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1.  Localized nodular synovitis of the infrapatellar fat pad 
Indian Journal of Orthopaedics  2013;47(3):313-316.
We report a case of localized nodular synovitis of the infrapatellar fat pad impinging on the patellofemoral joint causing limitation of extension. Arthroscopy involved use of a superolateral portal because location of lesion hindered access via a conventional anterior portal. The infrapatellar mass impinged in the patellofemoral joint upon knee extension and retracted upon flexion. Superior-superior triangulation allowed for complete excision of the mass.
doi:10.4103/0019-5413.111514
PMCID: PMC3687912  PMID: 23798766
Arthroscopy; infrapatellar fat pad; localized nodular synovitis
2.  Short-term protein intake increases fractional synthesis rate of muscle protein in the elderly: meta-analysis 
Nutrition Research and Practice  2010;4(5):375-382.
The precise effects of protein intake on fractional synthesis rate (FSR) of muscle protein are still under debate. The sample size of these studies was small and the conclusions in young and elderly subjects were inconsistent. To assess the effect of dietary protein intake on the FSR level, we conducted a meta-analysis of controlled protein intake trials. Random-effects models were used to calculate the weighted mean differences (WMDs). Ten studies were included and effects of short-term protein intake were evaluated. In an overall pooled estimate, protein intake significantly increased the FSR (20 trials, 368 participants; WMD: 0.025%/h; 95%CI: 0.019-0.031; P < 0.0001). Meta-regression analysis suggested that the protein dose was positively related to the effect size (regression coefficient = 0.108%/h; 95%CI: 0.035, 0.182; P = 0.009). A subgroup analysis indicated that protein intake significantly increased FSR when the protein dose was ≤ 0.80 g/kg BW (16 trials, 308 participants; WMD: 0.027%/h; 95%CI: 0.019-0.031; P < 0.0001), but did not affect FSR when the protein dose was > 0.80 g/kg BW (4 trials, 60 participants; WMD: 0.016%/h; 95%CI: 0.004-0.029; P = 0.98). In conclusion, this study is the first integrated results showing that a short-term protein intake is effective at improving the FSR of muscle protein in the healthy elderly as well as young subjects. This beneficial effect seems to be dose-dependent when the dose levels of protein range from 0.08 to 0.80 g/kg BW.
doi:10.4162/nrp.2010.4.5.375
PMCID: PMC2981720  PMID: 21103083
Protein intakes; fractional synthesis rate; muscle protein; meta-analysis
3.  A novel psychrophilic alkaline phosphatase from the metagenome of tidal flat sediments 
BMC Biotechnology  2015;15(1):1.
Background
Alkaline phosphatase (AP) catalyzes the hydrolytic cleavage of phosphate monoesters under alkaline conditions and plays important roles in microbial ecology and molecular biology applications. Here, we report on the first isolation and biochemical characterization of a thermolabile AP from a metagenome.
Results
The gene encoding a novel AP was isolated from a metagenomic library constructed with ocean-tidal flat sediments from the west coast of Korea. The metagenome-derived AP (mAP) gene composed of 1,824 nucleotides encodes a polypeptide with a calculated molecular mass of 64 kDa. The deduced amino acid sequence of mAP showed a high degree of similarity to other members of the AP family. Phylogenetic analysis revealed that the mAP is shown to be a member of a recently identified family of PhoX that is distinct from the well-studied classical PhoA family. When the open reading frame encoding mAP was cloned and expressed in recombinant Escherichia coli, the mature mAP was secreted to the periplasm and lacks an 81-amino-acid N-terminal Tat signal peptide. Mature mAP was purified to homogeneity as a monomeric enzyme with a molecular mass of 56 kDa. The purified mAP displayed typical features of a psychrophilic enzyme: high catalytic activity at low temperature and a remarkable thermal instability. The optimal temperature for the enzymatic activity of mAP was 37°C and complete thermal inactivation of the enzyme was observed at 65°C within 15 min. mAP was activated by Ca2+ and exhibited maximal activity at pH 9.0. Except for phytic acid and glucose 1-phosphate, mAP showed phosphatase activity against various phosphorylated substrates indicating that it had low substrate specificity. In addition, the mAP was able to remove terminal phosphates from cohesive and blunt ends of linearized plasmid DNA, exhibiting comparable efficiency to commercially available APs that have been used in molecular biology.
Conclusions
The presented mAP enzyme is the first thermolabile AP found in cold-adapted marine metagenomes and may be useful for efficient dephosphorylation of linearized DNA.
doi:10.1186/s12896-015-0115-2
PMCID: PMC4335783  PMID: 25636680
Alkaline phosphatase; Metagenome; PhoX; Escherichia coli
4.  Role of Bcl-xL/Beclin-1 in synergistic apoptotic effects of secretory TRAIL-armed adenovirus in combination with mitomycin C and hyperthermia on colon cancer cells 
Apoptosis  2014;19(11):1603-1615.
In this study, we attempted to develop a multimodality approach using chemotherapeutic agent mitomycin C, biologic agent tumor necrosis factor-related apoptosis-inducing ligand (TRAIL/Apo-2L), and mild hyperthermia to treat colon cancer. For this study, human colon cancer LS174T, LS180, HCT116 and CX-1 cells were infected with secretory TRAIL-armed adenovirus (Ad.TRAIL) and treated with chemotherapeutic agent mitomycin C and hyperthermia. The combinatorial treatment caused a synergistic induction of apoptosis which was mediated through an increase in caspase activation. The combinational treatment promoted the JNK-Bcl-xL-Bak pathway which transmitted the synergistic effect through the mitochondria-dependent apoptotic pathway. JNK signaling led to Bcl-xL phosphorylation at serine 62, dissociation of Bak from Bcl-xL, oligomerization of Bak, alteration of mitochondrial membrane potential, and subsequent cytochrome c release. Overexpression of dominant-negative mutant of Bcl-xL (S62A), but not dominant-positive mutant of Bcl-xL (S62D), suppressed the synergistic death effect. Interestingly, Beclin-1 was dissociated from Bcl-xL and overexpression of dominant-negative mutant of Bcl-xL (S62A), but not dominant-positive mutant of Bcl-xL (S62D), suppressed dissociation of Beclin-1 from Bcl-xL. A combinatorial treatment of mitomycin C, Ad.TRAIL and hyperthermia induced Beclin-1 cleavage, but the Beclin-1 cleavage was abolished in Beclin-1 double mutant (D133A/D146A) knock-in HCT116 cells, suppressing the apoptosis induced by the combination therapy. We believe that this study supports the application of the multimodality approach to colon cancer therapy.
doi:10.1007/s10495-014-1028-6
PMCID: PMC4196052  PMID: 25156145
Mitomycin C; Ad.TRAIL; Hyperthermia; Mitochondria-dependent pathway; Bcl-xL; Beclin-1
5.  Changes in Bone Mineral Density of Both Proximal Femurs after Total Knee Arthroplasty 
Clinics in Orthopedic Surgery  2014;6(1):43-48.
Background
This study investigated the effects of total knee arthroplasty (TKA) on bone mineral density (BMD) of the proximal femur in patients who underwent the procedure.
Methods
Forty-eight patients scheduled to undergo unilateral TKA because of primary knee osteoarthritis were included in this study, which was conducted at a medical center between October 2006 and October 2009. In these 48 patients, 96 hips were evaluated. Measurement of BMD was performed preoperatively and one month, three months, six months, and one year after unilateral TKA. Repeated measured analysis of variance and paired t-tests for comparison of two repeated samples were used to compare differences between time points (preoperation, one, three, six, and 12 months) and between the operative and nonoperative sides.
Results
Preoperatively, BMD of the femoral neck, trochanter, and total hip on the operative side were lower than on the nonoperative side; however, there was no statistical difference. BMD of both femoral neck areas was significantly lower than preoperative BMD at one month and three months after TKA. BMD of both trochanter areas was significantly lower than preoperative BMD at one month and three months after TKA. BMD of both total hips was significantly lower than preoperative BMD at three months after TKA. However, no statistical differences of changes in BMD were observed between the operative and nonoperative sides at each measurement time.
Conclusions
According to our results, TKA was found to affect both proximal femurs during the acute period. However, TKA did not affect a change in BMD of the proximal femur during one year postoperative.
doi:10.4055/cios.2014.6.1.43
PMCID: PMC3942601  PMID: 24605188
Proximal hip; Bone mineral density; Total knee arthroplasty
6.  Generating In Vivo Cloning Vectors for Parallel Cloning of Large Gene Clusters by Homologous Recombination 
PLoS ONE  2013;8(11):e79979.
A robust method for the in vivo cloning of large gene clusters was developed based on homologous recombination (HR), requiring only the transformation of PCR products into Escherichia coli cells harboring a receiver plasmid. Positive clones were selected by an acquired antibiotic resistance, which was activated by the recruitment of a short ribosome-binding site plus start codon sequence from the PCR products to the upstream position of a silent antibiotic resistance gene in receiver plasmids. This selection was highly stringent and thus the cloning efficiency of the GFPuv gene (size: 0.7 kb) was comparable to that of the conventional restriction-ligation method, reaching up to 4.3 × 104 positive clones per μg of DNA. When we attempted parallel cloning of GFPuv fusion genes (size: 2.0 kb) and carotenoid biosynthesis pathway clusters (sizes: 4 kb, 6 kb, and 10 kb), the cloning efficiency was similarly high regardless of the DNA size, demonstrating that this would be useful for the cloning of large DNA sequences carrying multiple open reading frames. However, restriction analyses of the obtained plasmids showed that the selected cells may contain significant amounts of receiver plasmids without the inserts. To minimize the amount of empty plasmid in the positive selections, the sacB gene encoding a levansucrase was introduced as a counter selection marker in receiver plasmid as it converts sucrose to a toxic levan in the E. coli cells. Consequently, this method yielded completely homogeneous plasmids containing the inserts via the direct transformation of PCR products into E. coli cells.
doi:10.1371/journal.pone.0079979
PMCID: PMC3823602  PMID: 24244585
7.  Genome Sequence of the Thermotolerant Yeast Kluyveromyces marxianus var. marxianus KCTC 17555 
Eukaryotic Cell  2012;11(12):1584-1585.
Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548).
doi:10.1128/EC.00260-12
PMCID: PMC3536290  PMID: 23193140
8.  Identification of repurposed small molecule drugs for chordoma therapy 
Cancer Biology & Therapy  2013;14(7):638-647.
Chordoma is a rare, slow growing malignant tumor arising from remnants of the fetal notochord. Surgery is the first choice for chordoma treatment, followed by radiotherapy, although postoperative complications remain significant. Recurrence of the disease occurs frequently due to the anatomy of the tumor location and violation of the tumor margins at the initial surgery. Currently, there are no effective drugs available for patients with chordoma. Due to the rarity of the disease, there is limited opportunity to test agents in clinical trials and no concerted effort to develop agents for chordoma in the pharmaceutical industry. To rapidly and efficiently identify small molecules that inhibit chordoma cell growth, we screened the NCGC Pharmaceutical Collection (NPC) containing approximately 2800 clinically approved and investigational drugs at 15 different concentrations in chordoma cell lines, U-CH1 and U-CH2. We identified a group of drugs including bortezomib, 17-AAG, digitoxin, staurosporine, digoxin, rubitecan, and trimetrexate that inhibited chordoma cell growth, with potencies from 10 to 370 nM in U-CH1 cells, but less potently in U-CH2 cells. Most of these drugs also induced caspase 3/7 activity with a similar rank order as the cytotoxic effect on U-CH1 cells. Cantharidin, digoxin, digitoxin, staurosporine, and bortezomib showed similar inhibitory effect on cell lines and 3 primary chordoma cell cultures. The combination treatment of bortezomib with topoisomerase I and II inhibitors increased the therapeutic potency in U-CH2 and patient-derived primary cultures. Our results provide information useful for repurposing currently approved drugs for chordoma and potential approach of combination therapy.
doi:10.4161/cbt.24596
PMCID: PMC3742493  PMID: 23792643
chordoma; NCGC Pharmaceutical Collection; cell viability; caspase 3/7; U-CH1; U-CH2; qHTS
9.  The Genome Organization of Thermotoga maritima Reflects Its Lifestyle 
PLoS Genetics  2013;9(4):e1003485.
The generation of genome-scale data is becoming more routine, yet the subsequent analysis of omics data remains a significant challenge. Here, an approach that integrates multiple omics datasets with bioinformatics tools was developed that produces a detailed annotation of several microbial genomic features. This methodology was used to characterize the genome of Thermotoga maritima—a phylogenetically deep-branching, hyperthermophilic bacterium. Experimental data were generated for whole-genome resequencing, transcription start site (TSS) determination, transcriptome profiling, and proteome profiling. These datasets, analyzed in combination with bioinformatics tools, served as a basis for the improvement of gene annotation, the elucidation of transcription units (TUs), the identification of putative non-coding RNAs (ncRNAs), and the determination of promoters and ribosome binding sites. This revealed many distinctive properties of the T. maritima genome organization relative to other bacteria. This genome has a high number of genes per TU (3.3), a paucity of putative ncRNAs (12), and few TUs with multiple TSSs (3.7%). Quantitative analysis of promoters and ribosome binding sites showed increased sequence conservation relative to other bacteria. The 5′UTRs follow an atypical bimodal length distribution comprised of “Short” 5′UTRs (11–17 nt) and “Common” 5′UTRs (26–32 nt). Transcriptional regulation is limited by a lack of intergenic space for the majority of TUs. Lastly, a high fraction of annotated genes are expressed independent of growth state and a linear correlation of mRNA/protein is observed (Pearson r = 0.63, p<2.2×10−16 t-test). These distinctive properties are hypothesized to be a reflection of this organism's hyperthermophilic lifestyle and could yield novel insights into the evolutionary trajectory of microbial life on earth.
Author Summary
Genomic studies have greatly benefited from the advent of high-throughput technologies and bioinformatics tools. Here, a methodology integrating genome-scale data and bioinformatics tools is developed to characterize the genome organization of the hyperthermophilic, phylogenetically deep-branching bacterium Thermotoga maritima. This approach elucidates several features of the genome organization and enables comparative analysis of these features across diverse taxa. Our results suggest that the genome of T. maritima is reflective of its hyperthermophilic lifestyle. Ultimately, constraints imposed on the genome have negative impacts on regulatory complexity and phenotypic diversity. Investigating the genome organization of Thermotogae species will help resolve various causal factors contributing to the genome organization such as phylogeny and environment. Applying a similar analysis of the genome organization to numerous taxa will likely provide insights into microbial evolution.
doi:10.1371/journal.pgen.1003485
PMCID: PMC3636130  PMID: 23637642
10.  Complete Genome Sequence of the Probiotic Bacterium Bifidobacterium bifidum Strain BGN4 
Journal of Bacteriology  2012;194(17):4757-4758.
Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B. bifidum BGN4, a strain that had been isolated from the fecal sample of a healthy breast-fed infant, and annotated 1,835 coding sequences.
doi:10.1128/JB.00988-12
PMCID: PMC3415514  PMID: 22887663
11.  Network context and selection in the evolution to enzyme specificity 
Science (New York, N.Y.)  2012;337(6098):1101-1104.
Enzymes are thought to have evolved highly specific catalytic activities from promiscuous ancestral proteins. By analyzing a genome-scale model of Escherichia coli metabolism, we found that 37% of its enzymes act on a variety of substrates and catalyze 65% of the known metabolic reactions. However, it is not apparent why these generalist enzymes remain. Here, we show that there are marked differences between generalist enzymes and specialist enzymes, known to catalyze a single chemical reaction on one particular substrate in vivo. Specialist enzymes (i) are frequently essential, (ii) maintain higher metabolic flux, and (iii) require more regulation of enzyme activity to control metabolic flux in dynamic environments than do generalist enzymes. Furthermore, these properties are conserved in Archaea and Eukarya. Thus, the metabolic network context and environmental conditions influence enzyme evolution toward high specificity.
doi:10.1126/science.1216861
PMCID: PMC3536066  PMID: 22936779
12.  Comparative multi-omics systems analysis of Escherichia coli strains B and K-12 
Genome Biology  2012;13(5):R37.
Background
Elucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced.
Results
We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. A genome-scale metabolic network of E. coli B was reconstructed and used to identify genetic bases of the phenotypes unique to B compared with K-12 through in silico complementation testing. This systems analysis revealed that E. coli B is well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella. Furthermore, E. coli B has an additional type II secretion system and a different cell wall and outer membrane composition predicted to be more favorable for protein secretion. In contrast, E. coli K-12 showed a higher expression of heat shock genes and was less susceptible to certain stress conditions.
Conclusions
This integrative systems approach provides a high-resolution system-wide view and insights into why two closely related strains of E. coli, B and K-12, manifest distinct phenotypes. Therefore, systematic understanding of cellular physiology and metabolism of the strains is essential not only to determine culture conditions but also to design recombinant hosts.
doi:10.1186/gb-2012-13-5-r37
PMCID: PMC3446290  PMID: 22632713
13.  Role of Bax in quercetin-induced apoptosis in human prostate cancer cells 
Biochemical Pharmacology  2008;75(12):2345-2355.
The aim of this study was to investigate the effect of quercetin, a flavonoid, on the apoptotic pathway in a human prostate cell line (LNCaP). We observed that treatment of cells for 24 h with quercetin induced cell death in a dose-dependent manner. A sustained inhibition of the major survival signal, Akt, occurred in quercetin-treated cells. Treatment of LNCaP cells with an apoptosis inducing concentration of quercetin (100 μM) resulted in a rapid decrease in the inhibitory Ser(473) phosphorylation of Akt leading to inhibition of its kinase activity. Quercetin treatment (100 μM) also caused a decrease in Ser(136) phosphorylation of Bad, which is a downstream target of Akt. Protein interaction assay revealed that during treatment with quercetin, Bcl-xL dissociated from Bax and then associated with Bad. Our results also show that quercetin decreases the Bcl-xL:Bax ratio and increases translocation and multimerization of Bax to the mitochondrial membrane. The translocation is accompanied by cytochrome c release, and procaspases-3, -8 and -9 cleavage and increased poly (ADP-ribose) polymerase (PARP) cleavage. Similar results were observed in human colon cancer HCT116Bax+/+ cell line, but not HCT116Bax−/− cell line. Interestingly, at similar concentrations (100 μM), quercetin treatment did not affect the viability or rate of apoptosis in normal human prostate epithelial cell line (PrEC) and rat prostate epithelial cell line (YPEN-1). Our results indicate that the apoptotic processes caused by quercetin are mediated by the dissociation of Bax from Bcl-xL and the activation of caspase families in human prostate cancer cells.
doi:10.1016/j.bcp.2008.03.013
PMCID: PMC3266687  PMID: 18455702
Quercetin; apoptosis; caspase; PI3K/Akt pathway; cytochrome c; Bax; Bad; Bcl-xL
14.  Astaxanthin protects against MPTP/MPP+-induced mitochondrial dysfunction and ROS production in vivo and in vitro 
Astaxanthin (AST) is a powerful antioxidant that occurs naturally in a wide variety of living organisms. We have investigated the role of AST in preventing 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced apoptosis of the substantia nigra (SN) neurons in the mouse model of Parkinson’s disease (PD) and 1-methyl-4-phenylpyridinium (MPP+)-induced cytotoxicity of SH-SY5Y human neuroblastoma cells. In in vitro study, AST inhibits MPP+-induced production of intracellular reactive oxygen species (ROS) and cytotoxicity in SH-SY5Y human neuroblastoma cells. Preincubation of AST (50 μM) significantly attenuates MPP+-induced oxidative damage. Furthermore, AST is able to enhance the expression of Bcl-2 protein but reduce the expression of α-synuclein and Bax, and suppress the cleavage of caspase-3. Our results suggest that the protective effects of AST on MPP+-induced apoptosis may be due to its anti-oxidative properties and anti-apoptotic activity via induction of expression of superoxide dismutase (SOD) and catalase and regulating the expression of Bcl-2 and Bax. Pretreatment with AST (30mg /kg) markedly increases tyrosine hydroxylase (TH)-positive neurons and decreases the argyrophilic neurons compared with the MPTP model group. In summary, AST shows protection from MPP+/MPTP-induced apoptosis in the SH-SY5Y cells and PD model mouse SN neurons, and this effect may be attributable to upregulation of the expression of Bcl-2 protein, downregulation of the expression of Bax and α-synuclein, and inhibition of the activation of caspase-3. These data indicate that AST may provide a valuable therapeutic strategy for the treatment of progressive neurodegenerative disease such as Parkinson’s disease.
doi:10.1016/j.fct.2010.10.029
PMCID: PMC3010303  PMID: 21056612
Astaxanthin; Parkinson’s disease; MPTP; Apoptosis; Substantia nigra neuron
15.  Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli 
PLoS ONE  2011;6(10):e26172.
Adaptive laboratory evolution (ALE) under controlled conditions has become a valuable approach for the study of the genetic and biochemical basis for microbial adaptation under a given selection pressure. Conventionally, the timescale in ALE experiments has been set in terms of number of generations. As mutations are believed to occur primarily during cell division in growing cultures, the cumulative number of cell divisions (CCD) would be an alternative way to set the timescale for ALE. Here we show that in short-term ALE (up to 40–50 days), Escherichia coli, under growth rate selection pressure, was found to undergo approximately 1011.2 total cumulative cell divisions in the population to produce a new stable growth phenotype that results from 2 to 8 mutations. Continuous exposure to a low level of the mutagen N-methyl-N′-nitro-N-nitrosoguanidine was found to accelerate this timescale and led to a superior growth rate phenotype with a much larger number of mutations as determined with whole-genome sequencing. These results would be useful for the fundamental kinetics of the ALE process in designing ALE experiments and provide a basis for its quantitative description.
doi:10.1371/journal.pone.0026172
PMCID: PMC3196513  PMID: 22028828
17.  Adaptive Evolution of Escherichia coli K-12 MG1655 during Growth on a Nonnative Carbon Source, l-1,2-Propanediol▿ †  
Applied and Environmental Microbiology  2010;76(13):4158-4168.
Laboratory adaptive evolution studies can provide key information to address a wide range of issues in evolutionary biology. Such studies have been limited thus far by the inability of workers to readily detect mutations in evolved microbial strains on a genome scale. This limitation has now been overcome by recently developed genome sequencing technology that allows workers to identify all accumulated mutations that appear during laboratory adaptive evolution. In this study, we evolved Escherichia coli K-12 MG1655 with a nonnative carbon source, l-1,2-propanediol (l-1,2-PDO), for ∼700 generations. We found that (i) experimental evolution of E. coli for ∼700 generations in 1,2-PDO-supplemented minimal medium resulted in acquisition of the ability to use l-1,2-PDO as a sole carbon and energy source so that the organism changed from an organism that did not grow at all initially to an organism that had a growth rate of 0.35 h−1; (ii) six mutations detected by whole-genome resequencing accumulated in the evolved E. coli mutant over the course of adaptive evolution on l-1,2-PDO; (iii) five of the six mutations were within coding regions, and IS5 was inserted between two fuc regulons; (iv) two major mutations (mutations in fucO and its promoter) involved in l-1,2-PDO catabolism appeared early during adaptive evolution; and (v) multiple defined knock-in mutant strains with all of the mutations had growth rates essentially matching that of the evolved strain. These results provide insight into the genetic basis underlying microbial evolution for growth on a nonnative substrate.
doi:10.1128/AEM.00373-10
PMCID: PMC2897412  PMID: 20435762
18.  Effect of hyperthermia in combination with TRAIL on the JNK-Bim signal transduction pathway and growth of xenograft tumors 
Journal of cellular biochemistry  2010;110(5):1073-1081.
Approximately 25% of patients with colorectal cancer develop metastases to the liver, and surgery is currently the best treatment available. But there are several patients who are unresectable, and isolated hepatic perfusion (IHP) offers a different approach in helping to treat these patients. IHP is a method used for isolating the liver and delivering high doses of chemotherapeutic agents. The efficacy of IHP has been improved by combining hyperthermia not only with chemotherapeutics but with other deliverable agents such as tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). In this study, we used human colorectal cancer CX-1 cells and treated them with hyperthermia and TRAIL, causing cytotoxicity. We were able to demonstrate that the numbers of live cells were significantly reduced with hyperthermia and 10 ng/ml of TRAIL combined. We also showed that the effect of hyperthermia on TRAIL in our studies was enhancement of the apoptotic pathway by the promotion of JNK and BimEL activity as well as PARP cleavage. We have also used our CX-1 cells to generate tumors in Balb/c nude mice. With intra-tumoral injections of TRAIL combined with hyperthermia at 42°C, we were able to show a delayed onset of tumor growth in our xenograft model.
doi:10.1002/jcb.22619
PMCID: PMC2967443  PMID: 20544795
Hyperthermia; TRAIL; JNK; Bim; xenograft tumor
19.  Neuroprotective Effects of Astaxanthin in Oxygen-Glucose Deprivation in SH-SY5Y Cells and Global Cerebral Ischemia in Rat 
Astaxanthin (ATX), a naturally occurring carotenoid pigment, is a powerful biological antioxidant. In the present study, we investigated whether ATX pharmacologically offers neuroprotection against oxidative stress by cerebral ischemia. We found that the neuroprotective efficacy of ATX at the dose of 30 mg/kg (n = 8) was 59.5% compared with the control group (n = 3). In order to make clear the mechanism of ATX neuroprotection, the up-regulation inducible nitric oxide synthase (iNOS) and heat shock proteins (HSPs) together with the oxygen glucose deprivation (OGD) in SH-SY5Y cells were also investigated. The induction of various factors involved in oxidative stress processes such as iNOS was suppressed by the treatment of ATX at 25 and 50 µM after OGD-induced oxidative stress. In addition, Western blots showed that ATX elevated of heme oxygenase-1 (HO-1; Hsp32) and Hsp70 protein levels in in vitro. These results suggest that the neuroprotective effects of ATX were related to anti-oxidant activities in global ischemia.
doi:10.3164/jcbn.10-29
PMCID: PMC2935152  PMID: 20838567
astaxanthin; global ischemia; oxidative stress; neuroprotection; nitric oxide synthase; heat shock protein
20.  Molecular cloning and biochemical characterization of a novel erythrose reductase from Candida magnoliae JH110 
Background
Erythrose reductase (ER) catalyzes the final step of erythritol production, which is reducing erythrose to erythritol using NAD(P)H as a cofactor. ER has gained interest because of its importance in the production of erythritol, which has extremely low digestibility and approved safety for diabetics. Although ERs were purified and characterized from microbial sources, the entire primary structure and the corresponding DNA for ER still remain unknown in most of erythritol-producing yeasts. Candida magnoliae JH110 isolated from honeycombs produces a significant amount of erythritol, suggesting the presence of erythrose metabolizing enzymes. Here we provide the genetic sequence and functional characteristics of a novel NADPH-dependent ER from C. magnoliae JH110.
Results
The gene encoding a novel ER was isolated from an osmophilic yeast C. magnoliae JH110. The ER gene composed of 849 nucleotides encodes a polypeptide with a calculated molecular mass of 31.4 kDa. The deduced amino acid sequence of ER showed a high degree of similarity to other members of the aldo-keto reductase superfamily including three ER isozymes from Trichosporonoides megachiliensis SNG-42. The intact coding region of ER from C. magnoliae JH110 was cloned, functionally expressed in Escherichia coli using a combined approach of gene fusion and molecular chaperone co-expression, and subsequently purified to homogeneity. The enzyme displayed a temperature and pH optimum at 42°C and 5.5, respectively. Among various aldoses, the C. magnoliae JH110 ER showed high specific activity for reduction of erythrose to the corresponding alcohol, erythritol. To explore the molecular basis of the catalysis of erythrose reduction with NADPH, homology structural modeling was performed. The result suggested that NADPH binding partners are completely conserved in the C. magnoliae JH110 ER. Furthermore, NADPH interacts with the side chains Lys252, Thr255, and Arg258, which could account for the enzyme's absolute requirement of NADPH over NADH.
Conclusions
A novel ER enzyme and its corresponding gene were isolated from C. magnoliae JH110. The C. magnoliae JH110 ER with high activity and catalytic efficiency would be very useful for in vitro erythritol production and could be applied for the production of erythritol in other microorganisms, which do not produce erythritol.
doi:10.1186/1475-2859-9-43
PMCID: PMC2902421  PMID: 20529366
21.  The Quantitative Analysis of Back Muscle Degeneration after Posterior Lumbar Fusion: Comparison of Minimally Invasive and Conventional Open Surgery 
Asian Spine Journal  2009;3(2):89-95.
Study Design
Prospective controlled study.
Purpose
The results of conventional open surgery was compared with those from minimally invasive transforaminal lumbar interbody fusion (MI-TLIF) for lumbar fusion to determine which approach resulted in less postoperative paraspinal muscle degeneration.
Overview of Literature
MI TLIF is new surgical technique that appears to minimize iatrogenic injury. However, there aren't any reports yet that have quantitatively analyzed and proved whether there's difference in back muscle injury and degeneration between the minimally invasive surgery and conventional open surgery in more than 1 year follow-up after surgery.
Methods
This study examined a consecutive series of 48 patients who underwent lumbar fusion in our hospital during the period, March 2006 to March 2008, with a 1-year follow-up evaluation using MRI. There were 17 cases of conventional open surgery and 31 cases of MI-TLIF (31 cases of single segment fusion and 17 cases of multi-segment fusion). The digital images of the paravertebral back muscles were analyzed and compared using the T2-weighted axial images. The point of interest was the paraspinal muscle of the intervertebral disc level from L1 to L5. Picture archiving and communication system viewing software was used for quantitative analysis of the change in fat infiltration percentage and the change in cross-sectional area of the paraspinal muscle, before and after surgery.
Results
A comparison of the traditional posterior fusion method with MI-TLIF revealed single segment fusion to result in an average increase in fat infiltration in the paraspinal muscle of 4.30% and 1.37% and a decrease in cross-sectional area of 0.10 and 0.07 before and after surgery, respectively. Multi-segment fusion showed an average 7.90% and 2.79% increase in fat infiltration and a 0.16 and 0.10 decrease in cross-sectional area, respectively. Both single and multi segment fusion showed less change in the fat infiltration percentage and cross-sectional area, particularly in multi segment fusion. There was no significant difference between the two groups in terms of the radiologic results.
Conclusions
A comparison of conventional open surgery with MI-TLIF upon degeneration of the paraspinal muscle with a 1 year follow-up evaluation revealed that both single and multi segment fusion showed less change in fat infiltration percentage and cross-sectional area in the MI-TLIF but there was no significant difference between the two groups. This suggests that as time passes after surgery, there is no significant difference in the level of degeneration of the paraspinal muscle between surgical techniques.
doi:10.4184/asj.2009.3.2.89
PMCID: PMC2852079  PMID: 20404953
Paraspainal muscle; Fat degeneration; MRI; Posterior fusion
22.  Quercetin augments TRAIL-induced apoptotic death: involvement of the ERK signal transduction pathway 
Biochemical pharmacology  2008;75(10):1946-1958.
Combined treatment with quercetin and TRAIL induced cytotoxicity and enhanced annexin V staining and poly (ADP-ribose) polymerase (PARP) cleavage in human prostate cancer cell lines DU-145 and PC-3. These indicators of apoptosis resulted from the activation of caspase-8, -9, and -3. Although the expression levels of FLIPs, cIAP1, cIAP2, and the Bcl-2 family were not changed in quercetin-treated cells, significant downregulation of survivin occurred. Knockdown survivin by siRNA significantly increased TRAIL-induced apoptosis. We hypothesized that quercetin-induced activation of MAPK (ERK, p38, JNK) is responsible for downregulation of survivin gene expression. To test this hypothesis, we selectively inhibited MAPK during treatment with quercetin. Our data demonstrated that inhibitor of ERK (PD98059), but not p38 MAPK (SB203580) or JNK (SP600125), significantly maintained the intracellular level of survivin during treatment with quercetin. Interestingly, PD98059 also prevented quercetin-induced deacetylation of histone H3. Data from survivin promoter activity assay suggest that the Sp1 transcription factor binds to the survivin promoter region and quercetin inhibits its binding activity through deacetylation of histone H3. Quercetin-induced activation of the ERK-MSK1 signal transduction pathway may be responsible for deacetylation of histone H3. Taken together, our findings suggest that quercetin enhances TRAIL induced apoptosis by inhibition of survivin expression, through ERK-MSK1-mediated deacetylation of H3.
doi:10.1016/j.bcp.2008.02.016
PMCID: PMC2430102  PMID: 18377872
Quercetin; TRAIL; Apoptosis; Survivin; ERK
23.  Role of p53, PUMA, and Bax in wogonin-induced apoptosis in human cancer cells 
Biochemical pharmacology  2008;75(10):2020-2033.
We observed that treatment of prostate cancer cells for 24 h with wogonin, a naturally occurring monoflavonoid, induced cell death in a dose- and time-dependent manner. Exposure of wogonin to LNCaP cells was associated with increased intracellular levels of p21Cip-1, p27Kip-1, p53, and PUMA, oligomerization of Bax, release of cytochrome c from the mitochondria, and activation of caspases. We also confirmed the role of p53 by noting that knock-in in p53 expression by transfecting p53 DNA increased wogonin-induced apoptosis in p53-null PC-3 cells. To study the mechanism of PUMA upregulation, we determined the activities of PUMA promoter in the wogonin treated and untreated cells. Increase of the intracellular levels of PUMA protein was due to increase in transcriptional activity. Data from chromatin immunoprecipitation (ChIP) analyses revealed that wogonin activated the transcription factor p53 binding activity to the PUMA promoter region. We observed that the upregulation of PUMA mediated wogonin cytotoxicity. Further characterization of the transcriptional response to wogonin in HCT116 human colon cancer cells demonstrated that PUMA induction was p53-dependent; deficiency in either p53 or PUMA significantly protected HCT116 cells against wogonin-induced apoptosis. Also, wogonin promoted mitochondrial translocation and multimerization of Bax. Interestingly, wogonin (100 μM) treatment did not affect the viability of normal human prostate epithelial cells (PrEC). Taken together, these results indicate that p53-dependent transcriptional induction of PUMA and oligomerization of Bax play important roles in the sensitivity of cancer cells to apoptosis induced by caspase activation through wogonin.
doi:10.1016/j.bcp.2008.02.023
PMCID: PMC2424318  PMID: 18377871
Wogonin; apoptosis; p53; PUMA; Bax
24.  Folding machineries displayed on a cation-exchanger for the concerted refolding of cysteine- or proline-rich proteins 
BMC Biotechnology  2009;9:27.
Background
Escherichia coli has been most widely used for the production of valuable recombinant proteins. However, over-production of heterologous proteins in E. coli frequently leads to their misfolding and aggregation yielding inclusion bodies. Previous attempts to refold the inclusion bodies into bioactive forms usually result in poor recovery and account for the major cost in industrial production of desired proteins from recombinant E. coli. Here, we describe the successful use of the immobilized folding machineries for in vitro refolding with the examples of high yield refolding of a ribonuclease A (RNase A) and cyclohexanone monooxygenase (CHMO).
Results
We have generated refolding-facilitating media immobilized with three folding machineries, mini-chaperone (a monomeric apical domain consisting of residues 191–345 of GroEL) and two foldases (DsbA and human peptidyl-prolyl cis-trans isomerase) by mimicking oxidative refolding chromatography. For efficient and simple purification and immobilization simultaneously, folding machineries were fused with the positively-charged consecutive 10-arginine tag at their C-terminal. The immobilized folding machineries were fully functional when assayed in a batch mode. When the refolding-facilitating matrices were applied to the refolding of denatured and reduced RNase A and CHMO, both of which contain many cysteine and proline residues, RNase A and CHMO were recovered in 73% and 53% yield of soluble protein with full enzyme activity, respectively.
Conclusion
The refolding-facilitating media presented here could be a cost-efficient platform and should be applicable to refold a wide range of E. coli inclusion bodies in high yield with biological function.
doi:10.1186/1472-6750-9-27
PMCID: PMC2676282  PMID: 19323835
25.  Culture Conditions and Characterizations of a New Phytase-Producing Fungal Isolate, Aspergillus sp. L117 
Mycobiology  2005;33(4):223-229.
A novel fungal strain Aspergillus sp. L117 that produced acid-stable and thermostable phytase was isolated on basis of the clearing zone on PSM plate and the ability of Na-phytate hydrolysis. The phytase of isolate showed a 3-fold higher activity than that of A. ficuun NRRL3135. The Aspergillus sp. L117 produced maximal level of phytase at initial pH of 5.0 and 30℃. The optimal pH and temperature for phytase activity were 5.5 and 50℃, respectively. The phytase showed totally stable activity after 20 min of exposure between 30 and 90℃, and even at 100℃. The highest level of residual phytase activity was obtained at pH 5.5, and still retained the stability at the broadest pH ranges (2.0 to 7.0) of all the aforementioned phytases. Storage stability of phytase was preserved over 96% of initial activities for 60 days at 4, -20, and -70℃ and to retain even 70% of the initial activity at room temperature.
doi:10.4489/MYCO.2005.33.4.223
PMCID: PMC3774891  PMID: 24049505
Acid-stable and thermostable phytase; Aspergillus sp.; Phosphatase

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