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1.  Clinical features and risk factors for post-partum depression in a large cohort of Chinese women with recurrent major depressive disorder 
Journal of Affective Disorders  2012;136(3):983-987.
Background
Post partum depression (PPD) is relatively common in China but its clinical characteristics and risk factors have not been studied. We set out to investigate whether known risk factors for PPD could be found in Chinese women.
Methods
A case control design was used to determine the impact of known risk factors for PPD in a cohort of 1970 Chinese women with recurrent DSM-IV major depressive disorder (MDD). In a within-case design we examined the risk factors for PPD in patients with recurrent MDD. We compared the clinical features of MDD in cases with PPD to those without MDD. Odds ratios were calculated using logistic and ordinal regression.
Results
Lower occupational and educational statuses increased the risk of PPD, as did a history of pre-menstrual symptoms, stressful life events and elevated levels of the personality trait of neuroticism. Patients with PPD and MDD were more likely to experience a comorbid anxiety disorder, had a younger age of onset of MDD, have higher levels of neuroticism and dysthymia.
Limitations
Results obtained in this clinical sample may not be applicable to PPD within the community. Data were obtained retrospectively and we do not know whether the correlations we observe have the same causes as those operating in other populations.
Conclusions
Our results are consistent with the hypothesis that the despite cultural differences between Chinese and Western women, the phenomenology and risk factors for PPD are very similar.
doi:10.1016/j.jad.2011.06.047
PMCID: PMC3315022  PMID: 21824665
Postpartum depression; Major depressive disorder; Neuroticism; Anxiety disorder
2.  Variation of Second Cancer Risk by Family History of Retinoblastoma Among Long-Term Survivors  
Journal of Clinical Oncology  2012;30(9):950-957.
Purpose
To evaluate the risk of second cancer (SC) in long-term survivors of retinoblastoma (Rb) according to classification of germline mutation, based on family history of Rb and laterality.
Patients and Methods
We assembled a cohort of 1,852 1-year survivors of Rb (bilateral, n = 1,036; unilateral, n = 816). SCs were ascertained by medical records and self-reports and confirmed by pathology reports. Classification of RB1 germline mutation, inherited or de novo, was inferred by laterality of Rb and positive family history of Rb. Standardized incidence ratios and cumulative incidence for all SCs combined and for soft tissue sarcomas, bone cancers, and melanoma were calculated. The influence of host- and therapy-related risk factors for SC was assessed by Poisson regression for bilateral survivors.
Results
We observed a relative risk (RR) of 1.37 (95% CI, 1.00 to 1.86) for SCs in bilateral survivors associated with a family history of Rb, adjusted for treatment, age, and length of follow-up. The risk for melanoma was significantly elevated for survivors with a family history of Rb (RR, 3.08; 95% CI, 1.23 to 7.16), but risks for bone or soft tissue sarcomas were not elevated. The cumulative incidence of SCs 50 years after diagnosis of bilateral Rb, with adjustment for competing risk of death, was significantly higher for survivors with a family history (47%; 95% CI, 35% to 59%) than survivors without a family history (38%; 95% CI, 32% to 44%; P = .004).
Conclusion
Rb survivors with bilateral disease and an inherited germline mutation are at slightly higher risk of an SC compared with those with a de novo germline mutation, in particular melanoma, perhaps because of shared genetic alterations.
doi:10.1200/JCO.2011.37.0239
PMCID: PMC3341108  PMID: 22355046
3.  Comparative intrinsic optical signal imaging of wild-type and mutant mouse retinas 
Optics Express  2012;20(7):7646-7654.
Functional measurement is important for retinal study and disease diagnosis. Transient intrinsic optical signal (IOS) response, tightly correlated with functional stimulation, has been previously detected in normal retinas. In this paper, comparative IOS imaging of wild-type (WT) and rod-degenerated mutant mouse retinas is reported. Both 2-month and 1-year-old mice were measured. In 2-month-old mutant mice, time course and peak value of the stimulus-evoked IOS were significantly delayed (relative to stimulus onset) and reduced, respectively, compared to age matched WT mice. In 1-year-old mutant mice, stimulus-evoked IOS was totally absent. However, enhanced spontaneous IOS responses, which might reflect inner neural remodeling in diseased retina, were observed in both 2-month and 1-year-old mutant retinas. Our experiments demonstrate the potential of using IOS imaging for noninvasive and high resolution identification of disease-associated retinal dysfunctions. Moreover, high spatiotemporal resolution IOS imaging may also lead to advanced understanding of disease-associated neural remodeling in the retina.
doi:10.1364/OE.20.007646
PMCID: PMC3387536  PMID: 22453443
(170.2655) Functional monitoring and imaging; (170.4580) Optical diagnostics for medicine; (170.3880) Medical and biological imaging; (330.5380) Physiology
4.  GLIPR-2 Overexpression in HK-2 Cells Promotes Cell EMT and Migration through ERK1/2 Activation 
PLoS ONE  2013;8(3):e58574.
The epithelial-to-mesenchymal transition (EMT) of tubular epithelial cells in the adult kidney is one of the key events in renal interstitial fibrosis. Glioma pathogenesis related-2 (GLIPR-2) has been shown to be up-regulated in proximal tubular cells (PTCs) in the fibrotic kidney. However, the biological function of GLIPR-2 remains unknown. In this study, we found that GLIPR-2 expression is elevated in the kidney tissue samples of patients with diabetic nephropathy (DN). Human proximal renal tubular epithelial cells (HK-2 cells) were transfected with pcDNA3.0-GLIPR-2 and selected with G418. To identify the biological function of GLIPR-2, an epithelial-to-mesenchymal transition (EMT) PCR array analysis was performed, and genes that had statistically significantly altered expression levels with more than a two-fold difference compared with the pcDNA3.0-transfected HK-2 cells were considered. Key elements of the EMT process, such as E-cadherin and vimentin, were transcriptionally activated in the pcDNA3.0-GLIPR-2-transfected sublines. In addition, α-SMA gene expression, which is a marker of myofibroblasts, increased in the pcDNA3.0-GLIPR-2-transfected HK-2 cells. The cell migration assay demonstrated that the transfection of HK-2 with GLIPR-2 promoted cell migration following an EMT. Additionally, consistent with the effects of increased EGFR expression levels, we found that the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) was highly elevated in the pcDNA3.0-GLIPR-2-transfected group. Our study demonstrates that GLIPR-2 overexpression in HK-2 cells can potentiate EMT-like processes in this cell type through the ERK1/2 signaling pathway. GLIPR-2 may be responsible for the development of renal fibrosis by increasing the accumulation of interstitial fibroblasts.
doi:10.1371/journal.pone.0058574
PMCID: PMC3596275
5.  Change point-cure models with application to estimating the change-point effect of age of diagnosis among prostate cancer patients 
Journal of applied statistics  2012;39(4):901-911.
Previous research on prostate cancer survival trends in the United States National Cancer Institute’s Surveillance Epidemiology and End Results database has indicated a potential change-point in the age of diagnosis of prostate cancer around age 50. Identifying a change-point value in prostate cancer survival and cure could have important policy and health care management implications. Statistical analysis of this data has to address two complicating features: (1) change-point models are not smooth functions and so present computational and theoretical difficulties; and (2) models for prostate cancer survival need to account for the fact that many men diagnosed with prostate cancer can be effectively cured of their disease with early treatment. We develop a cure survival model that allows for change-point effects in covariates to investigate a potential change-point in the age of diagnosis of prostate cancer. Our results do not indicate that age under 50 is associated with increased hazard of death from prostate cancer.
doi:10.1080/02664763.2011.626849
PMCID: PMC3337711  PMID: 22544992
cure models; change-point models; right censoring; smoothing; survival analysis
6.  Specificity of RGS10A as a key component in the RANKL signaling mechanism for osteoclast differentiation 
Journal of cell science  2007;120(Pt 19):3362-3371.
Summary
Significant progress has been made in studies of the mechanisms by which RANKL induces terminal osteoclast differentiation. However, many crucial details in the RANKL-evoked signaling pathway for osteoclast differentiation remain to be defined. We characterized genes specifically expressed in osteoclasts by differential screening of a human osteoclastoma cDNA library, and found that the regulator of G-protein signaling 10A (RGS10A), but not the RGS10B isoform, was specifically expressed in human osteoclasts. The expression of RGS10A is also induced by RANKL in osteoclast precursors and is prominently expressed in mouse osteoclast-like cells. RGS10A silencing by RNA interference blocked intracellular [Ca2+]i oscillations, the expression of NFAT2, and osteoclast terminal differentiation in both bone marrow cells and osteoclast precursor cell lines. Reintroduction of RGS10A rescued the impaired osteoclast differentiation. RGS10A silencing also resulted in premature osteoclast apoptosis. RGS10A silencing affected the RANKL-[Ca2+]i oscillation-NFAT2 signaling pathway but not other RANKL-induced responses. Our data demonstrate that target components of RGS10A are distinct from those of RGS12 in the RANKL signaling mechanism. Our results thus show the specificity of RGS10A as a key component in the RANKL-evoked signaling pathway for osteoclast differentiation, which may present a promising target for therapeutic intervention.
doi:10.1242/jcs.008300
PMCID: PMC3587975  PMID: 17881498
Differential screening; RGS10 RNA interference; [Ca2+]i oscillations; Osteoclast differentiation; RANKL signaling pathway
7.  Maternal age affects brain metabolism in adult children of mothers affected by Alzheimer’s disease 
Neurobiology of Aging  2011;33(3):624.e1-624.e9.
Cognitively normal (NL) individuals with a maternal history of late-onset Alzheimer’s disease (MH) show reduced brain glucose metabolism on FDG-PET as compared to those with a paternal history (PH) and those with negative family history (NH) of Alzheimer’s disease (AD). This FDG-PET study investigates whether metabolic deficits in NL MH are associated with advancing maternal age at birth. Ninety-six NL individuals with FDG-PET were examined, including 36 MH, 24 PH, and 36 NH. Regional-to-whole brain gray matter standardized FDG uptake value ratios were examined for associations with parental age across groups using automated regions-of-interest and statistical parametric mapping. Groups were comparable for clinical and neuropsychological measures. Brain metabolism in AD-vulnerable regions was lower in MH compared to NH and PH, and negatively correlated with maternal age at birth only in MH. There were no associations between paternal age and metabolism in any group. Evidence for a maternally inherited, maternal age-related mechanism provides further insight on risk factors and genetic transmission in late-onset AD.
doi:10.1016/j.neurobiolaging.2011.03.003
PMCID: PMC3155000  PMID: 21514691
Alzheimer’s disease; family history; PET imaging; glucose metabolism; age at birth; early detection
8.  Surgery and Brain Atrophy In Cognitively Normal Elderly Subjects and Subjects Diagnosed with Mild Cognitive Impairment 
Anesthesiology  2012;116(3):603-612.
Background
Structural MRI is used to longitudinally monitor the progression of Alzheimer's disease from its presymptomatic to symptomatic phases. Using magnetic resonance imaging data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), we tested the hypothesis that surgery would affect brain parameters associated with progression of dementia.
Materials and Methods
Brain images from the neuroimaging initiative database were used to study normal volunteer subjects and patients with mild cognitive impairment for the age group 55 to 90 inclusive. We compared changes in regional brain anatomy for three visits that defined two inter-visit intervals for a surgical cohort (n=41) and a propensity matched non-surgical control cohort (n = 123). The first interval for the surgical cohort contained the surgical date. Regional brain volumes were determined with Freesurfer and quantitatively described with J-image software (University of California at San Francisco). Statistical analysis used Repeated Measures ANCOVA (SPSS, v.18.0; Chicago, IL).
Results
We found that surgical patients, during the first follow-up interval (5–9 months), but not subsequently, had increased rates of atrophy for cortical gray matter and hippocampus, and lateral ventricle enlargement, as compared to non-surgical controls. A composite score of five cognitive tests during this interval showed reduced performance for surgical patients with mild cognitive impairment.
Conclusions
Elderly subjects after surgery experienced an increased rate of brain atrophy during the initial evaluation interval, a time associated with enhanced risk for postoperative cognitive dysfunction. Although there was no difference in atrophy rate by diagnosis, subjects with mild cognitive impairment suffered greater subsequent cognitive effects.
doi:10.1097/ALN.0b013e318246ec0b
PMCID: PMC3418798  PMID: 22293721
9.  Endogenous Type-I Interferon Activity is not Associated with Depression or Fatigue in Systemic Lupus Erythematosus 
Journal of neuroimmunology  2010;223(1-2):13-19.
Patients with systemic lupus erythematosus (SLE) often suffer from depression and fatigue in addition to the physical manifestations of the autoimmune disease. Elevated production of type-I interferons (IFN-I) has been found in lupus patients and IFN-I can precipitate a variety of neuropsychiatric side effects. This study was conducted to evaluate the relationship between dysregulated IFN-I production and the presence of depression or fatigue in lupus patients. Through cross-sectional and longitudinal analysis we found no significant correlation between abnormal IFN-I levels (as measured by peripheral blood expression of IFN-I-stimulated genes) and neuropsychiatric manifestations. Elevation of endogenous serum IFN-I levels is unlikely to account for the depression and fatigue associated with SLE.
doi:10.1016/j.jneuroim.2010.03.018
PMCID: PMC3580233  PMID: 20416954
Systemic lupus erythematosus; depression; fatigue; type I interferon
10.  Pleiotropic interferon-dependent and -independent effects of IRF5 on the pathogenesis of experimental lupus 
Genetic polymorphisms of IRF5 are associated with an increased risk of lupus in humans. Here, we examined the role of IRF5 in the pathogenesis of pristane-induced lupus in mice. The pathological response to pristane in IRF5−/− mice shared many features with IFN-I receptor (IFNAR) −/− and TLR7−/− mice: production of anti-Sm/RNP autoantibodies, glomerulonephritis, generation of Ly6Chi monocytes, and IFN-I production all were greatly attenuated. Lymphocyte activation following pristane injection was greatly diminished in IRF5−/− mice and helper T cell differentiation was deviated from TH1 in wild type mice toward TH2 in IRF5−/− mice. TH cell development was skewed similarly in TLR7−/− or IFNAR−/− mice, suggesting that IRF5 alters T cell activation and differentiation by affecting cytokine production. Indeed, production of IFN-I, IL-12, and IL-23 in response to pristane was markedly decreased, whereas IL-4 increased. Unexpectedly, plasmacytoid dendritic cells (pDC) were not recruited to the site of inflammation in IRF5−/− or MyD88−/− mice, but were recruited normally in IFNAR−/− and TLR7−/− mice. In striking contrast to wild type mice, pristane did not stimulate local expression of CCL19 and CCL21 in IRF5−/− mice, suggesting that IRF5 regulates chemokine-mediated pDC migration independently of its effects on IFN-I. Collectively, these data indicate that altered production of IFN-I and other cytokines in IRF5−/− mice prevents pristane from inducing lupus pathology by broadly affecting T and B lymphocyte activation/differentiation. Additionally, we uncovered a new, IFN-I independent, role of IRF5 in regulating chemokines involved in the homing of pDCs and certain lymphocyte subsets.
doi:10.4049/jimmunol.1103113
PMCID: PMC3580234  PMID: 22422888
11.  Novel pycnodysostosis mouse model uncovers cathepsin K function as a potential regulator of osteoclast apoptosis and senescence 
Human molecular genetics  2007;16(4):410-423.
Pycnodysostosis is a genetic bone disease featuring the unique bone homeostasis disorders of osteolysis and osteopetrosis in the same organism. The pathomechanism for pycnodysostosis has been largely unknown due to the unavailability of a pycnodysostosis mouse model with all the traits of the disease. We generated cathepsin K−/− mouse strains in the 129/Sv and C57BL/6J backgrounds and found that, only in the 129/Sv background, cathepsin K−/− mice exhibit many characteristics of the human pycnodysostosis-like phenotype. Our data indicated that 129/Sv cathepsin K−/− osteoclasts (OCs) lacked normal apoptosis and senescence and exhibited over-growth both in vitro and in vivo. These abnormalities resulted in an unusually high OC number, which is consistent with a recent case study of human pycnodysostosis. Our results show that cathepsin K function has different effects around the skeleton due to site-specific variations in bone homeostasis, such as phenotypes of osteopetrosis in tibiae and osteolysis in calvariae as a result of cathepsin K mutation. Our data demonstrated that the expression levels of p19, p53 and p21 were significantly reduced in 129/Sv cathepsin K−/− OCs and forced expression of cathepsin K in pre-OCs induced premature senescence and increased expression of p19, p53 and p21. This is the first evidence that cathepsin K plays a key role in OC apoptosis and senescence, revealing the importance of OC senescence in bone homeostasis. The finding of this novel cathepsin K function provides insight into the pathomechanism of pycnodysostosis and may provide new drug targets for diseases involved in OC-related abnormal bone homeostasis.
doi:10.1093/hmg/ddl474
PMCID: PMC3578583  PMID: 17210673
12.  Molecular Basis for Viral Selective Replication in Cancer Cells: Activation of CDK2 by Adenovirus-Induced Cyclin E 
PLoS ONE  2013;8(2):e57340.
Adenoviruses (Ads) with deletion of E1b55K preferentially replicate in cancer cells and have been used in cancer therapies. We have previously shown that Ad E1B55K protein is involved in induction of cyclin E for Ad replication, but this E1B55K function is not required in cancer cells in which deregulation of cyclin E is frequently observed. In this study, we investigated the interaction of cyclin E and CDK2 in Ad-infected cells. Ad infection significantly increased the large form of cyclin E (cyclin EL), promoted cyclin E/CDK2 complex formation and increased CDK2 phosphorylation at the T160 site. Activated CDK2 caused pRb phosphorylation at the S612 site. Repression of CDK2 activity with the chemical inhibitor roscovitine or with specific small interfering RNAs significantly decreased pRb phosphorylation, with concomitant repression of viral replication. Our results suggest that Ad-induced cyclin E activates CDK2 that targets the transcriptional repressor pRb to generate a cellular environment for viral productive replication. This study reveals a new molecular basis for oncolytic replication of E1b-deleted Ads and will aid in the development of new strategies for Ad oncolytic virotherapies.
doi:10.1371/journal.pone.0057340
PMCID: PMC3577715  PMID: 23437375
13.  Signaling and transcriptional regulation in osteoblast commitment and differentiation 
The major event that triggers osteogenesis is the transition of mesenchymal stem cells into bone forming, differentiating osteoblast cells. Osteoblast differentiation is the primary component of bone formation, exemplified by the synthesis, deposition and mineralization of extracellular matrix. Although not well understood, osteoblast differentiation from mesenchymal stem cells is a well-orchestrated process. Recent advances in molecular and genetic studies using gene targeting in mouse enable a better understanding of the multiple factors and signaling networks that control the differentiation process at a molecular level. Osteoblast commitment and differentiation are controlled by complex activities involving signal transduction and transcriptional regulation of gene expression. We review Wnt signaling pathway and Runx2 regulation network, which are critical for osteoblast differentiation. Many other factors and signaling pathways have been implicated in regulation of osteoblast differentiation in a network manner, such as the factors Osterix, ATF4, and SATB2 and the TGF-beta, Hedgehog, FGF, ephrin, and sympathetic signaling pathways. This review summarizes the recent advances in the studies of signaling transduction pathways and transcriptional regulation of osteoblast cell lineage commitment and differentiation. The knowledge of osteoblast commitment and differentiation should be applied towards the development of new diagnostic and therapeutic alternatives for human bone diseases.
PMCID: PMC3571113  PMID: 17485283
Osteoblast; Runx2; Osterix; ATF4; SATB2; Wnt signaling; TGF-Beta signaling; hedgehog signaling; fgf signaling; ephrin signaling; sympathetic signaling; Review
14.  Overexpression of a Fungal β-Mannanase from Bispora sp. MEY-1 in Maize Seeds and Enzyme Characterization 
PLoS ONE  2013;8(2):e56146.
Background
Mannans and heteromannans are widespread in plants cell walls and are well-known as anti-nutritional factors in animal feed. To remove these factors, it is common practice to incorporate endo-β-mannanase into feed for efficient nutrition absorption. The objective of this study was to overexpress a β-mannanase gene directly in maize, the main ingredient of animal feed, to simplify the process of feed production.
Methodology/Principal Findings
The man5A gene encoding an excellent β-mannanase from acidophilic Bispora sp. MEY-1 was selected for heterologous overexpression. Expression of the modified gene (man5As) was driven by the embryo-specific promoter ZM-leg1A, and the transgene was transferred to three generations by backcrossing with commercial inbred Zheng58. Its exogenous integration into the maize embryonic genome and tissue specific expression in seeds were confirmed by PCR and Southern blot and Western blot analysis, respectively. Transgenic plants at BC3 generation showed agronomic traits statistically similar to Zheng58 except for less plant height (154.0 cm vs 158.3 cm). The expression level of MAN5AS reached up to 26,860 units per kilogram of maize seeds. Compared with its counterpart produced in Pichia pastoris, seed-derived MAN5AS had higher temperature optimum (90°C), and remained more β-mannanase activities after pelleting at 80°C, 100°C or 120°C.
Conclusion/Significance
This study shows the genetically stable overexpression of a fungal β-mannanase in maize and offers an effective and economic approach for transgene containment in maize for direct utilization without any purification or supplementation procedures.
doi:10.1371/journal.pone.0056146
PMCID: PMC3569411  PMID: 23409143
15.  Subacute Intranasal Administration of Tissue Plasminogen Activator Increases Functional Recovery and Axonal Remodeling after Stroke in Rats 
Neurobiology of Disease  2011;45(2):804-809.
As a thrombolytic agent, application of recombinant tissue plasminogen activator (tPA) to ischemic stroke is limited by the narrow time window and side effects on brain edema and hemorrhage. This study examined whether tPA, administered by intranasal delivery directly targeting the brain and spinal cord, provides therapeutic benefit during the subacute phase after stroke. Adult male Wistar rats were subjected to permanent right middle cerebral artery occlusion (MCAo). Animals were treated intranasally with saline, 60 μg or 600 μg recombinant human tPA at 7 and 14 days after MCAo (n=8/group), respectively. An adhesive-removal test and a foot-fault test were used to monitor functional recovery. Biotinylated dextran amine (BDA) was injected into the left motor cortex to anterogradely label the corticorubral tract (CRT) and the corticospinal tract (CST). Naive rats (n=6) were employed as normal control. Animals were euthanized 8 weeks after stroke. Compared with saline treated animals, significant functional improvements were evident in rats treated with 600 μg tPA (p<0.05), but not in 60 μg tPA treated rats. Furthermore, 600 μg tPA treatment significantly enhanced both CRT and CST sprouting originating from the contralesional cortex sprouting into the denervated side of the red nucleus and cervical gray matter compared with control group (p<0.01), respectively. The behavioral outcomes were highly correlated with CRT and CST axonal remodeling. Our data suggest that delayed tPA intranasal treatment provides therapeutic benefits for neurological recovery after stroke by, at least in part, promoting neuronal remodeling in the brain and spinal cord.
doi:10.1016/j.nbd.2011.11.004
PMCID: PMC3259280  PMID: 22115941
functional recovery; middle cerebral artery occlusion; neuronal remodeling; tissue plasminogen activator
16.  Principled sure independence screening for Cox models with ultra-high-dimensional covariates 
Journal of multivariate analysis  2012;105(1):397-411.
It is rather challenging for current variable selectors to handle situations where the number of covariates under consideration is ultra-high. Consider a motivating clinical trial of the drug bortezomib for the treatment of multiple myeloma, where overall survival and expression levels of 44760 probesets were measured for each of 80 patients with the goal of identifying genes that predict survival after treatment. This dataset defies analysis even with regularized regression. Some remedies have been proposed for the linear model and for generalized linear models, but there are few solutions in the survival setting and, to our knowledge, no theoretical support. Furthermore, existing strategies often involve tuning parameters that are difficult to interpret. In this paper we propose and theoretically justify a principled method for reducing dimensionality in the analysis of censored data by selecting only the important covariates. Our procedure involves a tuning parameter that has a simple interpretation as the desired false positive rate of this selection. We present simulation results and apply the proposed procedure to analyze the aforementioned myeloma study.
doi:10.1016/j.jmva.2011.08.002
PMCID: PMC3293491  PMID: 22408278
Cox model; Multiple myeloma; Sure independence screening; Ultra-high-dimensional covariates; Variable selection
17.  Dielectrophoretic Capture of E. coli Cells at Nanoelectrode Arrays 
Electrophoresis  2011;32(17):2358-2365.
This paper reports capture and detection of pathogenic bacteria based on AC dielectrophoresis (DEP) and electrochemical impedance spectroscopy (EIS) employing an embedded vertically aligned carbon nanofiber (VACNF) nanoelectrode array (NEA) vs. a macroscopic indium tin oxide (ITO) transparent electrode in “points-and-lid” configuration. The nano-DEP device was fabricated using photolithography processes to define an exposed active region on a randomly distributed NEA and a microfluidic channel on ITO to guide the flow of labeled E. coli cells, respectively, and then bond them into a fluidic chip. A high frequency (100 kHz) AC field was applied to generate positive DEP at the tips of exposed CNFs. Enhanced electric field gradient was achieved due to reduction in electrode size down to nanometer scale which helped to overcome the large hydrodynamic drag force experienced by E. coli cells at high flow velocities (up to 1.6 mm/sec). This DEP device was able to effectively capture a significant number of E. coli. Significant decrease in the absolute impedance (|Z|) at the NEA was observed by EIS experiments. The results obtained in this study suggest the possibility of integration of a fully functional electronic device for rapid, reversible and label-free capture and detection of pathogenic bacteria.
doi:10.1002/elps.201100020
PMCID: PMC3560303  PMID: 21823128
Bacterial Capture; Dielectrophoresis; Dielectrophoretic Impedance Measurement; Nanoelectrode Array; Vertically Aligned Carbon Nanofibers
18.  RGS12 Is Essential for RANKL-Evoked Signaling for Terminal Differentiation of Osteoclasts In Vitro 
How RANKL evokes [Ca2+]i oscillations and leads to osteoclast differentiation is unclear. We identified a new signaling protein, RGS12, and found that RGS12 is essential for [Ca2+]i oscillations and osteoclast differentiation induced by RANKL. RGS12 may play a critical role in the RANKL-evoked PLCγ– calcium channels–[Ca2+]i oscillation–NFAT2 pathway.
Introduction
RANKL-induced [Ca2+]i oscillations play a switch-on role in NFAT2 expression and osteoclast differentiation. However, RANKL evokes [Ca2+]i oscillations and leads to osteoclast differentiation by an unknown mechanism. In this study, we identified a new RANKL-induced signaling protein, regulator of G signaling protein 12 (RGS12), and investigated its effect on osteoclast differentiation in vitro.
Materials and Methods
We used a genome-wide screening approach to identify genes that are specifically or prominently expressed in osteoclasts. To study the role of the RGS12 in osteoclast differentiation, we used vector and lentivirus-based RNAi gene silencing technology to silence the RGS12 gene in the monocyte progenitor cell lines and primary bone marrow–derived monocytes (BMMs). The interaction between RGS12 and N-type calcium channels was elucidated using co-immunoprecipitation and immunoblotting.
Results
We found that RGS12 was prominently expressed in osteoclast-like cells (OLCs) induced by RANKL. This result was further confirmed at both the mRNA and protein level in human osteoclasts and mouse OLCs. Silence of RGS12 expression using vector and lentivirus based RNA interference (RNAi) impaired phosphorylation of phospholipase C (PLC)γ and blocked [Ca2+]i oscillations, NFAT2 expression, and osteoclast differentiation in RANKL-induced RAW264.7 cells and BMMs. We further found that N-type calcium channels were expressed in OLCs after RANKL stimulation and that RGS12 directly interacted with the N-type calcium channels.
Conclusions
These results reveal that RGS12 is essential for the terminal differentiation of osteoclasts induced by RANKL. It is possible that RGS12 regulates osteoclast differentiation through a PLC γ–calcium channel–[Ca2+]i oscillation–NFAT2 pathway.
doi:10.1359/jbmr.061007
PMCID: PMC3559086  PMID: 17042716
regulator of G signaling protein 12; RANKL; calcium oscillations; osteoclast differentiation; calcium channels
19.  Baculovirus Superinfection: A Probable Restriction Factor on the Surface Display of Proteins for Library Screening 
PLoS ONE  2013;8(1):e54631.
In addition to the expression of recombinant proteins, baculoviruses have been developed as a platform for the display of complex eukaryotic proteins on the surface of virus particles or infected insect cells. Surface display has been used extensively for antigen presentation and targeted gene delivery but is also a candidate for the display of protein libraries for molecular screening. However, although baculovirus gene libraries can be efficiently expressed and displayed on the surface of insect cells, target gene selection is inefficient probably due to super-infection which gives rise to cells expressing more than one protein. In this report baculovirus superinfection of Sf9 cells has been investigated by the use of two recombinant multiple nucleopolyhedrovirus carrying green or red fluorescent proteins under the control of both early and late promoters (vAcBacGFP and vAcBacDsRed). The reporter gene expression was detected 8 hours after the infection of vAcBacGFP and cells in early and late phases of infection could be distinguished by the fluorescence intensity of the expressed protein. Simultaneous infection with vAcBacGFP and vAcBacDsRed viruses each at 0.5 MOI resulted in 80% of infected cells co-expressing the two fluorescent proteins at 48 hours post infection (hpi), and subsequent infection with the two viruses resulted in similar co-infection rate. Most Sf9 cells were re-infectable within the first several hours post infection, but the re-infection rate then decreased to a very low level by 16 hpi. Our data demonstrate that Sf9 cells were easily super-infectable during baculovirus infection, and super-infection could occur simultaneously at the time of the primary infection or subsequently during secondary infection by progeny viruses. The efficiency of super-infection may explain the difficulties of baculovirus display library screening but would benefit the production of complex proteins requiring co-expression of multiple polypeptides.
doi:10.1371/journal.pone.0054631
PMCID: PMC3554712  PMID: 23365677
20.  The HECTD3 E3 Ubiquitin Ligase Suppresses Cisplatin-Induced Apoptosis via Stabilizing MALT11 2 
Neoplasia (New York, N.Y.)  2013;15(1):39-48.
Homologous to the E6-associated protein carboxyl terminus domain containing 3 (HECTD3) is an E3 ubiquitin ligase with unknown functions. Here, we show that HECTD3 confers cancer cell resistance to cisplatin. To understand the molecular mechanisms, we performed a yeast two-hybrid analysis and identified mucosa-associated lymphoid tissue 1 (MALT1) as an HECTD3-interacting protein. HECTD3 promotes MALT1 ubiquitination with nondegradative polyubiquitin chains by direct interacting with the MALT1 through its N-terminal destruction of cyclin domain. HECTD3 does not target MALT1 for degradation but stabilize it. HECTD3 depletion dramatically decreases the levels of MALT1 in MCF7 and HeLa cells treated with cisplatin, which is correlated to an increase in apoptosis. Knockdown of MALT1 likewise increases cisplatin-induced apoptosis in these cancer cells. However, HECTD3 over-expression leads to a decreased cisplatin-induced apoptosis, whereas overexpression of MALT1 partially rescues HECTD3 depletion-induced apoptosis. These findings suggest that HECTD3 promotes cell survival through stabilizing MALT1. Our data have important implications in cancer therapy by providing novel molecular targets.
PMCID: PMC3556937  PMID: 23358872
21.  Phosphogenesis in the 2460 and 2728 million-year-old banded iron formations as evidence for biological cycling of phosphate in the early biosphere 
Ecology and Evolution  2013;3(1):115-125.
The banded iron formation deposited during the first 2 billion years of Earth's history holds the key to understanding the interplay between the geosphere and the early biosphere at large geological timescales. The earliest ore-scale phosphorite depositions formed almost at ∼2.0–2.2 billion years ago bear evidence for the earliest bloom of aerobic life. The cycling of nutrient phosphorus and how it constrained primary productivity in the anaerobic world of Archean–Palaeoproterozoic eons are still open questions. The controversy centers about whether the precipitation of ultrafine ferric oxyhydroxide due to the microbial Fe(II) oxidation in oceans earlier than 1.9 billion years substantially sequestrated phosphate, and whether this process significantly limited the primary productivity of the early biosphere. In this study, we report apatite radial flowers of a few micrometers in the 2728 million-year-old Abitibi banded iron formation and the 2460 million-year-old Kuruman banded iron formation and their similarities to those in the 535 million-year-old Lower Cambrian phosphorite. The lithology of the 535 Million-year-old phosphorite as a biosignature bears abundant biomarkers that reveal the possible similar biogeochemical cycling of phosphorus in the Later Archean and Palaeoproterozoic oceans. These apatite radial flowers represent the primary precipitation of phosphate derived from the phytoplankton blooms in the euphotic zones of Neoarchean and Palaoeproterozoic oceans. The unbiased distributions of the apatite radial flowers within sub-millimeter bands do not support the idea of an Archean Crisis of Phosphate. This is the first report of the microbial mediated mineralization of phosphorus before the Great Oxidation Event when the whole biosphere was still dominated by anaerobic microorganisms.
doi:10.1002/ece3.443
PMCID: PMC3568848  PMID: 23404127
Banded iron formation; great oxidation event; iron oxide; phosphate; Precambrian; primary productivity
22.  Stat3 Is Required to Maintain the Full Differentiation Potential of Mammary Stem Cells and the Proliferative Potential of Mammary Luminal Progenitors 
PLoS ONE  2012;7(12):e52608.
Stat3 has a defined role in mammary gland where it is a critical mediator of cell death during post-lactational regression. On the other hand, Stat3 is required for the self-renewal of embryonic stem cells and is sufficient for the induction of a naïve pluripotent state in epiblast stem cells. Mammary stem cells (MaSCs) have a high capacity for self-renewal and can grow robustly in transplantation experiments in vivo. However, a role for Stat3 in MaSCs has not been investigated. Here we show that depletion of Stat3 from basal cells results in reduced primary transplantation efficiency and diminishes the potential to generate ductal, but not alveolar, outgrowths. In addition, Stat3 is required for maximal proliferation of luminal progenitors.
doi:10.1371/journal.pone.0052608
PMCID: PMC3527594  PMID: 23285109
23.  Joint Models of Longitudinal Data and Recurrent Events with Informative Terminal Event 
Statistics in biosciences  2012;4(2):262-281.
This article presents semiparametric joint models to analyze longitudinal data with recurrent event (e.g. multiple tumors, repeated hospital admissions) and terminal event such as death. A broad class of transformation models for the cumulative intensity of the recurrent events and the cumulative hazard of the terminal event is considered, which includes the proportional hazards model and the proportional odds model as special cases. We propose to estimate all the parameters using the nonparametric maximum likelihood estimators (NPMLE). We provide the simple and efficient EM algorithms to implement the proposed inference procedure. Asymptotic properties of the estimators are shown to be asymptotically normal and semiparametrically efficient. Finally, we evaluate the performance of the method through extensive simulation studies and a real-data application.
doi:10.1007/s12561-012-9061-x
PMCID: PMC3516390  PMID: 23227131
Joint models; Longitudinal data; Nonparametric maximum likelihood; Random effects; Recurrent events; Repeated measures; Terminal event; Transformation models
24.  An Evaluation of Multiple Behavioral Risk Factors for Cancer in a Working Class, Multi-Ethnic Population 
Journal of data science : JDS  2006;4(3):291-306.
Behavioral risk factors for cancer tend to cluster within individuals, which can compound risk beyond that associated with the individual risk factors alone. There has been increasing attention paid to the prevalence of multiple risk factors (MRF) for cancer, and to the importance of designing interventions that help individuals reduce their risks across multiple behaviors simultaneously. The purpose of this paper is to develop methodology to identify an optimal linear combination of multiple risk factors (score function) which would facilitate evaluation of cancer interventions.
PMCID: PMC3516398  PMID: 23227033
Community based research; conditional logistic regression; multiple risk factors; random effects
25.  Association Analysis between SNPs in IL-28B Gene and the Progress of Hepatitis B Infection in Han Chinese 
PLoS ONE  2012;7(12):e50787.
Objective
As a candidate gene association study, we investigated the genetic association of SNPs in IL-28B genes with different outcomes of HBV infection, including LC and HCC occurrence.
Methods
Chinese Han subjects were categorized into two groups: 406 LC caused by CHB and 406 HCC caused by CHB. Genomic DNA was isolated from whole blood samples, SNPs were detected using high resolution melting curve (HRM) method. PCR amplification was carried out under the same conditions in a 96-well plate in Real-Time PCR System. Then 341 LC and 356 HCC patients caused by HBV infection were analyzed as a verification by independent sample. 393 CHB patients and 244 health subjects were included as control.
Results
CHB patients who progress to LC or HCC showed a significant different frequency in rs12979860 (p = 0.046). Patients with HCC carried more frequently the T alleles in rs12979860 comparison to LC. Same results were found in the independent sample.
Conclusion
IL-28B rs12979860 C/T polymorphism T allele appears to be more prevalent in patients with HCC than in LC. Carriage of this allele seems to enhance the risk for developing HCC. Gene polymorphism of IL-28B may confer symptomatic specificity in progress and extent of hepatitis B infection.
doi:10.1371/journal.pone.0050787
PMCID: PMC3515436  PMID: 23227209

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