• ALGAE
• /
• v.17 no.1
• /
• pp.59-68
• /
• 2002

A phylogenetic affinity between charophytes and embryophytes (land plants) has been explained by a few chloroplast genomic characters including gene and intron (Manhart and Palmer 1990; Baldauf et al. 1990; Lew and Manhart 1993). Here we show that a charophyte, Spirogyra maxima, has the largest operon of angiosperm chloroplast genomes, rpl23 operon (trnⅠ-rpl23-rpl2-rps19-rpl22-rps3-rpl16-rpl14-rps8-infA-rpl36-rps11-rpoA) containing both embryophyte introns, rpl16.i and rpl2.i. The rpl23 gene cluster of Spirogyra contains a distinct eubacterial promoter sequence upstream of rpl23, which is the first gene of the green algal rpl23 gene cluster. This sequence is completely absent in angiosperms but is present in non-flowering plants. The results imply that, in the rpl23 gene cluster, early charophytes had at least two promoters, one upstream of trnⅠ and and another upstream of rpl23, which partially or completely lost its function in land plants. A comparison of gene clusters of prokaryotes, algal chloroplast DNAs and land plant cpDNAs indicated a loss of numerous genes in chlorophyll a+b eukaryotes. A phylogenetic analysis using presence/absence of genes and introns as characters produced trees with a strongly supported clade containing chlorophyll a+b eukaryotes. Spirogyra and embryophytes formed a clade characterized by the loss of rpl5 and rps9 and the gain of trnⅠ (CAU) and introns in rpl2 and rpl16. The analyses support the hypothesis that the rpl23 gene cluster and the rpl2 and rpl16 introns of land plants originated from a common ancestor of Spirogyra and land plants.

• Journal of the Korea Institute of Information and Communication Engineering
• /
• v.23 no.12
• /
• pp.1679-1686
• /
• 2019

The main purpose of this research is to propose an approach for solving the packet loss problem by quickly adapting to topology change when nodes move in RPL-based IoT environment. In order to enhance mobility, every node is aware of the mobility of its neighbor nodes and quantifies the mobility level based on the number of control messages and all received packets. According to the mobility level, the DIO timer is changed. The proposed approach allows nodes to change their DIO timers according to their mobility levels to adapt topology changes and update paths to the sink. The performance of the proposed approach is evaluated using a Contiki-based Cooja simulator in various moving speeds. The simulation results show that the proposed approach copes with mobility scenarios better than the standard RPL by ascertaining that the packet delivery ratio is improved by 31.03%.

• Animal Bioscience
• /
• v.36 no.11
• /
• pp.1666-1684
• /
• 2023

Objective: Our objective was to examine the relationships of supplemental rumen-protected lysine (RPL) or lysine + methionine (RPLM) on lactational performance, plasma amino acids (AA) concentration, and nitrogen use efficiency of lactating dairy cows by using a meta-analysis approach. Methods: A total of 56 articles comprising 77 experiments with either RPL or RPLM supplementation were selected and analyzed using a mixed model methodology by considering the treatments and other potential covariates as fixed effects and different experiments as random effects. Results: In early lactating cows, milk yield was linearly increased by RPL (β₁ = 0.013; p<0.001) and RPLM (β₁ = 0.014; p<0.028) but 3.5% fat-corrected milk (FCM) and energy-corrected milk (ECM) (kg/d) was increased by only RPL. RPL and RPLM did not affect dry matter intake (DMI) but positively increased (p<0.05) dairy efficiency (Milk yield/DMI and ECM/DMI). As a percentage, milk fat, protein, and lactose were unchanged by RPL or RPLM but the yield of all components was increased (p<0.05) by feeding RPL while only milk protein was increased by feeding RPLM. Plasma Lys concentration was linearly increased (p<0.05) with increasing supplemental RPL while plasma Met increased (p<0.05) by RPLM supplementation. The increase in plasma Lys had a strong linear relationship (R² = 0.693 in the RPL dataset and R² = 0.769 in the RPLM dataset) on milk protein synthesis (g/d) during early lactation. Nitrogen metabolism parameters were not affected by feeding RPL or RPLM, either top-dress or when supplemented to deficient diets. Lactation performance did not differ between AA-deficient or AA-adequate diets in response to RPL or RPLM supplementation. Conclusion: RPL or RPLM showed a positive linear relationship on the lactational performance of dairy cows whereas greater improvement effects were observed during early lactation. Supplementing RPL or RPLM is recommended on deficient-AA diet but not on adequate-AA diet.

• Journal of Microbiology and Biotechnology
• /
• v.19 no.3
• /
• pp.238-249
• /
• 2009

The genus Listeria consists of six closely related species and forms three phylogenetic groups: L. monocytogenes-L. innocua, L. ivanovii-L. seeligeri-L. welshimeri, and L. grayi. In this report, we attempted to examine the evolutionary relationship in the L. monocytogenes-L. innocua group by probing the nucleotide sequences of 23S rRNA and 16S rRNA, and the gene clusters lmo0029-lmo0042, ascB-dapE, rplS-infC, and prs-ldh in L. monocytogenes serovars 1/2a, 4a, and 4b, and L. innocua. Additionally, we assessed the status of L. monocytogenes-specific inlA and inlB genes and 10 L. innocua-specific genes in these species/serovars, together with phenotypic characterization by using in vivo and in vitro procedures. The results indicate that L. monocytogenes serovar 4a strains are genetically similar to L. innocua in the lmo0035-lmo0042, ascB-dapE, and rplS-infC regions and also possess L. innocua-specific genes lin0372 and lin1073. Furthermore, both L. monocytogenes serovar 4a and L. innocua exhibit impaired intercellular spread ability and negligible pathogenicity in mouse model. On the other hand, despite resembling L. monocytogenes serovars 1/2a and 4b in having a nearly identical virulence gene cluster, and inlA and inlB genes, these serovar 4a strains differ from serovars 1/2a and 4b by harboring notably altered actA and plcB genes, displaying strong phospholipase activity and subdued in vivo and in vitro virulence. Thus, by possessing many genes common to L. monocytogenes serovars 1/2a and 4b, and sharing many similar gene deletions with L. innocua, L. monocytogenes serovar 4a represents a possible evolutionary intermediate between L. monocytogenes serovars 1/2a and 4b and L. innocua.

• Journal of Ginseng Research
• /
• v.44 no.1
• /
• pp.135-144
• /
• 2020

Background: Panax species are important herbal medicinal plants in the Araliaceae family. Recently, we reported the complete chloroplast genomes and 45S nuclear ribosomal DNA sequences from seven Panax species, two (P. quinquefolius and P. trifolius) from North America and five (P. ginseng, P. notoginseng, P. japonicus, P. vietnamensis, and P. stipuleanatus) from Asia. Methods: We conducted phylogenetic analysis of these chloroplast sequences with 12 other Araliaceae species and comprehensive comparative analysis among the seven Panax whole chloroplast genomes. Results: We identified 1,128 single nucleotide polymorphisms (SNP) in coding gene sequences, distributed among 72 of the 79 protein-coding genes in the chloroplast genomes of the seven Panax species. The other seven genes (including psaJ, psbN, rpl23, psbF, psbL, rps18, and rps7) were identical among the Panax species. We also discovered that 12 large chloroplast genome fragments were transferred into the mitochondrial genome based on sharing of more than 90% sequence similarity. The total size of transferred fragments was 60,331 bp, corresponding to approximately 38.6% of chloroplast genome. We developed 18 SNP markers from the chloroplast genic coding sequence regions that were not similar to regions in the mitochondrial genome. These markers included two or three species-specific markers for each species and can be used to authenticate all the seven Panax species from the others. Conclusion: The comparative analysis of chloroplast genomes from seven Panax species elucidated their genetic diversity and evolutionary relationships, and 18 species-specific markers were able to discriminate among these species, thereby furthering efforts to protect the ginseng industry from economically motivated adulteration.