif (LaM) followed by a linker and RNA recognition motif (RRM), is found in seven La-related proteins: LARP1, LARP1B, LARP3 (La protein), LARP4, LARP4B, LARP6, and LARP7 in humans. Several LARPs have been characterized for their distinct activity in a specific aspect of RNA metabolism. The La-modules vary among the LARPs in ...
DOI:
10.1080/15476286.2020.1860376

7. A novel intron mutation in FBN-1 gene identified in a pregnant woman with Marfan syndrome

Author:
Wu, Yuduo; Sun, Hairui; He, Yihua; Zhang, Hongjia
Source:
Hereditas 2021 v.158 no.1 pp. 6
ISSN:
1601-5223
Subject:
mutation,   etc   ; exons; introns; pregnancy; pregnant women;     Show all 5 Subjects
Abstract:
... Marfan syndrome (MFS) is one of the most common hereditary connective tissue diseases, with great individual heterogeneity. We reported a Chinese pregnancy with Clinical diagnosis of MFS, performed whole-exome sequencing, and screened for the genetic abnormality. We also conducted an in vitro mini-gene splicing assay to demonstrate the predicted harmful effects of an intronic variant of FBN-1. Exo ...
DOI:
10.1186/s41065-020-00170-w

8. Phosphorylation of OsFD1 by OsCIPK3 promotes the formation of RFT1-containing florigen activation complex for long-day flowering in rice

Author:
Peng, Qiang; Zhu, Chunmei; Liu, Tao; Zhang, Shuo; Feng, Shijing; Wu, Changyin
Source:
Molecular plant 2021
ISSN:
1674-2052
Subject:
mutation,   etc   ; domestication; florigen; phosphorylation; protein kinases; rice;     Show all 6 Subjects
Abstract:
... Heading date is a critical trait that determines the regional adaptability and grain productivity of many crops. Although rice is a facultative short-day plant, its domestication led to the Ghd7-Ehd1-Hd3a/RFT1 pathway for adaptation to long-day conditions (LDs). The formation of the “florigen activation complex” (FAC) containing florigen Hd3a has been characterized. However, the molecular composit ...
DOI:
10.1016/j.molp.2021.04.003

9. Computing the Beta Parameter in IDW Interpolation by Using a Genetic Algorithm

Author:
Bărbulescu, Alina; Șerban, Cristina; Indrecan, Marina-Larisa
Source:
Water 2021 v.13 no.6
ISSN:
2073-4441
Subject:
mutation,   etc   ; algorithms; hydrologic data; kriging; water;     Show all 5 Subjects
Abstract:
... This article proposes a new approach for determining the optimal parameter (β) in the Inverse Distance Weighted Method (IDW) for spatial interpolation of hydrological data series. This is based on a genetic algorithm (GA) and finds a unique β for the entire study region, while the classical one determines different βs for different interpolated series. The algorithm is proposed in four scenarios c ...
DOI:
10.3390/w13060863

10. Artificial Metalloproteins with Dinuclear Iron–Hydroxido Centers

Author:
Miller, Kelsey R.; Biswas, Saborni; Jasniewski, Andrew; Follmer, Alec H.; Biswas, Ankita; Albert, Therese; Sabuncu, Sinan; Bominaar, Emile L.; Hendrich, Michael P.; Moënne-Loccoz, Pierre; Borovik, A. S.
Source:
Journal of the American Chemical Society 2021 v.143 no.5 pp. 2384-2393
ISSN:
1520-5126
Subject:
mutation,   etc   ; X-ray diffraction; ligands; metalloproteins; spectroscopy;     Show all 5 Subjects
Abstract:
... Dinuclear iron centers with a bridging hydroxido or oxido ligand form active sites within a variety of metalloproteins. A key feature of these sites is the ability of the protein to control the structures around the Fe centers, which leads to entatic states that are essential for function. To simulate this controlled environment, artificial proteins have been engineered using biotin–streptavidin ( ...
DOI:
10.1021/jacs.0c12564

11. Farnesyltransferase inhibition in HGPS

Author:
Misteli, Tom
Source:
Cell 2021 v.184 no.2 pp. 293
ISSN:
0092-8674
Subject:
mutation,   etc   ; ; atherosclerosis; geranylgeranyl diphosphate synthase; heart failure;     Show all 5 Subjects
Abstract:
... The ultra-rare, pediatric premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS) is caused by mutation of LMNA, encoding the nuclear architectural protein lamin A. Patients develop atherosclerosis and typically die of heart failure in their teens. FDA-approved Zokinvy prevents farnesylation of lamin A, reduces vascular stiffness, and extends survival in HGPS patients. To view this Be ...
DOI:
10.1016/j.cell.2020.12.029

12. Taming fitness: Organism‐environment interdependencies preclude long‐term fitness forecasting

Author:
Doulcier, Guilhem; Takacs, Peter; Bourrat, Pierrick
Source:
BioEssays 2021 v.43 no.1 pp. e2000157
ISSN:
0265-9247
Subject:
mutation,   etc   ; evolutionary biology; progeny; reproductive performance;     Show all 4 Subjects
Abstract:
... Fitness is a central but notoriously vexing concept in evolutionary biology. The propensity interpretation of fitness is often regarded as the least problematic account for fitness. It ties an individual's fitness to a probabilistic capacity to produce offspring. Fitness has a clear causal role in evolutionary dynamics under this account. Nevertheless, the propensity interpretation faces its share ...
DOI:
10.1002/bies.202000157

13. Highly efficient and genotype-independent barley gene editing based on anther culture

Author:
Han, Yong; Broughton, Sue; Liu, Li; Zhang, Xiao-Qi; Zeng, Jianbin; He, Xiaoyan; Li, Chengdao
Source:
Plant communications 2021 v.2 no.2 pp. 100082
ISSN:
2590-3462
Subject:
mutation; mutation rate,   etc   ; anther culture; barley; callus; genes; genetic transformation; genomics; genotype; phenology;     Show all 10 Subjects
Abstract:
... Recalcitrance to tissue culture and genetic transformation is the major bottleneck for gene manipulation in crops. In barley, immature embryos of Golden Promise have typically been used as explants for transformation. However, the genotype dependence of this approach limits the genetic modification of commercial varieties. Here, we developed an anther culture-based system that permits the effectiv ...
DOI:
10.1016/j.xplc.2020.100082

14. A new method towards the detection of DNA mutation by Surface-Enhanced Raman Spectroscopy

Author:
Zeng, Jiayu; Dong, Meiyu; Zhu, Bixue; Chen, Dongmei; Li, Yang
Source:
Talanta 2021 v.223 pp. 121746
ISSN:
0039-9140
Subject:
frameshift mutation; point mutation,   etc   ; Raman spectroscopy; breathing; detection; genes; hydrophobicity; ions; nanosilver; single-stranded DNA; titanium;     Show all 11 Subjects
Abstract:
... It is generally believed that the self-folding of single-stranded DNA depends on the hydrophobic effect of its internal bases, but the folding of a single-stranded DNA in a solution was not disordered and would be affected by the stacking effect of adjacent bases. In this work, we developed a new method to explore the stacking between adjacent bases using Surface-Enhanced Raman Spectroscopy (SERS) ...
DOI:
10.1016/j.talanta.2020.121746

15. Streptomycin and nalidixic acid elevate the spontaneous genome-wide mutation rate in Escherichia coli

Author:
Ozdemirel, Huseyin Ozgur; Ulusal, Dilara; Kucukyildirim Celik, Sibel
Source:
Genetica 2021 v.149 no.1 pp. 73-80
ISSN:
0016-6707
Subject:
mutation accumulation; mutation rate,   etc   ; Escherichia coli; antibiotic resistance; genotoxicity tests; nalidixic acid; public health; streptomycin;     Show all 8 Subjects
Abstract:
... Since antibiotic resistance is a growing public health problem worldwide, it is important to understand how antibiotics and spontaneous mutations cooperate and shape the genome-wide mutation rate and spectrum. Here, we quantitatively evaluate genome-wide mutational profiles of Escherichia coli after long-term subinhibitory exposure to a broad-spectrum (streptomycin) and a narrow-spectrum antibioti ...
DOI:
10.1007/s10709-021-00114-w

16. Low mutation rates promote the evolution of advantageous traits by preventing interference from deleterious mutations

Author:
Aoyagi Blue, Yuta; Sakai, Satoki
Source:
Genetica 2020 v.148 no.2 pp. 101-108
ISSN:
0016-6707
Subject:
mutation; mutation rate,   etc   ; genome; phenotype; probability;     Show all 5 Subjects
Abstract:
... We studied how mutation rates promote the evolution of advantageous traits in an asexual population. First, to examine the effects of mutation rates on the evolution of an advantageous trait (high competitive ability), we carried out simulation analyses with competition between individuals for survival. Second, to examine the mechanism underlying the promotion of advantageous trait evolution, we c ...
DOI:
10.1007/s10709-020-00091-6

17. Cataract-causing G18V eliminates the antagonization by ATP against the crowding-induced destabilization of human γS-crystallin

Author:
He, Yuan; Kang, Jian; Song, Jianxing
Source:
Biochemical and biophysical research communications 2020 v.530 no.3 pp. 554-560
ISSN:
0006-291X
Subject:
mutation,   etc   ; cataract; humans; research;     Show all 4 Subjects
Abstract:
... In lens, ∼90% of ocular proteins are αβγ-crystallins with concentrations ≥400 mg/ml, which need to remain soluble for the whole life-span and their aggregation leads to cataract. The G18V mutation of human γS-crystallin causes hereditary childhood-onset cortical cataract. Mysteriously, despite being a metabolically-quiescent organ, lens maintains ATP concentrations of 3–7 mM. Very recently, we fou ...
DOI:
10.1016/j.bbrc.2020.07.070

18. TGIF1 and SF1 polymorphisms are associated with litter size in Small Tail Han sheep

Author:
Zhang, Zhuangbiao; He, Xiaoyun; Liu, Qiuyue; Tang, Jishun; Di, Ran; Chu, Mingxing
Source:
Reproduction in domestic animals 2020 v.55 no.9 pp. 1145-1153
ISSN:
0936-6768
Subject:
mutation,   etc   ; litter size; loci;     Show all 3 Subjects
Abstract:
... TGF‐β induced factor homeobox 1 (TGIF1) and splicing factor 1 (SF1) are important for mammalian reproduction; however, the effects of these genes on litter size in sheep remain unexplored. In this study, we genotyped 768 ewes from seven sheep breeds at two loci: g.37871539C>T, a synonymous mutation of TGIF1; and g.42314637T>C, a 3′UTR variant of SF1. Our analysis of polymorphism revealed only two ...
DOI:
10.1111/rda.13753

19. 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

20. The Developmental Gene Hypothesis for Punctuated Equilibrium: Combined Roles of Developmental Regulatory Genes and Transposable Elements

Author:
Casanova, Emily L.; Konkel, Miriam K.
Source:
BioEssays 2020 v.42 no.2 pp. e1900173
ISSN:
0265-9247
Subject:
mutation,   etc   ; Animalia; fossils; morphogenesis;     Show all 4 Subjects
Abstract:
... Theories of the genetics underlying punctuated equilibrium (PE) have been vague to date. Here the developmental gene hypothesis is proposed, which states that: 1) developmental regulatory (DevReg) genes are responsible for the orchestration of metazoan morphogenesis and their extreme conservation and mutation intolerance generates the equilibrium or stasis present throughout much of the fossil rec ...
DOI:
10.1002/bies.201900173
PubMed:
31943266
PubMed Central:
PMC7029956