Hyun Joo

ClustalXeed : a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment

BackgroundThere is an increasing demand to assemble and align large-scale biological sequence data sets. The commonly used multiple sequence alignment programs are still limited in their ability to handle very large amounts of sequences because the system lacks a scalable high-performance computing (HPC) environment with a greatly extended data storage capacity.ResultsWe designed ClustalXeed, a software system for multiple sequence alignment with incremental improvements over previous versions of the ClustalX and ClustalW-MPI software. The primary advantage of ClustalXeed over other multiple sequence alignment software is its ability to align a large family of protein or nucleic acid sequences. To solve the conventional memory-dependency problem, ClustalXeed uses both physical random access memory (RAM) and a distributed file-allocation system for distance matrix construction and pair-align computation. The computation efficiency of disk-storage system was markedly improved by implementing an efficient load-balancing algorithm, called idle node-seeking task algorithm (INSTA). The new editing option and the graphical user interface (GUI) provide ready access to a parallel-computing environment for users who seek fast and easy alignment of large DNA and protein sequence sets.ConclusionsClustalXeed can now compute a large volume of biological sequence data sets, which were not tractable in any other parallel or single MSA program. The main developments include: 1) the ability to tackle larger sequence alignment problems than possible with previous systems through markedly improved storage-handling capabilities. 2) Implementing an efficient task load-balancing algorithm, INSTA, which improves overall processing times for multiple sequence alignment with input sequences of non-uniform length. 3) Support for both single PC and distributed cluster systems.

Impact of IL2 and IL2RB Genetic Polymorphisms in Kidney Transplantation

Patient genetic make-up may contribute to a higher risk for acute rejection episodes (AREs). Because interleukin-2 (IL2) and IL2 receptor β (IL2RB) play key roles in immune modulation, we investigated the effect of single-nucleotide polymorphisms (SNPs) in the IL2 gene (rs2069762; T>G, promoter; and rs2069763; G>T, exon 1, Leu38Leu) and IL2RB gene (rs228942: C>A, exon 1, Asp391Glu; and rs228953: C>T, exon 8, Gly250Gly) on renal ARE risk in 61 ARE patients and 276 control renal allograft recipients in Korea. The genotype frequencies of the IL2 and IL2RB SNPs showed Hardy-Weinberg equilibrium in both ARE and control groups. No significant difference in the genotype frequencies of the 2 IL2 SNPs was detected between non-ARE and ARE subjects (P > .05). The occurrence of AREs was significantly associated with genetic variants of the IL2RB gene (rs228942: odds ratio [OR] 2.11, 95% confidence interval [CI] 1.19-3.74; P = .0096, dominant model; rs228953: OR 1.58, 95% CI 1.04-2.38; P = .029, codominant model). In the haplotype-based analysis, the AC haplotype of IL2RB (χ(2) = 4.738; P = .0295) showed associations with ARE. Our results demonstrate that genetic variants of IL2RB may be associated with the development of AREs and may help predict ARE risk in kidney transplantation patients.

Paclitaxel stimulates chromosomal fusion and instability in cells with dysfunctional telomeres: Implication in multinucleation and chemosensitization

The anticancer effect of paclitaxel is attributable principally to irreversible promotion of microtubule stabilization and is hampered upon development of chemoresistance by tumor cells. Telomere shortening, and eventual telomere erosion, evoke chromosomal instability, resulting in particular cellular responses. Using telomerase-deficient cells derived from mTREC-/-p53-/- mice, here we show that, upon telomere erosion, paclitaxel propagates chromosomal instability by stimulating chromosomal end-to-end fusions and delaying the development of multinucleation. The end-to-end fusions involve both the p- and q-arms in cells in which telomeres are dysfunctional. Paclitaxel-induced chromosomal fusions were accompanied by prolonged G2/M cell cycle arrest, delayed multinucleation, and apoptosis. Telomere dysfunctional cells with mutlinucleation eventually underwent apoptosis. Thus, as telomere erosion proceeds, paclitaxel stimulates chromosomal fusion and instability, and both apoptosis and chemosensitization eventually develop.

SIRT1 suppresses cellular accumulation of β-TrCP E3 ligase via protein degradation.

β-Transducin repeat-containing protein (β-TrCP), an E3 ligase, promotes the degradation of substrate proteins in response to various stimuli. Even though several β-TrCP substrates have been identified to date, limited information of its upstream regulators is available. Here, we showed that SIRT1 suppresses β-TrCP protein synthesis via post-translational degradation. SIRT1 depletion led to a significant increase in the β-TrCP accumulation without affecting the mRNA level. Consistently, β-TrCP protein accumulation induced by resveratrol was further enhanced upon SIRT1 depletion. Rescue of SIRT1 reversed the effect of resveratrol, leading to reduced β-TrCP protein levels. Proteasomal inhibition led to recovery of β-TrCP in cells with SIRT1 overexpression. Notably, the recovered β-TrCP colocalized mostly with SIRT1. Thus, SIRT1 acts as a negative regulator of β-TrCP synthesis via promoting protein degradation.

Identification and characterization of a novel bacterial ATP-sensitive K+ channel

Five bacterial species that are most likely to have putative prokaryotic inward rectifier K+ (Kir) channels were selected by in silico sequence homology and membrane topology analyses with respect to the number of transmembrane domains (TMs) and the presence of K+ selectivity filter and/or ATP binding sites in reference to rabbit heart inward rectifier K+ channel (Kir6.2). A dot blot assay with genomic DNAs when probed with whole rabbit Kir6.2 cDNA further supported the in silico analysis by exhibiting a stronger hybridization in species with putative Kir’s compared to one without a Kir. Among them, Chromobacterium violaceum gave rise to a putative Kir channel gene, which was PCR-cloned into the bacterial expression vector pET30b(+), and its expression was induced in Escherichia coli and confirmed by gel purification and immunoblotting. On the other hand, this putative bacterial Kir channel was functionally expressed in Xenopus oocytes and its channel activity was measured electrophysiologically by using two electrode voltage clamping (TEVC). Results revealed a K+ current with characteristics similar to those of the ATP-sensitive K+ (K-ATP) channel. Collectively, cloning and functional characterization of bacterial ion channels could be greatly facilitated by combining the in silico analysis and heterologous expression in Xenopus oocytes.

Study of the association of -667 aquaporin-2 (AQP-2) A/G promoter polymorphism with the incidence and clinical course of chronic kidney disease in Korea

Background. Impaired urinary concentration is uniformly present with advanced disease in chronic renal failure. Aquaporin-2 (AQP-2) is known to be expressed in the renal collecting duct cells and participates in urinary concentration in response to vasopressin. Recently, the study of AQP expression in various forms of chronic kidney disease (CKD) demonstrated a reduction in AQP-2 expression associated with a loss of nephrons and the presence of chronic interstitial fibrosis. No information on aquaporin genetic variations in CKD is available to date. The aim of our study was to evaluate the possible impact of aquaporin-2 genotype on the development and clinical course of CKD. Methods. Blood samples from 259 patients with CKD and 106 ethnicity-, age-, and sex-matched healthy controls were collected, and genomic DNA was extracted. AQP-2 -667 genotype was assessed by PCR, followed by restriction fragment length polymorphism analysis. Results. There were no significant differences in genotype and allele frequencies between the patients and healthy controls (pu2009=u20090.3936, pu2009=u20090.2941, respectively). In all, 79 (30.5%) patients had the AQP-2 -667 wild-type A/A, 123 (47.5%) were heterozygous for the G allele, and 57 (22.0%) patients showed homozygosity. After subclassification of CKD according to underlying disease, no significant differences were observed between those patients and controls (pu2009=u20090.72 for diabetic nephropathy, pu2009=u20090.52 for hypertensive nephropathy, pu2009=u20090.27 for chronic glomerulonephritis, and pu2009=u20090.80 for unknown etiology). Genotype and allele frequencies of the AQP-2 gene polymorphism (rs3759126) of hypertensive patients in pre-ESRD did not show a noticeable difference compared with normal blood pressure patients in pre-ESRD (pu2009=u20090.50). No correlation was found to exist between the AQP-2 gene polymorphism (rs3759126) and serum electrolyte levels in pre-ESRD patients (pu2009=u20090.38 for serum sodium level and pu2009=u20090.44 for serum potassium level). Conclusion. Our data indicate that no association exists between the -667 AQP-2 A/G polymorphism and susceptibility to CKD or its clinical course.

Cells with dysfunctional telomeres are susceptible to reactive oxygen species hydrogen peroxide via generation of multichromosomal fusions and chromosomal fragments bearing telomeres

During genotoxic stress, reactive oxygen species hydrogen peroxide (H(2)O(2)) is a prime mediator of the DNA damage response. Telomeres function both to assist in DNA damage repair and to inhibit chromosomal end-to-end fusion. Here, we show that telomere dysfunction renders cells susceptible to H(2)O(2), via generation of multichromosomal fusion and chromosomal fragments. H(2)O(2) caused formation of multichromosomal end-to-end fusions involving more than three chromosomes, preferentially when telomeres were erosive. Interestingly, extensive chromosomal fragmentation (yielding small-sized fragments) occurred only in cells exhibiting such multichromosomal fusions. Telomeres were absent from fusion points, being rather present in the small fragments, indicating that H(2)O(2) cleaves chromosomal regions adjacent to telomeres. Restoration of telomere function or addition of the antioxidant N-acetylcysteine prevented development of chromosomal aberrations and rescued the observed hypersensitivity to H(2)O(2). Thus, chromosomal regions adjacent to telomeres become sensitive to reactive oxygen species hydrogen peroxide when telomeres are dysfunctional, and are cleaved to produce multichromosomal fusions and small chromosomal fragments bearing the telomeres.

PCHM: A bioinformatic resource for high-throughput human mitochondrial proteome searching and comparison

Mitochondrial proteins associated with a wide spectrum of human diseases and currently large amounts of tissue or organ specific human mitochondrial proteome datasets are generated. However, high-throughput comparative proteomic methods have yet to be applied to extract subtle differences among mitochondria from different tissues or muscle types. The aim of this work was to provide an integrated way to identify and compare huge mitochondrial protein or peptide mass spectral data sets acquired from expert mitochondrial proteome or biomarker discovery community. Proteome comparison of human mitochondria (PCHM) is a web-based analysis environment for manual or automatic analysis of individual peptide mass fingerprints alongside a database of proteins and peptides identified in various organs for human mitochondrial proteins. PCHM provides a suite of graphical tools that allow the virtual plot of peptide mass fingerprinting (PMF) spectra and a fully automatic protein function classification based on gene ontology (GO) annotation system. The new virtual PMF plot is very useful to validate fragmented ion loses of any identical proteins and to remove unwanted foreign ion peaks. Fully automatic protein function classifier provides an easier way to compare the subtle differences of compositionally biased mitochondrial protein functions. PCHM also provides a variety of query algorithms aid in browsing, searching, and accessing complete annotations of data relevant to each mitochondrial protein of interest, which link external databases and users. PCHM will be a useful tool for the systematic and functional characterization of the mitochondrial proteins in relation to human diseases or biological research applications. PCHM can be accessed freely via a web interface http://pchm.inje.ac.kr.

Does strong hypertrophic condition induce fast mitochondrial DNA mutation of rabbit heart

Homo- and heteroplasmic mitochondrial DNA (mtDNA) mutations were observed and identified in an isoproterenol-induced rabbit model of cardiac hypertrophy. Genes encoding proteins essential for catalyzing mitochondrial electron transfer and for generating the proton motive force, such as NADH dehydrogenases (ND2, ND3, ND4, and ND6), cytochrome b, and ATPase 8, showed increased susceptibility for mutation. Specifically, five mutations caused amino acid changes and were located in Complex I and Complex V gene clusters. To our knowledge, this is the first demonstration of a relationship between cardiac hypertrophy induced by a strong sympathetic load and rapid mtDNA mutations.

Pharmacokinetic effect of voriconazole on cyclosporine in the treatment of aspergillosis after renal transplantation.

Azole antifungal agents are essential drugs in the treatment of fungal infections in renal transplant patients. As azoles, these antifungal agents are inhibitors of CYP3A4 and P-glycoprotein (P-gp); and thus therapeutic drug monitoring is important. We evaluated a patient with cutaneous and pulmonary aspergillosis who was successfully treated with voriconazole and a low cyclosporine trough level (3.2 - 27.9 ng/ml) for 3 months. During that period, the patient showed good allograft function with the co-administration of voriconazole and cyclosporine. We measured the patients genotype of MDR1, CYP3A4, CYP3A5 and CYP2C19 enzymes in addition to the intracellular concentration of cyclosporine in peripheral blood mononuclear cells (PBMCs). The intracellular concentration of cyclosporine in PBMC is 3.2 times higher with no functionally defected alleles in MDR1, CYP3A4, CYP3A5 or CYP2C19 enzymes when cyclosporine is co-administered with voriconazole ex vivo. Although other confounding factors causing immunological modulation may exist, it is plausible that low serum and high intracellular cyclosporine concentrations, due to the inhibition of P-gp activity by voriconazole, also contribute to an immunosuppressive state.