scholarly journals Influence of Non-canonical DNA Bases on the Genomic Diversity of Tevenvirinae

2021 ◽  
Vol 12 ◽  
Author(s):  
Nikita A. Nikulin ◽  
Andrei A. Zimin
Keyword(s):  
Life Cycle ◽  
Comparative Analysis ◽  
Essential Role ◽  
Phage Therapy ◽  
Genomic Diversity ◽  
Dna Bases ◽  
Model Organisms ◽  
Major Influence ◽  
Evolutionary Analysis ◽  
Canonical Bases

The Tevenvirinae viruses are some of the most common viruses on Earth. Representatives of this subfamily have long been used in the molecular biology studies as model organisms – since the emergence of the discipline. Tevenvirinae are promising agents for phage therapy in animals and humans, since their representatives have only lytic life cycle and many of their host bacteria are pathogens. As confirmed experimentally, some Tevenvirinae have non-canonical DNA bases. Non-canonical bases can play an essential role in the diversification of closely related viruses. The article performs a comparative and evolutionary analysis of Tevenvirinae genomes and components of Tevenvirinae genomes. A comparative analysis of these genomes and the genes associated with the synthesis of non-canonical bases allows us to conclude that non-canonical bases have a major influence on the divergence of Tevenvirinae viruses within the same habitats. Supposedly, Tevenvirinae developed a strategy for changing HGT frequency in individual populations, which was based on the accumulation of proteins for the synthesis of non-canonical bases and proteins that used those bases as substrates. Owing to this strategy, ancestors of Tevenvirinae with the highest frequency of HGT acquired genes that allowed them to exist in a certain niche, and ancestors with the lowest HGT frequency preserved the most adaptive of those genes. Given the origin and characteristics of genes associated with the synthesis of non-canonical bases in Tevenvirinae, one can assume that other phages may have similar strategies. The article demonstrates the dependence of genomic diversity of closely related Tevenvirinae on non-canonical bases.

scholarly journals Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12173
Author(s):  
Jiajing Sheng ◽  
Xuan She ◽  
Xiaoyu Liu ◽  
Jia Wang ◽  
Zhongli Hu
Keyword(s):  
Comparative Analysis ◽  
Codon Usage ◽  
Related Species ◽  
Influencing Factor ◽  
Model Organisms ◽  
Evolutionary Analysis ◽  
Optimal Codons ◽  
Chloroplast Genomes ◽  
Representative Species ◽  
Usage Patterns

Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4–11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.

Zophobas atratus (Fabricius, 1775) – new genus and species of darkling beetles (Coleoptera, Tenebrionidae) for the fauna of Ukraine

2018 ◽  
Vol 14 (1) ◽  
pp. 10-24
Author(s):  
V. N. Fursov ◽  
L. S. Cherney
Keyword(s):  
Life Cycle ◽  
Comparative Analysis ◽  
Sexual Dimorphism ◽  
Antennal Segment ◽  
Laboratory Culture ◽  
Important Species ◽  
Darkling Beetles ◽  
Zophobas Atratus ◽  
Sensory Zone ◽  
Coleoptera Tenebrionidae

Darkling beetle Zophobas atratus (Coleoptera, Tenebrionidae) is recorded here for the first time as a new species for the fauna of Ukraine. Detailed study on morphology of preimaginal stages and biology of this species recently introduced to Ukraine, is given here. Zophobas atratus is an important species being easily reared in laboratory cultures and widely distributed in North and South America, Europe, and Asia. Detailed descriptions of all life stages, including egg, young and older larvae, pupa and adult of Z. atratus are required for further taxonomical study of the genus Zophobas, which isn’t yet definitively established. New identification keys for adults and larvae of the genera of tribe Tenebrionini are presented here, based on a comparative analysis of the taxonomic characters of adults and larvae of Z. atratus and species from the genera Tenebrio and Neatus. Comparative analysis of morphology of larva of Z. atratus and larvae of the tribe Cteniopodini of close subfamily Alleculinae was conducted here. The subfamily Alleculinae previously had the rank of family Alleculidae, but our analysis confirmed the reliability of its current taxonomic position as subfamily. The study of morphology of larvae of 1st and 2nd instars of Z. atratus revealed that they are characterized by special taxonomic structures that are not characteristic for oldest instars of larvae of Z. atratus. These characters include absence of spines on caudal segment, presence of a set of 4 setae at posterior margin of tergites of prothorax, metathorax, and 1st to 8th abdominal segments, strongly convex 2nd antennal segment and sensory zone in the form of an open ring on its apex, and etc. Moreover, structure of antenna of larvae of Z. atratus is similar to that of oldest larvae of most species of darkling beetles of the fauna of Ukraine. The most distinctive features of Z. atratus are: sexual dimorphism in structure of clypeus of adults; filiform sclerotized antenna of larva with a continuous sensory zone at apex of 2nd segment, weakly developed 3rd segment; fusion of sclerotized pleurites of 1st–8th abdominal segments with their tergites; sexual dimorphism in structure of 9th abdominal segment of pupa, and presence of two hooks on apex of its appendages. The data of original study of features of life cycle of Z. atratus are given. The pictures and photos of details of morphology of egg, larvae, pupa and adult of Z. atratus are presented. It was recored that life cycle of Z. atratus from laying of egg to the emergence of adult continues from 169 up to 181 days. Adults lived maximum up to 206 days. Maturation of eggs in female after copulation continues 10-11 days. Stage of egg continues 7 days, larva – up to 151 days, including pre-pupal period from 6 to 22 days, pupa – from 8 to 21 days. Twelve larval stages of Z. atratus were recorded in laboratory culture.

scholarly journals The ATXN2 Orthologs CID3 and CID4, Act Redundantly to In-Fluence Developmental Pathways throughout the Life Cycle of Arabidopsis thaliana

2021 ◽  
Vol 22 (6) ◽  
pp. 3068
Author(s):  
Zaira M. López-Juárez ◽  
Laura Aguilar-Henonin ◽  
Plinio Guzmán
Keyword(s):  
Arabidopsis Thaliana ◽  
Life Cycle ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Leaf Growth ◽  
Transcriptome Profiling ◽  
Developmental Pathways ◽  
Model Organisms ◽  
Key Factors

RNA-binding proteins (RBPs) are key elements involved in post-transcriptional regulation. Ataxin-2 (ATXN2) is an evolutionarily conserved RBP protein, whose function has been studied in several model organisms, from Saccharomyces cerevisiae to the Homo sapiens. ATXN2 interacts with poly(A) binding proteins (PABP) and binds to specific sequences at the 3′UTR of target mRNAs to stabilize them. CTC-Interacting Domain3 (CID3) and CID4 are two ATXN2 orthologs present in plant genomes whose function is unknown. In the present study, phenotypical and transcriptome profiling were used to examine the role of CID3 and CID4 in Arabidopsis thaliana. We found that they act redundantly to influence pathways throughout the life cycle. cid3cid4 double mutant showed a delay in flowering time and a reduced rosette size. Transcriptome profiling revealed that key factors that promote floral transition and floral meristem identity were downregulated in cid3cid4 whereas the flowering repressor FLOWERING LOCUS C (FLC) was upregulated. Expression of key factors in the photoperiodic regulation of flowering and circadian clock pathways, were also altered in cid3cid4, as well as the expression of several transcription factors and miRNAs encoding genes involved in leaf growth dynamics. These findings reveal that ATXN2 orthologs may have a role in developmental pathways throughout the life cycle of plants.

scholarly journals Interaction of Pestiviral E1 and E2 Sequences in Dimer Formation and Intracellular Retention

2021 ◽  
Vol 22 (14) ◽  
pp. 7285
Author(s):  
Yu Mu ◽  
Birke Andrea Tews ◽  
Christine Luttermann ◽  
Gregor Meyers
Keyword(s):  
Life Cycle ◽  
Cell Surface ◽  
Double Mutant ◽  
Essential Role ◽  
Infectious Clone ◽  
Intracellular Localization ◽  
Dimer Formation ◽  
Covalent Linkage ◽  
Crucial Step ◽  
Retention Signal

Pestiviruses contain three envelope proteins: Erns, E1, and E2. Expression of HA-tagged E1 or mutants thereof showed that E1 forms homodimers and -trimers. C123 and, to a lesser extent, C171, affected the oligomerization of E1 with a double mutant C123S/C171S preventing oligomerization completely. E1 also establishes disulfide linked heterodimers with E2, which are crucial for the recovery of infectious viruses. Co-expression analyses with the HA-tagged E1 wt/E1 mutants and E2 wt/E2 mutants demonstrated that C123 in E1 and C295 in E2 are the critical sites for E1/E2 heterodimer formation. Introduction of mutations preventing E1/E2 heterodimer formation into the full-length infectious clone of BVDV CP7 prevented the recovery of infectious viruses, proving that C123 in E1 and C295 in E2 play an essential role in the BVDV life cycle, and further support the conclusion that heterodimer formation is the crucial step. Interestingly, we found that the retention signal of E1 is mandatory for intracellular localization of the heterodimer, so that absence of the E1 retention signal directs the heterodimer to the cell surface even though the E2 retention signal is still present. The covalent linkage between E1 and E2 plays an essential role for this process.

scholarly journals Numerical Analysis on Performance of the Middle-Pressure Jet Grouting Method for Ground Improvement

Geosciences ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 313
Author(s):  
Shinya Inazumi ◽  
Sudip Shakya ◽  
Takahiro Komaki ◽  
Yasuharu Nakanishi
Keyword(s):  
Life Cycle ◽  
Comparative Analysis ◽  
Ground Improvement ◽  
Cement Slurry ◽  
Mechanical Agitation ◽  
High Quality ◽  
Jet Grouting ◽  
Computer Aided ◽  
Improvement Method ◽  
Cae System

This study focused on the middle-pressure jet grouting method, which has a complicated development mechanism for the columnar soil-improved body, with the aim of establishing a computer-aided engineering (CAE) system that can simulate the performance on a computer. Furthermore, in order to confirm the effect of middle-pressure jet grouting with mechanical agitation and mixing, a comparative analysis was performed with different jet pressures, the development situation was visualized, and the performance of this method was evaluated. The results of MPS-CAE as one of the CAE systems showed that the cement slurry jet ratio in the planned improvement range, including the periphery of the mixing blade, by the middle-pressure jet grouting together with the mechanical agitation and mixing was increased and a high quality columnar soil-improved body was obtained. It is expected that the introduction of CAE will contribute to the visualization of the ground, and that CAE will be an effective tool for the visual management of construction for ground improvement and the maintenance of improved grounds during the life cycle of the ground-improvement method.

Project Implementation Decision Using Software Development Life Cycle Models: A Comparative Approach

2021 ◽  
Vol 28 (1) ◽  
Author(s):  
M.A. Adeagbo ◽  
J.E.T. Akinsola ◽  
A.A. Awoseyi ◽  
F. Kasali
Keyword(s):  
Life Cycle ◽  
Comparative Analysis ◽  
Software Development ◽  
Cost Estimation ◽  
Comparative Approach ◽  
Project Implementation ◽  
Development Life Cycle ◽  
Software Development Life Cycle ◽  
Waterfall Model ◽  
Spiral Model

Selection of a suitable Software Development Life Cycle (SDLC) model for project implementation is somewhat confusing as there are a lot of SDLC models with similar strengths and weaknesses. Also, the solutions proffered among the researchers so far have been the  qualitative comparative analysis of SDLC models. Hence, this paper proposes a comparative analysis of SDLC models using quantitative approach in relation to strengths and weaknesses of SDLC models. The study adapted comparative analysis and Software Development Life Cycle (SDLC) models features’ classification using ten characteristics such as project complexity, project size, project duration, project with risk, implementation/initial cost, error discovery, associated cost, risk analysis, maintenance and cost estimation. A quantitative measure that employs online survey using experts in software design and engineering, project management and system analysis was carried out for the evaluation of SDLC models. Purposeful Stratified Random Sampling (SRS) technique was used to gather the data for analysis using XLSTAT after pre-processing, taking into consideration both benefit and cost criteria. The overall performance evaluation showed that Spiral-Model is the best followed by V-Model and lastly Waterfall Model with comparative values of 38.63%, 35.76% and 25.61% respectively. As regards cost estimation, Waterfall Model is the most efficient with value of 41%, then V-Model with 31% and lastly Spiral Model with 28%. V-Model has great error recovery capability with value of 45% which is closely followed by Spiral Model with 37% and lastly Waterfall Model with 18%. The study revealed that, a model with efficient risk assurance does not guarantee efficient cost management. In the future work, more characteristics regarding SDLC models shall be considered.

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