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1.  Meta-analysis of genetic variants associated with human exceptional longevity 
Aging (Albany NY)  2013;5(9):653-661.
Despite evidence from family studies that there is a strong genetic influence upon exceptional longevity, relatively few genetic variants have been associated with this trait. One reason could be that many genes individually have such weak effects that they cannot meet standard thresholds of genome wide significance, but as a group in specific combinations of genetic variations, they can have a strong influence. Previously we reported that such genetic signatures of 281 genetic markers associated with about 130 genes can do a relatively good job of differentiating centenarians from non-centenarians particularly if the centenarians are 106 years and older. This would support our hypothesis that the genetic influence upon exceptional longevity increases with older and older (and rarer) ages. We investigated this list of markers using similar genetic data from 5 studies of centenarians from the USA, Europe and Japan. The results from the meta-analysis show that many of these variants are associated with survival to these extreme ages in other studies. Since many centenarians compress morbidity and disability towards the end of their lives, these results could point to biological pathways and therefore new therapeutics to increase years of healthy lives in the general population.
PMCID: PMC3808698  PMID: 24244950
centenarian; exceptional longevity; genetic association study; aging; gene; lifespan; meta-analysis
2.  Differential Expression of Secreted Phosphoprotein 1 in the Motor Cortex among Primate Species and during Postnatal Development and Functional Recovery 
PLoS ONE  2013;8(5):e65701.
We previously reported that secreted phosphoprotein 1 (SPP1) mRNA is expressed in neurons whose axons form the corticospinal tract (CST) of the rhesus macaque, but not in the corresponding neurons of the marmoset and rat. This suggests that SPP1 expression is involved in the functional or structural specialization of highly developed corticospinal systems in certain primate species. To further examine this hypothesis, we evaluated the expression of SPP1 mRNA in the motor cortex from three viewpoints: species differences, postnatal development, and functional/structural changes of the CST after a lesion of the lateral CST (l-CST) at the mid-cervical level. The density of SPP1-positive neurons in layer V of the primary motor cortex (M1) was much greater in species with highly developed corticospinal systems (i.e., rhesus macaque, capuchin monkey, and humans) than in those with less developed corticospinal systems (i.e., squirrel monkey, marmoset, and rat). SPP1-positive neurons in the macaque monkey M1 increased logarithmically in layer V during postnatal development, following a time course consistent with the increase in conduction velocity of the CST. After an l-CST lesion, SPP1-positive neurons increased in layer V of the ventral premotor cortex, in which compensatory changes in CST function/structure may occur, which positively correlated with the extent of finger dexterity recovery. These results further support the concept that the expression of SPP1 may reflect functional or structural specialization of highly developed corticospinal systems in certain primate species.
doi:10.1371/journal.pone.0065701
PMCID: PMC3669139  PMID: 23741508
3.  Revision of tumor prosthesis of the knee joint 
Background
Among 40 patients with primary malignant tumors of the knee joint who underwent reconstruction of the affected limb with tumor prosthesis, revision was required in 7 due to stem breakage or loosening.
Subjects and methods
In the 7 cases undergoing revision, conditions and background factors at the time of breakage, the breakage site, time of revision, models of previous and new prostheses, stem diameters before and after revision, details of the revision (blood loss, operative time), and the presence or absence of adjuvant therapy were determined.
Results
The replacement site was the distal femur in 5 and proximal tibia in 2. Revision was performed 6 years and 2 months after the previous prosthesis placement on average. The broken prosthesis model was KMFTR in 4 and HMRS and the physio-hinge type in one each. Revision due to loosening was performed in a case requiring replacement with Growing Kotz prosthesis. The model was switched to HMRS in 3, and the stem diameter was changed to 12 mm in 3 KMFTR breakage cases. The mean stem diameters were 11.2 and 10.2 mm in the non-revision and revision groups. The respective resection rates were 36 and 45%. The mean functional evaluation was 70.1% before and 76.2% after revision.
Conclusion
To reduce the risk of tumor prosthesis breakage, the amount of bone resection should be limited to 30% or less in the affected bone, the stem diameter should be at least 12 mm, and the stem shape should be fitted to the anatomical shape of the femur.
doi:10.1007/s00590-011-0848-0
PMCID: PMC3376781  PMID: 22754428
Limb salvage; Revision; Tumor prostheses; Malignant bone tumor
4.  Lifespan-Extending Effects of Royal Jelly and Its Related Substances on the Nematode Caenorhabditis elegans 
PLoS ONE  2011;6(8):e23527.
Background
One of the most important challenges in the study of aging is to discover compounds with longevity-promoting activities and to unravel their underlying mechanisms. Royal jelly (RJ) has been reported to possess diverse beneficial properties. Furthermore, protease-treated RJ (pRJ) has additional pharmacological activities. Exactly how RJ and pRJ exert these effects and which of their components are responsible for these effects are largely unknown. The evolutionarily conserved mechanisms that control longevity have been indicated. The purpose of the present study was to determine whether RJ and its related substances exert a lifespan-extending function in the nematode Caenorhabditis elegans and to gain insights into the active agents in RJ and their mechanism of action.
Principal Findings
We found that both RJ and pRJ extended the lifespan of C. elegans. The lifespan-extending activity of pRJ was enhanced by Octadecyl-silica column chromatography (pRJ-Fraction 5). pRJ-Fr.5 increased the animals' lifespan in part by acting through the FOXO transcription factor DAF-16, the activation of which is known to promote longevity in C. elegans by reducing insulin/IGF-1 signaling (IIS). pRJ-Fr.5 reduced the expression of ins-9, one of the insulin-like peptide genes. Moreover, pRJ-Fr.5 and reduced IIS shared some common features in terms of their effects on gene expression, such as the up-regulation of dod-3 and the down-regulation of dod-19, dao-4 and fkb-4. 10-Hydroxy-2-decenoic acid (10-HDA), which was present at high concentrations in pRJ-Fr.5, increased lifespan independently of DAF-16 activity.
Conclusions/Significance
These results demonstrate that RJ and its related substances extend lifespan in C. elegans, suggesting that RJ may contain longevity-promoting factors. Further analysis and characterization of the lifespan-extending agents in RJ and pRJ may broaden our understanding of the gene network involved in longevity regulation in diverse species and may lead to the development of nutraceutical interventions in the aging process.
doi:10.1371/journal.pone.0023527
PMCID: PMC3153499  PMID: 21858156
6.  RNA Editing Genes Associated with Extreme Old Age in Humans and with Lifespan in C. elegans 
PLoS ONE  2009;4(12):e8210.
Background
The strong familiality of living to extreme ages suggests that human longevity is genetically regulated. The majority of genes found thus far to be associated with longevity primarily function in lipoprotein metabolism and insulin/IGF-1 signaling. There are likely many more genetic modifiers of human longevity that remain to be discovered.
Methodology/Principal Findings
Here, we first show that 18 single nucleotide polymorphisms (SNPs) in the RNA editing genes ADARB1 and ADARB2 are associated with extreme old age in a U.S. based study of centenarians, the New England Centenarian Study. We describe replications of these findings in three independently conducted centenarian studies with different genetic backgrounds (Italian, Ashkenazi Jewish and Japanese) that collectively support an association of ADARB1 and ADARB2 with longevity. Some SNPs in ADARB2 replicate consistently in the four populations and suggest a strong effect that is independent of the different genetic backgrounds and environments. To evaluate the functional association of these genes with lifespan, we demonstrate that inactivation of their orthologues adr-1 and adr-2 in C. elegans reduces median survival by 50%. We further demonstrate that inactivation of the argonaute gene, rde-1, a critical regulator of RNA interference, completely restores lifespan to normal levels in the context of adr-1 and adr-2 loss of function.
Conclusions/Significance
Our results suggest that RNA editors may be an important regulator of aging in humans and that, when evaluated in C. elegans, this pathway may interact with the RNA interference machinery to regulate lifespan.
doi:10.1371/journal.pone.0008210
PMCID: PMC2788130  PMID: 20011587
7.  High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line 
BMC Research Notes  2009;2:153.
Background
THP-1 is a human monocytic leukemia cell line derived from a patient with acute monocytic leukemia. The cell line differentiates into macrophage-like cells by stimulation with phorbol myristate acetate (PMA). Although it has been used frequently as a model for macrophage differentiation in research including the FANTOM4/Genome Network Project, there are few reports on its genomic constitution. Therefore, we attempted to reveal the genomic aberrations in these cells with the microarray-based comparative genomic hybridization (aCGH) technique.
Findings
We report large aberrations, including deletions 6p, 12p, 17p, and trisomy 8, and revealed breakpoints in the MLL and MLLT3 genes. Moreover, we found novel genomic aberrations such as a hemizygous narrow deletion partially containing the TP73 gene and homozygous deletions, including the CDKN2A, CDKN2B and PTEN genes.
Conclusion
In this study, we identified 119 aberrant regions in autosomal chromosomes, and at least 16 of these aberrations were less than 100 kb, most of which were undetectable in the previous works. We also revealed a total of 4.6 Mb of homozygous deleted regions. Our results will provide a base to precisely understand studies involving the THP-1 cell line, especially the huge amount of data generated from the FANTOM4/Genome Network Project.
doi:10.1186/1756-0500-2-153
PMCID: PMC2729307  PMID: 19635138
8.  Integrative Genome-Wide Expression Analysis Bears Evidence of Estrogen Receptor-Independent Transcription in Heregulin-Stimulated MCF-7 Cells 
PLoS ONE  2008;3(3):e1803.
Heregulin ß-1 (HRG) is an extracellular ligand that activates mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-OH kinase (PI3K)/Akt signaling pathways through ErbB receptors. MAPK and Akt have been shown to phosphorylate the estrogen receptor (ER) at Ser-118 and Ser-167, respectively, thereby mimicking the effects of estrogenic activity such as estrogen responsive element (ERE)-dependent transcription. In the current study, integrative analysis was performed using two tiling array platforms, comprising histone H3 lysine 9 (H3K9) acetylation and RNA mapping, together with array comparative genomic hybridization (CGH) analysis in an effort to identify HRG-regulated genes in ER-positive MCF-7 breast cancer cells. Through application of various threshold settings, 333 (326 up-regulated and 7 down-regulated) HRG-regulated genes were detected. Prediction of upstream transcription factors (TFs) and pathway analysis indicated that 21% of HRG-induced gene regulation may be controlled by the MAPK cascade, while only 0.6% of the gene expression is controlled by ERE. A comparison with previously reported estrogen (E2)-regulated gene expression data revealed that only 12 common genes were identified between the 333 HRG-regulated (3.6%) and 239 E2-regulated (5.0%) gene groups. However, with respect to enriched upstream TFs, 4 common TFs were identified in the 14 HRG-regulated (28.6%) and 13 E2-regulated (30.8%) gene groups. These results indicated that while E2 and HRG may induce common TFs, the regulatory mechanisms that govern HRG- and E2-induced gene expression differ.
doi:10.1371/journal.pone.0001803
PMCID: PMC2266794  PMID: 18350142
9.  Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression 
BMC Genomics  2004;5:16.
Background
Gene expression is regulated mainly by transcription factors (TFs) that interact with regulatory cis-elements on DNA sequences. To identify functional regulatory elements, computer searching can predict TF binding sites (TFBS) using position weight matrices (PWMs) that represent positional base frequencies of collected experimentally determined TFBS. A disadvantage of this approach is the large output of results for genomic DNA. One strategy to identify genuine TFBS is to utilize local concentrations of predicted TFBS. It is unclear whether there is a general tendency for TFBS to cluster at promoter regions, although this is the case for certain TFBS. Also unclear is the identification of TFs that have TFBS concentrated in promoters and to what level this occurs. This study hopes to answer some of these questions.
Results
We developed the cluster score measure to evaluate the correlation between predicted TFBS clusters and promoter sequences for each PWM. Non-promoter sequences were used as a control. Using the cluster score, we identified a PWM group called PWM-PCP, in which TFBS clusters positively correlate with promoters, and another PWM group called PWM-NCP, in which TFBS clusters negatively correlate with promoters. The PWM-PCP group comprises 47% of the 199 vertebrate PWMs, while the PWM-NCP group occupied 11 percent. After reducing the effect of CpG islands (CGI) against the clusters using partial correlation coefficients among three properties (promoter, CGI and predicted TFBS cluster), we identified two PWM groups including those strongly correlated with CGI and those not correlated with CGI.
Conclusion
Not all PWMs predict TFBS correlated with human promoter sequences. Two main PWM groups were identified: (1) those that show TFBS clustered in promoters associated with CGI, and (2) those that show TFBS clustered in promoters independent of CGI. Assessment of PWM matches will allow more positive interpretation of TFBS in regulatory regions.
doi:10.1186/1471-2164-5-16
PMCID: PMC375527  PMID: 15053842
promoter; tissue-specific gene expression; position weight matrix; regulatory motif

Results 1-9 (9)