In silico study on <i>Arabidopsis BAG</i> gene expression in response to environmental stresses

Nawkar, Ganesh M.,Maibam, Punyakishore,Park, Joung Hun,Woo, Su Gyeong,Kim, Cha Young,Lee, Sang Yeol,Kang, Chang Ho Springer Vienna 2017 Protoplasma Vol.254 No.1

<P>BAG (Bcl-2 athanogene) family proteins are conserved in a wide range of eukaryotes, and they have been proposed to play a crucial role in plant programmed cell death (PCD). During the past decade, with the help of advanced bioinformatics tools, seven homologs of <I>BAG</I> genes have been identified in the <I>Arabidopsis</I> genome; these genes are involved in pathogen attack and abiotic stress conditions. In this study, gene expression of <I>Arabidopsis BAG</I> family members under environmental stresses was analyzed using the Botany Array Resource (BAR) expression browser tool and the in silico data were partially confirmed by qRT-PCR analysis for the selected stress- and hormone-treated conditions related to environmental stresses. Particularly, the induction of <I>AtBAG6</I> gene in response to heat shock was confirmed by using GUS reporter lines. The loss of the <I>AtBAG6</I> gene resulted into impairment in basal thermotolerance of plant and showed enhanced cell death in response to heat stress. To elucidate the regulatory mechanisms of <I>BAG</I> genes, we analyzed ∼1-kbp promoter regions for the presence of stress-responsive elements. Our transcription profiling finally revealed that the <I>Arabidopsis BAG</I> genes differentially respond to environmental stresses under the control of specifically organized upstream regulatory elements.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00709-016-0961-3) contains supplementary material, which is available to authorized users.</P>

Determinants of muscle carnosine content

Harris, R. C.,Wise, J. A.,Price, K. A.,Kim, H. J.,Kim, C. K.,Sale, C. Springer Vienna 2012 Amino acids Vol.43 No.1

<P>The main determinant of muscle carnosine (M-Carn) content is undoubtedly species, with, for example, aerobically trained female vegetarian athletes [with <I>circa</I> 13 mmol/kg dry muscle (dm)] having just 1/10th of that found in trained thoroughbred horses. Muscle fibre type is another key determinant, as type II fibres have a higher M-Carn or muscle histidine containing dipeptide (M-HCD) content than type I fibres. In vegetarians, M-Carn is limited by hepatic synthesis of β-alanine, whereas in omnivores this is augmented by the hydrolysis of dietary supplied HCD’s resulting in muscle levels two or more times higher. β-alanine supplementation will increase M-Carn. The same increase in M-Carn occurs with administration of an equal molar quantity of carnosine as an alternative source of β-alanine. Following the cessation of supplementation, M-Carn returns to pre-supplementation levels, with an estimated t<SUB>1/2</SUB> of 5–9 weeks. Higher than normal M-Carn contents have been noted in some chronically weight-trained subjects, but it is unclear if this is due to the training <I>per se</I>, or secondary to changes in muscle fibre composition, an increase in β-alanine intake or even anabolic steroid use. There is no measureable loss of M-Carn with acute exercise, although exercise-induced muscle damage may result in raised plasma concentrations in equines. Animal studies indicate effects of gender and age, but human studies lack sufficient control of the effects of diet and changes in muscle fibre composition.</P>

Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification

Bao, Yiming,Chetvernin, Vyacheslav,Tatusova, Tatiana Springer Vienna 2014 Archives of virology Vol.159 No.12

<P>The number of viral genome sequences in the public databases is increasing dramatically, and these sequences are playing an important role in virus classification. Pairwise sequence comparison is a sequence-based virus classification method. A program using this method calculates the pairwise identities of virus sequences within a virus family and displays their distribution, and visual analysis helps to determine demarcations at different taxonomic levels such as strain, species, genus and subfamily. Subsequent comparison of new sequences against existing ones allows viruses from which the new sequences were derived to be classified. Although this method cannot be used as the only criterion for virus classification in some cases, it is a quantitative method and has many advantages over conventional virus classification methods. It has been applied to several virus families, and there is an increasing interest in using this method for other virus families/groups. The Pairwise Sequence Comparison (PASC) classification tool was created at the National Center for Biotechnology Information. The tool’s database stores pairwise identities for complete genomes/segments of 56 virus families/groups. Data in the system are updated every day to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool (http://www.ncbi.nlm.nih.gov/sutils/pasc/) makes it easy to navigate and perform analyses. Multiple new viral genome sequences can be tested simultaneously with this system to suggest the taxonomic position of virus isolates in a specific family. PASC eliminates potential discrepancies in the results caused by different algorithms and/or different data used by researchers.</P>

Resection frequency map after awake resective surgery for non-lesional neocortical epilepsy involving eloquent areas

Kim, Young-Hoon,Kim, Chi Heon,Kim, June Sic,Lee, Sang Kun,Chung, Chun Kee Springer Vienna 2011 Acta neurochirurgica Vol.153 No.9

<P><B>Background</B></P><P>The resection of eloquent areas is challenging due to postoperative neurological deficits. The purpose of this study was to assess the efficacy and risk of awake brain surgery for non-lesional epilepsy involving the eloquent areas or their adjacent areas and to advocate the generation of a resection frequency map.</P><P><B>Methods</B></P><P>We enrolled 55 patients who underwent awake surgery between 1994 and 2007 for non-lesional epilepsy involving the primary sensori-motor or language areas. All patients underwent two-staged operations including subdural electrode monitoring and awake resective surgery. For each case, the preoperative and postoperative images were spatially normalized and compared on a standard atlas, and the resection map was then computed by summing up each resected area on the atlas.</P><P><B>Results</B></P><P>The postoperative seizure outcome was Engel class I in 27 patients (49.1%), II in nine (16.4%), III in 14 (25.5%) and IV in five (9.1%). Ten patients (18.2%) experienced postoperative neurological deficits including seven transient (12.7%) and three permanent, but mild ones (5.5%). The neurological complication rate of purely eloquent area resection was 36.8% (7/19). The resection frequency map computed in this study showed that the resection of eloquent areas was tolerable, with the exception of the Broca’s area.</P><P><B>Conclusions</B></P><P>Awake resective surgery with intraoperative brain mapping is an effective and safe treatment option for non-lesional epilepsy involving eloquent areas. The resection frequency map can show the resected area of a group as well as individuals and provide an objective measure of neurological risk.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00701-011-1074-6) contains supplementary material, which is available to authorized users.</P>

Complete genome sequence of a novel avian paramyxovirus isolated from wild birds in South Korea

Jeong, Jipseol,Kim, Youngsik,An, Injung,Wang, Seung-Jun,Kim, Yongkwan,Lee, Hyun-Jeong,Choi, Kang-Seuk,Im, Se-Pyeong,Min, Wongi,Oem, Jae-Ku,Jheong, Weonhwa Springer Vienna 2018 Archives of virology Vol.163 No.1

<P>A novel avian paramyxovirus (APMV), Cheonsu1510, was isolated from wild bird feces in South Korea and serologically and genetically characterized. In hemagglutination inhibition tests, antiserum against Cheonsu1510 showed low reactivity with other APMVs and <I>vice versa</I>. The complete genome of Cheonsu1510 comprised 15,408 nucleotides, contained six open reading frames (3’-N-P-M-F-HN-L-5’), and showed low sequence identity to other APMVs (< 63%) and a unique genomic composition. Phylogenetic analysis revealed that Cheonsu1510 was related to but distinct from APMV-1, -9, and -15. These results suggest that Cheonsu1510 represents a new APMV serotype, APMV-17.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00705-017-3588-6) contains supplementary material, which is available to authorized users.</P>

Novel reassortant clade 2.3.4.4 avian influenza A (H5N8) virus in a grey heron in South Korea in 2017

Woo, Chanjin,Kwon, Jung-Hoon,Lee, Dong-Hun,Kim, Youngsik,Lee, Kwanghee,Jo, Seong-Deok,Son, Ki dong,Oem, Jae-Ku,Wang, Seung-Jun,Kim, Yongkwan,Shin, Jeonghwa,Song, Chang-Seon,Jheong, Weonhwa,Jeong, Jips Springer Vienna 2017 Archives of virology Vol.162 No.12

<P>We report the identification of a novel reassortant clade 2.3.4.4 H5N8 virus from a dead grey heron in Korea in 2017. Outbreaks of clade 2.3.4.4 H5 HPAIVs have been reported worldwide, and they have evolved into multiple genotypes among wild birds. Phylogenetic analysis indicated that this virus likely originated from Qinghai Lake and Western Siberia and further evolved through reassortment with Eurasian LPAI during the 2016 fall migration of wild birds. Enhanced surveillance and comparative genetic analysis will help to monitor the further evolution and dissemination of clade 2.3.4.4 HPAIVs.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00705-017-3547-2) contains supplementary material, which is available to authorized users.</P>

Plasmodesmal receptor-like kinases identified through analysis of rice cell wall extracted proteins

Jo, Yeonhwa,Cho, Won Kyong,Rim, Yeonggil,Moon, Juyeon,Chen, Xiong-Yan,Chu, Hyosub,Kim, Cha Young,Park, Zee-Yong,Lucas, William J.,Kim, Jae-Yean Springer Vienna 2011 Protoplasma Vol.248 No.1

<P>In plants, plasmodesmata (PD) are intercellular channels that function in both metabolite exchange and the transport of proteins and RNAs. Currently, many of the PD structural and regulatory components remain to be elucidated. Receptor-like kinases (RLKs) belonging to a notably expanded protein family in plants compared to the animal kingdom have been shown to play important roles in plant growth, development, pathogen resistance, and cell death. In this study, cell biological approaches were used to identify potential PD-associated RLK proteins among proteins contained within cell walls isolated from rice callus cultured cells. A total of 15 rice RLKs were investigated to determine their subcellular localization, using an <I>Agrobacterium</I>-mediated transient expression system. Of these six PD-associated RLKs were identified based on their co-localization with a viral movement protein that served as a PD marker, plasmolysis experiments, and subcellular localization at points of wall contact between spongy mesophyll cells. These findings suggest potential PD functions in apoplasmic signaling in response to environmental stimuli and developmental inputs.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00709-010-0251-4) contains supplementary material, which is available to authorized users.</P>

Isoprenyl carboxyl methyltransferase inhibitors: a brief review including recent patents

Yang, Woo Seok,Yeo, Seung-Gu,Yang, Sungjae,Kim, Kyung-Hee,Yoo, Byong Chul,Cho, Jae Youl Springer Vienna 2017 Amino acids Vol.49 No.9

<P>Among the enzymes involved in the post-translational modification of Ras, isoprenyl carboxyl methyltransferase (ICMT) has been explored by a number of researchers as a significant enzyme controlling the activation of Ras. Indeed, inhibition of ICMT exhibited promising anti-cancer activity against various cancer cell lines. This paper reviews patents and research articles published between 2009 and 2016 that reported inhibitors of ICMT as potential chemotherapeutic agents targeting Ras-induced growth factor signaling. Since ICMT inhibitors can modulate Ras signaling pathway, it might be possible to develop a new class of anti-cancer drugs targeting Ras-related cancers. Researchers have discovered indole-based small-molecular ICMT inhibitors through high-throughput screening. Researchers at Duke University identified a prototypical inhibitor, cysmethynil. At Singapore University, Ramanujulu and his colleagues patented more potent compounds by optimizing cysmethynil. In addition, Rodriguez and Stevenson at Universidad Complutense De Madrid and Cancer Therapeutics CRC PTY Ltd., respectively, have developed inhibitors based on formulas other than the indole base. However, further optimization of chemicals targeted to functional groups is needed to improve the characteristics of ICMT inhibitors related to their application as drugs, such as solubility, effectiveness, and safety, to facilitate clinical use.</P>