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Journal articles on the topic 'Genome structure'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Kim, Sang-Chul, Young-Ho Ha, Beom Kyun Park, et al. "Comparative analysis of the complete chloroplast genome of Papaveraceae to identify rearrangements within the Corydalis chloroplast genome." PLOS ONE 18, no. 9 (2023): e0289625. http://dx.doi.org/10.1371/journal.pone.0289625.

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Chloroplast genomes are valuable for inferring evolutionary relationships. We report the complete chloroplast genomes of 36 Corydalis spp. and one Fumaria species. We compared these genomes with 22 other taxa and investigated the genome structure, gene content, and evolutionary dynamics of the chloroplast genomes of 58 species, explored the structure, size, repeat sequences, and divergent hotspots of these genomes, conducted phylogenetic analysis, and identified nine types of chloroplast genome structures among Corydalis spp. The ndh gene family suffered inversion and rearrangement or was lost

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2

Khaitovich, A. B. "CORONAVIRUS (GENOME STRUCTURE, REPLICATION)." Crimea Journal of Experimental and Clinical Medicine 10, no. 4 (2021): 78–95. http://dx.doi.org/10.37279/2224-6444-2020-10-4-78-95.

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The overview presented in the article is a continuation of the publication on coronaviruses. The paper examines modern data on the structure of the genome and the replication process in various types of coronaviruses that cause diseases in humans and are of medical importance. The structure of the genomes of coronaviruses and the functions of genes that encode the structure of viral particles are presented; describes the function of structural genes and auxiliary genes; the role of genes encoding non-structural proteins in the structure of the viral particle and replication of coronaviruses is

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Mauger, David M., Michael Golden, Daisuke Yamane, et al. "Functionally conserved architecture of hepatitis C virus RNA genomes." Proceedings of the National Academy of Sciences 112, no. 12 (2015): 3692–97. http://dx.doi.org/10.1073/pnas.1416266112.

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Hepatitis C virus (HCV) infects over 170 million people worldwide and is a leading cause of liver disease and cancer. The virus has a 9,650-nt, single-stranded, messenger-sense RNA genome that is infectious as an independent entity. The RNA genome has evolved in response to complex selection pressures, including the need to maintain structures that facilitate replication and to avoid clearance by cell-intrinsic immune processes. Here we used high-throughput, single-nucleotide resolution information to generate and functionally test data-driven structural models for three diverse HCV RNA genome

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Bernaola-Galván, Pedro, Pedro Carpena, Cristina Gómez-Martín, and Jose L. Oliver. "Compositional Structure of the Genome: A Review." Biology 12, no. 6 (2023): 849. http://dx.doi.org/10.3390/biology12060849.

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As the genome carries the historical information of a species’ biotic and environmental interactions, analyzing changes in genome structure over time by using powerful statistical physics methods (such as entropic segmentation algorithms, fluctuation analysis in DNA walks, or measures of compositional complexity) provides valuable insights into genome evolution. Nucleotide frequencies tend to vary along the DNA chain, resulting in a hierarchically patchy chromosome structure with heterogeneities at different length scales that range from a few nucleotides to tens of millions of them. Fluctuati

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Andrzejewska, Angelika, Małgorzata Zawadzka, Julita Gumna, David J. Garfinkel, and Katarzyna Pachulska-Wieczorek. "In vivostructure of the Ty1 retrotransposon RNA genome." Nucleic Acids Research 49, no. 5 (2021): 2878–93. http://dx.doi.org/10.1093/nar/gkab090.

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AbstractLong terminal repeat (LTR)-retrotransposons constitute a significant part of eukaryotic genomes and influence their function and evolution. Like other RNA viruses, LTR-retrotransposons efficiently utilize their RNA genome to interact with host cell machinery during replication. Here, we provide the first genome-wide RNA secondary structure model for a LTR-retrotransposon in living cells. Using SHAPE probing, we explore the secondary structure of the yeast Ty1 retrotransposon RNA genome in its native in vivo state and under defined in vitro conditions. Comparative analyses reveal the st

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Mukherjee, Partha, Youakim Badr, Srushti Karvekar, and Shanmugapriya Viswanathan. "Coronavirus Genome Sequence Similarity and Protein Sequence Classification." Journal of Digital Science 3, no. 2 (2021): 3–18. http://dx.doi.org/10.33847/2686-8296.3.2_1.

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The world currently is going through a serious pandemic due to the coronavirus disease (COVID-19). In this study, we investigate the gene structure similarity of coronavirus genomes isolated from COVID-19 patients, Severe Acute Respiratory Syndrome (SARS) patients and bats genes. We also explore the extent of similarity between their genome structures to find if the new coronavirus is similar to either of the other genome structures. Our experimental results show that there is 82.42% similarity between the CoV-2 genome structure and the bat genome structure. Moreover, we have used a bidirectio

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Nicolas Calderon, Kevin, Johan Fabian Galindo, and Clara Isabel Bermudez-Santana. "Evaluation of Conserved RNA Secondary Structures within and between Geographic Lineages of Zika Virus." Life 11, no. 4 (2021): 344. http://dx.doi.org/10.3390/life11040344.

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Zika virus (ZIKV), without a vaccine or an effective treatment approved to date, has globally spread in the last century. The infection caused by ZIKV in humans has changed progressively from mild to subclinical in recent years, causing epidemics with greater infectivity, tropism towards new tissues and other related symptoms as a product of various emergent ZIKV–host cell interactions. However, it is still unknown why or how the RNA genome structure impacts those interactions in differential evolutionary origin strains. Moreover, the genomic comparison of ZIKV strains from the sequence-based

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Zhang, Hui, Yao Xiong, Wenhai Xiao, and Yi Wu. "Investigation of Genome Biology by Synthetic Genome Engineering." Bioengineering 10, no. 2 (2023): 271. http://dx.doi.org/10.3390/bioengineering10020271.

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Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design–build–test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and fu

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9

Zhou, Tianming, Ruochi Zhang, and Jian Ma. "The 3D Genome Structure of Single Cells." Annual Review of Biomedical Data Science 4, no. 1 (2021): 21–41. http://dx.doi.org/10.1146/annurev-biodatasci-020121-084709.

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The spatial organization of the genome in the cell nucleus is pivotal to cell function. However, how the 3D genome organization and its dynamics influence cellular phenotypes remains poorly understood. The very recent development of single-cell technologies for probing the 3D genome, especially single-cell Hi-C (scHi-C), has ushered in a new era of unveiling cell-to-cell variability of 3D genome features at an unprecedented resolution. Here, we review recent developments in computational approaches to the analysis of scHi-C, including data processing, dimensionality reduction, imputation for e

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10

Fujishiro, Shin, Naoko Tokuda, and Masaki Sasai. "2P267 Computational chromosome conformation sampling of human diploid genome(21B. Genome biology:Genome structure,Poster)." Seibutsu Butsuri 54, supplement1-2 (2014): S239. http://dx.doi.org/10.2142/biophys.54.s239_3.

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11

Jackman, Shaun D., Lauren Coombe, René L. Warren, et al. "Complete Mitochondrial Genome of a Gymnosperm, Sitka Spruce (Picea sitchensis), Indicates a Complex Physical Structure." Genome Biology and Evolution 12, no. 7 (2020): 1174–79. http://dx.doi.org/10.1093/gbe/evaa108.

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Abstract Plant mitochondrial genomes vary widely in size. Although many plant mitochondrial genomes have been sequenced and assembled, the vast majority are of angiosperms, and few are of gymnosperms. Most plant mitochondrial genomes are smaller than a megabase, with a few notable exceptions. We have sequenced and assembled the complete 5.5-Mb mitochondrial genome of Sitka spruce (Picea sitchensis), to date, one of the largest mitochondrial genomes of a gymnosperm. We sequenced the whole genome using Oxford Nanopore MinION, and then identified contigs of mitochondrial origin assembled from the

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12

Makałowski, W. "The human genome structure and organization." Acta Biochimica Polonica 48, no. 3 (2001): 587–98. http://dx.doi.org/10.18388/abp.2001_3893.

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Genetic information of human is encoded in two genomes: nuclear and mitochondrial. Both of them reflect molecular evolution of human starting from the beginning of life (about 4.5 billion years ago) until the origin of Homo sapiens species about 100,000 years ago. From this reason human genome contains some features that are common for different groups of organisms and some features that are unique for Homo sapiens. 3.2 x 10(9) base pairs of human nuclear genome are packed into 23 chromosomes of different size. The smallest chromosome - 21st contains 5 x 10(7) base pairs while the biggest one

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13

White, K. Andrew. "Regulation of RNA Virus Processes by Viral Genome Structure." Proceedings 50, no. 1 (2020): 68. http://dx.doi.org/10.3390/proceedings2020050068.

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The genomes of RNA viruses contain a variety of RNA sequences and structures that regulate different steps in virus reproduction. Events that are controlled by RNA elements include (i) the translation of viral proteins, (ii) the replication of viral RNA genomes, and (iii) the transcription of viral subgenomic mRNAs. Studies of members of the family Tombusviridae, which possess plus-strand RNA genomes, have revealed novel ways in which the RNA genome structure is utilized to control different viral processes. Recent advances in our understanding of RNA-based viral regulation in select tombusvir

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14

Lloyd, Vett K., and Kathleen Fitzpatrick. "Genome and chromosome structure: Twelve dynamic and evolving genomes." Fly 2, no. 3 (2008): 141–44. http://dx.doi.org/10.4161/fly.6379.

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15

Cassidy, Liam D., and Ashok R. Venkitaraman. "Genome instability mechanisms and the structure of cancer genomes." Current Opinion in Genetics & Development 22, no. 1 (2012): 10–13. http://dx.doi.org/10.1016/j.gde.2012.02.003.

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16

Andrews, Ryan J., Julien Roche, and Walter N. Moss. "ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV." PeerJ 6 (December 18, 2018): e6136. http://dx.doi.org/10.7717/peerj.6136.

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In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing

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17

Khaitovich, A. B., and P. A. Yermachkova. "CORONAVIRUS (GENOME STRUCTURE, REPLICATION)." Crimea Journal of Experimental and Clinical Medicine 11, no. 1 (2022): 61–75. http://dx.doi.org/10.37279/2224-6444-2021-11-1-61-75.

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The publication analyzes studies on identified mutations and their impact on the variability of coronaviruses; on the identified genotypes (lines, clusters, clades) in SARS-CoV-2, which are important for: assessing the biological properties of coronaviruses; determination of the epidemiological pathways for the introduction and spread of the virus; studying the evolution and origin of the virus; determining the effect of the virus on clinical manifestations; drug development that targets some of the targets of the virus. The work describes the genotypes (clusters, types, lines) of SARS-CoV-2 a

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18

Rusk, Nicole. "Variability in genome structure." Nature Methods 16, no. 5 (2019): 359. http://dx.doi.org/10.1038/s41592-019-0410-2.

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19

Ondřej, M. "Structure of Plant Genome." Biotechnology & Biotechnological Equipment 8, no. 1 (1994): 3–6. http://dx.doi.org/10.1080/13102818.1994.10818744.

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20

Bernardi, Giorgio. "Genome structure and evolution." Journal of Molecular Evolution 33, no. 1 (1991): 3. http://dx.doi.org/10.1007/bf02100189.

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21

Bernardi, G. "Genome structure and evolution:Foreword." Journal of Molecular Evolution 33, no. 4 (1991): 402. http://dx.doi.org/10.1007/bf02102870.

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Bernardi, Giorgio. "Genome structure and evolution." Journal of Molecular Evolution 37, no. 2 (1993): 91–92. http://dx.doi.org/10.1007/bf02407343.

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23

Saint Girons, I., S. J. Norris, U. Göbel, J. Meyer, E. M. Walker, and R. Zuerner. "Genome structure of spirochetes." Research in Microbiology 143, no. 6 (1992): 615–21. http://dx.doi.org/10.1016/0923-2508(92)90119-9.

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24

Philipp, Wolfgang J., David C. Schwartz, Amalio Telenti, and Stewart T. Cole. "Mycobacterial genome structure (minireview)." Electrophoresis 19, no. 4 (1998): 573–76. http://dx.doi.org/10.1002/elps.1150190418.

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25

Boyd, Patricia S., Janae B. Brown, Joshua D. Brown, et al. "NMR Studies of Retroviral Genome Packaging." Viruses 12, no. 10 (2020): 1115. http://dx.doi.org/10.3390/v12101115.

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Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments prov

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26

Zhou, Chenxi, Tania Duarte, Rocio Silvestre, et al. "Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes." Gates Open Research 2 (September 5, 2018): 41. http://dx.doi.org/10.12688/gatesopenres.12856.1.

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Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding

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Zhou, Chenxi, Tania Duarte, Rocio Silvestre, et al. "Insights into population structure of East African sweetpotato cultivars from hybrid assembly of chloroplast genomes." Gates Open Research 2 (July 21, 2020): 41. http://dx.doi.org/10.12688/gatesopenres.12856.2.

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Background: The chloroplast (cp) genome is an important resource for studying plant diversity and phylogeny. Assembly of the cp genomes from next-generation sequencing data is complicated by the presence of two large inverted repeats contained in the cp DNA. Methods: We constructed a complete circular cp genome assembly for the hexaploid sweetpotato using extremely low coverage (<1×) Oxford Nanopore whole-genome sequencing (WGS) data coupled with Illumina sequencing data for polishing. Results: The sweetpotato cp genome of 161,274 bp contains 152 genes, of which there are 96 protein coding

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Mohanta, Tapan Kumar, Awdhesh Kumar Mishra, and Ahmed Al-Harrasi. "The 3D Genome: From Structure to Function." International Journal of Molecular Sciences 22, no. 21 (2021): 11585. http://dx.doi.org/10.3390/ijms222111585.

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The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding fact

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Ulloa, Mauricio, Ibrokhim Y. Abdurakhmonov, Claudia Perez-M., Richard Percy, and James McD Stewart. "Genetic diversity and population structure of cotton (Gossypium spp.) of the New World assessed by SSR markers." Botany 91, no. 4 (2013): 251–59. http://dx.doi.org/10.1139/cjb-2012-0192.

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A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understanding its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representing five allotetraploids (AD1–AD5 genomes), 23 Asiatic diploids of the Old World (A1 and A2 genomes), and 82 diploids of the New World subgenus Houzingenia (D1–D11 genomes) species were assessed using simple sequence repeats (SSR) markers with wide genome coverage. The mean genetic distance (GD) be

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Campbell, Matthew A., James T. Van Leuven, Russell C. Meister, Kaitlin M. Carey, Chris Simon, and John P. McCutcheon. "Genome expansion via lineage splitting and genome reduction in the cicada endosymbiont Hodgkinia." Proceedings of the National Academy of Sciences 112, no. 33 (2015): 10192–99. http://dx.doi.org/10.1073/pnas.1421386112.

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Comparative genomics from mitochondria, plastids, and mutualistic endosymbiotic bacteria has shown that the stable establishment of a bacterium in a host cell results in genome reduction. Although many highly reduced genomes from endosymbiotic bacteria are stable in gene content and genome structure, organelle genomes are sometimes characterized by dramatic structural diversity. Previous results from Candidatus Hodgkinia cicadicola, an endosymbiont of cicadas, revealed that some lineages of this bacterium had split into two new cytologically distinct yet genetically interdependent species. It

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Yang, Heng, Renzhi Chen, and Ke Li. "Bridging Sequence-Structure Alignment in RNA Foundation Models." Proceedings of the AAAI Conference on Artificial Intelligence 39, no. 20 (2025): 21929–37. https://doi.org/10.1609/aaai.v39i20.35500.

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The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the seamless flow of genomic information between RNA sequences and structures. In this study, we introduce OmniGenome, an RNA FM trained to align RNA sequences with respect to secondary structures through structure-contextualized modelling. This alignment enables free and bidirectional mappings between sequences and structures by utilizing a flexible RNA modelling paradigm that supports versatile in

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Mazur, Andrzej, and Piotr Koper. "Rhizobial plasmids — replication, structure and biological role." Open Life Sciences 7, no. 4 (2012): 571–86. http://dx.doi.org/10.2478/s11535-012-0058-8.

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AbstractSoil bacteria, collectively named rhizobia, can establish mutualistic relationships with legume plants. Rhizobia often have multipartite genome architecture with a chromosome and several extrachromosomal replicons making these bacteria a perfect candidate for plasmid biology studies. Rhizobial plasmids are maintained in the cells using a tightly controlled and uniquely organized replication system. Completion of several rhizobial genome-sequencing projects has changed the view that their genomes are simply composed of the chromosome and cryptic plasmids. The genetic content of plasmids

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Szlachta, Karol, Arkadi Manukyan, Heather M. Raimer, et al. "Topoisomerase II contributes to DNA secondary structure-mediated double-stranded breaks." Nucleic Acids Research 48, no. 12 (2020): 6654–71. http://dx.doi.org/10.1093/nar/gkaa483.

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Abstract DNA double-stranded breaks (DSBs) trigger human genome instability, therefore identifying what factors contribute to DSB induction is critical for our understanding of human disease etiology. Using an unbiased, genome-wide approach, we found that genomic regions with the ability to form highly stable DNA secondary structures are enriched for endogenous DSBs in human cells. Human genomic regions predicted to form non-B-form DNA induced gross chromosomal rearrangements in yeast and displayed high indel frequency in human genomes. The extent of instability in both analyses is in concorda

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Zhang, Qinfen, Yuanzhu Gao, Matthew L. Baker, et al. "The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization." PLOS Pathogens 19, no. 4 (2023): e1011341. http://dx.doi.org/10.1371/journal.ppat.1011341.

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Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mu

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Brickner, Jason. "Genetic and epigenetic control of the spatial organization of the genome." Molecular Biology of the Cell 28, no. 3 (2017): 364–69. http://dx.doi.org/10.1091/mbc.e16-03-0149.

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Eukaryotic genomes are spatially organized within the nucleus by chromosome folding, interchromosomal contacts, and interaction with nuclear structures. This spatial organization is observed in diverse organisms and both reflects and contributes to gene expression and differentiation. This leads to the notion that the arrangement of the genome within the nucleus has been shaped and conserved through evolutionary processes and likely plays an adaptive function. Both DNA-binding proteins and changes in chromatin structure influence the positioning of genes and larger domains within the nucleus.

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Xia, Lei, Han Wang, Xiaokun Zhao, et al. "Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber." International Journal of Molecular Sciences 24, no. 10 (2023): 8943. http://dx.doi.org/10.3390/ijms24108943.

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Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, ph

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Sorimachi, Kenji. "Evolution based on genome structure: the “diagonal genome universe”." Natural Science 02, no. 10 (2010): 1104–12. http://dx.doi.org/10.4236/ns.2010.210137.

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Alzahrani, Dhafer, Enas Albokhari, Abidina Abba, and Samaila Yaradua. "The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis." Science Progress 104, no. 4 (2021): 003685042110599. http://dx.doi.org/10.1177/00368504211059973.

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Caylusea hexagyna and Ochradenus baccatus are two species in the Resedaceae family. In this study, we analysed the complete plastid genomes of these two species using high-throughput sequencing technology and compared their genomic data. The length of the plastid genome of C. hexagyna was 154,390 bp while that of O. baccatus was 153,380 bp. The lengths of the inverted repeats (IR) regions were 26,526 bp and 26,558 bp, those of the large single copy (LSC) regions were 83,870 bp and 83,023 bp; and those of the small single copy (SSC) regions were 17,468 bp and 17,241 bp in C. hexagyna and O. bac

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Panzenhagen, Pedro, Devendra H. Shah, Dalia dos Prazeres Rodrigues, and Carlos Adam Conte Junior. "Worldwide Population Dynamics of Salmonella Saintpaul: Outbreaks, Epidemiology, and Genome Structure." Genes 16, no. 3 (2025): 254. https://doi.org/10.3390/genes16030254.

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Background/Objectives: Salmonella Saintpaul (SSa) is increasingly linked to foodborne outbreaks in Brazil and globally. Despite its rising public health significance, its epidemiology, genomic diversity, and pathogenic potential remain underexplored. This study addresses these gaps through a comprehensive global analysis of SSa population dynamics, outbreak patterns, and genetic structures, along with an in-depth phenotypic and genomic characterization of strain PP_BR059, isolated from a hospitalized patient in Ceará, Brazil. Methods: We analyzed 1,953 publicly available SSa genomes using core

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Poblete, Simón, and Horacio V. Guzman. "Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models." Viruses 13, no. 8 (2021): 1555. http://dx.doi.org/10.3390/v13081555.

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Three-dimensional RNA domain reconstruction is important for the assembly, disassembly and delivery functionalities of a packed proteinaceus capsid. However, to date, the self-association of RNA molecules is still an open problem. Recent chemical probing reports provide, with high reliability, the secondary structure of diverse RNA ensembles, such as those of viral genomes. Here, we present a method for reconstructing the complete 3D structure of RNA genomes, which combines a coarse-grained model with a subdomain composition scheme to obtain the entire genome inside proteinaceus capsids based

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Wu, Xiaobing, Tao Zheng, Zhigang Jiang, and Lei Wei. "The mitochondrial genome structure of the clouded leopard (Neofelis nebulosa)." Genome 50, no. 2 (2007): 252–57. http://dx.doi.org/10.1139/g06-143.

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The complete 16 844 bp mitochondrial genome of Neofelis nebulosa has been sequenced and compared with the complete mitochondrial genomes of Felis catus and the Acinonyx jubatus . The base composition of the mitochondrial genome of N. nebulosa is as follows: A, 5343 bp (31.7%); C, 4441 bp (26.4%); G, 2491 bp (14.8%); T, 4569 bp (27.1%). The genome complement and the gene order of this mitochondrial genome was found to be typical of those reported for other mammals. Several unusual features of this genome, however, were found. First, in protein-coding regions, AT bias in the genome was not preva

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Oakley, Aaron J. "Hidden Glutathione Transferases in the Human Genome." Biomolecules 13, no. 8 (2023): 1240. http://dx.doi.org/10.3390/biom13081240.

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With the development of accurate protein structure prediction algorithms, artificial intelligence (AI) has emerged as a powerful tool in the field of structural biology. AI-based algorithms have been used to analyze large amounts of protein sequence data including the human proteome, complementing experimental structure data found in resources such as the Protein Data Bank. The EBI AlphaFold Protein Structure Database (for example) contains over 230 million structures. In this study, these data have been analyzed to find all human proteins containing (or predicted to contain) the cytosolic glu

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Durrant, Matthew G., and Ami S. Bhatt. "Microbiome genome structure drives function." Nature Microbiology 4, no. 6 (2019): 912–13. http://dx.doi.org/10.1038/s41564-019-0473-y.

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Vinson, Valda. "The structure of the genome." Science 361, no. 6405 (2018): 888.4–888. http://dx.doi.org/10.1126/science.361.6405.888-d.

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Martin-Didonet, Claudia C. G., Leda S. Chubatsu, Emanuel M. Souza, et al. "Genome Structure of the GenusAzospirillum." Journal of Bacteriology 182, no. 14 (2000): 4113–16. http://dx.doi.org/10.1128/jb.182.14.4113-4116.2000.

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ABSTRACT Azospirillum species are plant-associated diazotrophs of the alpha subclass of Proteobacteria. The genomes of five of the six Azospirillum species were analyzed by pulsed-field gel electrophoresis. All strains possessed several megareplicons, some probably linear, and 16S ribosomal DNA hybridization indicated multiple chromosomes in genomes ranging in size from 4.8 to 9.7 Mbp. The nifHDK operon was identified in the largest replicon.

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Spaan, W., D. Cavanagh, and M. C. Horzinek. "Coronaviruses: Structure and Genome Expression." Journal of General Virology 69, no. 12 (1988): 2939–52. http://dx.doi.org/10.1099/0022-1317-69-12-2939.

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Samudrala, Ram. "Modeling genome structure and function." Pure and Applied Chemistry 74, no. 6 (2002): 907–14. http://dx.doi.org/10.1351/pac200274060907.

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The ongoing genomics revolution has led to the creation and enumeration of all the genes encoded within several organisms. The next steps are to catalog all proteins, their structures, and their functions in different contexts. At the same time, scientists have been pursuing experimental and theoretical approaches to integrate this information to gain understanding of the behavior of entire systems. In this work, we provide a framework for obtaining structures for all tractable protein sequences encoded by a genome, and using the resulting structures to aid in understanding function. Our aim i

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Tang, Lei. "From genome structure to function." Nature Methods 20, no. 12 (2023): 1869. http://dx.doi.org/10.1038/s41592-023-02107-3.

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Levi, Laura I., Emily A. Madden, Jeremy Boussier, et al. "Chikungunya Virus RNA Secondary Structures Impact Defective Viral Genome Production." Microorganisms 12, no. 9 (2024): 1794. http://dx.doi.org/10.3390/microorganisms12091794.

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Chikungunya virus (CHIKV) is a mosquito-borne RNA virus that poses an emerging threat to humans. In a manner similar to other RNA viruses, CHIKV encodes an error-prone RNA polymerase which, in addition to producing full-length genomes, gives rise to truncated, non-functional genomes, which have been coined defective viral genomes (DVGs). DVGs have been intensively studied in the context of therapy, as they can inhibit viral replication and dissemination in their hosts. In this work, we interrogate the influence of viral RNA secondary structures on the production of CHIKV DVGs. We experimentall

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Seemann, Stefan E., Aashiq H. Mirza, Claus H. Bang-Berthelsen, et al. "Does rapid sequence divergence preclude RNA structure conservation in vertebrates?" Nucleic Acids Research 50, no. 5 (2022): 2452–63. http://dx.doi.org/10.1093/nar/gkac067.

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Abstract Accelerated evolution of any portion of the genome is of significant interest, potentially signaling positive selection of phenotypic traits and adaptation. Accelerated evolution remains understudied for structured RNAs, despite the fact that an RNA’s structure is often key to its function. RNA structures are typically characterized by compensatory (structure-preserving) basepair changes that are unexpected given the underlying sequence variation, i.e., they have evolved through negative selection on structure. We address the question of how fast the primary sequence of an RNA can cha

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