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https://www.readbyqxmd.com/read/29233223/a-stretched-conformation-of-dna-with-a-biological-role
#1
Niklas Bosaeus, Anna Reymer, Tamás Beke-Somfai, Tom Brown, Masayuki Takahashi, Pernilla Wittung-Stafshede, Sandra Rocha, Bengt Nordén
We have discovered a well-defined extended conformation of double-stranded DNA, which we call Σ-DNA, using laser-tweezers force-spectroscopy experiments. At a transition force corresponding to free energy change ΔG = 1·57 ± 0·12 kcal (mol base pair)-1 60 or 122 base-pair long synthetic GC-rich sequences, when pulled by the 3'-3' strands, undergo a sharp transition to the 1·52 ± 0·04 times longer Σ-DNA. Intriguingly, the same degree of extension is also found in DNA complexes with recombinase proteins, such as bacterial RecA and eukaryotic Rad51...
January 2017: Quarterly Reviews of Biophysics
https://www.readbyqxmd.com/read/29229516/dissimilar-substitution-rates-between-two-strands-of-dna-influence-codon-usage-pattern-in-some-human-genes
#2
Binata Halder, Arup Kumar Malakar, Supriyo Chakraborty
We illustrated the descriptive aspects of codon usage of some important human genes and their expression potential in E. coli. By comparing the results of various codon usage parameters, effects that are due to selection and mutational pressures have been deciphered. The variation in GC3s explains a significant proportion of the variation in codon usage patterns. The codons CGC, CGG, CTG and GCG showed strong positive correlation with GC3, which suggested that codon usage had been influenced by GC bias. We also found that ACC (Thr, RSCU-1...
December 8, 2017: Gene
https://www.readbyqxmd.com/read/29220511/unbiased-estimate-of-synonymous-and-non-synonymous-substitution-rates-with-non-stationary-base-composition
#3
Laurent Guéeguen, Laurent Duret
The measurement of synonymous and non-synonymous substitution rates (dS and dN) is useful for assessing selection operating on protein sequences or for investigating mutational processes affecting genomes. In particular, the ratio dNdS is expected to be a good proxy for ω, the ratio of fixation robabilities of non-synonymous mutations relative to that of neutral mutations. Standard methods for estimating dN, dS or ω rely on the assumption that the base composition of sequences is at the equilibrium of the evolutionary process...
December 6, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29218897/codon-bias-among-synonymous-rare-variants-is-associated-with-alzheimer-s-disease-imaging-biomarker
#4
Jason E Miller, Manu K Shivakumar, Shannon L Risacher, Andrew J Saykin, Seunggeun Lee, Kwangsik Nho, Dokyoon Kim
Alzheimer's disease (AD) is a neurodegenerative disorder with few biomarkers even though it impacts a relatively large portion of the population and is predicted to affect significantly more individuals in the future. Neuroimaging has been used in concert with genetic information to improve our understanding in relation to how AD arises and how it can be potentially diagnosed. Additionally, evidence suggests synonymous variants can have a functional impact on gene regulatory mechanisms, including those related to AD...
2018: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/29203807/mitochondrial-genomic-variation-and-phylogenetic-relationships-of-three-groups-in-the-genus-scaphoideus-hemiptera-cicadellidae-deltocephalinae
#5
Yimin Du, Wu Dai, Christopher H Dietrich
The widespread leafhopper genus Scaphoideus Uhler is the most diverse genus in Scaphoideini and includes some species that are serious pests and vectors of plant pathogens. Here the first Scaphoideus mitogenome sequences are provided for three species, S. maai, S. nigrivalveus and S. varius, representing three main species groups in the Oriental region based on color pattern. The lengths of these three mitogenomes were 15,188, 15,235 and 15,207 bp, respectively. Gene order of three mitogenomes is highly conserved and identical to that of the putative ancestral insect...
December 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29199828/efficient-co-production-of-mannanase-and-cellulase-by-transformation-of-a-codon-optimized-endo-mannanase-gene-from-aspergillus-niger-into-trichoderma-reesei
#6
Xianhua Sun, Xianli Xue, Mengzhu Li, Fei Gao, Zhenzhen Hao, Huoqing Huang, Huiying Luo, Lina Qin, Bin Yao, Xiaoyun Su
Cellulase and mannase are both important enzyme additives of animal feeds. Expressing the two enzymes simultaneously within one microbial host could potentially lead to cost saving in animal feeding. For this purpose, we codon optimized the Aspergillus niger Man5A gene to the codon usage bias of Trichoderma reesei. By comparing the free energy and the local structure of the nucleotide sequences, one optimized sequence was finally selected and transformed into the T. reesei pyridine auxotrophic strain TU-6. The codon optimized gene was expressed to a higher level than the original one...
December 4, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29198972/analysis-of-codon-usage-bias-of-crimean-congo-hemorrhagic-fever-virus-and-its-adaptation-to-hosts
#7
Siddiq Ur Rahman, Xiaoting Yao, Xiangchen Li, Dekun Chen, Shiheng Tao
Crimean-Congo hemorrhagic fever virus (CCHFV) is a negative-sense, single stranded RNA virus with a three-segmented genome that belongs to the genus Nairovirus within the family Bunyaviridae. CCHFV uses Hyalomma ticks as a vector to infect humans with a wide range of clinical signs, from asymptomatic to Zika-like syndrome. Despite significant progress in genomic analyses, the influences of viral relationships with different hosts on overall viral fitness, survival, and evading the host's immune systems remain unknown...
November 30, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29195856/codon-usage-and-expression-level-of-human-mitochondrial-13-protein-coding-genes-across-six-continents
#8
Supriyo Chakraborty, Arif Uddin, Tarikul Huda Mazumder, Monisha Nath Choudhury, Arup Kumar Malakar, Prosenjit Paul, Binata Halder, Himangshu Deka, Gulshana Akthar Mazumder, Riazul Ahmed Barbhuiya, Masuk Ahmed Barbhuiya, Warepam Jesmi Devi
The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes...
November 28, 2017: Mitochondrion
https://www.readbyqxmd.com/read/29172233/stronger-selective-constraint-on-downstream-genes-in-the-oxidative-phosphorylation-pathway-of-cetaceans
#9
Ran Tian, Shixia Xu, Simin Chai, Daiqing Yin, Harold Zakon, Guang Yang
The oxidative phosphorylation (OXPHOS) pathway is an efficient way to produce energy via adenosine triphosphate (ATP), which is critical for sustaining an energy supply for cetaceans in a hypoxic environment. Several studies have shown that natural selection may shape the evolution of the genes involved in OXPHOS. However, how network architecture drives OXPHOS protein sequence evolution remains poorly explored. Here, we investigated the evolutionary patterns of genes in the OXPHOS pathway across six cetacean genomes within the framework of a functional network...
November 24, 2017: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29170068/enhanced-heat-tolerance-in-transgenic-silkworm-via-overexpression-of-pyrococcus-furiosus-superoxide-reductase
#10
Liang Jiang, Chunlin Huang, Bingbing Wang, Huizhen Guo, Qiang Sun, Fei Xia, Guowen Xu, Qingyou Xia
Heat shock causes a serious harm to organisms by accelerating the production of reactive oxygen species (ROS). Pyrococcus furiosus superoxide reductase (PfSOR) is an enzyme that efficiently detoxifies ROS. In order to generate a silkworm strain with high heat tolerance for sericulture, we synthesized an artificial DNA sequence encoding PfSOR based on the codon bias of Bombyx mori. PfSOR was successfully overexpressed in transgenic silkworm (named A4SOR) and BmE cells, as determined by RT-PCR and western blot analyses...
November 20, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29157661/analysis-of-codon-usage-pattern-of-mitochondrial-protein-coding-genes-in-different-hookworms
#11
Bornali Deb, Arif Uddin, Gulshana Akthar Mazumder, Supriyo Chakraborty
The phenomenon of unequal usage of synonymous codons encoding an amino acid in which some codons are more preferred to others is the codon usage bias (CUB) and it is species specific. Analysis of CUB helps in understanding evolution at molecular level and acquires significance in mRNA translation, design of transgenes and new gene discovery. In our current study, we analyzed synonymous codon usage pattern and the factors influencing it on mitochondrial protein coding genes of 6 different hookworms i.e. Ancylostoma ceylanicum, Ancylostoma duodenale, Necator americanus, Ancylostoma tubaeforme, Ancylostoma caninum and Uncinaria sanguinis as no work was reported yet...
November 17, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/29155926/codon-usage-and-codon-pair-patterns-in-non-grass-monocot-genomes
#12
Purabi Mazumdar, RofinaYasmin Binti Othman, Katharina Mebus, N Ramakrishnan, Jennifer Ann Harikrishna
Background and Aims: Studies on codon usage in monocots have focused on grasses, and observed patterns of this taxon were generalized to all monocot species. Here, non-grass monocot species were analysed to investigate the differences between grass and non-grass monocots. Methods: First, studies of codon usage in monocots were reviewed. The current information was then extended regarding codon usage, as well as codon-pair context bias, using four completely sequenced non-grass monocot genomes (Musa acuminata, Musa balbisiana, Phoenix dactylifera and Spirodela polyrhiza) for which comparable transcriptome datasets are available...
November 16, 2017: Annals of Botany
https://www.readbyqxmd.com/read/29155419/catching-hidden-variation-systematic-correction-of-reference-minor-allele-annotation-in-clinical-variant-calling
#13
Yury A Barbitoff, Igor V Bezdvornykh, Dmitrii E Polev, Elena A Serebryakova, Andrey S Glotov, Oleg S Glotov, Alexander V Predeus
PurposeWe comprehensively assessed the influence of reference minor alleles (RMAs), one of the inherent problems of the human reference genome sequence.MethodsThe variant call format (VCF) files provided by the 1000 Genomes and Exome Aggregation Consortium (ExAC) consortia were used to identify RMA sites. All coding RMA sites were checked for concordance with UniProt and the presence of same codon variants. RMA-corrected predictions of functional effect were obtained with SIFT, PolyPhen-2, and PROVEAN standalone tools and compared with dbNSFP v2...
October 26, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29137642/effects-of-mrna-secondary-structure-on-the-expression-of-hev-orf2-proteins-in-escherichia-coli
#14
Nouredine Behloul, Wenjuan Wei, Sarra Baha, Zhenzhen Liu, Jiyue Wen, Jihong Meng
BACKGROUND: Viral protein expression in Escherichia coli (E. coli) is a powerful tool for structural/functional studies as well as for vaccine and diagnostics development. However, numerous factors such as codon bias, mRNA secondary structure and nucleotides distribution, have been indentified to hamper this heterologous expression. RESULTS: In this study, we combined computational and biochemical methods to analyze the influence of these factors on the expression of different segments of hepatitis E virus (HEV) ORF 2 protein and hepatitis B virus surface antigen (HBsAg)...
November 14, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/29132309/significant-differences-in-terms-of-codon-usage-bias-between-bacteriophage-early-and-late-genes-a-comparative-genomics-analysis
#15
Oriah Mioduser, Eli Goz, Tamir Tuller
BACKGROUND: Viruses undergo extensive evolutionary selection for efficient replication which effects, among others, their codon distribution. In the current study, we aimed at understanding the way evolution shapes the codon distribution in early vs. late viral genes in terms of their expression during different stages in the viral replication cycle. To this end we analyzed 14 bacteriophages and 11 human viruses with available information about the expression phases of their genes. RESULTS: We demonstrated evidence of selection for distinct composition of synonymous codons in early and late viral genes in 50% of the analyzed bacteriophages...
November 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29121951/increasing-the-cpg-dinucleotide-abundance-in-the-hiv-1-genomic-rna-inhibits-viral-replication
#16
Irati Antzin-Anduetza, Charlotte Mahiet, Luke A Granger, Charlotte Odendall, Chad M Swanson
BACKGROUND: The human immunodeficiency virus type 1 (HIV-1) structural protein Gag is necessary and sufficient to form viral particles. In addition to encoding the amino acid sequence for Gag, the underlying RNA sequence could encode cis-acting elements or nucleotide biases that are necessary for viral replication. Furthermore, RNA sequences that inhibit viral replication could be suppressed in gag. However, the functional relevance of RNA elements and nucleotide biases that promote or repress HIV-1 replication remain poorly understood...
November 9, 2017: Retrovirology
https://www.readbyqxmd.com/read/29115457/identification-of-biomarkers-for-childhood-obesity-based-on-expressional-correlation-and-functional-similarity
#17
Zheng-Lun Zhu, Qiu-Meng Yang, Chen Li, Jun Chen, Min Xiang, Ming-Min Chen, Min Yan, Zheng-Gang Zhu
The aim of the current study was to identify potential biomarkers of childhood obesity, and investigate molecular mechanisms and candidate agents in order to improve therapeutic strategies for childhood obesity. The GSE9624 gene expression profile was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in omental adipose tissues were analyzed with limma package by comparing samples from obese and normal control children. Two‑way hierarchical clustering was applied using the pheatmap package...
October 27, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29098364/generation-of-an-arginine-trna-adapted-saccharomyces-cerevisiae-strain-for-effective-heterologous-protein-expression
#18
Marcel Noßmann, Jana Pieper, Falk Hillmann, Axel A Brakhage, Thomas Munder
The tRNA population reflects the codon bias of the organism and affects the translation of heterologous target mRNA molecules. In this study, Saccharomyces cerevisiae strains with modified levels of rare tRNA were engineered, that allowed efficient generation of recombinant proteins with unfavorable codon usage. We established a novel synthetic tRNA expression cassette and verified functional nonsense suppressor tRNA(GlnS)CUA generation in a stop codon read-through assay with a modified β-galactosidase reporter gene...
November 2, 2017: Current Genetics
https://www.readbyqxmd.com/read/29093502/comprehensive-analysis-of-correlations-among-codon-usage-bias-gene-expression-and-substitution-rate-in-arachis-duranensis-and-arachis-ipa%C3%A3-nsis-orthologs
#19
Hui Song, Hongjun Gao, Jing Liu, Pei Tian, Zhibiao Nan
The relationship between evolutionary rates and gene expression in model plant orthologs is well documented. However, little is known about the relationships between gene expression and evolutionary trends in Arachis orthologs. We identified 7,435 one-to-one orthologs, including 925 single-copy and 6,510 multiple-copy sequences in Arachis duranensis and Arachis ipaënsis. Codon usage was stronger for shorter polypeptides, which were encoded by codons with higher GC contents. Highly expressed coding sequences had higher codon usage bias, GC content, and expression breadth...
November 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29079855/somatic-mutation-driven-codon-transition-bias-in-human-cancer
#20
Hyeonju Son, Hyundeok Kang, Hyun Seok Kim, Sangwoo Kim
Accumulation of DNA mutations alters amino acid sequence in the key domains of oncoproteins, leading to cellular malignant transformation. Due to redundancy of the genetic code, the same amino acid alteration can be achieved by multiple distinct genetic mutations, which are considered functionally identical and not actively distinguished in the current cancer genome research. For the first time, we analyzed the distribution of codon level transitions acquired by somatic mutations in human cancers. By analyzing the ~2...
October 27, 2017: Scientific Reports
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