• Molecules and Cells
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• v.27 no.5
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• pp.539-546
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• 2009

In Saccharomyces cerevisiae, ribosomal protein L7, one of the ~46 ribosomal proteins of the 60S subunit, is encoded by paralogous RPL7A and RPL7B genes. The amino acid sequence identity between RPl7a and RPl7b is 97 percent; they differ by only 5 amino acid residues. Interestingly, despite the high sequence homology, Rpl7b is detected in both the cytoplasm and the nucleolus, whereas Rpl7a is detected exclusively in the cytoplasm. A site-directed mutagenesis experiment revealed that the change in the amino acid sequence of Rpl7b does not influence its subcellular localization. In addition, introns of RPL7A and RPL7B did not affect the subcellular localization of Rpl7a and Rpl7b. Remarkably, Rpl7b was detected exclusively in the cytoplasm in rpl7a knockout mutant, and overexpression of Rpl7a resulted in its accumulation in the nucleolus, indicating that the subcellular localization of Rpl7a and Rpl7b is influenced by the intracellular level of Rpl7a. Rpl7b showed a wide range of localization patterns, from exclusively cytoplasmic to exclusively nucleolar, in knockout mutants for some rRNA-processing factors, nuclear pore proteins, and large ribosomal subunit assembly factors. Rpl7a, however, was detected exclusively in the cytoplasm in these mutants. Taken together, these results suggest that although Rpl7a and Rpl7b are paralogous and functionally replaceable with each other, their precise physiological roles may not be identical.

• ALGAE
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• v.17 no.1
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• pp.59-68
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• 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.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.11 no.4
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• pp.2002-2019
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• 2017

RPL routing protocol for low-power and lossy networks is an Internet Engineering Task Force (IETF) recommended IPv6 based protocol for routing over Low power Lossy Networks (LLNs). RPL is proposed for networks with characteristics like small packet size, low bandwidth, low data rate, lossy wireless links and low power. RPL is a proactive routing protocol that creates a Directed Acyclic Graph (DAG) of the network topology. RPL is increasingly used for Internet of Things (IoT) which comprises of heterogeneous networks and applications. RPL proposes a single path routing strategy. The forwarding technique of RPL does not support multiple paths between source and destination. Multipath routing is an important strategy used in both sensor and ad-hoc network for performance enhancement. Multipath routing is also used to achieve multi-fold objectives including higher reliability, increase in throughput, fault tolerance, congestion mitigation and hole avoidance. In this paper, M-RPL (Multi-path extension of RPL) is proposed, which aims to provide temporary multiple paths during congestion over a single routing path. Congestion is primarily detected using buffer size and packet delivery ratio at forwarding nodes. Congestion is mitigated by creating partially disjoint multiple paths and by avoiding forwarding of packets through the congested node. Detailed simulation analysis of M-RPL against RPL in both grid and random topologies shows that M-RPL successfully mitigates congestion and it enhances overall network throughput.

• Fisheries and Aquatic Sciences
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• v.19 no.4
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• pp.21.1-21.11
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• 2016

Background: The evaluation of suitable reference genes as normalization controls is a prerequisite requirement for launching quantitative reverse transcription-PCR (RT-qPCR)-based expression study. In order to select the stable reference genes in abalone Haliotis discus hannai tissues (gill and hepatopancreas) under heavy metal exposure conditions (Cu, Zn, and Cd), 12 potential candidate housekeeping genes were subjected to expression stability based on the comprehensive ranking while integrating four different statistical algorithms (geNorm, NormFinder, BestKeeper, and ${\Delta}CT$ method). Results: Expression stability in the gill subset was determined as RPL7 > RPL8 > ACTB > RPL3 > PPIB > RPL7A > EF1A > RPL4 > GAPDH > RPL5 > UBE2 > B-TU. On the other hand, the ranking in the subset for hepatopancreas was RPL7 > RPL3 > RPL8 > ACTB > RPL4 > EF1A > RPL5 > RPL7A > B-TU > UBE2 > PPIB > GAPDH. The pairwise variation assessed by the geNorm program indicates that two reference genes could be sufficient for accurate normalization in both gill and hepatopancreas subsets. Overall, both gill and hepatopancreas subsets recommended ribosomal protein genes (particularly RPL7) as stable references, whereas traditional housekeepers such as ${\beta}-tubulin$ (B-TU) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes were ranked as unstable genes. The validation of reference gene selection was confirmed with the quantitative assay of MT transcripts. Conclusions: The present analysis showed the importance of validating reference genes with multiple algorithmic approaches to select genes that are truly stable. Our results indicate that expression stability of a given reference gene could not always have consensus across tissue types. The data from this study could be a good guide for the future design of RT-qPCR studies with respect to metal regulation/detoxification and other related physiologies in this abalone species.

• Journal of Communications and Networks
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• v.17 no.6
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• pp.647-655
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• 2015

Low-power and lossy networks (LLNs) comprised of thousands of embedded networking devices can be used in a variety of applications, such as smart grid automated metering infrastructures (AMIs) and wireless sensor networks. Connecting these LLNs to the Internet has even greater potential, leading to the emerging concept of the Internet of Things (IoT). With the goal of integrating LLNs into IoT, the IETF has recently standardized RPL and 6LoWPAN to allow the use of IPv6 on LLNs. Although there already exist several studies on the the performance of RPL and embedded IPv6 stack in LLN, performance measurement and characterization of TCP over RPL in multihop LLNs is yet to be studied. In this article, we present a comprehensive experimental study on the performance of TCP over RPL in an embedded IPv6-based LLN running over a 30-node multihop IEEE 802.15.4 testbed network. Our results and findings are aimed at investigating how embedded TCP interoperates with common Linux TCP and underlying RPL (and vice versa), which furthers our understanding of the performance trade-offs when choosing TCP over RPL in IPv6-based LLNs.

• Clinical and Experimental Reproductive Medicine
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• v.47 no.2
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• pp.122-129
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• 2020

Objective: The survival of a semi-allogeneic fetus depends on several immunological mechanisms, and it has been suggested that recurrent pregnancy loss (RPL) could develop as a result of one or more immunological abnormalities. Methods: Compatibility between partners for human leukocyte antigen (HLA) genotypes and the relationships between maternal killer-cell immunoglobulin-like receptor (KIR) and paternal HLA-Bw4/Bw6 and HLA-C1/C2 supra-groups were investigated in 25 couples with RPL in comparison to healthy couples with children. HLA and KIR genotyping was performed using polymerase chain reaction with sequence-specific primers and/or sequence-specific oligonucleotides. Results: HLA class I incompatibility between partners, especially in HLA-B alleles, was more common in the RPL group (p= 0.01). HLA-C2 homozygosity was more frequent in the male partners of RPL couples than in other groups (p= 0.03). The KIR2DL5 gene frequency was significantly higher in both the female and male partners of RPL couples, whereas the KIR2DS3 gene frequency in male partners of RPL couples was significantly reduced (p= 0.03). The presence of KIR2DL3 in women with RPL was correlated with the presence of HLA-C2 alleles in their spouses (p= 0.03). Conclusion: Our data from a Turkish population suggest that male HLA-C2 homozygosity may play an important role in RPL. Additionally, an incidental match between male HLA-C2 and female HLA-C1 ligand KIR receptors might perturb the balance between activatory and inhibitory KIR-ligand interactions during pregnancy in couples affected by RPL. The roles of orphan KIR2DL5 and orphan KIR2DS3 in RPL remain obscure.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.2
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• pp.168-172
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• 2006

In this study. the transcriptional features of a 2.8 kb region spanning the sigH and rplA genes of Bacillus subtilis were clarified using synthetic oligonucleotides complementary to the transcripts of the rpmG, secE, nusG, and rplK genes. The 5' ends of three transcripts corresponding to this region were located and mapped on the chromosome via primer extension analysis. Three regions, designated Prg, Pn, and Prk, which partially share the consensus sequence recognized by ${\sigma}^A$ RNA polymerase, were theorized to function as promoter elements. The rpmG and secE genes of B. subtilis were cotranscribed from the designated prg promoter, whereas the nusG and rplK genes were transcribed separately from the Pn and Prk promoters, respectively. Accordingly, the transcriptional features, as well as the gene organization, of the region encompassing the sigH and rplA genes of B. subtilis, including the rpmG-secE-nusG-rplK genes, were determined to be distinct from those of Escherichia coli. Divergences in terms of gene organization and transcriptional features within the relevant region would serve as excellent criteria for the delineation of phylogenetic relationships among bacteria.

• Journal of KIISE
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• v.43 no.11
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• pp.1233-1244
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• 2016

In the IoT network environments for LLNs(Low power and Lossy networks), IPv6 Routing Protocol for Low Power and Lossy networks(RPL) has been proposed by IETF(Internet Engineering Task Force). The goal of RPL is to create a directed acyclic graph, without loops. As recommended by the IETF standard, RPL route recovery mechanisms in the event of a failure of a node should avoid loop, loop detection, DIO Poisoning. In this process, route recovery time and control message might be increased in the sub-tree because of the repeated route search. In this paper, we suggested RPL route recovery method to solve the routing overhead problem in the sub-tree during a loss of a link in the RPL routing protocol based on IoT wireless networks. The proposed method improved local repair process by utilizing a route that could not be selected as the preferred existing parents. This reduced the traffic control packet, especially in the disconnected node's sub tree. It also resulted in a quick recovery. Our simulation results showed that the proposed RPL local repair reduced the recovery time and the traffic of control packets of RPL. According to our experiment results, the proposed method improved the recovery performance of RPL.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.51 no.1
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• pp.95-106
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• 2018

To evaluate appropriate reference genes for the normalization of quantitative reverse transcription PCR (RT-qPCR) data with embryonic and larval samples from Russian sturgeon Acipenser gueldenstaedtii, the expression stability of eight candidate housekeeping genes, including beta-actin (ACTB), elongation factor-1A (EF1A), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), histone 2A (H2A), ribosomal protein L5 (RPL5), ribosomal protein L7 (RPL7), succinate dehydrogenase (SDHA), and ubiquitin-conjugating enzyme E2 (UBE2A), were tested using embryonic samples from 12 developmental stages and larval samples from 11 ontogenic stages. Based on the stability rankings from three statistic software packages, geNorm, NormFinder, and BestKeeper, the expression stability of the embryonic subset was ranked as UBE2A>H2A>SDHA>GAPDH>RPL5>EF1A>ACTB>RPL7. On the other hand, the ranking in the larval subset was determined as UBE2A>GAPDH>SDHA>RPL5>RPL7>H2A>EF1A>AC TB. When the two subsets were combined, the overall ranking was UBE2A>SDHA>H2A>RPL5>GAPDH>EF1A>ACTB>RPL7. Taken together, our data suggest that UBE2A and SDHA are recommended as suitable references for developmental and ontogenic samples of this sturgeon species, whereas traditional housekeepers such as ACTB and GAPDH may not be suitable candidates.

• Journal of the Korea Institute of Information Security & Cryptology
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• v.26 no.3
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• pp.655-659
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• 2016

In this paper, we propose new detection and detour methods against packet drop attacks for availability in the Internet of Things (IoT) based on the IEEE 802.15.4e and RPL protocol standards that employ IPv6. We consider the rank value of RPL and the consecutive packet drops to improve the detection metrics, and also take into account the use of both sibling and child nodes on a RPL routing path to construct the detour method. Our simulation results show that the proposed detection method is faster than the previous result, and the detour method improves the detour success rate.