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Genomics of PHA Synthesizing Bacteria
Published in Martin Koller, The Handbook of Polyhydroxyalkanoates, 2020
Parveen K. Sharma, Jilagamazhi Fu, Nisha Mohanan, David B. Levin
A large number (120) of Halomonas sp. genome sequences (draft, permanent, and finished) are available on the IMG platform (https://img.jgi.doe.gov). Complete genome sequences of Halomonas sp. SF2003 and H. smyrnensis AAD6T have been recently published [13,81]. We selected 15 genomes of Halomonas species for further study. The genome size of Halomonas species varies from 2.87 to 5.33 Mb, with gene contents between 2,636 to 4,807. The H. halocynthiae DSM 14573 genome is 2.87 Mb, while the H. titanicae BH1 genome is 5.33 Mb (see Table 3.4). The % GC ratio is in the range of 0.52–0.62. A maximum of 1,002 genes was horizontally transferred into H. anticariensis DSM 16096. The 15 genomes of Halomonas spp. had up to 77.4% average nucleotide identity with Halomonas anticariensis SDSM16096. Analyses of genome size, gene counts, and % average nucleotide identity (ANI) indicate that there is wide diversity among the genomes of Halomonas species.
“Omics”
Published in Kirk A. Phillips, Dirk P. Yamamoto, LeeAnn Racz, Total Exposure Health, 2020
A mosaic of several individuals is represented in the Genome Reference Consortium’s (GRC) human reference genome version GRCh38. Several large genome sequencing projects have captured a large amount of the variability, and GRCH38 has 261 alternate scaffolds to account for the “benign” variability in ethnically diverse populations. It is estimated that unrelated individuals would differ at ~15 million positions and carry as many as 2,000 structural variations like copy number variations (duplications and deletions) and genome rearrangements like inversions and translocations. Based on a genome size of 3.2 billion nucleotides, it can be expected that each human may have ~3 million nucleotide differences from the reference genome (1 every 300 base pair (bp)). Thus, variants (alleles) have to be contextualized and could be benign or associated with a phenotype or disease or yet to be determined significance (Jackson et al. 2018). Allelic variants are referred as single nucleotide variants (SNVs), and when present in >1% of the population are called polymorphisms (SNP). About 11 million SNPs in the human genome have been cataloged with any one individual carrying about 3 million of them (Chong et al. 2015). Currently, about 4,100 mutations linked to a phenotype have been documented; their current count and statistical breakdown of the spectrum of phenotypes associated with the genes can be found at (https://www.omim.org/statistics/geneMap).
Nanomaterials for the Delivery of Therapeutic Nucleic Acids
Published in Klaus D. Sattler, st Century Nanoscience – A Handbook, 2020
Michael Riley, Wilfred Vermerris
Adenoviruses are double-stranded linear DNA (dsDNA) viruses from the family Adenoviridae, with a genome of approximately 36 kilobasepairs (kb) (Graham and Prevec 1995). Unlike retroviruses, adenoviral vectors do not integrate into the host genome, limiting their long-term expression potential. This limitation, however, makes adenoviral vectors a prime candidate for vaccine development. Due to its large genome size, adenovirus-derived vectors can accommodate large DNA inserts, which increases their potential use in gene therapy applications involving entire genes (as opposed to short DNA or RNA fragments). One of the major drawbacks of adenoviral vectors is the immune response they trigger in patients receiving the recombinant virus. This could not only be detrimental to the patient’s overall health but also reduce the effectiveness of the therapeutic DNA being delivered.
Removal of antibiotic resistance genes (ARGs) in various wastewater treatment processes: An overview
Published in Critical Reviews in Environmental Science and Technology, 2022
The removal of ARGs by UV irradiation has been widely explored, as shown in Table 7. The removal efficiency of ARGs by UV irradiation was investigated using four types of ARBs (McKinney & Pruden, 2012). It was found that 5 log reduction of ARBs was achieved by UV irradiation, ranging from 10 to 20 mJ/cm2. Even ARBs from the same genus displayed different response to UV irradiation (Shen et al., 2020), reflecting different response of bacteria to various wavelengths, resulting in different ARGs inactivation degree (Chen et al., 2009). A negative correlation was also found between genome size and ARB as well as ARGs removal (Liu et al., 2020; Krzeminski et al., 2020). Generally, higher irradiation resulted in higher removal efficiency of ARGs (Liu & Hu, 2020; Zhang, Zhuang, et al., 2015).
Hexavalent chromium bioremediation with insight into molecular aspect: an overview
Published in Bioremediation Journal, 2021
Sreejita Ghosh, Amrita Jasu, Rina Rani Ray
Another highly tolerant fungal strain of Aspergillus flavus strain TERIBR1 exhibited a capacity to withstand and survive under chromium stress as high as 250 mg/l. The genome size of this strain was found to be around 37.7 Mb and it codes for about 13,587 genes for chromium stress tolerance (Singh et al. 2019). It has been reported that some naturally induced mutations or genetic polymorphisms in the strain of Aspergillus flavus to adapt to chromium stress and employ various mechanisms to combat or overcome this heavy metal stress (Jaiswar et al. 2018). Thus, the structural modifications in transporter proteins and enzymes have been found to confer resistivity against hexavalent chromium pollution.
Saccharomyces cerevisiae and newly isolated Candida boidinii co-fermentation of industrial tea waste for improved bioethanol production
Published in Energy Sources, Part A: Recovery, Utilization, and Environmental Effects, 2022
Ekin Demiray, Eda Açıkel, Sevgi Ertuğrul Karatay, Gönül Dönmez
Candida boidinii belongs to the Ascomycota division and can be isolated in various environments such as wine fermentation, soil, seawater, or sugar-contained crops. Its genome size is around 19.000.000 bp with 5900 protein-coding genes. GC content of C. boidinii species is also ranged between 30.9% and 32.7%. (Camiolo et al. 2017). The morphology of the species is long-ovoid to cylindrical shapes with 2–4 × 4–20 µm. Cells can be found single, in pairs, or chains. A pellicle formation can also be observed (Kurtzman, Fell, and Boekhout 2011).