Publications by authors named "Yinghua Shen"

19 Publications

  • Page 1 of 1

Mobility Prediction Using a Weighted Markov Model Based on Mobile User Classification.

Sensors (Basel) 2021 Mar 3;21(5). Epub 2021 Mar 3.

School of Information and Communications Engineering, Communication University of China, Beijing 100024, China.

The vast amounts of mobile communication data collected by mobile operators can provide important insights regarding epidemic transmission or traffic patterns. By analyzing historical data and extracting user location information, various methods can be used to predict the mobility of mobile users. However, existing prediction algorithms are mainly based on the historical data of all users at an aggregated level and ignore the heterogeneity of individual behavior patterns. To improve prediction accuracy, this paper proposes a weighted Markov prediction model based on mobile user classification. The trajectory information of a user is extracted first by analyzing real mobile communication data, where the complexity of a user's trajectory is measured using the mobile trajectory entropy. Second, classification criteria are proposed based on different user behavior patterns, and all users are classified with machine learning algorithms. Finally, according to the characteristics of each user classification, the step threshold and the weighting coefficients of the weighted Markov prediction model are optimized, and mobility prediction is performed for each user classification. Our results show that the optimized weighting coefficients can improve the performance of the weighted Markov prediction model.
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http://dx.doi.org/10.3390/s21051740DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7959290PMC
March 2021

A Group-Based Distance Learning Method for Semisupervised Fuzzy Clustering.

IEEE Trans Cybern 2020 Oct 7;PP. Epub 2020 Oct 7.

Learning a proper distance for clustering from prior knowledge falls into the realm of semisupervised fuzzy clustering. Although most existing learning methods take prior knowledge (e.g., pairwise constraints) into account, they pay little attention to local knowledge of data, which, however, can be utilized to optimize the distance. In this article, we propose a novel distance learning method, which learns from the Group-level information, for semisupervised fuzzing clustering. We first present a new format of constraint information, called Group-level constraints, by elevating the pairwise constraints (must-links and cannot-links) from point level to Group level. The Groups, generated around data points contained in the pairwise constraints, carry not only the local information of data (the relation between close data points) but also more background information under some given limited prior knowledge. Then, we propose a novel method to learn a distance by using the Group-level constraints, namely, Group-based distance learning, in order to optimize the performance of fuzzy clustering. The distance learning process aims to pull must-link Groups as close as possible while pushing cannot-link Groups as far as possible. We formulate the learning process with the weights of constraints by invoking some linear and nonlinear transformations. The linear Group-based distance learning method is realized by means of semidefinite programming, and the nonlinear learning method is realized by using the neural network, which can explicitly provide nonlinear mappings. Experimental results based on both synthetic and real-world datasets show that the proposed methods yield much better performance compared to other distance learning methods using pairwise constraints.
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http://dx.doi.org/10.1109/TCYB.2020.3023373DOI Listing
October 2020

Should chromosomal microarray be offered to fetuses with ultrasonographic soft markers in second trimester: A prospective cohort study and meta-analysis.

Prenat Diagn 2020 12 31;40(12):1569-1577. Epub 2020 Aug 31.

International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

Objective: To evaluate whether chromosomal microarray (CMA) should be offered to fetuses with ultrasonographic soft markers (USMs) in the second trimester.

Methods: A prospective cohort study and meta-analysis were conducted. In the prospective cohort study, 564 fetuses with USMs were enrolled. In the meta-analysis, eligible articles describing copy number variations in fetuses with USMs were included.

Results: In the prospective cohort study, the diagnostic yields of CMA over non-invasive prenatal testing (NIPT) and karyotyping were significantly higher in fetuses with mild ventriculomegaly (MVM) than those in local control cohorts with normal ultrasound. However, the yields of CMA over NIPT and karyotyping in fetuses with other USMs were similar to controls. About ten studies, involving 405 fetuses with MVM and 1412 fetuses with other USMs, were included in the meta-analysis. The pooled diagnostic yields of CMA over NIPT and karyotyping in fetuses with MVM were 4.9% and 3.2%, respectively. In fetuses with other USMs, the yields of CMA over NIPT and karyotyping were 1.2% and 0.4%, respectively.

Conclusion: It is reasonable to offer CMA as a first-tier test to fetuses with MVM. However, for fetuses with other USMs, the considerations to perform CMA should not differ from pregnancies with normal ultrasound.
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http://dx.doi.org/10.1002/pd.5815DOI Listing
December 2020

Pharmacokinetics, Pharmacodynamics and Safety of Belimumab in Chinese Patients with Systemic Lupus Erythematosus: A Phase I, Open-Label Study.

Rheumatol Ther 2020 Mar 17;7(1):191-200. Epub 2020 Jan 17.

GlaxoSmithKline, Shanghai, China.

Introduction: The B cell survival factor B lymphocyte stimulator (BLyS) is elevated in patients with systemic lupus erythematosus (SLE) and associated with disease activity. Belimumab, a monoclonal antibody specific for soluble BLyS, is approved for the treatment of adults with active, autoantibody-positive SLE receiving standard therapy. Ethnicity is one of the factors that can potentially affect the pharmacokinetics (PK) of therapeutic monoclonal antibodies, and therefore their efficacy and safety.

Methods: This phase 1, open-label study (200909) evaluated the pharmacokinetics (PK, primary objective), pharmacodynamics (PD), and safety (secondary objectives) of belimumab in Chinese patients with SLE (N = 20). Blood samples were taken up to 84 days after a single intravenous (IV) dose of belimumab 10 mg/kg.

Results: Peak serum concentrations of belimumab (C) were obtained within the 1-h infusion. Geometric mean C, area under the concentration-time curve (time 0 to last quantifiable concentration), terminal half-life, systemic clearance, and volume of distribution were 221 μg/mL, 2395 day·μg/mL, 14.6 days, 4.06 mL/day/kg, and 85.7 mL/kg, respectively. Decreases in CD20, CD20/CD27 naïve, CD20/CD69 active, CD20/CD138 plasmacytoid, CD19/CD27/CD38 SLE subset, and CD20/CD138 plasma B Cells post-dose were accompanied by an increase in CD20/CD27 memory B cells. Four cases of upper respiratory tract infection (three mild, one moderate) and one case of mild pharyngitis were possibly drug-related; all resolved during the study.

Conclusion: PK of a single belimumab 10 mg/kg IV dose in Chinese patients with SLE were similar to those observed previously in Japanese and American (white and African-American) patients with SLE. PD results were consistent with belimumab inhibiting BLyS, and belimumab was well tolerated. These data support the use of belimumab in Chinese patients with SLE.

Trial Registration: ClinicalTrials.gov identifier, NCT02880852.
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http://dx.doi.org/10.1007/s40744-020-00193-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7021845PMC
March 2020

Prenatal Diagnosis of Microdeletions or Microduplications in the Proximal, Central, and Distal Regions of Chromosome 22q11.2: Ultrasound Findings and Pregnancy Outcome.

Front Genet 2019 30;10:813. Epub 2019 Aug 30.

International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.

Several recurrent microdeletions and microduplications in the proximal, central, and distal regions of chromosomal 22q11.2 have been identified. However, due to a limited number of patients reported in the literature, highly variable clinical phenotypes, and incomplete penetrance, the pathogenicity of some microdeletions/microduplications in 22q11.2 central and distal regions is unclear. Hence, the genetic counseling and subsequent pregnancy decision are extremely challenging, especially when they are found in structurally normal fetuses. Here, we reported 27 consecutive cases diagnosed prenatally with 22q11.2 microdeletions or microduplications by chromosomal microarray analysis in our center. The prenatal ultrasound features, inheritance of the microdeletions/microduplications, and their effects on the pregnancy outcome were studied. We found that fetuses with 22q11.2 microdeletions were more likely to present with structure defects in the ultrasound, as compared with fetuses with 22q11.2 microduplications. Both the prenatal ultrasound findings and the inheritance of the microdeletions/microduplications affected the parent's decision of pregnancy. Those with structure defects in prenatal ultrasound or occurred often resulted in termination of the pregnancy, whereas those with normal ultrasound and inherited from healthy parent were likely to continue the pregnancy and led to normal birth. Our study emphasized that proximal, central, and distal 22q11.2 deletions or duplications were different from each other, although some common features were shared among them. More studies are warranted to demonstrate the underlying mechanisms of different clinical features of these recurrent copy-number variations, thereby to provide more information for genetic counseling of 22q11.2 microdeletions and microduplications when they are detected prenatally.
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http://dx.doi.org/10.3389/fgene.2019.00813DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728414PMC
August 2019

Improved Efficacy in a Fabry Disease Model Using a Systemic mRNA Liver Depot System as Compared to Enzyme Replacement Therapy.

Mol Ther 2019 04 6;27(4):878-889. Epub 2019 Mar 6.

Translate Bio, Lexington, MA 02141, USA. Electronic address:

Fabry disease is a lysosomal storage disorder caused by the deficiency of α-galactosidase A. Enzyme deficiency results in a progressive decline in renal and cardiac function, leading to cardiomyopathy and end-stage renal disease. Current treatments available, including enzyme replacement therapies, have provided significant benefit to patients; however, unmet medical needs remain. mRNA therapy, with drug-like properties, has the unique ability to produce therapeutic proteins endogenously. Here we describe the sustained delivery of therapeutic human α-galactosidase protein in vivo via nanoparticle-formulated mRNA in mouse and non-human primate, with a demonstration of efficacy through clinically relevant biomarker reduction in a mouse Fabry disease model. Multi-component nanoparticles formulated with lipids and lipid-like materials were developed for the delivery of mRNA encoding human α-galactosidase protein. Upon delivery of human GLA mRNA to mice, serum GLA protein levels reached as high as ∼1,330-fold over normal physiological values.
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http://dx.doi.org/10.1016/j.ymthe.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6453518PMC
April 2019

Approximation of Fuzzy Sets by Interval Type-2 Trapezoidal Fuzzy Sets.

IEEE Trans Cybern 2020 Nov 3;50(11):4722-4734. Epub 2019 Jan 3.

In this paper, we propose a gradient-based method to approximate a fuzzy set through a trapezoidal fuzzy set (TFS). By adding some constraints in the formulated optimization problem, the major characteristics of the fuzzy set such as the core, the major part of the support, and the shape of the membership function could be preserved; also the form of the optimized result as a TFS is guaranteed. We regard the optimized TFS as the "skeleton" (blueprint) of the original fuzzy set. Based on this skeleton, we further extend the TFS to a higher type, that is, an interval type-2 TFS (IT2 TFS), so that more information about the original fuzzy set could be captured but the number of the parameters used to describe the original fuzzy set is still maintained low (nine parameters are required for an IT2 TFS). The principle of justifiable granularity is used to ensure that the formed type-2 information granule exhibits a sound interpretation. Both synthetic fuzzy sets and those constructed by the fuzzy C -means algorithm applied to the publicly available data have been used to demonstrate the usefulness of the proposed approximation methods.
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http://dx.doi.org/10.1109/TCYB.2018.2886725DOI Listing
November 2020

Clustering Homogeneous Granular Data: Formation and Evaluation.

IEEE Trans Cybern 2019 Apr 26;49(4):1391-1402. Epub 2018 Feb 26.

In this paper, we develop a comprehensive conceptual and algorithmic framework to cope with a problem of clustering homogeneous information granules. While there have been several approaches to coping with granular (viz. non-numeric) data, the origin of granular data themselves considered there is somewhat unclear and, as a consequence, the results of clustering start lacking some full-fledged interpretation. In this paper, we offer a holistic view at clustering information granules and an evaluation of the results of clustering. We start with a process of forming information granules with the use of the principle of justifiable granularity (PJG). With this regard, we discuss a number of parameters used in this development of information granules as well as quantify the quality of the granules produced in this manner. In the sequel, Fuzzy C -Means is applied to cluster the derived information granules, which are represented in a parametric manner and associated with weights resulting from the usage of the PJG. The quality of clustering results is evaluated through the use of the reconstruction criterion (quantifying the concept of information granulation and degranulation). A suite of experiments using synthetic and publicly available datasets is reported to quantify the performance of the proposed approach and highlight its key features.
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http://dx.doi.org/10.1109/TCYB.2018.2802453DOI Listing
April 2019

An open-label clinical trial of agalsidase alfa enzyme replacement therapy in children with Fabry disease who are naïve to enzyme replacement therapy.

Drug Des Devel Ther 2016 25;10:1771-81. Epub 2016 May 25.

Shire, Lexington, MA, USA.

Background: Following a drug manufacturing process change, safety/efficacy of agalsidase alfa were evaluated in enzyme replacement therapy (ERT)-naïve children with Fabry disease.

Methods: In an open-label, multicenter, Phase II study (HGT-REP-084; Shire), 14 children aged ≥7 years received 0.2 mg/kg agalsidase alfa every other week for 55 weeks. Primary endpoints: safety, changes in autonomic function (2-hour Holter monitoring). Secondary endpoints: estimated glomerular filtration rate, left ventricular mass index (LVMI), midwall fractional shortening, pharmacodynamic parameters, and patient-reported quality-of-life.

Results: Among five boys (median 10.2 [range 6.7, 14.4] years) and nine girls (14.8 [10.1, 15.9] years), eight patients experienced infusion-related adverse events (vomiting, n=4; nausea, n=3; dyspnea, n=3; chest discomfort, n=2; chills, n=2; dizziness, n=2; headache, n=2). One of these had several hypersensitivity episodes. However, no patient discontinued for safety reasons and no serious adverse events occurred. One boy developed immunoglobulin G (IgG) and neutralizing antidrug antibodies. Overall, no deterioration in cardiac function was observed in seven patients with low/abnormal SDNN (standard deviation of all filtered RR intervals; <100 ms) and no left ventricular hypertrophy: mean (SD) baseline SDNN, 81.6 (20.9) ms; mean (95% confidence interval [CI]) change from baseline to week 55, 17.4 (2.9, 31.9) ms. Changes in SDNN correlated with changes in LVMI (r=-0.975). No change occurred in secondary efficacy endpoints: mean (95% CI) change from baseline at week 55 in LVMI, 0.16 (-3.3, 3.7) g/m(2.7); midwall fractional shortening, -0.62% (-2.7%, 1.5%); estimated glomerular filtration rate, 0.15 (-11.4, 11.7) mL/min/1.73 m(2); urine protein, -1.8 (-6.0, 2.4) mg/dL; urine microalbumin, 0.6 (-0.5, 1.7) mg/dL; plasma globotriaosylceramide (Gb3), -5.71 (-10.8, -0.6) nmol/mL; urinary Gb3, -1,403.3 (-3,714.0, 907.4) nmol/g creatinine, or clinical quality-of-life outcomes.

Conclusion: Fifty-five weeks' agalsidase alfa ERT at 0.2 mg/kg every other week was well tolerated. Disease progression may be slowed when ERT is started prior to major organ dysfunction.

Trial Registration: https://ClinicalTrials.gov identifier NCT01363492.
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http://dx.doi.org/10.2147/DDDT.S102761DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4887054PMC
March 2017

Online 2D-LC-MS/MS assay to quantify therapeutic protein in human serum in the presence of pre-existing antidrug antibodies.

Anal Chem 2015 Aug 7;87(16):8555-63. Epub 2015 Aug 7.

Bioanalytical and Biomarker Development, Research and Nonclinical Development, Shire, Lexington, Massachusetts 02421, United States.

The formation of antidrug antibodies (ADA) can interfere with the accurate quantitation of therapeutic proteins, leading to significantly underestimated drug concentrations and confounded pharmacokinetic (PK) data interpretation. Although highly desirable, development of ADA-tolerant bioanalytical methods enabling unbiased measurement of both free and ADA-bound drug presents a considerable challenge. We report herein the development and validation of a robust LC-MS assay capable of quantifying therapeutic protein immunoglobulin A1 protease (IgAP) in human serum in the presence of pre-existing anti-IgAP antibodies. The procedure included sodium dodecyl sulfate (SDS) denaturation and chemical reduction of serum proteins to dissociate ADA-drug bindings, followed by tryptic digestion of protein pellets and subsequent LC-MS analysis of the surrogate IgAP peptide using stable isotope labeled peptide internal standard. Substantial enhancements in the sensitivity and selectivity were achieved by the combination of online two-dimensional reversed-phase LC (2D-LC) operated in high and low pH buffers, respectively, for efficient enrichment and quantitation of the surrogate peptide by multiple-reaction monitoring (MRM) mass spectrometry. Unlike ligand-binding assay, our method is not prone to interferences from ADA, allowing accurate and precise measurement of the IgAP in the range of 0.05 to 10 μg/mL in 25 μL of human serum with a wide range of anti-IgAP antibody levels. The intra- and inter-run precision (coefficient of variation (CV%)) was within 11.5% and 10.5%, respectively, and the bias was within ±7.1% for all quality control (QC) concentrations. With little modification, the described method can readily be applicable to the quantitation of other biotherapeutic proteins in the ADA-positive clinical matrices.
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http://dx.doi.org/10.1021/acs.analchem.5b02293DOI Listing
August 2015

Delta frequency optogenetic stimulation of the thalamic nucleus reuniens is sufficient to produce working memory deficits: relevance to schizophrenia.

Biol Psychiatry 2015 Jun 28;77(12):1098-107. Epub 2015 Feb 28.

Brandeis University, Waltham, Massachusetts. Electronic address:

Background: Low-frequency (delta/theta) oscillations in the thalamocortical system are elevated in schizophrenia during wakefulness and are also induced in the N-methyl-D-asparate receptor hypofunction rat model. To determine whether abnormal delta oscillations might produce functional deficits, we used optogenetic methods in awake rats. We illuminated channelrhodopsin-2 in the thalamic nucleus reuniens (RE) at delta frequency and measured the effect on working memory (WM) performance (the RE is involved in WM, a process affected in schizophrenia [SZ]).

Methods: We injected RE with adeno-associated virus to transduce cells with channelrhodopsin-2. An optical fiber was implanted just dorsal to the hippocampus in order to illuminate RE axon terminals.

Results: During optogenetic delta frequency stimulation, rats displayed a strong WM deficit. On the following day, performance was normal if illumination was omitted.

Conclusions: The optogenetic experiments show that delta frequency stimulation of a thalamic nucleus is sufficient to produce deficits in WM. This result supports the hypothesis that delta frequency bursting in particular thalamic nuclei has a causal role in producing WM deficits in SZ. The action potentials in these bursts may "jam" communication through the thalamus, thereby interfering with behaviors dependent on WM. Studies in thalamic slices using the N-methyl-D-asparate receptor hypofunction model show that delta frequency bursting is dependent on T-type Ca(2+) channels, a result that we confirmed here in vivo. These channels, which are strongly implicated in SZ by genome-wide association studies, may thus be a therapeutic target for treatment of SZ.
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http://dx.doi.org/10.1016/j.biopsych.2015.01.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4444380PMC
June 2015

The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing.

PLoS One 2010 Jan 26;5(1):e8888. Epub 2010 Jan 26.

Department of Pathology, Harvard Medical School and Immune Disease Institute, Boston, Massachusetts, United States of America.

Background: We recently showed that enzymes of the TET family convert 5-mC to 5-hydroxymethylcytosine (5-hmC) in DNA. 5-hmC is present at high levels in embryonic stem cells and Purkinje neurons. The methylation status of cytosines is typically assessed by reaction with sodium bisulfite followed by PCR amplification. Reaction with sodium bisulfite promotes cytosine deamination, whereas 5-methylcytosine (5-mC) reacts poorly with bisulfite and is resistant to deamination. Since 5-hmC reacts with bisulfite to yield cytosine 5-methylenesulfonate (CMS), we asked how DNA containing 5-hmC behaves in bisulfite sequencing.

Methodology/principal Findings: We used synthetic oligonucleotides with different distributions of cytosine as templates for generation of DNAs containing C, 5-mC and 5-hmC. The resulting DNAs were subjected in parallel to bisulfite treatment, followed by exposure to conditions promoting cytosine deamination. The extent of conversion of 5-hmC to CMS was estimated to be 99.7%. Sequencing of PCR products showed that neither 5-mC nor 5-hmC undergo C-to-T transitions after bisulfite treatment, confirming that these two modified cytosine species are indistinguishable by the bisulfite technique. DNA in which CMS constituted a large fraction of all bases (28/201) was much less efficiently amplified than DNA in which those bases were 5-mC or uracil (the latter produced by cytosine deamination). Using a series of primer extension experiments, we traced the inefficient amplification of CMS-containing DNA to stalling of Taq polymerase at sites of CMS modification, especially when two CMS bases were either adjacent to one another or separated by 1-2 nucleotides.

Conclusions: We have confirmed that the widely used bisulfite sequencing technique does not distinguish between 5-mC and 5-hmC. Moreover, we show that CMS, the product of bisulfite conversion of 5-hmC, tends to stall DNA polymerases during PCR, suggesting that densely hydroxymethylated regions of DNA may be underrepresented in quantitative methylation analyses.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008888PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811190PMC
January 2010

LC/MS analysis of cellular RNA reveals NAD-linked RNA.

Nat Chem Biol 2009 Dec 11;5(12):879-81. Epub 2009 Oct 11.

Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.

We developed a general method to detect cellular small molecule-RNA conjugates that does not rely on the reactivity of the small molecule. This technique revealed NAD-linked RNA in Escherichia coli and Streptomyces venezuelae. Subsequent characterization showed that NAD is a 5' modification of RNA, cannot be installed in vitro through aberrant transcriptional initiation, is only found among smaller cellular RNAs and is present at a surprisingly high abundance of approximately 3,000 copies per cell.
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http://dx.doi.org/10.1038/nchembio.235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2842606PMC
December 2009

A chemical screen for biological small molecule-RNA conjugates reveals CoA-linked RNA.

Proc Natl Acad Sci U S A 2009 May 28;106(19):7768-73. Epub 2009 Apr 28.

Howard Hughes Medical Institute and Department of Chemistry and Chemical Biology, 12 Oxford Street, Harvard University, Cambridge, MA 02138, USA.

Compared with the rapidly expanding set of known biological roles for RNA, the known chemical diversity of cellular RNA has remained limited primarily to canonical RNA, 3'-aminoacylated tRNAs, nucleobase-modified RNAs, and 5'-capped mRNAs in eukaryotes. We developed two methods to detect in a broad manner chemically labile cellular small molecule-RNA conjugates. The methods were validated by the detection of known tRNA and rRNA modifications. The first method analyzes small molecules cleaved from RNA by base or nucleophile treatment. Application to Escherichia coli and Streptomyces venezuelae RNA revealed an RNA-linked hydroxyfuranone or succinyl ester group, in addition to a number of other putative small molecule-RNA conjugates not previously reported. The second method analyzes nuclease-generated mononucleotides before and after treatment with base or nucleophile and also revealed a number of new putative small molecule-RNA conjugates, including 3'-dephospho-CoA and its succinyl-, acetyl-, and methylmalonyl-thioester derivatives. Subsequent experiments established that these CoA species are attached to E. coli and S. venezuelae RNA at the 5' terminus. CoA-linked RNA cannot be generated through aberrant transcriptional initiation by E. coli RNA polymerase in vitro, and CoA-linked RNA in E. coli is only found among smaller (approximately < 200 nucleotide) RNAs that have yet to be identified. These results provide examples of small molecule-RNA conjugates and suggest that the chemical diversity of cellular RNA may be greater than previously understood.
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http://dx.doi.org/10.1073/pnas.0900528106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674394PMC
May 2009

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1.

Science 2009 May 16;324(5929):930-5. Epub 2009 Apr 16.

Department of Pathology, Harvard Medical School and Immune Disease Institute, 200 Longwood Avenue, Boston, MA 02115, USA.

DNA cytosine methylation is crucial for retrotransposon silencing and mammalian development. In a computational search for enzymes that could modify 5-methylcytosine (5mC), we identified TET proteins as mammalian homologs of the trypanosome proteins JBP1 and JBP2, which have been proposed to oxidize the 5-methyl group of thymine. We show here that TET1, a fusion partner of the MLL gene in acute myeloid leukemia, is a 2-oxoglutarate (2OG)- and Fe(II)-dependent enzyme that catalyzes conversion of 5mC to 5-hydroxymethylcytosine (hmC) in cultured cells and in vitro. hmC is present in the genome of mouse embryonic stem cells, and hmC levels decrease upon RNA interference-mediated depletion of TET1. Thus, TET proteins have potential roles in epigenetic regulation through modification of 5mC to hmC.
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http://dx.doi.org/10.1126/science.1170116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2715015PMC
May 2009

Translation of DNA into a library of 13,000 synthetic small-molecule macrocycles suitable for in vitro selection.

J Am Chem Soc 2008 Nov 29;130(46):15611-26. Epub 2008 Oct 29.

Howard Hughes Medical Institute and the Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

DNA-templated organic synthesis enables the translation, selection, and amplification of DNA sequences encoding synthetic small-molecule libraries. Previously we described the DNA-templated multistep synthesis and model in vitro selection of a pilot library of 65 macrocycles. In this work, we report several key developments that enable the DNA-templated synthesis of much larger (>10,000-membered) small-molecule libraries. We developed and validated a capping-based approach to DNA-templated library synthesis that increases final product yields, simplifies the structure and preparation of reagents, and reduces the number of required manipulations. To expand the size and structural diversity of the macrocycle library, we augmented the number of building blocks in each DNA-templated step from 4 to 12, selected 8 different starting scaffolds which result in 4 macrocycle ring sizes and 2 building-block orientations, and confirmed the ability of the 36 building blocks and 8 scaffolds to generate DNA-templated macrocycle products. We computationally generated and experimentally validated an expanded set of codons sufficient to support 1728 combinations of step 1, step 2, and step 3 building blocks. Finally, we developed new high-resolution LC/MS analysis methods to assess the quality of large DNA-templated small-molecule libraries. Integrating these four developments, we executed the translation of 13,824 DNA templates into their corresponding small-molecule macrocycles. Analysis of the resulting libraries is consistent with excellent (>90%) representation of desired macrocycle products and a stringent test of sequence specificity suggests a high degree of sequence fidelity during translation. The quality and structural diversity of this expanded DNA-templated library provides a rich starting point for the discovery of functional synthetic small-molecule macrocycles.
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http://dx.doi.org/10.1021/ja805649fDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648815PMC
November 2008

Construction of SH-EP1-alpha4beta2-hAPP695 cell line and effects of nicotinic agonists on beta-amyloid in the cells.

Cell Mol Neurobiol 2008 Jan 3;28(1):103-12. Epub 2007 Oct 3.

School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.

(1) Nicotinic acetylcholine receptors in central nervous system are thought to be new targets for Alzheimer's disease. However, the most involved nicotinic receptor subtype in Alzheimer's disease is unclear. alpha4beta2 receptor is the most widely spread subtype in brain, involving in several important aspects of cognitive and other functions. We constructed cell line by transfecting human amyloid precursor protein (695) gene into SH-EP1 cells which have been transfected with human nicotinic receptor alpha4 subunit and beta2 subunit gene, to observe effects of alpha4beta2 receptors activation on beta-amyloid, expecting to provide a new cell line for drug screening and research purpose. (2) Liposome transfection was used to express human amyloid precursor protein (695) gene in SH-EP1-alpha4beta2 cells. Function of the transfected alpha4beta2 receptors was tested by patch clamp. Effects of nicotine and epibatidine (selective alpha4beta2 nicotinic receptor agonist) on beta-amyloid were detected by Western blot and ELISA. Effects of nicotine and epibatidine on amyloid precursor protein (695) mRNA level were measured using real-time PCR. (3) Human amyloid precursor protein (695) gene was stably expressed in SH-EP1-alpha4beta2 cells; Nicotine (1 muM) and epibatidine (0.1 muM) decreased intracellular and secreted beta-amyloid in the cells; and activation of alpha4beta2 receptors did not affect amyloid precursor protein (695) mRNA level. (4) These results suggest that the constructed cell line, expressing both amyloid precursor protein (695) gene and human nicotinic receptor alpha4 subunit and beta2 subunit gene, might be useful for screening specific nicotinic receptor agonists against Alzheimer's disease. Alteration of Abeta level induced by activation of alpha4beta2 nAChR in our study might occur at a post-translational level.
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http://dx.doi.org/10.1007/s10571-007-9218-1DOI Listing
January 2008

Studies of neutral and ionic CuAr and CuKr van der Waals complexes.

J Phys Chem A 2005 Nov;109(44):10077-83

Dartmouth College, Department of Chemistry, Hanover, New Hampshire 03755, USA.

Ab initio calculations of the interaction potential between Cu (or Cu(+)) and Ar (or Kr) have been carried out. A range of theoretical methods, including Hartree-Fock (HF), Moeller-Plesset perturbation methods to second order (MP2), and single and double excitation coupled cluster methods, with the perturbational effect of triple excitations (CCSD(T)), were employed with relativistic pseudopotential basis sets. The effects of bond functions and diffuse polarization (f, g, h) functions were tested on the calculation of the weak intermolecular interactions. Potential energy curves were obtained for all four complexes by MP2 and CCSD(T) methods. For CuKr, even with the largest basis set used, a binding energy that is only 37% of the measured value was obtained. Possible reasons for the disagreement are discussed.
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http://dx.doi.org/10.1021/jp050211wDOI Listing
November 2005

Density functional theory study of the Jahn-Teller effect and spin-orbit coupling for copper and gold trimers.

J Phys Chem A 2005 Jan;109(3):512-9

Dartmouth College, Department of Chemistry, Hanover, New Hampshire 03755, USA.

The Born-Oppenheimer potential energy hypersurfaces of copper and gold trimers were calculated using density functional theory with an analytic potential. The calculated Jahn-Teller distortion energies, pseudorotation barriers, dissociation, and isomerization energies for the two trimers are discussed. Global minima from the surfaces were optimized using the density functional theory method as well as the coupled cluster-singles-doubles-with-triples energies technique. The agreement of the optimized structures with the analytic potential was very good. The Mulliken population analysis compared favorably with the experimental electron spin resonance results. Spin-orbit coupling was subsequently included and the effect was significant for gold, but negligible for copper. The spin-orbit effect suppressed the Jahn-Teller distortion of the gold trimer, and the potential surface with the spin-orbit effect included was also obtained. The spin-orbit splitting for the D(3h) geometry of the gold trimer was in excellent agreement with the most recent infrared spectroscopic results.
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http://dx.doi.org/10.1021/jp040502pDOI Listing
January 2005