CiteULike: jyuh's Lu

Multidimensional scaling for large genomic data sets

Jengnan Tzeng — 2008-04-05T06:29:03-00:00

BMC Bioinformatics, Vol. 9 (04 April 2008), 179.

Therapy for Helicobacter pylori infection can be improved: sequential therapy and beyond.

DY Graham — 2008-07-19T16:02:51-00:00

Drugs, Vol. 68, No. 6. (2008), pp. 725-736.

As with other bacterial infections, successful treatment of Helicobacter pylori infections depends on the use of antibacterial agents to which the organism is susceptible. In this article, we use the proposed report card grading scheme (i.e. grade A, B, C, D, F) for the outcome of clinical trials, where intention-to-treat cure rates >95% = A, 90-95% = B, 85-89% = C, 81-84% = D and <81% = F. The goal of therapy is to consistently cure >95% of patients (e.g. provide grade A results). Like tuberculosis, H. pylori infections are difficult to cure and successful treatment generally requires the administration of several antibacterial agents simultaneously. Duration of therapy is also important and depends upon whether resistance is present; 14 days is often best. With few exceptions, worldwide increasing macrolide resistance now undermines the effectiveness of the legacy triple therapy (e.g. a proton pump inhibitor [PPI], clarithromycin and amoxicillin) and, in most areas, cure rates have declined to unacceptable levels (e.g. grade F). The development of sequential therapy was one response to this problem. Sequential therapy has repeatedly been shown in head-to-head studies to be superior to legacy triple therapy. Sequential therapy, as originally described, is the sequential administration of a dual therapy (a PPI plus amoxicillin) followed by a Bazzoli-type triple therapy (a PPI plus clarithromycin and tinidazole) and has been shown to be especially useful where there is clarithromycin resistance. However, the cure rates of the original sequential treatment are grade B and can probably be further improved by changes in dose, duration or administration, such as by continuing the amoxicillin into the triple therapy arm. The sequential approach may also be more complicated than necessary, based on the fact that the same four drugs have also been given concomitantly (at least nine publications with >700 patients) as a quadruple therapy with excellent success. This article discusses the approach to therapy in the modern era where antimicrobial resistance is an increasing problem and legacy triple therapy is no longer an acceptable initial choice. Methods to achieve acceptable eradication rates (e.g. grade A or B results) are discussed and, specifically, sequential therapy is considered both conceptually and practically. Suggestions are provided regarding how sequential therapy might be improved to become a grade A therapy as well as how to identify situations where it can be expected to yield unacceptable results. New uses for current drugs are discussed and suggestions for subsequent randomized comparisons to overcome phenotypic and genotypic resistance are given. We propose a change in focus from comparative studies (designed to prove that a new therapy is superior to a known inferior therapy) to demanding that efficacious therapies meet or exceed a pre-specified level of success (i.e. grade A or B result). To do so, coupled with less concern about the effect of recommendations on the pharmaceutical industry, should provide clinicians with much higher quality information, and improve the quality of medical care and recommendations regarding treatment. Ultimately, there is little or no justification for comparative testing that includes an arm with known unacceptably low results. H. pylori gastritis is an infectious disease and should be approached and treated as such.

Methicillin-resistant Staphylococcus aureus carriage, infection and transmission in dialysis patients, healthcare workers and their family members.

PL Lu — 2008-07-08T13:35:34-00:00

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association, Vol. 23, No. 5. (May 2008), pp. 1659-1665.

BACKGROUND: Carriage and subsequent infection with methicillin resistant S. aureus (MRSA) and its transmission between hospital and community settings have not been studied in dialysis patients and their contacts. METHODS: Surveillance for nasal MRSA carriage and infection among dialysis patients, healthcare workers (HCWs) and their family members in a dialysis centre was prospectively undertaken during three time periods within 1 year. Molecular typing was used to determine epidemiological relationship. RESULTS: Among 1687 samples collected, MRSA colonization rates were 2.41% (2/83) for peritoneal dialysis patients and 2.36% (12/509) for haemodialysis patients. Five (5/14) subjects subsequently had MRSA infection. The clinical MRSA isolates had the same molecular type as the colonized strains of the same person, indicating MRSA colonization preceded clinical infection. Significantly higher MRSA nasal carriage rates were observed among family members of HCWs than family members of dialysis patients (P = 0.0024). Only three major clones were observed. Pulmonary diseases (OR: 4.873, 95% CI: 1.668-14.235), recent admission to a hospital (OR: 2.797, 95% CI: 1.291-6.059) and recent antibiotics usage (OR: 2.319, 95% CI: 1.053-5.104) were also significantly associated with MRSA carriage. CONCLUSION: Transmission of MRSA among dialysis patients, HCWs and their family members in a dialysis unit could be inferred. Monitoring and eradication of MRSA from patients, HCWs and their family members should be considered to prevent continuous spread between healthcare facilities and the community.

Significance of plasma von Willebrand factor level and von Willebrand factor-cleaving protease activity in patients with chronic renal diseases.

GY Lu — 2008-06-28T12:52:07-00:00

Chinese medical journal, Vol. 121, No. 2. (20 January 2008), pp. 133-136.

BACKGROUND: von Willebrand factor (vWF) mediates the initial capture of platelets to vascular subendothelium and is essential for platelet aggregation under high fluid shear stress as in arterial stenosis. On release from endothelial cells, vWF is rapidly cleaved by ADAMTS13/vWF-cleaving protease (vWF-CP). We investigated the clinical significance of changes in plasma vWF and vWF-CP activities in chronic renal disease. METHODS: Plasma vWF and vWF-CP activities were measured using enzyme-linked immunosorbent assay (ELISA) and residual collagen binding assay respectively in patients with lupus nephritis (n = 31), primary nephritic syndrome (n = 25), diabetic nephropathy (n = 45), chronic glomerulonephritis (n = 38) and 40 normal controls. The relation of their levels with pathological and renal status was analyzed. RESULTS: In all diseased patients the levels of vWF were significantly higher and vWF-CP activity significantly lower than the controls (both P < 0.01). vWF in the four subgroups did not correlate with the stage of disease but correlated negatively with vWF-CP activity. vWF-CP activity was not changed two weeks after renal transplantation. Renal biopsy demonstrated that the vWF level in stage IV was higher than in stages II and III while vWF-CP activity was lower in patients with lupus nephritis. After eight-week treatment, the vWF level significantly decreased and the vWF-CP activity significantly increased in systemic lupus erythema, disease activity index < 9, but not with index = 9. Even though the vWF-CP activity was significantly lower in membranous nephropathy than in minimal change disease, mesangial proliferative glomerulonephritis or IgA glomerulonephritis, the vWF level was not significantly different. CONCLUSIONS: The alterations of plasma vWF and vWF-CP activities were associated with different renal pathologies. Injury to endothelial cells and autoantibodies against vWF-CP activity may result in higher vWF level and lower vWF-CP activity in chronic renal disease and thus a mechanism for worsening of chronic renal disease and thrombosis.

Measurement of microalbuminuria using protein chip electrophoresis.

S Pandey — 2008-06-08T06:02:27-00:00

American journal of clinical pathology, Vol. 129, No. 3. (March 2008), pp. 432-438.

Microalbuminuria reflects the progression of nephropathy and cardiovascular disease in diabetic and hypertensive patients. Most commercially available tests currently used to measure microalbuminuria are immunoassays. We developed a microfluidics-based assay using the P200 protein chip (Caliper Life Sciences, Mountain View, CA, and Agilent Technologies, Santa Clara, CA) and 2100 Bioanalyzer (Agilent Technologies) to detect microalbuminuria. The method integrates and automates the electrophoretic separation and fluorescent detection of proteins from 14 to 200 kd. The assay was linear up to 750 mg/L and demonstrated good sensitivity with a lower detection limit of 7.5 mg/L. Intrachip and interchip coefficients of variation ranged from 0% to 4% and 4.9% to 13.5%, respectively. When albumin was measured by chip and immunoturbidimetry in diabetic urine samples, the chip consistently showed higher albumin concentrations. The discrepancy may be due to the chip's ability to detect immunounreactive albumin. Overall, this simple, cost-effective assay offers a sensitive and accurate measurement of microalbuminuria that can be easily implemented in a clinical laboratory.

Diagnostic strategy to improve the efficiency of screening diabetes--ROC analysis for fasting plasma glucose.

J Lu — 2008-06-06T15:22:58-00:00

Diabetes research and clinical practice, Vol. 80, No. 3. (June 2008)

Using the optimal receiver operating characteristic curve to design a predictive genetic test, exemplified with type 2 diabetes.

Q Lu — 2008-06-06T15:23:14-00:00

American journal of human genetics, Vol. 82, No. 3. (March 2008), pp. 641-651.

Current extensive genetic research into common complex diseases, especially with the completion of genome-wide association studies, is bringing to light many novel genetic risk loci. These new discoveries, along with previously known genetic risk variants, offer an important opportunity for researchers to improve health care. We describe a method of quick evaluation of these new findings for potential clinical practice by designing a new predictive genetic test, estimating its classification accuracy, and determining the sample size required for the verification of this accuracy. The proposed predictive test is asymptotically more powerful than tests built on any other existing method and can be extended to scenarios where loci are linked or interact. We illustrate the approach for the case of type 2 diabetes. We incorporate recently discovered risk factors into the proposed test and find a potentially better predictive genetic test. The area under the receiver operating characteristic (ROC) curve (AUC) of the proposed test is estimated to be higher (AUC = 0.671) than for the existing test (AUC = 0.580).

Optimal waist circumference cutoffs for abdominal obesity in Chinese.

Yuqian Bao — 2008-06-06T03:39:38-00:00

Atherosclerosis (18 March 2008)

OBJECTIVE: To determine the appropriate cutoffs for visceral fat area (VFA) measured by magnetic resonance imaging linking to risk of the metabolic syndrome (MetS) and the corresponding waist circumference in Chinese. METHODS AND RESULTS: Totally 1140 individuals (men 525, women 615) aged from 35 to 75 years were included. The components of the MetS were defined by International Diabetes Federation (IDF) and Chinese Diabetes Society (CDS) definition, respectively. Receive operating characteristic curve analyses were used to determine the appropriate cutoffs of VFA and corresponding waist circumference in the prediction of the MetS. The optimal VFA cutoff was near 80cm(2) in identifying the MetS with two or more components but not including overweight/obesity by either of the two definitions in all subjects. There was no difference in men by ages while women aged <50 years tended to have lower VFA cutoff than those aged >/=50 years by the two definitions. The appropriate waist circumference cutoffs were 90cm in men and 85cm in women for the MetS. CONCLUSION: The optimal cutoff of waist circumference for abdominal obesity is 90cm for men and 85cm for women in Chinese.

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics.

Zhi John Lu — 2008-06-04T15:50:49-00:00

Nucleic acids research (19 May 2008)

Given an mRNA sequence as input, the OligoWalk web server generates a list of small interfering RNA (siRNA) candidate sequences, ranked by the probability of being efficient siRNA (silencing efficacy greater than 70%). To accomplish this, the server predicts the free energy changes of the hybridization of an siRNA to a target mRNA, considering both siRNA and mRNA self-structure. The free energy changes of the structures are rigorously calculated using a partition function calculation. By changing advanced options, the free energy changes can also be calculated using less rigorous lowest free energy structure or suboptimal structure prediction methods for the purpose of comparison. Considering the predicted free energy changes and local siRNA sequence features, the server selects efficient siRNA with high accuracy using a support vector machine. On average, the fraction of efficient siRNAs selected by the server that will be efficient at silencing is 78.6%. The OligoWalk web server is freely accessible through internet at http://rna.urmc.rochester.edu/servers/oligowalk.

Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.

Zhi John Lu — 2008-06-04T15:50:55-00:00

Nucleic acids research (15 May 2008)

Both siRNA and antisense oligodeoxynucleotides (ODNs) inhibit the expression of a complementary gene. In this study, fundamental differences in the considerations for RNA interference and antisense ODNs are reported. In siRNA and antisense ODN databases, positive correlations are observed between the cost to open the mRNA target self-structure and the stability of the duplex to be formed, meaning the sites along the mRNA target with highest potential to form strong duplexes with antisense strands also have the greatest tendency to be involved in pre-existing structure. Efficient siRNA have less stable siRNA-target duplex stability than inefficient siRNA, but the opposite is true for antisense ODNs. It is, therefore, more difficult to avoid target self-structure in antisense ODN design. Self-structure stabilities of oligonucleotide and target correlate to the silencing efficacy of siRNA. Oligonucleotide self-structure correlations to efficacy of antisense ODNs, conversely, are insignificant. Furthermore, self-structure in the target appears to correlate with antisense ODN efficacy, but such that more effective antisense ODNs appear to target mRNA regions with greater self-structure. Therefore, different criteria are suggested for the design of efficient siRNA and antisense ODNs and the design of antisense ODNs is more challenging.

Hypotheses in genome-wide association scans

Michael Nothnagel — 2008-05-14T10:47:27-00:00

European Journal of Human Genetics, Vol. aop, No. current.

GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations

Qingwei Xu — 2008-03-25T19:23:05-00:00

BMC Bioinformatics, Vol. 9, No. Suppl 1. (2008)

BACKGROUND:The most renowned biological ontology, Gene Ontology (GO) is widely used for annotations of genes and gene products of different organisms. However, there are shortcomings in the Resource Description Framework (RDF) data file provided by the GO consortium: 1) Lack of sufficient semantic relationships between pairs of terms coming from the three independent GO sub-ontologies, that limit the power to provide complex semantic queries and inference services based on it. 2) The term-centric view of GO annotation data and the fact that all information is stored in a single file. This makes attempts to retrieve GO annotations based on big volume datasets unmanageable. 3) No support of GOSlim.RESULTS:We propose a RDF model, GORouter, which encodes heterogeneous original data in a uniform RDF format, creates additional ontology mappings between GO terms, and introduces a set of inference rulebases. Furthermore, we use the Oracle Network Data Model (NDM) as the native RDF data repository and the table function RDF_MATCH to seamlessly combine the result of RDF queries with traditional relational data. As a result, the scale of GORouter is minimized; information not directly involved in semantic inference is put into relational tables.CONCLUSION:Our work demonstrates how to use multiple semantic web tools and techniques to provide a mixture of semantic query and inference solutions of GO and its associations. GORouter is licensed under Apache License Version 2.0, and is accessible via the website: http://www.scbit.org/gorouter/.

CSCDB: The cAMP and cGMP signaling components database.

Jianxin Lu — 2008-05-16T02:41:44-00:00

Genomics (7 May 2008)

Adenylate cyclases, guanylate cyclases, cyclic nucleotide phosphodiesterases, and cyclic nucleotide-binding proteins constitute the core of cAMP and cGMP signaling components. Using a combination of BLAST and profile search methods, we found that cyclic nucleotide-binding proteins exhibited diverse domain architectures. In addition to the domain architectures involved in the characterized functional groups, a cyclic nucleotide-binding domain was also fused to various domains involved in pyridine nucleotide-disulfide oxidoreductase, acetyltransferase, thioredoxin reductase, glutaminase, rhodanese, ferredoxin, and diguanylate cyclase, implying the versatile functions of cyclic nucleotide-binding proteins. We constructed the CSCDB database to accumulate the components of cAMP and cGMP signaling pathways in the complete genomes. User-friendly interfaces were created for easier browsing, searching, and downloading the data. Besides harboring the sequence itself, each entry provided detailed annotation information, such as sequence features, chromosomal localization, functional domains, transmembrane region, and sequence similarity against several major databases. Currently, CSCDB contains 4234 entries covering 466 organisms, including 35 eukaryotes, 382 bacteria, and 29 archaea. CSCDB can be freely accessible on the web at http://cscdb.com.cn.

Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass

Enrico Petretto — 2008-04-29T07:16:46-00:00

Nature Genetics, Vol. 40, No. 5. (28 April 2008), pp. 546-552.

Loss of the glycine N-methyltransferase gene leads to steatosis and hepatocellular carcinoma in mice.

ML Martínez-Chantar — 2008-05-14T15:55:30-00:00

Hepatology (Baltimore, Md.), Vol. 47, No. 4. (April 2008), pp. 1191-1199.

Glycine N-methyltransferase (GNMT) is the main enzyme responsible for catabolism of excess hepatic S-adenosylmethionine (SAMe). GNMT is absent in hepatocellular carcinoma (HCC), messenger RNA (mRNA) levels are significantly lower in livers of patients at risk of developing HCC, and GNMT has been proposed to be a tumor-susceptibility gene for liver cancer. The identification of several children with liver disease as having mutations of the GNMT gene further suggests that this enzyme plays an important role in liver function. In the current study we studied development of liver pathologies including HCC in GNMT-knockout (GNMT-KO) mice. GNMT-KO mice have elevated serum aminotransferase, methionine, and SAMe levels and develop liver steatosis, fibrosis, and HCC. We found that activation of the Ras and Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathways was increased in liver tumors from GNMT-KO mice coincidently with the suppression of the Ras inhibitors Ras-association domain family/tumor suppressor (RASSF) 1 and 4 and the JAK/STAT inhibitors suppressor of cytokine signaling (SOCS) 1-3 and cytokine-inducible SH2-protein. Finally, we found that methylation of RASSF1 and SOCS2 promoters and the binding of trimethylated lysine 27 in histone 3 to these 2 genes was increased in HCC from GNMT-KO mice. Conclusion: These data demonstrate that loss of GNMT induces aberrant methylation of DNA and histones, resulting in epigenetic modulation of critical carcinogenic pathways in mice.

Epigenetic inhibition of nuclear receptor small heterodimer partner is associated with and regulates hepatocellular carcinoma growth.

N He — 2008-05-14T15:55:57-00:00

Gastroenterology, Vol. 134, No. 3. (March 2008), pp. 793-802.

BACKGROUND & AIMS: Aberrant hypermethylation of promoter regions in cytosine-guanine dinucleotides (CpG) islands has been shown to be associated with transcriptional silencing of tumor-suppressor genes in many cancers. This study evaluated the methylation profile and the tumor-suppressive function of the small heterodimer partner (SHP, NR0B2) in the development of human hepatocellular carcinoma (HCC). METHODS: Human HCC pathologic specimens and cell lines were used as model systems in this study. RESULTS: The expression of SHP is diminished in HCC pathologic specimens and cell lines by epigenetic silencing owing to SHP promoter hypermethylation. In vitro methylation decreased SHP promoter transactivation and nuclear receptor LRH-1 binding, an event that was reversed by demethylation. Overexpression of SHP inhibited HCC foci formation, arrested HCC tumor growth in xenografted nude mice, and increased the sensitivity of HCC cells to apoptotic stimuli. Further analysis of a total of 19 normal liver and 57 HCC specimens showed that down-regulation of SHP gene expression may be a common denominator of HCC. CONCLUSIONS: We propose that SHP functions as a novel tumor suppressor in the development of HCC. These findings provide new insight into the molecular mechanisms leading to this common cancer and may have both diagnostic and therapeutic applications.

Efficient siRNA selection using hybridization thermodynamics.

ZJ Lu — 2008-02-05T06:02:58-00:00

Nucleic Acids Res, Vol. 36, No. 2. (February 2008), pp. 640-647.

Small interfering RNA (siRNA) are widely used to infer gene function. Here, insights in the equilibrium of siRNA-target hybridization are used for selection of efficient siRNA. The accessibilities of siRNA and target mRNA for hybridization, as measured by folding free energy change, are shown to be significantly correlated with efficacy. For this study, a partition function calculation that considers all possible secondary structures is used to predict target site accessibility; a significant improvement over calculations that consider only the predicted lowest free energy structure or a set of low free energy structures. The predicted thermodynamic features, in addition to siRNA sequence features, are used as input for a support vector machine that selects functional siRNA. The method works well for predicting efficient siRNA (efficacy >70%) in a large siRNA data set from Novartis. The positive predictive value (percentage of sites predicted to be efficient for silencing that are) is as high as 87.6%. The sensitivity and specificity are 22.7 and 96.5%, respectively. When tested on data from different sources, the positive predictive value increased 8.1% by adding equilibrium terms to 25 local sequence features. Prediction of hybridization affinity using partition functions is now available in the RNAstructure software package.

Interventions designed to improve the quality and efficiency of medication use in managed care: a critical review of the literature - 2001-2007

Christine Lu — 2008-04-08T06:32:55-00:00

BMC Health Services Research, Vol. 8 (07 April 2008), 75.

Highly efficient deletion method for the engineering of plasmid DNA with single-stranded oligonucleotides.

LY Lu — 2008-05-11T14:27:59-00:00

BioTechniques, Vol. 44, No. 2. (February 2008)

The lamda phage Red recombination system has been used to modify plasmid, bacterial artificial chromosome (BAC), and chromosomal DNA in a highly precise and versatile manner Linear double-stranded DNA fragments or synthetic single-stranded oligonucleotides (SSOs) with short flanking homologies (<50 bp) to the target loci can be used as substrates to direct changes, including point mutations, insertions, and deletions. In attempts to explore mechanistic bases under this recombination process, we and others have previously identified factors that influence SSO-mediated single base substitutions. In this report, we focus our study on SSO-mediated deletion on plasmids. We found that SSOs as short as 63 bp were sufficient to mediate deletion as long as 2 kb with efficiency higher than 1%. Strand bias was consistently observed, and SSOs with sequences identical to the nascent lagging strand during replication always resulted in higher efficiency. Unlike SSO-mediated single nucleotide substitution, homology on each side of SSO flanking the fragment to be deleted was important for successful deletion, and abolishing the host methyl-directed mismatch repair (MMR) system did not lead to detectable changes in deletion efficiency. Finally, we showed that by optimizing its design, SSO-mediated deletion was efficient enough to make it possible to manipulate plasmids without selectable markers.

Gender differences in renal nuclear receptors and aryl hydrocarbon receptor in 5/6 nephrectomized rats.

H Lu — 2008-05-05T13:55:40-00:00

Kidney international, Vol. 70, No. 11. (December 2006), pp. 1920-1928.

This study was aimed at delineating molecular pathways essential in gender-different pathogenesis of chronic kidney diseases (CKD). Renal transcripts of nuclear receptors and metabolic enzymes in male and female kidneys from 5/6 nephrectomized (Nx) rats 7 weeks post-Nx were examined using branched DNA signal amplification assay. Nx-males had marked kidney injury coupled with anemia and malnutrition. Nx-females had moderate renal injury, and were free of albuminuria, anemia, and malnutrition. Nx-males had systemic and renal inflammation, which were largely absent in Nx-females. Blood 17beta-estradiol, testosterone, and corticosterone did not change, whereas urinary testosterone decreased in both genders. Compared to males, female kidneys had higher androgen receptor (AR) and aryl hydrocarbon receptor (AhR) but lower estrogen receptor alpha (ERalpha). Compared to Nx-males, female remnant kidneys had less decreases in ERalpha and peroxisome proliferator-activated receptor alpha (PPARalpha), had no induction of AR and decrease of acyl-CoA oxidase, whereas had induction of cytochrome P450 4a1 (Cyp4a1) but decrease of AhR. Renal protein expression of a 52-kDa isoform of Wilm's tumor 1 (WT1), transcription factor critical in nephrogenesis, decreased dramatically in Nx-males but largely preserved in Nx-females. In conclusion, gender divergences in basal expression and alteration of ERalpha, AR, AhR, WT1, and PPARalpha/Cyp4a1 during CKD may explain gender differences in CKD progression and outcome of renal transplantation.

Covariate adjustment for two-sample treatment comparisons in randomized clinical trials: A principled yet flexible approach.

Anastasios A Tsiatis — 2008-05-03T09:53:30-00:00

Statistics in medicine (24 October 2007)

There is considerable debate regarding whether and how covariate-adjusted analyses should be used in the comparison of treatments in randomized clinical trials. Substantial baseline covariate information is routinely collected in such trials, and one goal of adjustment is to exploit covariates associated with outcome to increase precision of estimation of the treatment effect. However, concerns are routinely raised over the potential for bias when the covariates used are selected post hoc and the potential for adjustment based on a model of the relationship between outcome, covariates, and treatment to invite a 'fishing expedition' for that leading to the most dramatic effect estimate. By appealing to the theory of semiparametrics, we are led naturally to a characterization of all treatment effect estimators and to principled, practically feasible methods for covariate adjustment that yield the desired gains in efficiency and that allow covariate relationships to be identified and exploited while circumventing the usual concerns. The methods and strategies for their implementation in practice are presented. Simulation studies and an application to data from an HIV clinical trial demonstrate the performance of the techniques relative to the existing methods. Copyright (c) 2007 John Wiley & Sons, Ltd.

OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression

Lawrence Hunter — 2008-02-02T00:42:17-00:00

BMC Bioinformatics, Vol. 9 (31 January 2008), 78.

Epigallocatechin-3-gallate inhibits growth of activated hepatic stellate cells by enhancing the capacity of glutathione synthesis.

Y Fu — 2008-04-20T00:36:29-00:00

Molecular pharmacology, Vol. 73, No. 5. (May 2008), pp. 1465-1473.

Activation of hepatic stellate cells (HSC), the key effectors in hepatic fibrogenesis, is characterized by enhanced cell proliferation and overproduction of extracellular matrix. Oxidative stress promotes HSC activation. Glutathione (GSH) is the most important intracellular antioxidant, whose synthesis is mainly regulated by glutamate-cysteine ligase (GCL). We reported previously that (-)-epigallocatechin-3-gallate (EGCG), the major and most active component in green tea extracts, inhibited HSC activation. The aim of this study is to elucidate the underlying mechanisms. We hypothesize that this inhibitory effect of EGCG might mainly result from its antioxidant capability by increasing de novo synthesis of GSH. In this report, we observe that EGCG enhances the levels of cytoplasmic and mitochondrial GSH and increases GCL activity by inducing gene expression of the catalytic subunit GCLc, leading to de novo synthesis of GSH. Real-time polymerase chain reaction and Western blotting analyses show that de novo synthesis of GSH is required for EGCG to regulate the expression of genes relevant to apoptosis and to cell proliferation. Additional experiments demonstrate that exogenous transforming growth factor (TGF)-beta1 suppresses GCLc gene expression and reduces the level of GSH in cultured HSC. Transient transfection assays and Western blotting analyses further display that EGCG interrupts TGF-beta signaling by reducing gene expression of TGF-beta receptors and Smad4, leading to increased expression of GCLc. These results support our hypothesis and collectively demonstrate that EGCG increases the level of cellular GSH in HSC by stimulating gene expression of GCLc, leading to the inhibition of cell proliferation of activated HSC in vitro.

S-Adenosylmethionine in cell growth, apoptosis and liver cancer.

SC Lu — 2008-04-19T09:39:19-00:00

Journal of gastroenterology and hepatology, Vol. 23 Suppl 1 (March 2008)

S-Adenosylmethionine (SAMe), the principal biological methyl donor, is synthesized from methionine and ATP in a reaction catalyzed by methionine adenosyltransferase (MAT). In mammals, two genes (MAT1A and MAT2A), encode for two homologous MAT catalytic subunits, while a third gene MAT2beta, encodes for the beta-subunit that regulates MAT2A-encoded isoenzyme. Normal liver expresses MAT1A, whereas extrahepatic tissues express MAT2A. MAT2A and MAT2 beta are induced in human hepatocellular carcinoma (HCC), which facilitate cancer cell growth. Patients with cirrhosis of various etiologies, including alcohol, have decreased hepatic MAT activity and SAMe biosynthesis. Consequences of hepatic SAMe deficiency as illustrated by the Mat1a knock-out mouse model include increased susceptibility to steatosis and oxidative liver injury, spontaneous development of steatohepatitis and HCC. Predisposition to HCC can be partly explained by the effect of SAMe on growth. Thus, SAMe inhibits the mitogenic effect of growth factors such as hepatocyte growth factor and, following partial hepatectomy, a fall in SAMe level is required for the liver to regenerate. During liver regeneration, the fall in hepatic SAMe is transient. If the fall were to persist, it would favor a proliferative phenotype and, ultimately, development of HCC. Not only does SAMe control liver growth, it also regulates apoptosis. Interestingly, SAMe is anti-apoptotic in normal hepatocytes but pro-apoptotic in liver cancer cells. In liver cancer cells but not in normal human hepatocytes, SAMe can selectively induce Bcl-x(S), an alternatively spliced isoform of Bcl-x(L) that promotes apoptosis. This should make SAMe an attractive agent for both chemoprevention and treatment of HCC.

Role of S-adenosyl-L-methionine in liver health and injury.

JM Mato — 2008-04-19T09:29:41-00:00

Hepatology (Baltimore, Md.), Vol. 45, No. 5. (May 2007), pp. 1306-1312.

S-adenosylmethionine (SAMe) has rapidly moved from being a methyl donor to a key metabolite that regulates hepatocyte growth, death, and differentiation. Biosynthesis of SAMe occurs in all mammalian cells as the first step in methionine catabolism in a reaction catalyzed by methionine adenosyltransferase (MAT). Decreased hepatic SAMe biosynthesis is a consequence of all forms of chronic liver injury. In an animal model of chronic liver SAMe deficiency, the liver is predisposed to further injury and develops spontaneous steatohepatitis and hepatocellular carcinoma. However, impaired SAMe metabolism, which occurs in patients with mutations of glycine N-methyltransferase (GNMT), can also lead to liver injury. This suggest that hepatic SAMe level needs to be maintained within a certain range, and deficiency or excess can both lead to abnormality. SAMe treatment in experimental animal models of liver injury shows hepatoprotective properties. Meta-analyses also show it is effective in patients with cholestatic liver diseases. Recent data show that exogenous SAMe can regulate hepatocyte growth and death, independent of its role as a methyl donor. This raises the question of its mechanism of action when used pharmacologically. Indeed, many of its actions can be recapitulated by methylthioadenosine (MTA), a by-product of SAMe that is not a methyl donor. A better understanding of why liver injury occurs when SAMe homeostasis is perturbed and mechanisms of action of pharmacologic doses of SAMe are essential in defining which patients will benefit from its use.

A Monte Carlo approach for change-point detection in the Cox proportional hazards model.

Mengling Liu — 2008-04-14T04:22:26-00:00

Statistics in medicine (6 February 2008)

Detecting a time lag of treatment effect or identifying change points in a hazard function is of great interest and importance in survival analysis. The testing procedures hereto are primarily based on analytical approximations for the asymptotic null distribution of either the likelihood ratio test or the score test. In the presence of random censoring and/or covariates, however, the justification for the limiting distribution often requires some technical assumptions and conditions that are difficult to verify in practice. Moreover, a satisfactory asymptotic theory for testing the existence of multiple change points in hazard function has not emerged. In this paper, we consider maximal score tests for detecting change point(s) in the Cox proportional hazards model with censored data. We propose to use a simple Monte Carlo approach for assessing the statistical significance of tests. The proposed approach is applicable for testing a single change point in the Cox model with covariates and sample stratifications over various types of candidate regions, including discrete time-point sets or disjoint intervals. We also show that the proposed test statistics and the Monte Carlo procedure are well applicable under situations with multiple change points. Simulation studies and an analysis of a real data from a randomized cancer trial are conducted to demonstrate the finite-sample performance of the proposed approach. Copyright (c) 2008 John Wiley & Sons, Ltd.

A Comparison of Two Bias-Corrected Covariance Estimators for Generalized Estimating Equations

Lu — 2007-09-04T09:34:45-00:00

Biometrics, Vol. 63, No. 3. (September 2007), pp. 935-941.

A DNA Damage-Induced p53 Serine 392 Kinase Complex Contains CK2, hSpt16, and SSRP1

David Keller — 2008-04-10T16:10:25-00:00

Molecular Cell, Vol. 7, No. 2. (February 2001), pp. 283-292.

Phosphorylation of the human p53 protein at Ser-392 has been shown to be responsive to UV but not [gamma] irradiation. Here we describe identification and purification of a mammalian UV-activated protein kinase complex that phosphorylates Ser-392 of p53 in vitro. This kinase complex contains casein kinase 2 (CK2) and the chromatin transcriptional elongation factor FACT (a heterodimer of hSpt16 and SSRP1). In vitro studies show that FACT alters the specificity of CK2 in the complex such that it selectively phosphorylates p53 over other substrates including casein. In addition, phosphorylation by the kinase complex enhances p53 activity. These results thus provide a potential mechanism for p53 activation by UV irradiation.

Therapeutic Potential of Angiostatin in Diabetic Nephropathy

Sarah Zhang — 2008-04-04T04:14:08-00:00

J Am Soc Nephrol, Vol. 17, No. 2. (1 February 2006), pp. 475-486.

Angiostatin is a proteolytic fragment of plasminogen and a potent angiogenic inhibitor. Previous studies have shown that angiostatin inhibits retinal neovascularization and reduces retinal vascular permeability in diabetic retinopathy. Here, it is reported for the first time that angiostatin is also implicated in diabetic nephropathy (DN). Angiostatin levels are dramatically decreased in the kidney of streptozotocin-induced diabetic rats. Consistently, diabetic kidneys also showed decreased expression and proteolytic activities of matrix metalloproteinase-2, an enzyme that releases angiostatin from plasminogen. Adenovirus-mediated delivery of angiostatin significantly alleviated albuminuria and attenuated the glomerular hypertrophy in diabetic rats. Moreover, angiostatin treatment downregulated the expression of vascular endothelial growth factor and TGF-[beta]1, two major pathogenic factors of DN, in diabetic kidneys. In cultured human mesangial cells, angiostatin blocked the overexpression of vascular endothelial growth factor and TGF-[beta]1 that were induced by high glucose while increasing the levels of pigment epithelium-derived factor, an endogenous inhibitor of DN. Moreover, angiostatin effectively inhibited the high-glucose-and TGF-[beta]1-induced overproduction of proinflammatory factors and extracellular matrix proteins via blockade of the Smad signaling pathway. These findings suggest that the decrease of angiostatin levels in diabetic kidney may contribute to the pathologic changes such as inflammation and fibrosis in DN. Therefore, angiostatin has therapeutic potential in DN as a result of its anti-inflammatory and antifibrosis activities. 10.1681/ASN.2005020217

Discovery and Characterization of Substituted Diphenyl Heterocyclic Compounds as Potent and Selective Inhibitors of Hepatitis C Virus Replication

Peiyong Huang — 2008-03-28T04:52:33-00:00

Antimicrob. Agents Chemother., Vol. 52, No. 4. (1 April 2008), pp. 1419-1429.

A novel small-molecule inhibitor, referred to here as R706, was discovered in a high-throughput screen of chemical libraries against Huh-7-derived replicon cells carrying autonomously replicating subgenomic RNA of hepatitis C virus (HCV). R706 was highly potent in blocking HCV RNA replication as measured by real-time reverse transcription-PCR and Western blotting of R706-treated replicon cells. Structure-activity iterations of the R706 series yielded a lead compound, R803, that was more potent and highly specific for HCV replication, with no significant inhibitory activity against a panel of HCV-related positive-stranded RNA viruses. Furthermore, HCV genotype 1 replicons displayed markedly higher sensitivity to R803 treatment than a genotype 2a-derived replicon. In addition, R803 was tested by a panel of biochemical and cell-based assays for on-target and off-target activities, and the data suggested that the compound had a therapeutic window close to 100-fold, while its exact mechanism of action remained elusive. We found that R803 was more effective than alpha interferon (IFN-alpha) at blocking HCV RNA replication in the replicon model. In combination studies, R803 showed a weak synergistic effect with IFN-alpha/ribavirin but only additive effects with a protease inhibitor and an allosteric inhibitor of RNA-dependent RNA polymerase (20). We conclude that R803 and related heterocyclic compounds constitute a new class of HCV-specific inhibitors that could potentially be developed as a treatment for HCV infection. 10.1128/AAC.00525-07

Identification of pollution source of cadmium in soil: application of material flow analysis and a case study in Taiwan.

LT Lu — 2008-03-25T09:21:38-00:00

Environ Sci Pollut Res Int, Vol. 14, No. 1. (January 2007), pp. 49-59.

BACKGROUND: Since the 1970s, at least 200 hectares (ha) of farm-land has been polluted by the heavy metal cadmium (Cd). Consequently, the Cd pollution has led to contaminate the rice production and caused acute social panic. According to the recent investigation results performed by the Taiwan Environmental Protection Administration (TEPA), it is indicated that most of the Cd pollution incidents in Taiwan resulted from the waste-water discharge of stearate Cd factories. To prevent the Cd pollution incidents from spreading, the TEPA has either forced these factories to close down or assisted them in improving their production processes since the 1980s. Unfortunately, accidental incidents of Cd pollution still emerge in an endless stream, despite the strict governmental controls placed on these questionable factories. Whether this pollution has resulted from undetected or hidden pollution sources stemming from two decades ago or comes from some new source, will be an outstanding issue. Therefore, this study attempts to identify the pollution sources of Cd in soil in Taiwan as well as to find the solution to the above-mentioned, outstanding issue by way of a methodology termed Material Flow Analysis (MFA). METHODOLOGY: The MFA has proved to be a useful tool on providing quantitative information of the flow of substances through an economic to an environmental system. Based upon the supply-and-demand theory of MFA, researchers have successfully conducted an overview of the use of materials in many industries, the construction industry being one of these. Therefore, this study tries to establish a set of analytical processes by way of MFA for identifying the pollution source of Cd in soil in Taiwan. In addition, the spirit of Life Cycle Assessment (LCA) technique was also employed to identify the materials, and products should be ignored as a crucial pollution source in this study. RESULTS AND DISCUSSION: According to the MFA methodology applied in this study and on the basis of related studies performed by Taiwanese governmental authorities, we arrive at the following analysis results: (1) the total amount of Cd from the economic perspective of material and product flow was approximately 441.2 tons; (2) the wastewater directly discharged into irrigation water can be concluded to be the major pollution route of Cd in farmland soil in Taiwan; (3) material plastic stabilizer (cadmium oxide, CdO), Zn-Pd compounds and Cu compounds should be the crucial pollution sources to contaminate environment through the route of wastewater in Cd flow analysis; (4) the crucial pollution sources to contaminate environment through the route of wastewater in Cd flow analysis were five factories, Coin, Jili, Taiwan Dye, Guangzheng and Mingguan, and they were all categorized as stearate Cd industries; (5) the typical source of the Cd pollution in soil in Changhua County through the pollution route of wastewater should be the metal surfacing process industries. CONCLUSIONS: This study proved that MFA can be a good tool for identifying Cd flow as well as for recognizing the crux of the problem concerning incidents of Cd pollution. This study led to the conclusion that the causal relationship between farmland pollution caused by Cd and stearate Cd factories in Taiwan seemed quite close by way of MFA methodology. In addition, this study also found that the wastewater discharged from a single metal surfacing process factory will not cause remarkable farmland pollution. However, the wastewater simultaneously discharged from a group of pollution factories can result in a significant pollution incident. RECOMMENDATIONS AND OUTLOOK: This case study is only a small contribution to the understanding of the toxic material flow related to Cd in the environment. This study recommends that Taiwanese governmental authorities should not deal with problems on an ad hoc basis, but should instead deal with Cd pollution problems overall employing control measures. Finally, the more accurate information or data we can collect, the more reliable results we can identify. Therefore, the quality and quantity of related data used in this MFA model should be closely scrutinized in order to ensure the most correct and comprehensive investigation on the toxic material flow.

Association of a Functional Cytochrome P450 4F2 Haplotype with Urinary 20-HETE and Hypertension.

Hong Liu — 2008-03-25T09:08:07-00:00

J Am Soc Nephrol (30 January 2008)

Cytochrome P450 4F2 (CYP4F2) catalyzes the omega-hydroxylation of arachidonic acid to 20-hydroxyeicosatetraenoic acid (20-HETE), a natriuretic and vasoactive eicosanoid that participates in the development of hypertension. The relationship among CYP4F2 genetic variants in the regulatory region, formation of renal 20-HETE, and hypertension is unknown. Here are reported seven genetic variants around the CYP4F2 intronic regulatory region. Four of these variants made up two common haplotypes, Hap I (c.-91T/c.-48G/c.-13T/c.+34T) and Hap II (c.-91C/c.-48C/c.-13C/c.+34G). Hap I included a major functional variant, c.-91T-->C, which was identified by reporter assay and electrophoretic mobility shift assay. Transfected into HEK293 cells, the Hap I construct showed a trend toward higher basal transcriptional activity and exhibited significantly greater LPS-stimulated activity than Hap II; these findings were the result of different NF-kappaB binding affinity between the two constructs. In vivo, a case-control study demonstrated that homozygosity for Hap I doubled the risk for hypertension in a Chinese population, even after adjustment for risk factors including age, gender, and body mass index. This association was confirmed in a family-based association study. In addition, Hap I was associated with elevated urinary 20-HETE. These results indicate that a functional variant of the CYP4F2 regulatory region, which increases the binding affinity of NF-kappaB, increases the risk for hypertension, likely by modulating the production of 20-HETE.

Urinary neutrophil gelatinase-associated lipocalin (NGAL) is an early biomarker for renal tubulointerstitial injury in IgA nephropathy.

H Ding — 2008-03-20T02:08:54-00:00

Clin Immunol, Vol. 123, No. 2. (May 2007), pp. 227-234.

Renal tubulointerstitial injury plays an important role in the development of IgA nephropathy (IgAN), the most common form of glomerulonephritis. Few currently in use biomarkers can sensitively detect the earliest signs of renal tubular injury, hindering our efforts to launch preventive and therapeutic measures for this disorder in a timely manner. Neutrophil gelatinase-associated lipocalin (NGAL) is an acute phase protein that is rapidly released from not only neutrophils but also a variety of cell types upon inflammation and tissue injury. Its small molecular size and protease resistance could render it an excellent biomarker of renal injury in IgAN. In this study, we tested this hypothesis by measuring urinary levels of NGAL, creatinine and N-acetyl-beta-D-glucosaminidase (NAG) in 40 healthy individuals and 70 IgAN patients with various disease severities. The urinary NGAL levels and NGAL/creatinine values were significantly upregulated in Lee grade III IgAN patients, in correlation with progressive glomerular mesangial proliferation and tubulointerstitial injury. Compared with urinary NAG levels, the urinary NGAL levels elevated much more drastically and can be readily detected even in Lee grade II IgAN patients when their NAG levels showed almost no change. Our findings suggest the promising use of urinary NGAL as an early biomarker for tubulointerstitial injury of IgA nephropathy and perhaps other types of renal disease in general.

Semiparametric analysis of mixture regression models with competing risks data.

Wenbin Lu — 2008-03-17T09:13:46-00:00

Lifetime Data Anal (12 January 2008)

In the analysis of competing risks data, cumulative incidence function is a useful summary of the overall crude risk for a failure type of interest. Mixture regression modeling has served as a natural approach to performing covariate analysis based on this quantity. However, existing mixture regression methods with competing risks data either impose parametric assumptions on the conditional risks or require stringent censoring assumptions. In this article, we propose a new semiparametric regression approach for competing risks data under the usual conditional independent censoring mechanism. We establish the consistency and asymptotic normality of the resulting estimators. A simple resampling method is proposed to approximate the distribution of the estimated parameters and that of the predicted cumulative incidence functions. Simulation studies and an analysis of a breast cancer dataset demonstrate that our method performs well with realistic sample sizes and is appropriate for practical use.

Integration of statistical inference methods and a novel control measure to improve sensitivity and specificity of data analysis in expression profiling studies.

S Zang — 2008-03-15T03:22:49-00:00

J Biomed Inform, Vol. 40, No. 5. (October 2007), pp. 552-560.

Statistical methods have proven invaluable tools for enhancing the quality of microarray analysis. In this study, we used different methods such as significance analysis of microarrays (SAM) and Bayesian analysis of gene expression levels (BAGEL), to analyze the same set of raw data in an attempt to maximize the chance of identifying genes whose expression were significantly altered in gastric cancers. In addition, we examined the utility of an additional set of reference in controlling the variances and enhancing the quality of the results. Our results showed that BAGEL has the advantage of detecting small yet statistically significant differences, which might be of biological significance. Furthermore, introducing an additional control into the BAGEL, we were able to minimize the influence of the variances and significantly reduce number of potential false positive hits. BAGEL incorporates a novel control significantly improve the sensitivity and specificity of gene expression profiling analysis.

Investigation on glycosylation patterns of proteins from human liver cancer cell lines based on the multiplexed proteomics technology.

H Zhou — 2008-03-14T04:49:44-00:00

Arch Biochem Biophys, Vol. 459, No. 1. (1 March 2007), pp. 70-78.

Glycosylation, a very important post-translational modification of proteins, is increasingly coming into notice. However, large-scale, throughput investigations on glycosylated proteins are few. We applied a sensitive and fast fluorescence-based multiplexed proteomics (MP) technology which included two-dimensional gel electrophoresis (2-DE) followed by the fluorescence staining of glycoprotein and mass spectrometry identification for the purpose of constructing glycoprotein databases of the typical human hepatocellular carcinoma cell lines including Hep3B cell line without metastasis and MHCC97H with highly metastatic potential as well as the control non-tumor Chang liver cell. 74+/-2 (n=3), 78+/-3 (n=3) and 72+/-5 (n=3) glycoprotein spots were detected on 2-DE gels from Chang liver, Hep3B and MHCC97H cell sample using this MP technique, respectively. In all, 80 glycoproteins from three cell lines were successfully identified via peptide mass profiling using MALDI-TOF-MS/MS and the identified glycoproteins were annotated to our databases. In addition, we also found the glycosylation pattern differences among these three cell lines. The protein glycosylation alteration would be have great significance for the diagnosis of HCC and prediction of its metastasis. This study described the construction of glycosylation patterns of proteins and glycoproteome databases of human liver cells by the novel technological platform. The glycoproteome databases also provide essential basis for following study.

Staining method for protein analysis by capillary gel electrophoresis.

S Wu — 2008-03-13T16:14:25-00:00

Anal Chem, Vol. 79, No. 20. (15 October 2007), pp. 7727-7733.

A novel staining method and the associated fluorescent dye were developed for protein analysis by capillary SDS-PAGE. The method strategy is to synthesize a pseudo-SDS dye and use it to replace some of the SDS in SDS-protein complexes so that the protein can be fluorescently detected. The pseudo-SDS dye consists of a long, straight alkyl chain connected to a negative charged fluorescent head and binds to proteins just as SDS. The number of dye molecules incorporated with a protein depends on the dye concentration relative to SDS in the sample solution, since SDS and dye bind to proteins competitively. In this work, we synthesized a series of pseudo-SDS dyes, and tested their performances for capillary SDS-PAGE. FT-16 (a fluorescein molecule linked with a hexadodecyl group) seemed to be the best among all the dyes tested. Although the numbers of dye molecules bound to proteins (and the fluorescence signals from these protein complexes) were maximized in the absence of SDS, high-quality separations were obtained when co-complexes of SDS-protein-dye were formed. The migration time correlates well with protein size even after some of the SDS in the SDS-protein complexes was replaced by the pseudo-SDS dye. Under optimized experimental conditions and using a laser-induced fluorescence detector, limits of detection of as low as 0.13 ng/mL (bovine serum albumin) and dynamic ranges over 5 orders of magnitude in which fluorescence response is proportional to the square root of analyte concentration were obtained. The method and dye were also tested for separations of real-world samples from E. coli.

Ultrasensitive flow-based immunoassays using single-molecule counting.

J Todd — 2008-03-08T16:13:35-00:00

Clin Chem, Vol. 53, No. 11. (November 2007), pp. 1990-1995.

BACKGROUND: Immunoassay (IA) technology has expanded the clinical utility of protein biomarkers, but demands for increased sensitivity, dynamic reporting ranges, and small sample volumes have limited the potential clinical usefulness of many biomarkers. We assessed the performance, including limits of detection (LODs) and the dynamic reporting range, of an IA-based technology, Erenna Immunoassay System, for a series of biomarkers, including cardiac troponin I (cTnI). METHODS: Erenna IAs were used with 10 different and clinically important biomarkers to ascertain the LOD with various sample sizes (10 microL to 200 microL). RESULTS: The Erenna Immunoassay System generated LODs of 10-100 pg/L using 100 microL of sample. For cTnI, the LOD was 0.2 ng/L and a 10% CV was seen between 0.78 and 1.6 ng/L. CONCLUSIONS: The Erenna IA-based technology reproducibly measures protein biomarkers with detection limits of 10-100 pg/L, with a dynamic range of >4.5 logs in sample volumes of 50-150 microL.

Role of nuclear factor kappa B and reactive oxygen species in the tumor necrosis factor-alpha-induced epithelial-mesenchymal transition of MCF-7 cells.

R Dong — 2008-03-07T02:06:57-00:00

Braz J Med Biol Res, Vol. 40, No. 8. (August 2007), pp. 1071-1078.

Snail promoter The microenvironment of the tumor plays an important role in facilitating cancer progression and activating dormant cancer cells. Most tumors are infiltrated with inflammatory cells which secrete cytokines such as tumor necrosis factor-alpha (TNF-alpha). To evaluate the role of TNF-alpha in the development of cancer we studied its effects on cell migration with a migration assay. The migrating cell number in TNF-alpha-treated group is about 2-fold of that of the control group. Accordingly, the expression of E-cadherin was decreased and the expression of vimentin was increased upon TNF-alpha treatment. These results showed that TNF-alpha can promote epithelial-mesenchymal transition (EMT) of MCF-7 cells. Further, we found that the expression of Snail, an important transcription factor in EMT, was increased in this process, which is inhibited by the nuclear factor kappa B (NFkappaB) inhibitor aspirin while not affected by the reactive oxygen species (ROS) scavenger N-acetyl cysteine. Consistently, specific inhibition of NFkappaB by the mutant IkappaBalpha also blocked the TNF-alpha-induced upregulation of Snail promoter activity. Thus, the activation of NFkappaB, which causes an increase in the expression of the transcription factor Snail is essential in the TNF-alpha-induced EMT. ROS caused by TNF-alpha seemed to play a minor role in the TNF-alpha-induced EMT of MCF-7 cells, though ROS per se can promote EMT. These findings suggest that different mechanisms might be responsible for TNF-alpha- and ROS-induced EMT, indicating the need for different strategies for the prevention of tumor metastasis induced by different stimuli.

Instantaneous derivatization technology for simultaneous and homogeneous determination of multiple DNA targets.

J Miao — 2008-03-05T06:45:42-00:00

Anal Chem, Vol. 80, No. 5. (1 March 2008), pp. 1606-1613.

There are potential advantages, in terms of simplicity and speed, for detecting DNA hybridization steps directly without using any external labels, especially for the multiplexed assays. In the current paper, we describe the use of a carrier-resolved label-free multiplexed assay for the simultaneous detection of multiple DNA targets. Herein we demonstrate that this protocol, using three homogeneous carriers thermosensitive poly(N-isopropylacrylamide), polystyrene beads, and magnetic beads, respectively, for simultaneous determination of three short DNA fragments specific to hepatitis B virus. Briefly, one hybridization occurs between a mixture of three different capture probe DNAs immobilized onto three carriers and three targets in a single vessel, and then chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxylphenylglyoxal (TMPG) and the guanine nucleotide-rich regions within the target DNA. An excellent linearity is found within the range between 0.1 and 6.0 pmol with the lowest detection limit of 100 fmol. In contrast to current encoding strategies, every hybridization signal for the corresponding DNA target in our protocol is uniquely immobilized onto one carrier vehicle with a unique and intrinsic physical-chemical signature. Moreover, an instantaneous derivatization reaction is employed for the label-free determination of three targets in a single vessel. In addition, a simple CL setup is employed to read the carrier code instead of an expensive and complicated flow cytometer or imaging system commonly used for multiplexed assays. Further signal amplification is achieved by employing three amplified DNAs for second hybridization, which include a guanine nucleobase-rich sequence domain for the generation of light and an additional tethered nucleic acid domain complementary with one of the target DNA as an amplification platform. Such simple amplified CL transduction allows detection of DNA targets down to the 15-fmol level. This new protocol also provided a good capability in discriminating perfectly complementary DNA from single-base mismatches and noncomplementary sequences. Overall, the protocol described here may have value in a variety of clinical, environmental, and biodefense applications for which the accurate quantitative analysis of multiple DNA targets is desired.

Case-Cohort Designs and Analysis for Clustered Failure Time Data

Lu — 2006-11-30T10:31:26-00:00

Biometrics, Vol. 62, No. 4. (December 2006), pp. 1138-1148.

On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.

D Luca — 2008-02-29T16:04:34-00:00

Am J Hum Genet, Vol. 82, No. 2. (February 2008), pp. 453-463.

Resources being amassed for genome-wide association (GWA) studies include "control databases" genotyped with a large-scale SNP array. How to use these databases effectively is an open question. We develop a method to match, by genetic ancestry, controls to affected individuals (cases). The impact of this method, especially for heterogeneous human populations, is to reduce the false-positive rate, inflate other spuriously small p values, and have little impact on the p values associated with true positive loci. Thus, it highlights true positives by downplaying false positives. We perform a GWA by matching Americans with type 1 diabetes (T1D) to controls from Germany. Despite the complex study design, these analyses identify numerous loci known to confer risk for T1D.

Dimension reduction and coefficient estimation in multivariate linear regression

Yuan — 2007-05-25T21:59:04-00:00

Journal of the Royal Statistical Society: Series B (Statistical Methodology), Vol. 69, No. 3. (June 2007), pp. 329-346.

High prevalence of chronic kidney disease in population-based patients diagnosed with type 2 diabetes in downtown Shanghai.

B Lu — 2008-02-24T01:12:41-00:00

J Diabetes Complications, Vol. 22, No. 2. (r 2008), pp. 96-103.

OBJECTIVE: This study aimed to evaluate the prevalence of chronic kidney disease (CKD) and the risk factors associated with CKD among Chinese patients diagnosed with type 2 diabetes aged over 30 in downtown Shanghai and to assess the relationship between CKD and diabetic retinopathy (DR). METHODS: We investigated 1039 Chinese patients diagnosed with type 2 diabetes aged over 30 by randomized cluster sampling in downtown Shanghai, and 1009 patients in this study were analyzed based on data integrity. Body measurements including height, weight, waist circumference and hip circumference, resting blood pressure, fasting blood measures, and urinary albumin-to-creatinine ratio (ACR), as well as the digitally stored fundus images, were investigated. Glomerular filtration rate (GFR) was estimated using the Cockcroft-Gault equation. The prevalence of CKD was calculated, and the risk factors associated with CKD were evaluated using stepwise logistic regression. The relationship between CKD and DR was evaluated using Spearman correlation and the chi-square test. RESULTS: The following were the results found in this study: (a) The prevalence rate of CKD (Stages 1-5) was 63.9% in Chinese patients diagnosed with type 2 diabetes, 8.8% in those with CKD Stage 1, 22.3% in those with CKD Stage 2, and 32.8% in those with CKD Stages 3-5 (GFR<60 ml/min/1.73 m(2)). The prevalence of CKD increased with age. (b) CKD patients were older and had higher duration of diabetes, systolic blood pressure, urea nitrogen, uric acid, creatinine, and ACR of the first urine than those without CKD. (c) Male patients had a higher percentage of CKD Stages 3-5, and female patients had a higher percentage of CKD Stages 1-2. (d) CKD was significantly associated with duration of diabetes, older age, systolic blood pressure, and serum urea nitrogen based on logistic regression analysis. (e) Of the patients without CKD, 15.6% had DR, and of those with CKD, 27.6% had DR. The decrease in GFR was significantly correlated with DR after controlling for sex, age, and albuminuria staging. CONCLUSION: The high prevalence of CKD observed in Chinese patients diagnosed with type 2 diabetes aged over 30 in downtown Shanghai was similar to that in Western patients, and the cause of CKD is likely to be any of the following: type 2 diabetes, IgA nephropathy, hypertension, or any combination of these. The screening program for GFR in type 2 diabetic patients should be performed even on those with normoalbuminuria. The decrease in GFR might predict the occurrence of DR among patients diagnosed with type 2 diabetes.

High prevalence of albuminuria in population-based patients diagnosed with type 2 diabetes in the Shanghai downtown.

B Lu — 2008-02-24T01:07:34-00:00

Diabetes Res Clin Pract, Vol. 75, No. 2. (February 2007), pp. 184-192.

OBJECTIVE: The prevalence of albuminuria and the risk factors associated with albuminuria were evaluated among the Chinese patients diagnosed with type 2 diabetes aged over 30 in the Shanghai downtown. We also evaluated the variability of urinary albumin-to-creatinine ratio (ACR) among the three measurements and the relationship between diabetic retinopathy (DR) and albuminuria. METHODS: The 1039 Chinese patients diagnosed with type 2 diabetes aged over 30 were investigated by randomized cluster sampling in the Shanghai downtown and 1018 patients were analyzed in this study. Body mass measurements including height, weight, waist circumference and hip circumference, resting blood pressure, fasting blood measures, urinary ACR and the digitally stored fundus images were investigated. The prevalence of albuminuria was calculated and the risk factors associated with albuminuria were evaluated by stepwise logistic regression. The concordance of urinary ACR was evaluated by observed agreement. The relationship between albuminuria and DR was also evaluated. RESULTS: (1) The mean age of all patients was 66.10+/-11.54 years and the duration of diabetes was 7.89+/-7.16 years. (2) The prevalence of albuminuria was 49.6% among the Chinese patients diagnosed with type 2 diabetes aged over 30 in the Shanghai downtown, 41.4% with microalbuminuria and 8.2% with macroalbuminuria. (3) Microalbuminuria was significantly associated with systolic blood pressure, gender and waist circumference. Macroalbuminuria was significantly associated with systolic blood pressure and duration of diabetes. (4) Observed agreement among the three urinary ACR measurement for albuminuria staging was 73.3% (first versus second), 64.5% (first versus third) and 77.5% (second versus third). Observed agreement in the albuminuria staging between the single urinary ACR measurement and all three urinary ACR measurements was 85.8% (first versus all three), 87.6% (second versus all three) and 81.9% (third versus all three). (5) The percentage of DR in the macroalbuminuric group (59.2%) was significantly higher than that in the normalbuminuria group (16.1%) and microalbuminuria group (24.6%). (6) The macroalbuminuric patients with DR had significantly increased fasting blood glucose and HbA1c compared with the macroalbuminuric patients without DR. CONCLUSION: The prevalence of microalbuminuria observed in the Chinese patients diagnosed with type 2 diabetes aged over 30 in the Shanghai downtown reached up to 41.4% though the observations in our study might be representative of the diabetic patients of the Shanghai downtown. We agreed that at least two of the three urinary collections were done in a 3- to 6-month period because of the day-to-day variability in albumin excretion. The percentage of DR among the patients with macroalbuminuria was 59.2%, and the macroalbuminuric patients with the significantly high plasma glucose and DR were prone to diagnose DN.

Electrospray positive ionization tandem mass spectrometry of Amadori compounds.

J Wang — 2008-02-23T12:14:39-00:00

J Mass Spectrom, Vol. 43, No. 2. (February 2008), pp. 262-264.

Bayesian models based on test statistics for multiple hypothesis testing problems.

Yuan Ji — 2008-02-06T07:59:03-00:00

Bioinformatics (1 February 2008)

MOTIVATION: We propose a Bayesian method for the problem of multiple hypothesis testing that is routinely encountered in bioinformatics research, such as the differential gene expression analysis. Our algorithm is based on modeling the distributions of test statistics under both null and alternative hypotheses. We substantially reduce the complexity of the process of defining posterior model probabilities by modeling the test statistics directly instead of modeling the full data. Computationally, we apply a Bayesian FDR approach to control the number of rejections of null hypotheses. To check if our model assumptions for the test statistics are valid for various bioinformatics experiments, we also propose a simple graphical model-assessment tool. RESULTS: Using extensive simulations, we demonstrate the performance of our models and the utility of the model-assessment tool. In the end, we apply the proposed methodology to an siRNA screening and a gene expression experiment. CONTACT: yuanji@mdanderson.org.