Article
Multidisciplinary Sciences
Bert Ely
Summary: GC→AT transitions lead to a decrease in genomic GC content in prokaryotic genomes, while biased gene conversion serves to counteract this change by increasing genomic GC content in eukaryotic genomes. Additionally, in bacterial genomes, when GC base pairs make up more than 40% of the total genome, genomic GC content tends to decrease, but when they make up less than 40%, genomic GC content is relatively stable or increasing.
Article
Multidisciplinary Sciences
Zhidong Zhang, Guilin Liu, Yao Chen, Weizhen Xue, Qianyue Ji, Qiwu Xu, He Zhang, Guangyi Fan, He Huang, Ling Jiang, Jianwei Chen
Summary: This study compared hybrid assembly strategies for genome assembly of six bacterial isolates using different sequencing platforms, and found that stLFR sequencing data yielded more contiguity and gene function integrity compared to NGS. The research provides a cost-effective chromosome-level genome assembly strategy for large-scale sequencing of extremophile genomes with different GC contents.
Article
Forestry
Yan-Feng Song, Qing-Hua Yang, Xian-Gui Yi, Zhao-Qing Zhu, Xian-Rong Wang, Meng Li
Summary: The study utilized SCUB analysis to investigate codon usage bias in subg. Cerasus, revealing natural selection as the main influencing factor, with gene expression level and GC content also impacting the usage pattern. The findings showed a consistent codon usage pattern across the 36 species, highlighting the importance of locus mutations and no-preference codons in phylogenetic reconstruction within the subgenus.
Article
Multidisciplinary Sciences
Jiajing Sheng, Xuan She, Xiaoyu Liu, Jia Wang, Zhongli Hu
Summary: This study systematically analyzed the codon usage patterns of Miscanthus plants and related species, revealing a preference for A/T bases and A/T-ending codons in the chloroplast genomes. The results suggested that the codon usage patterns are mainly influenced by natural selection, and Arabidopsis thaliana, Populus trichocarpa, and Saccharomyces cerevisiae could be considered as preferential exogenous expression receptors.
Article
Plant Sciences
Peipei Zhang, Wenbo Xu, Xu Lu, Long Wang
Summary: This study systematically analyzed the codon usage bias in chloroplast genomes of nine Gynostemma species, revealing an overall weak bias and indicating that multiple factors, with natural selection potentially being the main determinant, influence codon usage patterns. The findings could provide valuable insights for optimizing and modifying codons to enhance gene expression in Gynostemma species, and could also serve as a reference for understanding organism evolution and phylogeny in other plant species.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Microbiology
Yu Fu, Fasheng Liang, Congjun Li, Alan Warren, Mann Kyoon Shin, Lifang Li
Summary: This study analyzed the macronuclear genome of ciliates and calculated several indices to investigate codon usage bias and its influencing factors. The results showed that ciliates preferred using codons ending with A or T, and codon usage bias was affected by gene mutation and natural selection.
Article
Forestry
Jing Chen, Wuqiang Ma, Xinwen Hu, Kaibing Zhou
Summary: The synonymous codon usage (SCU) bias in oil-tea camellia cpDNAs was analyzed, and a conserved bias was observed among the samples. The third position GC content (GC3) showed a preference for A or T, suggesting weak SCU bias. The correlation analysis revealed the relationship between GC content and expected number of codons (ENC). These findings provide insights for studying cpDNA gene expression and genetic engineering.
Article
Genetics & Heredity
Gun Li, Liang Zhang, Pei Xue
Summary: Studying the molecular identities and genetic diversity of Panicum species' chloroplast genomes is crucial for understanding gene evolutionary pressure and diversity. The analysis revealed that natural selection plays a major role in influencing the evolutionary process, and although the overall evolutionary differences among the 19 chloroplast genomes were not significant, the genetic diversity of specific genes varied with shorter sequences being more prone to instability. These findings contribute to a better understanding of the evolution of Panicum species' chloroplast genomes and provide valuable insights for further research on their evolutionary processes.
Article
Genetics & Heredity
Taha Alqahtani, Rekha Khandia, Nidhi Puranik, Ali M. Alqahtani, Yahia Alghazwani, Saad Ali Alshehri, Kumarappan Chidambaram, Mohammad Amjad Kamal
Summary: This study investigated 47 genes related to dementia and found that compositional, selectional, and mutational forces play a role in the development of the disease. Nucleotide components influence codon usage bias, with nucleotide A having a positive effect and GC having a negative effect. The preference for GC-ending codons is associated with higher gene expression, except for the TTG codon which behaves differently. The findings suggest that selection pressure, along with compositional constraint and mutational force, shapes codon usage.
FRONTIERS IN GENETICS
(2022)
Article
Microbiology
Diego Simon, Juan Cristina, Hector Musto
Summary: The genetic material of different life domains shows variation in GC content, with nucleotide composition being a simple way to characterize genomes across bacteria, archaea, and eukaryotes. The study on nucleotide composition is important for understanding genome evolution and the implications of genetic material in different organisms.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Konrad Pawlak, Pawel Blazej, Dorota Mackiewicz, Pawel Mackiewicz
Summary: Synonymous codon usage is influenced by mutations and selection at both the nucleotide and amino acid levels. The proposed mutation-selection model demonstrates that the selection of amino acids based on physicochemical properties can result in biases in codon usage. Alternative genetic codes tend to exhibit greater codon bias than the standard genetic code, and the mutational pressures on cytosine and guanine content further affect usage bias. The study emphasizes the importance of considering amino acid selection in understanding codon usage patterns.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Jianglin Zhou, Yaling Xing, Zhe Zhou, Shengqi Wang
Summary: This study investigated the evolution and codon usage patterns of the Usutu virus (USUV). They found that USUV is influenced by various factors in its codon usage, including natural selection, mutation pressure, and dinucleotide abundance. The study also observed a complex interaction of codon usage between USUV and its host, suggesting a potential risk of cross-species transmission and subsequent outbreaks. Therefore, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Kunshan Liu, Yaqi Ouyang, Ru Lin, Chenyu Ge, Mian Zhou
Summary: Codon usage bias plays an important role in regulating gene expression levels, mRNA and protein stabilities in P. pastoris. Extreme codon optimization in genes with strong negative correlation between codon usage bias and protein structural disorder tendency may not be favored, and may affect protein structural conformation more severely in structural disordered proteins.
JOURNAL OF BIOTECHNOLOGY
(2022)
Article
Veterinary Sciences
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Muazzam Ali Khan, Fazli Rahim, Hamid Ali, Dekun Chen, Wentao Ma
Summary: The beef tapeworm, Taenia saginata, is a zoonotic parasite that poses serious health risks with a worldwide distribution. This study analyzed the codon usage pattern in T. saginata genomes and provided valuable data for evolutionary studies.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Multidisciplinary Sciences
Min Li, Jiajia Wang, Renhuai Dai, Guy Smagghe, Xianyi Wang, Siying You
Summary: This study assembled and annotated the complete mitochondrial genomes of five Japanagallia species, and analyzed their codon usage patterns. The results showed that the codon usage bias of mitochondrial genes in Japanagallia species was influenced by both natural selection and mutation pressure. Phylogenetic analyses supported the monophyly of Megophthalminae and revealed the relationship between Japanagallia species and Durgade. The findings can contribute to future research on organism evolution, identification, and phylogeny relationships.
Article
Infectious Diseases
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Aleksander Nikolaevich Stojarov, Nitin Sharma, Bhaskar Bhaskar, Rajanish Giri
INFECTION GENETICS AND EVOLUTION
(2020)
Article
Materials Science, Multidisciplinary
Larisa V. Kordyukova, Ramil R. Mintaev, Artyom A. Rtishchev, Marina S. Kunda, Natalia N. Ryzhova, Sergei S. Abramchuk, Marina V. Serebryakova, Vladislav V. Khrustalev, Tatyana A. Khrustaleva, Victor V. Poboinev, Stanislav G. Markushin, Olga L. Voronina
MICROSCOPY AND MICROANALYSIS
(2020)
Article
Microbiology
Vladislav Victorovich Khrustalev, Rajanish Giri, Tatyana Aleksandrovna Khrustaleva, Shivani Krishna Kapuganti, Aleksander Nicolaevich Stojarov, Victor Vitoldovich Poboinev
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Vladislav V. Khrustalev, Larisa V. Kordyukova, Alexander M. Arutyunyan, Victor V. Poboinev, Tatyana A. Khrustaleva, Aleksander N. Stojarov, Lyudmila A. Baratova, Alena S. Sapon, Valery G. Lugin
Summary: This study reveals that the cytoplasmic tail (CT) of the influenza A/H1N1 virus hemagglutinin (HA) may form a short antiparallel beta-structure under the lipid membrane within the virion, which is crucial for virus pathogenesis.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Marina A. Yermalovich, Alina M. Dronina, Galina Semeiko, Elena O. Samoilovich, Vladislav V. Khrustalev, Aurelie Sausy, Judith M. Hubschen
Summary: Based on serological and molecular investigation of samples from measles and rubella discarded cases collected in Belarus between 2005 and 2019, this study provided comprehensive data on the epidemiology of EI, highlighting the prominent role of B19V in exanthematous diseases in Belarus. Additionally, the study revealed a previously underestimated diversity of subgenotype 1a sequences with a third subtype 1a3.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Vladislav V. Khrustalev
Summary: The study aimed to create a new version of the PentaFOLD algorithm and test its performance on various proteins and peptides. The algorithm was successful in designing vaccine peptides with stable secondary structure elements based on experimental results.
PROTEIN AND PEPTIDE LETTERS
(2021)
Article
Spectroscopy
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Victor Vitoldovich Poboinev, Aleksander Nicolaevich Stojarov, Larisa Valentinovna Kordyukova, Anastasia Aleksandrovna Akunevich
Summary: The study demonstrates the presence of three peak values in the fluorescence spectra of tryptophan, which vary depending on the polarity of the solvent. Smoothed spectra of Trp-containing proteins show a single fluorescence peak that can range between 330nm and 360nm, depending on different states within the protein.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)
Article
Biochemistry & Molecular Biology
Victor Vitoldovich Poboinev, Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Tihon Evgenyevich Kasko, Vadim Dmitrievich Popkov
Summary: Intrinsically disordered proteins play important regulatory roles in cells by binding to multiple targets and performing opposite functions. The PentUnFOLD algorithm is a physicochemical method that utilizes new propensity scales to identify different elements of secondary structure and determine the stability of protein regions. Unlike other methods, PentUnFOLD works with PDB files and can identify fragments that can transition between ordered and disordered states. The algorithm has also found specific amino acid residues that are enriched in these transitional regions.
Article
Biochemistry & Molecular Biology
Anastasia Aleksandrovna Akunevich, Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Victor Vitoldovich Poboinev, Nikolai Vladimirovich Shalygo, Aleksander Nicolaevich Stojarov, Alexander Migranovich Arutyunyan, Larisa Valentinovna Kordyukova, Yehor Gennadyevich Sapon
Summary: This study reveals the existence of EGF dimers under physiological conditions and identifies the involvement of the EGF C-terminal part in dimer formation. The substitution of D46G increases the stability of EGF dimers and leads to elongation and rearrangement of the intermolecular beta-structure.
Article
Genetics & Heredity
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Anna Vladimirovna Popinako
Summary: Amyloid-beta precursor protein (APP) is highly conserved in mammals. While cytosine usage is highest in fourfold degenerated sites of the APP coding region in placental mammals, in marsupial mammals, thymine usage is favored. However, in the human APP coding region, C to T and G to A transitions are the most frequent germline and somatic mutations. Mutational AT-pressure is also common in germline mutations in introns of the human APP gene, although several exceptional introns show deviations in germline mutation rates. The presence of lncRNA genes in complementary DNA strands may explain exceptional nucleotide usage biases observed in certain exons.
Article
Biochemistry & Molecular Biology
Victor Vitoldovich Poboinev, Vladislav Victorovich Khrustalev, Anastasia Aleksandrovna Akunevich, Nikolai Vladimirovich Shalygo, Aleksander Nikolaevich Stojarov, Tatyana Aleksandrovna Khrustaleva, Larisa Valentinovna Kordyukova
Summary: Researchers have studied the cytoplasmic domain of the influenza virus hemagglutinin (HA) and found that its beta structure is determined by its amino acid sequence rather than aggregation. They have also identified tripeptides that can block the interaction between HA CT and M1 protein.
Meeting Abstract
Biochemistry & Molecular Biology
A. A. Akunevich, V. V. Khrustalev, T. A. Khrustaleva, A. M. Arutyunyan, L. V. Kordyukova, V. V. Poboinev
Article
Biochemistry & Molecular Biology
Vladislav Victorovich Khrustalev
Article
Biochemistry & Molecular Biology
Vladislav Victorovich Khrustalev, Tatyana Aleksandrovna Khrustaleva, Victor Vitoldovich Poboinev, Carolina Igorevna Karchevskaya, Elizaveta Aleksandrovna Shablovskaya, Tatyana Germanovna Terechova
Meeting Abstract
Biochemistry & Molecular Biology
V. V. Khrustalev, T. A. Khrustaleva, A. M. Arutyunyan, E. V. Shtykova, M. V. Petoukhov, N. V. Fedorova, V. V. Poboinev, L. V. Kordyukova