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Other Double-Stranded DNA Viruses
Published in Paul Pumpens, Peter Pushko, Philippe Le Mercier, Virus-Like Particles, 2022
Paul Pumpens, Peter Pushko, Philippe Le Mercier
The HcDNAV, a large dsDNA virus of the single species Heterocapsa circularisquama DNA virus 01 from the unassigned genus Dinodnavirus, was isolated from Japanese coastal waters in August 1999 during a H. circularisquama bloom (Tarutani et al. 2001). The virus was icosahedral, lacking a tail, approximately 180–210 nm in diameter and contained an electron-dense core. Its genome size was estimated to be about 356 kb. In fact, this was the first report that has been isolated and maintained in culture of a virus infecting dinoflagellates. Later, Takano et al. (2018) performed detailed observation of the HcDNAV particle, and its infection process was conducted via field emission scanning electron microscopy and epifluorescence microscopy. Each 5-fold vertex of the icosahedral virion was decorated with a protrusion, which may be related to the entry process of HcDNAV into the host. The transverse groove of host cells is proposed to be the main virus-entry site.
ChIP-seq analysis
Published in Altuna Akalin, Computational Genomics with R, 2020
Figure 9.16 shows that the ChIP sample is clearly enriched in the peak regions. The percentage of reads in peaks will depend on the quality of the antibody (strength of enrichment), and the size of peaks which are bound by the protein of interest. If the total size of peaks is small, relative to the genome size, we can expect that the percentage of reads in peaks will be small.
Basic Microbiology
Published in Philip A. Geis, Cosmetic Microbiology, 2020
The chromosome of most bacteria is a closed circle of double-stranded DNA although a few species have linear genomes. Most bacteria are haploid, containing only one copy of the genome per cell. Genome sizes vary by species but are considered small for the most part when compared to eukaryotic genomes. Bacteria do not in general contain “junk” DNA sequences such as intronic sequences, removing the necessity for RNA splicing, but rather their protein-coding sequences are concentrated when compared to eukaryotic genomes. As mentioned previously, bacterial DNA is too large to fit within cells unless it is compact and organized, often in conjunction with contact with the plasma membrane into the nucleoid.
Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome
Published in Gut Microbes, 2022
Hao Jin, Lijun You, Feiyan Zhao, Shenghui Li, Teng Ma, Lai-Yu Kwok, Haiyan Xu, Zhihong Sun
The completeness and contamination of each of the recovered genomes were estimated using CheckM (v1.0.18)60 lineage-workflows with default parameters. 16S rRNA genes were predicted using barrnap (v.0.9, https://github.com/tseemann/barrnap). The estimated genome size was adjusted to account for its completeness and contamination: Estimated genome size = (genome size)/(completeness + contamination). The genome replication rate was calculated using the GRiD software (version 1.3).61 This method calculated the genome growth rate from reference genomes at ultra-low sequencing coverage (>0.2x) based on estimating the ratio between coverage at the peak (ori) and the terminus (ter) for the reference bacterial genome using redescending M estimator with Tukey’s biweight function. The GRiD value was directly proportional to the growth rate.
Early flowering, good grain quality mutants through gamma rays and EMS for enhancing per day productivity in rice (Oryza sativa L.)
Published in International Journal of Radiation Biology, 2021
Vinithashri Gautam, Manonmani Swaminathan, Manoharan Akilan, Anand Gurusamy, Meena Suresh, Bhuvaneswari Kaithamalai, A. John Joel
Induced mutagenesis aids in acquiring novel variations and can also be utilized as a potential source for the creation of variability (Novak and Brunner 1992). Understanding the mutations and their practical utility will help in the elucidation of the genetic, physiological and biochemical basis of traits. Because of its small genome size, it facilitates the release of higher quality sequences, and also due to synteny among the Poaceae, other crops do receive benefit from the findings of rice crop (Viana et al. 2019). Being the most utilized staple food crop, this cereal needs constant improvement to ensure food security in changing climatic trends. In the present study an attempt was made to develop early mutants by utilizing gamma rays and combination treatments (Gamma rays + EMS).
Blautia—a new functional genus with potential probiotic properties?
Published in Gut Microbes, 2021
Xuemei Liu, Bingyong Mao, Jiayu Gu, Jiaying Wu, Shumao Cui, Gang Wang, Jianxin Zhao, Hao Zhang, Wei Chen
The high performance and efficiency of next-generation sequencing technology have allowed novel insights into the whole genome of several bacteria.35 Bioinformatics is widely used to analyze bacterial genome information, enabling the research direction shift from phenotypic assessments to genomic evaluations and even prediction of potential probiotic functions.36 Compared with the abundance of well-known probiotics such as Bifidobacterium and Lactobacillus species and of their genomic data, fewer Blautia species have been isolated, so information on their genome is limited. Currently, there are 12 isolated Blautia species with a total of 195 genome assemblies according to the NCBI database. The genome size varies greatly and ranges from 3.17 to 6.07 Mb with a median of 3.49 Mb. The median GC content is 44.25%, and the median protein count is 3205 (These data were obtained from the NCBI database on September 1, 2020, and detailed information is presented in Table 3).