bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative experimental determination of primer–dimer formation risk by free‐solution conjugate electrophoresis
Authors: Desmarais Samantha M. , Leitner Thomas , Barron Annelise E. 
Published: January 2012

AbstractDNA barcodes are short, unique ssDNA primers that “mark” individual biomolecules. To gain better understanding of biophysical parameters constraining primer–dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag‐tag‐DNA conjugates to quantify dimerization risk between primer‐barcode pairs. Results obtained with this unique free‐solution conjugate electrophoresis approach are useful as quantitatively precise input data to parameterize computation models of dimerization risk. A set of fluorescently labeled, model primer‐barcode conjugates were designed with complementary regions of differing lengths to quantify heterodimerization as a function of temperature. Primer–dimer cases comprised two 30‐mer primers, one of which was covalently conjugated to a lab‐made, chemically synthesized poly‐N‐methoxyethylglycine drag‐tag, which reduced electrophoretic mobility of ssDNA to distinguish it from ds primer–dimers. The drag‐tags also provided a shift in mobility for the dsDNA species, which allowed us to quantitate primer–dimer formation. In the experimental studies, pairs of oligonucleotide primer barcodes with fully or partially complementary sequences were annealed, and then separated by free‐solution conjugate CE at different temperatures, to assess effects on primer–dimer formation. When less than 30 out of 30 base‐pairs were bonded, dimerization was inversely correlated to temperature. Dimerization occurred when more than 15 consecutive base‐pairs formed, yet non‐consecutive base‐pairs did not create stable dimers even when 20 out of 30 possible base‐pairs bonded. The use of free‐solution electrophoresis in combination with a peptoid drag‐tag and different fluorophores enabled precise separation of short DNA fragments to establish a new mobility shift assay for detection of primer–dimer formation.
Effect of the cytochrome P450 2D6*10 allele on risperidone metabolism in Japanese psychiatric patients
Authors: Suzuki Yutaro , Fukui Naoki , Tsuneyama Nobuto , Watanabe Junzo , Ono Shin , Sugai Takuro , Saito Mami , Inoue Yoshimasa , Someya Toshiyuki 
Published: January 2012

ObjectiveThe sum of the serum levels of risperidone (RIS) and 9‐hydroxyrisperidone (9‐OH‐RIS), which is the active moiety serum level, could be important for estimating the clinical effects of RIS. However, there have been no consistent results reported about the relationship between cytochrome P450 (CYP) 2D6*10 allele and plasma 9‐OH‐RIS or active moiety levels. We investigated the effect of the number of CYP2D6*10 alleles on steady‐state plasma RIS, 9‐OH‐RIS, and active moiety levels in Japanese patients.MethodsSteady‐state plasma RIS, 9‐OH‐RIS, and active moiety levels were measured in 64 patients treated with an average dosage of 4.6 mg/day.ResultsThe number of CYP2D6*10 alleles significantly affected dose‐corrected plasma RIS levels (p = 0.001), and the median concentrations in ng/ml/mg were 0.94 (0 allele) vs. 1.73 (1 allele) vs. 3.05 (2 alleles). The number of CYP2D6*10 alleles did not affect plasma 9‐OH‐RIS or active moiety levels.ConclusionThe present study shows that the number of CYP2D6*10 alleles affected plasma RIS levels but not plasma 9‐OH‐RIS and plasma active moiety levels. Because the plasma active moiety levels can influence antipsychotic effects or side effects, the genetic screening of the CYP2D6*10 allele for RIS in Asian populations may not be clinically important. Copyright © 2012 John Wiley & Sons, Ltd.
Systemic blockade of the hyaluronan receptor for endocytosis prevents lymph node metastasis of prostate cancer
Authors: Simpson Melanie A. , Weigel Janet A. , Weigel Paul H. 
Published: January 2012

AbstractTumor progression and metastasis are promoted by the remodeling of organized tissue architecture and engagement of molecular interactions that support tumor cell passage through endothelial barriers. Prostate tumor cells that secrete and turn over excessive quantities of pericellular hyaluronan (HA) exhibit accelerated growth kinetics and spontaneous lymph node metastasis in mice. The HA receptor for endocytosis (HARE) is an endocytic clearance receptor for HA in the liver that is also highly expressed in sinusoidal endothelium of lymph nodes and bone marrow, which are frequent sites of prostate cancer metastasis. In our study, we tested the hypothesis that HARE can act as an endothelial receptor for metastatic tumor cells with pericellular HA. In an orthotopic mouse model of prostate cancer, we delivered a monoclonal antibody against HARE that specifically blocks HA binding and internalization. This treatment fully blocked the formation of metastatic tumors in lymph nodes. No effects on primary tumor growth were observed and the antibody did not induce toxic outcomes in any other tissue. Our results implicate HARE for the first time in potentiation of tumor metastasis and suggest a novel mechanism by which tumor cell‐associated HA could promote tissue‐specific dissemination. “Published 2012 Wiley Periodicals, Inc. This article is a US Government work, and, as such, is in the public domain in the United States of America.”
Low values of 5‐hydroxymethylcytosine (5hmC), the “sixth base,” are associated with anaplasia in human brain tumors
Authors: Kraus Theo F.J. , Globisch Daniel , Wagner Mirko , Eigenbrod Sabina , Widmann David , Münzel Martin , Müller Markus , Pfaffeneder Toni , Hackner Benjamin , Feiden Wolfgang , Schüller Ulrich , Carell Thomas , Kretzschmar Hans A. 
Published: January 2012

Abstract5‐Methylcytosine (5mC) in genomic DNA has important epigenetic functions in embryonic development and tumor biology. 5‐Hydroxymethylcytosine (5hmC) is generated from 5mC by the action of the TET (Ten‐Eleven‐Translocation) enzymes and may be an intermediate to further oxidation and finally demethylation of 5mC. We have used immunohistochemistry (IHC) and isotope‐based liquid chromatography mass spectrometry (LC‐MS) to investigate the presence and distribution of 5hmC in human brain and brain tumors. In the normal adult brain, IHC identified 61.5% 5hmC positive cells in the cortex and 32.4% 5hmC in white matter (WM) areas. In tumors, positive staining of cells ranged from 1.1% in glioblastomas (GBMs) (WHO Grade IV) to 8.9% in Grade I gliomas (pilocytic astrocytomas). In the normal adult human brain, LC‐MS also showed highest values in cortical areas (1.17% 5hmC/dG [deoxyguanosine]), in the cerebral WM we measured around 0.70% 5hmC/dG. 5hmC levels were related to tumor differentiation, ranging from lowest values of 0.078% 5hmC/dG in GBMs (WHO Grade IV) to 0.24% 5hmC/dG in WHO Grade II diffuse astrocytomas. 5hmC measurements were unrelated to 5mC values. We find that the number of 5hmC positive cells and the amount of 5hmC/dG in the genome that has been proposed to be related to pluripotency and lineage commitment in embryonic stem cells is also associated with brain tumor differentiation and anaplasia.
Evaluation of the hybrid capture 2 assay for detecting anal high‐grade dysplasia
Authors: Goldstone Stephen E. , Lowe Brian , Rothmann Thomas , Nazarenko Irina 
Published: January 2012

AbstractHybrid Capture 2 (HC2) Human Papillomavirus (HPV) DNA Test® is FDA approved and is a proven aid in detecting HPV infections of the cervix and as an aid in diagnosing, with cytology, cervical disease. A prospective feasibility study was conducted to determine if HC2 testing has utility when screening for high‐grade anal dysplasia (AIN2+). We enrolled 298 patients (45% HIV+) who had AIN2+ screening with cytology, histology and HC2 testing for two specimens: a swab into liquid‐based cytology medium and either a swab or a brush collection in specimen transport medium (STM). High‐resolution anoscopy was performed on all patients with biopsy of AIN2+ suspicious lesions. Cytology was benign (42%), atypical squamous cells of undetermined significance (30%), low‐grade squamous intraepithelial lesion (18%), high‐grade squamous intraepithelial lesion (1%), ASCUS possibly high‐grade dysplasia (1.7%) and nondiagnostic (7%) and 36% had AIN2+ histology. Sensitivity and specificity for predicting AIN2+ histology for any abnormal cytology were 77 and 52%, whereas HC2 sensitivity and specificity were 91 and 40% (p = 0.005 for sensitivity), respectively. There was no significant difference in HC2 sensitivity or specificity between brush and swab or STM and residual cells from cytology. AIN2+ was found in 20% of patients with benign cytology. Only nine AIN2+ specimens were HC2−. This prospective study indicates that HC2 may be useful when screening for anal dysplasia; however, a larger study is recommended.
Percutaneous absorption in diseased skin: an overview
Authors: Chiang Audris , Tudela Emilie , Maibach Howard I. 
Published: January 2012

ABSTRACTThe stratum corneum's (SC) functions include protection from external hazardous environments, prevention of water loss and regulation of body temperature. While intact skin absorption studies are abundant, studies on compromised skin permeability are less common, although products are often used to treat affected skin. We reviewed literature on percutaneous absorption through abnormal skin models. Tape stripping is used to disrupt water barrier function. Studies demonstrated that physicochemical properties influence the stripping effect: water‐soluble drugs are more affected. Abrasion did not affect absorption as much. Freezing is commonly used to preserve skin. It does not seem to modify water absorption, but still increases the penetration of compounds. Comparatively, heating the skin consistently increased percutaneous absorption. Removing SC lipids may increase percutaneous absorption of drugs. Many organic solvents are employed to delipidize. Delipidization with chloroform–methanol increased hydrophilic compound permeability, but not lipophilic. Acetone pre‐treatment enhanced hydrophilic compound penetration. More data is needed to determine influence on highly lipophilic compound penetration. Sodium lauryl sulfate (SLS) induces irritant dermatitis and is frequently used as a model. Studies revealed that SLS increases hydrophilic compound absorption, but not lipophilic. However, skin irritation with other chemicals increases lipophilic penetration as much as hydrophilic. Animal studies show that UV exposure increases percutaneous absorption whereas human studies do not. Human studies show increased penetration in psoriatic and atopic dermatitis skin. The data summarized here begin to characterize flux alteration associated with damaged skin. Understanding the degree of alteration requires interpretation of involved conditions and the enlarging of our database to a more complete physicochemical spectrum. Copyright © 2012 John Wiley & Sons, Ltd.
Developing in vitro reporter gene assays to assess the hormone receptor activities of chemicals frequently detected in drinking water
Authors: Sun Hong , Si Chaozong , Bian Qian , Chen Xiaodong , Chen Liansheng , Wang Xinru 
Published: January 2012

ABSTRACTThe present study intended to develop receptor‐mediated luciferase reporter gene assays to evaluate and compare the estrogen receptor (ER), androgen receptor (AR) and thyroid hormone receptor (TR) activities of target chemicals. Di‐2‐ethylhexyl‐phthalate (DEHP), chlorpyrifos (CPF), 2,4‐dichlorophenoxyacetic acid (2,4‐D) and bisphenol A (BPA) are some of the most common contaminants in drinking water and are frequently detected in China and worldwide. The chemicals were tested at concentrations of 0.1, 1, 10 and 100 times their maximum contaminant level in drinking water. The results showed that BPA possessed various activities on ER, AR and TR. DEHP and CPF could suppress 17β‐estradiol or testosterone activity with different potencies, and DEHP possessed weaker anti‐thyroid hormone activity. 2,4‐D showed no agonist or antagonist activity against these hormone receptors, but it significantly enhanced the activity of testosterone through AR. Furthermore, the mixture of DEHP and CPF exhibited stronger ER and AR antagonist activities than each single component alone, but their combined effects were less than the expected effects based on the additive model. These results implied that the transcription activation mediated by hormone receptors was the potential endocrine‐disrupting mechanism of the test chemicals. Our study also provided useful tools for evaluation of their endocrine disrupting activity. Copyright © 2012 John Wiley & Sons, Ltd.
The inhibition of hyaluronan degradation reduced pro‐inflammatory cytokines in mouse synovial fibroblasts subjected to collagen‐induced arthritis
Authors: Campo Giuseppe M. , Avenoso Angela , D'Ascola Angela , Scuruchi Michele , Prestipino Vera , Nastasi Giancarlo , Calatroni Alberto , Campo Salvatore 
Published: January 2012

AbstractHyaluronan (HA) degradation produces small oligosaccharides that are able to increase pro‐inflammatory cytokines in rheumatoid arthritis synovial fibroblasts (RASF) by activating both CD44 and the toll‐like receptor 4 (TLR‐4). CD44 and TLR‐4 stimulation in turn activate the NF‐kB that induces the production of pro‐inflammatory cytokines. Degradation of HA occurs via two mechanisms: one exerted by reactive oxygen species (ROS) and one controlled by different enzymes in particular hyaluronidases (HYALs). We aimed to investigate the effects of inhibiting HA degradation (which prevents the formation of small HA fragments) on synovial fibroblasts obtained from normal DBA/J1 mice (NSF) and on synovial fibroblasts (RASF) obtained from mice subjected to collagen induced arthritis (CIA), both fibroblast types stimulated with tumor necrosis factor alpha (TNF‐α). TNF‐α stimulation produced high mRNA expression and the related protein production of CD44 and TLR‐4 in both NSF and RASF, and activation of NF‐kB was also found in all fibroblasts. TNF‐α also up‐regulated the inflammatory cytokines, interleukin‐1beta (IL‐1beta) and interleukin‐6 (IL‐6), and other pro‐inflammatory mediators, such as matrix metalloprotease‐13 (MMP‐13), inducible nitric oxide synthase (iNOS), as well as HA levels and small HA fragment production. Treatment of RASF with antioxidants and specific HYAL1, HYAL2, and HYAL3 small interference RNA (siRNAs) significantly reduced TLR‐4 and CD44 increase in the mRNA expression and the related protein synthesis, as well as the release of inflammatory mediators up‐regulated by TNF‐α. These data suggest that the inhibition of HA degradation during arthritis may contribute to reducing TLR‐4 and CD44 activation and the inflammatory mediators response. J. Cell. Biochem. 113: 1852–1867, 2012. © 2012 Wiley Periodicals, Inc.
TGFβ‐inducible early gene‐1 (TIEG1) mutations in hypertrophic cardiomyopathy
Authors: Bos J. Martijn , Subramaniam Malayannan , Hawse John R. , Christiaans Imke , Rajamannan Nalini M. , Maleszewski Joseph J. , Edwards William D. , Wilde Arthur A.M. , Spelsberg Thomas C. , Ackerman Michael J. 
Published: January 2012

AbstractHypertrophic cardiomyopathy (HCM) is the most common heritable cardiovascular disease. A recent study showed that male KLF10‐encoded TGFβ Inducible Early Gene‐1 knock‐out mice (TIEG−/−) develop HCM with 13‐fold up‐regulation of PTTG1‐encoded pituitary tumor‐transforming gene 1. We hypothesized TIEG1 could be a novel candidate gene in the pathogenesis of genotype negative HCM in humans, possibly through a loss of its repression on PTTG1 expression. A cohort of 923 unrelated patients from two independent HCM centers was analyzed for mutations in TIEG's four translated exons using DHPLC and direct DNA‐sequencing. Site directed mutagenesis was performed to clone novel variants. The effect of TIEG1 mutations on SMAD7 and PTTG1 promoters was studied using transient transfection and luciferase‐assays. Altered expression of PTTG1 in cardiac tissue was studied by immunohistochemistry (IHC) to determine levels of PTTG1 protein in hypertrophic diseases. Six novel TIEG1 missense mutations were discovered in six patients (two males/four females, mean age at diagnosis 56.2 ± 23 years, MLVWT 20.8 ± 4 mm). Compared to WT TIEG1, five TIEG1 mutants significantly increased PTTG1 promoter function similar to TIEG1−/−‐mice. By IHC, PTTG1‐protein expression was significantly increased in multiple models of hypertrophic cardiac disease, including TIEG1‐mutation positive HCM compared to normal hearts. This is the first article to associate mutations in TIEG1 to human disease with the discovery of six novel, HCM‐associated variants. Functional assays suggest a role for PTTG1 in the pathogenesis of TIEG1‐mediated HCM. Up‐regulation of PTTG1 seems to be a common pathway in hypertrophic heart disease, including TIEG1‐mediated HCM. J. Cell. Biochem. 113: 1896–1903, 2012. © 2012 Wiley Periodicals, Inc.
Heme induced oxidative stress attenuates sirtuin1 and enhances adipogenesis in mesenchymal stem cells and mouse pre‐adipocytes
Authors: Puri Nitin , Sodhi Komal , Haarstad Michael , Kim Dong Hyun , Bohinc Steven , Foglio Eleonora , Favero Gaia , Abraham Nader G. 
Published: January 2012

AbstractPatho‐physiological conditions with high oxidative stress, such as conditions associated with increased denatured heme‐proteins, are associated with enhanced adipogenic response. This effect predominantly manifests as adipocyte hypertrophy characterized by dysfunctional, pro‐inflammatory adipocytes exhibiting reduced expression of anti‐inflammatory hormone, adiponectin. To understand how increased levels of cellular heme, a pro‐oxidant molecule, modulates adipogenesis; the following study was designed to evaluate effects of heme on adipogenesis in human mesenchymal stem cells (hMSCs) and mouse pre‐adipocytes (3T3L1). Experiments were conducted in the absence and in the presence of a superoxide dismutase (SOD) mimetic (tempol, 100 µM). Heme (10 µM) increased (P < 0.05) adipogenesis in hMSCs and mouse pre‐adipocytes, where tempol alone (100 µmol/L) attenuated adipogenesis in these cells (P < 0.05). Tempol also reversed heme‐induced increase in adipogenesis in both hMSCs and mouse pre‐adipocytes (P < 0.05). In addition, heme exposed 3T3L1 exhibited reduced (P < 0.05) expression of transcriptional regulator—sirtuin 1 (Sirt1), along with, increased (P < 0.05) expression of adipogenic markers peroxisome proliferators‐activated receptor‐gamma (PPARγ), C/EBPα, and aP2. These effects of heme were rescued (P < 0.05) in cells concurrently treated with heme and tempol (P < 0.05) and prevented in cells over‐expressing Sirt1. Taken together, our results indicate that heme‐induced oxidative stress inhibits Sirt1, thus un‐inhibiting adipogenic regulators such as PPARγ and C/EBPα; which in turn induce increased adipogenesis along with adipocyte hypertrophy in pre‐adipocytes. Anti‐oxidant induced offsetting of these effects of heme supports the role of heme‐dependent oxidative stress in mediating such events. J. Cell. Biochem. 113: 1926–1935, 2012. © 2012 Wiley Periodicals, Inc.
Adsorption of butanol from aqueous solution onto a new type of macroporous adsorption resin: Studies of adsorption isotherms and kinetics simulation
Authors: Lin Xiaoqing , Wu Jinglan , Fan Jiansheng , Qian Wenbin , Zhou Xiqun , Qian Chen , Jin Xiaohong , Wang Lili , Bai Jianxin , Ying Hanjie 
Published: January 2012

AbstractBACKGROUND: Owing to the rapid depletion of petroleum fuel, the production of bio‐butanol has attracted much attention. However, low butanol productivity severely limits its potential industrial application. It is important to establish an approach for recovering low‐concentration butanol from fermentation broth. Experiments were conducted using batch adsorption mode under different conditions of initial butanol concentration and temperature. Batch adsorption data were fitted to Langmuir and Freundlich isotherms and the macropore diffusion, pseudo‐first‐ and second‐order models for kinetic study.RESULTS: The maximum adsorption capacity of butanol onto KA‐I resin increase with increasing temperature, ranged from 139.836 to 304.397 mg g−1. The equilibrium adsorption data were well fitted by the Langmuir isotherm. The adsorption kinetics was more accurately represented by the macropore diffusion model, which also clearly predicted the intraparticle distribution of the concentration. The effective pore diffusivity (Dp) was dependent upon temperature, but independent of initial butanol concentration, and was 0.251 × 10−10, 0.73 × 10−10, 1.32 × 10−10 and 4.31 × 10−10 m2 s−1 at 283.13, 293.13, 303.13 and 310.13 K, respectively.CONCLUSION: This work demonstrates that KA‐I resin is an efficient adsorbent for the removal of butanol from aqueous solutions and available for practical applications for future in situ product recovery of butanol from ABE fermentation broth. Copyright © 2012 Society of Chemical Industry
Enhancing separation of titanium and iron by three‐liquid‐phase extraction with 1,10‐phenanthroline as additive
Authors: Xie Keng , Huang Kun , Yang Liangrong , Liu Huizhou 
Published: January 2012

AbstractBACKGROUND: A three‐liquid‐phase system (TLPS) composed of an organic solvent‐rich top phase, a polymer‐rich middle phase and a salt‐rich bottom phase is a newly emerging separation medium. Due to low affinity of the polymer‐rich phase for metals it is necessary and important to search for a suitable complexing agent that has a definite affinity for the polymer‐rich middle phase and a high selectivity for the metal ion of interest.RESULTS: Addition of 1,10‐phenanthroline (phen) is effective in enhancing the separation of titanium and iron from magnesium in the TLPS consisting of trialkylphosphine oxide (TRPO)‐PEG 2000‐(NH4)2SO4. Hydrogen‐bonding interactions between PEG 2000 and phen molecules are the driving force for anchoring tri(phen)‐iron(II) sulfate complexes in the middle phase. Under the conditions (pH = 1.5, molar ratio of phen to iron(II) = 3.4:1), nearly 86% of titanium was extracted into the top phase while 100% of iron(II) was distributed in the middle phase, without any interference between the metal species. The separation factor of titanium and iron in the upper two phases was greater than 20 000.CONCLUSIONS: A single step of extraction and separation of titanium and iron from magnesium was realized in the TRPO‐PEG 2000‐(NH4)2SO4 TLPS with phen as additive. It highlights the effectiveness of TLPS in dealing with multi‐metal solutions and suggests a potential use of TLPS in the separation of iron and other target metals. As iron is ubiquitous the separation of iron is often needed in both analytical processes and the hydrometallurgical industry. Copyright © 2012 Society of Chemical Industry
Construction of microbial cell factories for industrial bioprocesses
Authors: Sauer Michael , Mattanovich Diethard 
Published: January 2012

AbstractThe development of industrial microbial processes is gaining unprecedented momentum. Increased concern for environmental issues and the prospect of declining petroleum resources has shifted the industrial focus increasingly to microorganisms as biocatalysts. At the same time systems biology and synthetic biology supply industry and academia with new tools to design optimal microbial cell factories.Among the tools are systems biology approaches allowing the modelling of cellular networks for rational strain design, single cell analyses methods for gaining insight into population hetereogeneity, and an exciting combination of tools from structural biology and synthetic biology, permitting the catalysis of new (unnatural) enzymatic reactions or the production of new (unnatural) chemicals.This perspective article outlines recent advances and new developments within the field of microbial cell factory design. Copyright © 2012 Society of Chemical Industry