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1.  Methicillin-Resistant Staphylococcus aureus Carriage among Students at a Historically Black University: A Case Study 
Background. Black people in the USA is afflicted with a higher rate of methicillin-resistant Staphylococcus aureus (MRSA) infection. This study determined the prevalence of MRSA carriage among black college students at a university setting. Methods. Hand and nasal swabs were collected and screened for MRSA by mannitol fermentation, coagulase, and DNase activities and their resistance to oxacillin. MRSA isolates were analyzed for antimicrobial resistance pattern, genetic profile for staphylococcal cassette chromosome mec (SCCmec) type, pulsed-field type, multilocus sequence type (ST), and the presence of Panton-Valentine leukocidin (PVL) gene. Results. MRSA was isolated from 1 of the 312 (0.3%) hand swabs and 2 of the 310 (0.65%) nasal swabs, respectively. All isolates lack multidrug resistance and have type IV SCCmec, characteristic of community-associated MRSA. These isolates were a ST8-MRSA-IVa-PVL(+) (USA300 strain), a ST8-MRSA-IVb-PVL(−), and a new MLST, ST2562-MRSA-IV-PVL(−), identified in this study. These isolates were thus not transmitted among students. Conclusion. We found a low rate of MRSA carriage among students in a black university. Our finding highlights the need of future study which involves multiinstitutions and other ethnic group to assess the association of black race with MRSA carriage.
doi:10.1155/2013/979734
PMCID: PMC3563209  PMID: 23401691
2.  Aging enhances the basal production of IL-6 and CCL2 in vascular smooth muscle cells 
Objective
Increased circulating cytokine levels are a prominent feature of aging that may contribute to atherosclerosis. However, the role vascular cells play in chronic inflammation induced by aging is not clear. Here, we examined the role of aging on inflammatory responses of vascular cells.
Methods and Results
In an ex vivo culture system, we examined the inflammatory response of aortas from young (2-4 months) and aged (16-18 months) mice under non-stimulatory conditions. We found that basal levels of interleukin (IL)-6 were increased in aged aortas. Aged aortic vascular smooth muscle cells (VSMC) exhibited a higher basal secretion of IL-6 than young VSMC. Gene and protein expression analysis revealed that aged VSMC exhibited upregulation of chemokines (e.g. CCL2), adhesion molecules (e.g., ICAM1), and innate immune receptors (e.g., Toll like receptor [TLR] 4), which all contribute to atherosclerosis. Using VSMC from aged TL4-/- and Myd88-/- mice, we demonstrate that signaling via TLR4 and its signal adaptor, MyD88, are in part responsible for the age-elevated basal IL-6 response.
Conclusion
Aging induces a proinflammatory phenotype in VSMC due in part to increased signaling of TLR4 and MyD88. Our results provide a potential explanation as to why aging leads to chronic inflammation and enhanced atherosclerosis.
doi:10.1161/ATVBAHA.111.236349
PMCID: PMC3241880  PMID: 22034510
aging; atherosclerosis; inflammation; mouse; vascular smooth muscle cells
3.  Degree-Strength Correlation Reveals Anomalous Trading Behavior 
PLoS ONE  2012;7(10):e45598.
Manipulation is an important issue for both developed and emerging stock markets. Many efforts have been made to detect manipulation in stock markets. However, it is still an open problem to identify the fraudulent traders, especially when they collude with each other. In this paper, we focus on the problem of identifying the anomalous traders using the transaction data of eight manipulated stocks and forty-four non-manipulated stocks during a one-year period. By analyzing the trading networks of stocks, we find that the trading networks of manipulated stocks exhibit significantly higher degree-strength correlation than the trading networks of non-manipulated stocks and the randomized trading networks. We further propose a method to detect anomalous traders of manipulated stocks based on statistical significance analysis of degree-strength correlation. Experimental results demonstrate that our method is effective at distinguishing the manipulated stocks from non-manipulated ones. Our method outperforms the traditional weight-threshold method at identifying the anomalous traders in manipulated stocks. More importantly, our method is difficult to be fooled by colluded traders.
doi:10.1371/journal.pone.0045598
PMCID: PMC3474833  PMID: 23082114
4.  An age-specific CD8+ T-cell pathway that impairs the effectiveness of strategies to prolong allograft survival1 
Age-related decline in immunity can impair cell-mediated responses during an infection, malignancy, and acute allograft rejection. Although much research has been allocated to understand the immune responses that impact the former two conditions, the cellular mechanisms by which aging impacts the immune acceptance of organ allografts are not completely clear. In this study, we examined how recipient age impacts the efficacy of therapies that modulate immune recognition of allografts using an immunogenic murine skin transplant model. We found that costimulatory blockade-based treatment failed to extend allograft survival in older recipients to the same extent as that observed in younger recipients. CD8+ T-cells were critical for the inability of aged recipients to achieve maximal allograft survival. Although aged mice displayed a larger number of effector memory T-cells prior to transplantation, these cells did not exhibit enhanced alloreactivity compared to young memory T-cells. In contrast, naïve aged CD8+ T-cells exhibited enhanced IFN-γ production to allostimulation compared to young naïve T-cells. Our results provide evidence that aging enhances CD8+ T-cell alloreactivity. This could impair the ability of costimulatory blockade-based therapies to prolong allograft survival. Thus, targeting CD8+ T cells in humans may be a way to improve outcomes in older patients requiring immune modulatory therapy.
doi:10.4049/jimmunol.1100441
PMCID: PMC3178732  PMID: 21873523
5.  Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes 
Nature  2012;483(7387):82-86.
The human X and Y chromosomes evolved from an ordinary pair of autosomes during the past 200–300 million years1–3. Due to genetic decay, the human MSY (male-specific region of Y chromosome) retains only three percent of the ancestral autosomes’ genes4,5. This evolutionary decay was driven by a series of five “stratification” events. Each event suppressed X-Y crossing over within a chromosome segment or “stratum”, incorporated that segment into the MSY, and subjected its genes to the erosive forces that attend the absence of crossing over2,6. The last of these events occurred 30 million years ago (mya), or 5 million years before the human and Old World monkey (OWM) lineages diverged. Although speculation abounds regarding ongoing decay and looming extinction of the human Y chromosome7–10, remarkably little is known about how many MSY genes were lost in the human lineage in the 25 million years that have followed its separation from the OWM lineage. To explore this question, we sequenced the MSY of the rhesus macaque, an OWM, and compared it to the human MSY. We discovered that, during the last 25 million years, MSY gene loss in the human lineage was limited to the youngest stratum (stratum 5), which comprises three percent of the human MSY. Within the older strata, which collectively comprise the bulk of the human MSY, gene loss evidently ceased more than 25 mya. Likewise, the rhesus MSY has not lost any older genes (from strata 1–4) during the past 25 million years, despite major structural differences from the human MSY. The rhesus MSY is simpler, with few amplified gene families or palindromes that might enable intrachromosomal recombination and repair. We present an empirical reconstruction of human MSY evolution in which each stratum transitioned from rapid, exponential loss of ancestral genes to strict conservation through purifying selection.
doi:10.1038/nature10843
PMCID: PMC3292678  PMID: 22367542
6.  Haptoglobin activates innate immunity to enhance acute transplant rejection in mice 
Immune tolerance to transplanted organs is impaired when the innate immune system is activated in response to the tissue necrosis that occurs during harvesting and implantation procedures. A key molecule in this immune pathway is the intracellular TLR signal adaptor known as myeloid differentiation primary response gene 88 (MyD88). After transplantation, MyD88 induces DC maturation as well as the production of inflammatory mediators, such as IL-6 and TNF-α. However, upstream activators of MyD88 function in response to transplantation have not been identified. Here, we show that haptoglobin, an acute phase protein, is an initiator of this MyD88-dependent inflammatory process in a mouse model of skin transplantation. Necrotic lysates from transplanted skin elicited higher inflammatory responses in DCs than did nontransplanted lysates, suggesting DC-mediated responses are triggered by factors released during transplantation. Analysis of transplanted lysates identified haptoglobin as one of the proteins upregulated during transplantation. Expression of donor haptoglobin enhanced the onset of acute skin transplant rejection, whereas haptoglobin-deficient skin grafts showed delayed acute rejection and antidonor T cell priming in a MyD88-dependent graft rejection model. Thus, our results show that haptoglobin release following skin necrosis contributes to accelerated transplant rejection, with potential implications for the development of localized immunosuppressive therapies.
doi:10.1172/JCI58344
PMCID: PMC3248290  PMID: 22156194
7.  A cluster of specified microRNAs in peripheral blood as biomarkers for metastatic non-small-cell lung cancer by stem-loop RT-PCR 
Purpose
To investigate the levels for some specified microRNAs in human’s peripheral blood so as to determine whether they can serve as biomarkers for metastatic non-small-cell lung cancer.
Methods
Use a quantitative stem-loop RT-PCR method to examine the serum levels for certain microRNAs including has-miR-125a-5p, has-miR-126, has-miR-183, has-miR-200, has-miR-221, and has-miR-222 from the patients with Stage IV, Stage I/II non-small-cell lung cancer and the controls.
Results
There was statistical difference in the serum levels for hsa-miR-126, hsa-miR-183, and hsa-miR-222 between the controls and the Stage IV patients, but not for has-miR-125a-5p, has-miR-200 and has-miR-221. It also showed statistical difference for hsa-miR-126 and hsa-miR-183 between the Stage I/II patients and Stage IV patients, but not between the controls and Stage I/II patients.
Conclusion
Hsa-miR-126 and hsa-miR-183 may serve as potential serum biomarkers for metastatic non-small-cell lung cancer.
doi:10.1007/s00432-011-1068-z
PMCID: PMC3249180  PMID: 22009180
microRNAs; Non-small-cell lung cancer; Stem-loop RT-PCR; Biomarker
8.  Imbalanced expression of mitogen-activated protein kinase phosphatase-1 and phosphorylated extracellular signal-regulated kinases in lung squamous cell carcinoma*  
Objective: Mitogen-activated protein kinases (MAPKs) are correlated with a more malignant phenotype in many cancers. This study was designed to evaluate the predictive value of the expression of MAPK phosphatase-1 (MKP-1) and phosphorylated extracellular signal-regulated kinase 1/2 (p-ERK1/2), as the key regulatory mechanism of the MAPKs, in lung squamous cell carcinoma (SCC). Methods: We assessed the expressions of MKP-1 and p-ERK1/2 in twenty subjects at different differentiation degree of SCC and five normal lungs by immunohistochemistry and real-time reverse transcriptase polymerase chain reaction (RT-PCR) analysis. Results: Immunohistochemistry and real-time RT-PCR assay showed that the expression of MKP-1 was gradually decreased as tissue type went from normal lung tissues to increasingly undifferentiated carcinoma, and it was negatively correlated with tumor differentiation (P<0.01). However, the expression of p-ERK1/2 or ERK1/2 was gradually increased as tissue type went from normal lung tissues to increasingly undifferentiated carcinoma, and it was positively correlated with tumor differentiation (P<0.01). Conclusions: Our data indicates the relevance of MKP-1 and p-ERK1/2 in SCC as a potential positive and negative prognostic factor. The imbalanced expression of MKP-1 and p-ERK1/2 may play a role in the development of SCC and these two molecules may be new targets for the therapy and prognosis of SCC.
doi:10.1631/jzus.B1100165
PMCID: PMC3190098  PMID: 21960346
Mitogen-activated protein kinase phosphatase-1 (MKP-1); Extracellular signal-regulated kinase (ERK); Lung squamous cell carcinoma (SCC); Prognostic factor
9.  Evaluation of biodistribution and antitumor effects of 188Re-rhk5 in a mouse model of lung cancer 
Oncology Letters  2011;2(5):865-870.
Targeting drugs to receptors involved in tumor angiogenesis is considered to be a novel and promising approach to improve cancer treatment. This study aimed to evaluate the anti-tumor efficacy of 188Re-labeled recombinant human plasminogen kringle 5 (188Re‑rhk5) through [18F]-fluorodeoxyglucose (FDG) micro-positron emission tomography (PET). Radiolabeled rhk5 was obtained by conjugating the hystidine (6 x His) group at the carbon end of rhk5 with fac-[188Re(H2O)3(CO)3]+. The biodistribution study of 188Re-rhk5 showed that 188Re-rhk5 had a high initial tumor uptake and prolonged tumor retention. The highest tumor uptake of 188Re-rhk5 (3.65±0.82% ID/g) was found 2 h after injection which decreased to 0.81±0.14% ID/g 12 h after injection. Following therapy, tumor size measurement indicated that 188Re-rhk5-treated tumors were smaller than 188Re-, rhk5- and saline-treated controls 6 days after the treatment. In vivo 18F-FDG micro-PET imaging showed significantly reduced tumor metabolism in the 188Re-rhk5-treated mice vs. those treated with rhk5, 188Re and saline control, 1 day after treatment. Moreover, the number of microvessels was significantly reduced after 188Re-rhk5 treatment as determined by CD31 staining. Our results demonstrate that specific delivery of 188Re-rhk5 allows preferential cytotoxicity to A549 lung cancer cells and tumor vasculature. 18F-FDG micro-PET is a non-invasive imaging tool that can be utilized to assess early tumor responses to 188Re-rhk5 therapy.
doi:10.3892/ol.2011.326
PMCID: PMC3408053  PMID: 22866142
10.  Paclitaxel based vs oxaliplatin based regimens for advanced gastric cancer 
AIM: To compare the efficacy and safety of paclitaxel combined with fluorouracil plus cisplatin (PCF), and oxaliplatin combined with fluorouracil plus leucovorin (FOLFOX-4) regimens for advanced gastric cancer (AGC).
METHODS: Ninety-four patients with AGC were randomly assigned to receive paclitaxel (50 mg/m2 iv) on days 1, 8 and 15, cisplatin (20 mg/m2 iv) and fluorouracil (750 mg/m2 iv) on days 1-5, or oxaliplatin (85 mg/m2 iv) and leucovorin (200 mg/m2 iv) on day 1, followed by bolus fluorouracil (400 mg/m2 iv) and fluorouracil (600 mg/m2 iv) on days 1 and 2. The primary end point was the 1-year survival time.
RESULTS: The overall response rate (ORR) of the patients was 48.0% and 45.5% to PCF and FOLFOX-4, respectively. The disease control rate (DCR) of PCF and FOLFOX-4 was 82.0% and 81.8%, respectively. The median survival times (MSTs) of the patients were 10.8 and 9.9 mo, respectively, after treatment with PCF and FOLFOX-4. The 1-year survival rate of the patients was 36.0% and 34.1%, respectively, after treatment with PCF and FOLFOX-4. No significant difference was observed in ORR, DCR, MST or 1-year survival rate between the two groups. The most common adverse events were anemia, nausea and vomiting, and grade 3/4 alopecia in PCF treatment group, and anemia, grade 1/2 neurotoxic effect and grade 3/4 neutropenia in FOLFOX-4 treatment group.
CONCLUSION: Patients with AGC have a similar response rate to PCF and FOLFOX-4 regimens with a similar survival rate. The PCF and FOLFOX-4 regimens are efficacious and tolerable as a promising therapy for AGC.
doi:10.3748/wjg.v17.i8.1082
PMCID: PMC3057154  PMID: 21448363
Paclitaxel; Oxaliplatin; Advanced gastric cancer
11.  Differential ability of novel attenuated targeted deletion mutants of Francisella tularensis subspecies tularensis strain SCHU S4 to protect mice against aerosol challenge with virulent bacteria: effects of host background and route of immunization 
Vaccine  2009;28(7):1824.
Francisella tularensis subspecies tularensis is a highly virulent facultative intracellular pathogen of humans and a potential biological weapon. A live vaccine strain, F. tularensis LVS, was developed more than 50 years ago by pragmatic attenuation of a strain of the less virulent holarctica subspecies. LVS was demonstrated to be highly effective in human volunteers who were exposed to intradermal challenge with fully virulent subsp. tularensis, but was less effective against aerosol exposure. LVS faces regulatory hurdles that to date have prevented its licensure for general use. Therefore, a better defined and more effective vaccine is being sought. To this end we have created gene deletion mutants in the virulent subsp. tularensis strain and tested them for their ability to elicit a protective immune response against systemic or aerosol challenge with the highly virulent wild-type subsp. tularensis strain, SCHU S4. Both oral and Intradermal (ID) primary vaccination routes were assessed in BALB/c and C3H/HeN mice as was oral boosting. One SCHU S4 mutant missing the heat shock gene, clpB, was significantly more attenuated than LVS whereas a double deletion mutant missing genes FTT0918 and capB was as attenuated as LVS. In general mice immunized with SCHU S4ΔclpB were significantly better protected against aerosol challenge than mice immunized with LVS. A single ID immunization of BALB/c mice with SCHU S4ΔclpB was at least as effective as any other regimen examined. Mice immunized with SCHU S4Δ0918ΔcapB were generally protected to a similar degree as mice immunized with LVS. A preliminary examination of immune responses to vaccination with LVS, SCHU S4ΔclpB, or SCHU S4Δ0918ΔcapB provided no obvious correlate to their relative efficacies.
doi:10.1016/j.vaccine.2009.12.001
PMCID: PMC2822029  PMID: 20018266
12.  Molecular Immune Responses to Aerosol Challenge with Francisella tularensis in Mice Inoculated with Live Vaccine Candidates of Varying Efficacy 
PLoS ONE  2010;5(10):e13349.
Background
Francisella tularensis is a facultative intracellular bacterial pathogen and the etiological agent of tularemia. The subspecies F. tularensis tularensis is especially virulent for humans when inhaled and respiratory tularemia is associated with high mortality if not promptly treated. A live vaccine strain (LVS) derived from the less virulent holarctica subspecies confers incomplete protection against aerosol challenge with subsp. tularensis. Moreover, correlates of protection have not been established for LVS.
Methodology/Principal Findings
In the present study we compare molecular immune responses elicited by LVS and two defined deletion mutants of clinical subsp. tularensis strain, SCHU S4, that confer enhanced protection in a mouse model. BALB/c mice were immunized intradermally then challenged with an aerosol of SCHU S4 six weeks later. Changes in the levels of a selected panel of cytokines and chemokines were examined in the lungs, spleens, and sera of vaccinated and challenged mice. Mostly, increased cytokine and chemokine levels correlated with increased bacterial burden. However, after adjusting for this variable, immunization with either of the two Schu S4 mutants resulted in higher levels of several pulmonary cytokines, versus those resulting after LVS immunization, including IL-17. Moreover, treatment of mice immunized with ΔclpB with anti-IL-17 antibodies post-challenge enhanced lung infection.
Conclusions/Significance
This is the first report characterizing local and systemic cytokine and chemokine responses in mice immunized with vaccines with different efficacies against aerosol challenge with virulent F. tularensis subsp. tularensis. It shows that increases in the levels of most of these immunomodulators, including those known to be critical for protective immunity, do not superficially correlate with protection unless adjusted for the effects of bacterial burden. Additionally, several cytokines were selectively suppressed in the lungs of naïve mice, suggesting that one mechanism of vaccine action is to overcome this pathogen-induced immunosuppression.
doi:10.1371/journal.pone.0013349
PMCID: PMC2953512  PMID: 20967278
13.  Aging Augments IL-17 T cell Alloimmune Responses 
As increasing numbers of elderly patients require solid organ transplantation, the need to better understand how aging modifies alloimmune responses increases. Here, we examined whether aged mice exhibit augmented, donor-specific memory responses prior to transplantation. We found that elevated donor-specific IL-17, but not IFN-γ, responses were observed in aged mice compared to young mice prior to transplantation. Further characterization of the heightened IL-17 alloimmune response with aging demonstrated that memory CD4+ T cells were required. Reduced IL-2 alloimmune responses with age contributed to the elevated IL-17 phenotype in vitro, and treatment with an anti-IL-17 antibody delayed the onset of acute allograft rejection. In conclusion, aging leads to augmented, donor-specific IL-17 immune responses that are important for the timing of acute allograft rejection in aged recipients. IL-17 targeting therapies may be useful for averting transplant rejection responses in older transplant recipients.
doi:10.1111/j.1600-6143.2008.02458.x
PMCID: PMC2626154  PMID: 18976294
14.  Dual Signaling of MyD88 and TRIF are Critical for Maximal TLR4-Induced Dendritic Cell Maturation† 
TLR4 is a unique TLR as downstream signaling occurs via two separate pathways: MyD88 and TRIF. Here, we compared and contrasted the interplay of these pathways between murine dendritic cells (DCs) and macrophages during LPS stimulation. During TLR4 activation, neither pathway on its own was critical for upregulation of costimulatory molecules in DCs, whereas the upregulation of costimulatory molecules was largely TRIF-dependent in macrophages. LPS-induced secreted factors, of which type I IFNs were one of the active components, played a larger role in promoting the upregulation of costimulatory molecules in macrophages than DCs. In both cell types, MyD88 and TRIF pathways together accounted for the inflammatory response to LPS activation. Furthermore, signaling of both adaptors allowed maximal T cell priming by LPS-matured DCs, with MyD88 playing a larger role than TRIF. In sum, in our experimental systems, TRIF signaling plays a more important role in LPS-induced macrophage activation than in DC activation.
PMCID: PMC2507878  PMID: 18641322
Rodent; dendritic cell
15.  Molecular immunology of experimental primary tularemia in mice infected by respiratory or intradermal routes with type A Francisella tularensis 
Molecular immunology  2008;45(10):2962-2969.
The type A subspecies of Francisella tularensis is a highly virulent facultative intracellular bacterial pathogen, and a potential biological weapon. Recently, there has been renewed interest in developing new vaccines and therapeutics against this bacterium. Natural cases of disease, tularemia, caused by the type A subspecies are very rare. Therefore, the United States Food and Drug Administration will rely on the so called Animal Rule for efficacy testing of anti-Francisella medicines. This requires the human disease to be modeled in one or more animal species in which the pathogenicity of the agent is reasonably well understood. Mice are natural hosts for F. tularensis, and might be able to satisfythis requirement. Tularemia pathogenesis appears to be primarily due to the host inflammatory responsewhich is poorly understood at the molecular level. Additionally, the extent to which this response varies depending on host and pathogen genetic background, or by pathogen challenge route or dose is unknown. Therefore, the present study examined sera and infected tissues from C57BL/6 and BALB/c mice challenged by natural intradermal and respiratory routes with one of two distinct type A strains of the pathogen for cytokine and chemokine responses that might help explain the morbidity associated with tularemia. The results show that the molecular immune response was mostly similar regardless of the variables examined. For instance, mRNA for the proinflammatory cytokine IL-6, and chemokines KC, and IP-10 was consistently upregulated at all sites of infection. Upregulation of mRNA for several other cytokines and chemokines occurred in a more tissue restricted manner. For instance, IFNIFN-γ was highly upregulated in the skin of BALB/c, but not C57BL/6 mice after ID inoculation of the pathogen, whilst IL-10 mRNA upregulation was only consistently seen in the skin and lungs.
doi:10.1016/j.molimm.2008.01.022
PMCID: PMC2715917  PMID: 18321578
16.  Somatic mutations affect key pathways in lung adenocarcinoma 
Ding, Li | Getz, Gad | Wheeler, David A. | Mardis, Elaine R. | McLellan, Michael D. | Cibulskis, Kristian | Sougnez, Carrie | Greulich, Heidi | Muzny, Donna M. | Morgan, Margaret B. | Fulton, Lucinda | Fulton, Robert S. | Zhang, Qunyuan | Wendl, Michael C. | Lawrence, Michael S. | Larson, David E. | Chen, Ken | Dooling, David J. | Sabo, Aniko | Hawes, Alicia C. | Shen, Hua | Jhangiani, Shalini N. | Lewis, Lora R. | Hall, Otis | Zhu, Yiming | Mathew, Tittu | Ren, Yanru | Yao, Jiqiang | Scherer, Steven E. | Clerc, Kerstin | Metcalf, Ginger A. | Ng, Brian | Milosavljevic, Aleksandar | Gonzalez-Garay, Manuel L. | Osborne, John R. | Meyer, Rick | Shi, Xiaoqi | Tang, Yuzhu | Koboldt, Daniel C. | Lin, Ling | Abbott, Rachel | Miner, Tracie L. | Pohl, Craig | Fewell, Ginger | Haipek, Carrie | Schmidt, Heather | Dunford-Shore, Brian H. | Kraja, Aldi | Crosby, Seth D. | Sawyer, Christopher S. | Vickery, Tammi | Sander, Sacha | Robinson, Jody | Winckler, Wendy | Baldwin, Jennifer | Chirieac, Lucian R. | Dutt, Amit | Fennell, Tim | Hanna, Megan | Johnson, Bruce E. | Onofrio, Robert C. | Thomas, Roman K. | Tonon, Giovanni | Weir, Barbara A. | Zhao, Xiaojun | Ziaugra, Liuda | Zody, Michael C. | Giordano, Thomas | Orringer, Mark B. | Roth, Jack A. | Spitz, Margaret R. | Wistuba, Ignacio I. | Ozenberger, Bradley | Good, Peter J. | Chang, Andrew C. | Beer, David G. | Watson, Mark A. | Ladanyi, Marc | Broderick, Stephen | Yoshizawa, Akihiko | Travis, William D. | Pao, William | Province, Michael A. | Weinstock, George M. | Varmus, Harold E. | Gabriel, Stacey B. | Lander, Eric S. | Gibbs, Richard A. | Meyerson, Matthew | Wilson, Richard K.
Nature  2008;455(7216):1069-1075.
Determining the genetic basis of cancer requires comprehensive analyses of large collections of histopathologically well-classified primary tumours. Here we report the results of a collaborative study to discover somatic mutations in 188 human lung adenocarcinomas. DNA sequencing of 623 genes with known or potential relationships to cancer revealed more than 1,000 somatic mutations across the samples. Our analysis identified 26 genes that are mutated at significantly high frequencies and thus are probably involved in carcinogenesis. The frequently mutated genes include tyrosine kinases, among them the EGFR homologue ERBB4; multiple ephrin receptor genes, notably EPHA3; vascular endothelial growth factor receptor KDR; and NTRK genes. These data provide evidence of somatic mutations in primary lung adenocarcinoma for several tumour suppressor genes involved in other cancers—including NF1, APC, RB1 and ATM—and for sequence changes in PTPRD as well as the frequently deleted gene LRP1B. The observed mutational profiles correlate with clinical features, smoking status and DNA repair defects. These results are reinforced by data integration including single nucleotide polymorphism array and gene expression array. Our findings shed further light on several important signalling pathways involved in lung adenocarcinoma, and suggest new molecular targets for treatment.
doi:10.1038/nature07423
PMCID: PMC2694412  PMID: 18948947
17.  Identification of Genes Contributing to the Virulence of Francisella tularensis SCHU S4 in a Mouse Intradermal Infection Model 
PLoS ONE  2009;4(5):e5463.
Background
Francisella tularensis is a highly virulent human pathogen. The most virulent strains belong to subspecies tularensis and these strains cause a sometimes fatal disease. Despite an intense recent research effort, there is very limited information available that explains the unique features of subspecies tularensis strains that distinguish them from other F. tularensis strains and that explain their high virulence. Here we report the use of targeted mutagenesis to investigate the roles of various genes or pathways for the virulence of strain SCHU S4, the type strain of subspecies tularensis.
Methodology/Principal Findings
The virulence of SCHU S4 mutants was assessed by following the outcome of infection after intradermal administration of graded doses of bacteria. By this route, the LD50 of the SCHU S4 strain is one CFU. The virulence of 20 in-frame deletion mutants and 37 transposon mutants was assessed. A majority of the mutants did not show increased prolonged time to death, among them notably ΔpyrB and ΔrecA. Of the remaining, mutations in six unique targets, tolC, rep, FTT0609, FTT1149c, ahpC, and hfq resulted in significantly prolonged time to death and mutations in nine targets, rplA, wbtI, iglB, iglD, purL, purF, ggt, kdtA, and glpX, led to marked attenuation with an LD50 of >103 CFU. In fact, the latter seven mutants showed very marked attenuation with an LD50 of ≥107 CFU.
Conclusions/Significance
The results demonstrate that the characterization of targeted mutants yielded important information about essential virulence determinants that will help to identify the so far little understood extreme virulence of F. tularensis subspecies tularensis.
doi:10.1371/journal.pone.0005463
PMCID: PMC2675058  PMID: 19424499
18.  Aging Impairs Recipient T Cell Intrinsic and Extrinsic Factors in Response to Transplantation 
PLoS ONE  2009;4(1):e4097.
Background
As increasing numbers of older people are listed for solid organ transplantation, there is an urgent need to better understand how aging modifies alloimmune responses. Here, we investigated whether aging impairs the ability of donor dendritic cells or recipient immunity to prime alloimmune responses to organ transplantation.
Principal Findings
Using murine experimental models, we found that aging impaired the host environment to expand and activate antigen specific CD8+ T cells. Additionally, aging impaired the ability of polyclonal T cells to induce acute allograft rejection. However, the alloimmune priming capability of donor dendritic cells was preserved with aging.
Conclusion
Aging impairs recipient responses, both T cell intrinsic and extrinsic, in response to organ transplantation.
doi:10.1371/journal.pone.0004097
PMCID: PMC2606020  PMID: 19119314
19.  Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF 
Genome Biology  2008;9(7):R110.
A comparison of two strains of the hospital pathogen Enterococcus faecalis suggests that mediators of virulence differ between strains and that virulence does not depend on mobile gene elements
Background
Enterococcus faecalis has emerged as a major hospital pathogen. To explore its diversity, we sequenced E. faecalis strain OG1RF, which is commonly used for molecular manipulation and virulence studies.
Results
The 2,739,625 base pair chromosome of OG1RF was found to contain approximately 232 kilobases unique to this strain compared to V583, the only publicly available sequenced strain. Almost no mobile genetic elements were found in OG1RF. The 64 areas of divergence were classified into three categories. First, OG1RF carries 39 unique regions, including 2 CRISPR loci and a new WxL locus. Second, we found nine replacements where a sequence specific to V583 was substituted by a sequence specific to OG1RF. For example, the iol operon of OG1RF replaces a possible prophage and the vanB transposon in V583. Finally, we found 16 regions that were present in V583 but missing from OG1RF, including the proposed pathogenicity island, several probable prophages, and the cpsCDEFGHIJK capsular polysaccharide operon. OG1RF was more rapidly but less frequently lethal than V583 in the mouse peritonitis model and considerably outcompeted V583 in a murine model of urinary tract infections.
Conclusion
E. faecalis OG1RF carries a number of unique loci compared to V583, but the almost complete lack of mobile genetic elements demonstrates that this is not a defining feature of the species. Additionally, OG1RF's effects in experimental models suggest that mediators of virulence may be diverse between different E. faecalis strains and that virulence is not dependent on the presence of mobile genetic elements.
doi:10.1186/gb-2008-9-7-r110
PMCID: PMC2530867  PMID: 18611278
20.  Virulence comparison in mice of distinct isolates of type A Francisella tularensis 
Microbial pathogenesis  2006;40(3):133-138.
Francisella tularensis subspecies tularensis (type A F. tularensis) is considered to be one of the most virulent of all bacterial pathogens. Mice are extremely susceptible to infection with this subspecies (LD100 via various inoculation routes is <10 cfu). However, it has not been established whether overt virulence differences exist amongst type A strains of F. tularensis. To this end, the present study compared the virulence of two distinct type A strains, FSC033 and SCHU S4, for naïve mice and mice immunized with the live vaccine strain of the pathogen, F. tularensis LVS. One nominal isolate of SCHU S4 was found to be completely avirulent. Another isolate was highly virulent, but all examined cases appeared somewhat less virulent than FSC033. The implication of these findings for future infection and immunity studies is discussed.
doi:10.1016/j.micpath.2005.12.004
PMCID: PMC1868512  PMID: 16448801
Francisella tularensis; Virulence; Mice
21.  A case of chylothorax treated curatively with Sapylin, a streptococcus preparation*  
Chylothorax is an uncommon disease where fatty fluid accumulates within the chest cavity. Conservative management, including repeated thoracentesis or pleurodesis, seems to be suitable to most cases. Herein, we present a case of efficacious pleurodesis by intrapleural injection of Sapylin, a streptococcus preparation, for the treatment of chylothorax. A 52-year-old non-smoking female farmer was diagnosed as idiopathic chylothorax after we ruled out possible causes including chest trauma, lymphoma, lung cancer, filariasis, tuberculosis, and etc. Two-time intra-thoracic injection of 3 Klinische Einheit (KE) Sapylin achieved rapid and effective control of chylothorax with no severe side effects. Sapylin may facilitate pleurodesis by producing a strong inflammatory response.
doi:10.1631/jzus.2007.B0885
PMCID: PMC2100160  PMID: 18257122
Chylothorax; Sapylin; Streptococcus preparation
22.  Resistance of Francisella tularensis Strains against Reactive Nitrogen and Oxygen Species with Special Reference to the Role of KatG▿  
Infection and Immunity  2007;75(3):1303-1309.
Francisella tularensis is a facultative intracellular bacterial pathogen capable of proliferating within host macrophages. The mechanisms that explain the differences in virulence between various strains of the species are not well characterized. In the present study, we show that both attenuated (strain LVS) and virulent (strains FSC200 and SCHU S4) strains of the pathogen replicate at similar rates in resting murine peritoneal exudate cells (PEC). However, when PEC were activated by exposure to gamma interferon (IFN-γ), they killed LVS more rapidly than virulent strains of the pathogen. Addition of NG-monomethyl-l-arginine, an inhibitor of inducible nitric oxide synthase, to IFN-γ-treated PEC, completely inhibited killing of the virulent strains, whereas it only partially blocked the killing of LVS. Similarly, in a cell-free system, SCHU S4 and FSC200 were more resistant to killing by H2O2 and ONOO− than F. tularensis LVS. Catalase encoded by katG is a bacterial factor that can detoxify bactericidal compounds such as H2O2 and ONOO−. To investigate its contribution to the virulence of F. tularensis, katG deletion-containing mutants of SCHU S4 and LVS were generated. Both mutants demonstrated enhanced susceptibility to H2O2 in vitro but replicated as effectively as the parental strains in unstimulated PEC. In mice, LVS-ΔkatG was significantly attenuated compared to LVS whereas SCHU S4-ΔkatG, despite slower replication, killed mice as quickly as SCHU S4. This implies that clinical strains of the pathogen have katG-independent mechanisms to combat the antimicrobial effects exerted by H2O2 and ONOO−, the loss of which could have contributed to the attenuation of LVS.
doi:10.1128/IAI.01717-06
PMCID: PMC1828546  PMID: 17210667
23.  Low dose aerosol infection of mice with virulent type A Francisella tularensis induces severe thymus atrophy and CD4+ CD8+ thymocyte depletion 
Microbial pathogenesis  2005;39(5-6):189-196.
Francisella tularensis is a gram-negative facultative intracellular bacterium and the causative agent of tularemia. Two subspecies (type A and B strains) of the pathogen exist, the former being much more virulent than the latter for humans and other higher mammals. In this study, we examined the effect of virulent strains of F. tularensis infection on the thymus and thymocytes and the potential mechanisms involved. Low-dose aerosol exposure of C57BL/6 mice with type A, but not type B, F. tularensis caused severe reduction in thymus weight and destruction of thymocytes, particularly CD4+ CD8+ thymocytes, by day 4 after infection. The depletion of thymocytes was accompanied by a significant increase in circulating cortisone levels and could be partially prevented by adrenalectomy. Moreover, thymus atrophy and thymocyte depletion following infection were abolished in mice deficient in tumor necrosis factor receptors 1 and 2, but not in FasL-deficient mice. The severe destruction of the thymus and selective depletion of immature thymocytes during type A F. tularensis infection may represent a key pathogenic mechanism in tularemia and could hinder the development of an effective primary immune response against this highly virulent pathogen.
doi:10.1016/j.micpath.2005.08.005
PMCID: PMC1564440  PMID: 16257504
Francisella tularensis; Thymus; Pathogenesis; Mouse model; Host response
24.  The diagnostic significance of the detection of cytokeratin 19 mRNA by quantitative RT-PCR in benign and malignant pleural effusions 
Objective: To evaluate the diagnostic significance of detecting cytokeratin 19 (CK19) mRNA by quantitative reverse transcription polymerase chain reaction (RT-PCR) in benign and malignant pleural effusions. Methods: CK19 mRNA was examined by quantitative RT-PCR and CK19 was detected by Enzyme-linked immunoadsorbent assay (ELISA) in 32 patients with malignant pleural effusions and 35 patients with benign pleural effusions. Results: On the threshold of 200 copies/μl, the positive rate of CK19 mRNA in patients with malignant pleural effusions was 62.5%. The positive rates of CK19 mRNA and CK19 in the malignant pleural effusions were significantly higher than those in the benign group (P<0.01). Furthermore, the positive rate of CK19 mRNA was higher than that of CK19 in the malignant group (P<0.05). Conclusion: Detection of CK19 mRNA can be a promising diagnostic marker in differential diagnosis of benign and malignant pleural effusions.
doi:10.1631/jzus.2004.1286
PMCID: PMC1388735  PMID: 15362202
Cytokeratin 19 mRNA; Quantitative reverse transcription polymerase chain reaction; Pleural effusions

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