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Volume 10, March

BioTech, Volume 9, Issue 4 (December 2020) – 7 articles

Cover Story (view full-size image): Transcripts are initiated in the 5′ and terminated at the 3′ LTR (green and purple). Reverse transcription, generates a cDNA which is inserted into genomic DNA with a short target site duplication (small arrow), leaving the allelic site unaffected. These two alleles, the occupied and empty site accumulate point mutations (illustrated as black dots). The evolutionary fate of these alleles depends on genetic drift and selection. With strong negative selection the occupied site will be lost quickly. Strong positive selection would cause the occupied site allele frequency to increase rapidly. Most extant insertions are selectively neutral, or nearly so and their fate is dependent on random variation (genetic drift) as illustrated in the graph. There are two stable frequencies for neutral alleles, when they are lost and when they are fixed: these alleles follow the famous U-shaped [...] Read more.
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Article
Retrotransposons and the Evolution of Genome Size in Pisum
BioTech 2020, 9(4), 24; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040024 - 26 Nov 2020
Viewed by 1054
Abstract
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of [...] Read more.
Here we investigate the plant population genetics of retrotransposon insertion sites in pea to find out whether genetic drift and the neutral theory of molecular evolution can account for their abundance in the pea genome. (1) We asked whether two contrasting types of pea LTR-containing retrotransposons have the frequency and age distributions consistent with the behavior of neutral alleles and whether these parameters can explain the rate of change of genome size in legumes. (2) We used the recently assembled v1a pea genome sequence to obtain data on LTR-LTR divergence from which their age can be estimated. We coupled these data to prior information on the distribution of insertion site alleles. (3) We found that the age and frequency distribution data are consistent with the neutral theory. (4) We concluded that demographic processes are the underlying cause of genome size variation in legumes. Full article
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Commentary
The Future of Biobanking: What Is Next?
BioTech 2020, 9(4), 23; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040023 - 23 Nov 2020
Cited by 2 | Viewed by 932
Abstract
Biobanks are an extraordinary tool for research and scientific progress. Since their origin, the debate on the main technical, regulatory and ethical aspects has not stopped. The future of biobanks should take into account many factors: the need to improve the technical standards [...] Read more.
Biobanks are an extraordinary tool for research and scientific progress. Since their origin, the debate on the main technical, regulatory and ethical aspects has not stopped. The future of biobanks should take into account many factors: the need to improve the technical standards of collection, conservation and use of the sample, the usefulness of achieving forms of harmonization and common governance, the improvement of biobank networks, including through public–private partnerships and improving the sustainability of these infrastructures. Full article
Review
RNF6 as an Oncogene and Potential Therapeutic Target—A Review
BioTech 2020, 9(4), 22; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040022 - 11 Nov 2020
Viewed by 947
Abstract
The RNF6 gene encodes Ring Finger Protein 6 (RNF6), which functions as a ubiquitin ligase. Its functions are not entirely known, but research shows that it is involved in human cancer development. Initially, this gene was considered to be a tumor suppressor. Numerous [...] Read more.
The RNF6 gene encodes Ring Finger Protein 6 (RNF6), which functions as a ubiquitin ligase. Its functions are not entirely known, but research shows that it is involved in human cancer development. Initially, this gene was considered to be a tumor suppressor. Numerous statistical analyses on cell lines and animals indicate, however, that RNF6 functions as an oncogene, involved in signaling pathways, including SHP1/STAT3, AKT/mTOR, Wnt/β-catenin, or ERα/Bcl-xL. Due to this fact, it has become a potential prognostic factor and therapeutic target. Studies in tumor cells and model organisms using inhibitors such as total saponins from Paris forrestii (TSPf), ellagic acid, or microRNA molecules show the effectiveness of inhibiting RNF6, and through it, the pathways of tumor cell proliferation. The results of the currently available studies are promising, but the function of RNF6 is not fully understood. More research is needed to assess the role of RNF6 and to check the safety and efficacy of inhibitors. Full article
(This article belongs to the Special Issue Feature Papers 2020)
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Article
Transcriptome Sequencing of the Striped Cucumber Beetle, Acalymma vittatum (F.), Reveals Numerous Sex-Specific Transcripts and Xenobiotic Detoxification Genes
BioTech 2020, 9(4), 21; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040021 - 27 Oct 2020
Cited by 1 | Viewed by 1206
Abstract
Acalymma vittatum (F.), the striped cucumber beetle, is an important pest of cucurbit crops in the contintental United States, damaging plants through both direct feeding and vectoring of a bacterial wilt pathogen. Besides providing basic biological knowledge, biosequence data for A. vittatum would [...] Read more.
Acalymma vittatum (F.), the striped cucumber beetle, is an important pest of cucurbit crops in the contintental United States, damaging plants through both direct feeding and vectoring of a bacterial wilt pathogen. Besides providing basic biological knowledge, biosequence data for A. vittatum would be useful towards the development of molecular biopesticides to complement existing population control methods. However, no such datasets currently exist. In this study, three biological replicates apiece of male and female adult insects were sequenced and assembled into a set of 630,139 transcripts (of which 232,899 exhibited hits to one or more sequences in NCBI NR). Quantitative analyses identified 2898 genes differentially expressed across the male–female divide, and qualitative analyses characterized the insect’s resistome, comprising the glutathione S-transferase, carboxylesterase, and cytochrome P450 monooxygenase families of xenobiotic detoxification genes. In summary, these data provide useful insights into genes associated with sex differentiation and this beetle’s innate genetic capacity to develop resistance to synthetic pesticides; furthermore, these genes may serve as useful targets for potential use in molecular-based biocontrol technologies. Full article
(This article belongs to the Special Issue Feature Papers 2020)
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Review
Metabolomics Community in Russia: History of Development, Key Participants, and Results
BioTech 2020, 9(4), 20; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040020 - 25 Oct 2020
Viewed by 1135
Abstract
Metabolomics is the latest trend in the “-omics” sciences, of which technologies are widely used today in all life sciences. Metabolomics gave impetus to the description of biochemical processes that occur in many organisms, search for new biomarkers of disease, and laid the [...] Read more.
Metabolomics is the latest trend in the “-omics” sciences, of which technologies are widely used today in all life sciences. Metabolomics gave impetus to the description of biochemical processes that occur in many organisms, search for new biomarkers of disease, and laid the foundation for new clinical laboratory diagnostics. The purpose of this review is to show how metabolomics is represented in Russian science, what main research areas were chosen, and to demonstrate the successes and main achievements of Russian scientists in this field. The review is dedicated to the 10th anniversary of Russian metabolomics and also touches on the history of the formation of Russian metabolomics and prospects for the future. Full article
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Article
Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex
BioTech 2020, 9(4), 19; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040019 - 23 Sep 2020
Viewed by 1360
Abstract
Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The [...] Read more.
Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1–5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours. Full article
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Editorial
Change of Title: From High-Throughput to BioTech
BioTech 2020, 9(4), 18; https://0-doi-org.brum.beds.ac.uk/10.3390/biotech9040018 - 22 Sep 2020
Viewed by 962
Abstract
Founded in 2012, High-Throughput (formerly Microarrays) is a MDPI peer-reviewed journal that has published 216 articles so far, 29 of which are frequently cited (10 to 100 times) reports [...] Full article
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