bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative RT‐PCR analysis of estrogen receptor gene expression in laser microdissected prostate cancer tissue
Authors: Walton Thomas J. , Li Geng , McCulloch Thomas A. , Seth Rashmi , Powe Desmond G. , Bishop Michael C. , Rees Robert C. 
Published: February 2009

AbstractBACKGROUNDReal‐time quantitative RT‐PCR analysis of laser microdissected tissue is considered the most accurate technique for determining tissue gene expression. The discovery of estrogen receptor beta (ERβ) has focussed renewed interest on the role of estrogen receptors in prostate cancer, yet few studies have utilized the technique to analyze estrogen receptor gene expression in prostate cancer.METHODSFresh tissue was obtained from 11 radical prostatectomy specimens and from 6 patients with benign prostate hyperplasia. Pure populations of benign and malignant prostate epithelium were laser microdissected, followed by RNA isolation and electrophoresis. Quantitative RT‐PCR was performed using primers for androgen receptor (AR), estrogen receptor beta (ERβ), estrogen receptor alpha (ERα), progesterone receptor (PGR) and prostate specific antigen (PSA), with normalization to two housekeeping genes. Differences in gene expression were analyzed using the Mann–Whitney U‐test. Correlation coefficients were analyzed using Spearman's test.RESULTSSignificant positive correlations were seen when AR and AR‐dependent PSA, and ERα and ERα‐dependent PGR were compared, indicating a representative population of RNA transcripts. ERβ gene expression was significantly over‐expressed in the cancer group compared with benign controls (P < 0.01). In contrast, PGR expression was significantly down‐regulated in the cancer group (P < 0.05). There were no significant differences in AR, ERα or PSA expression between the groups. This study represents the first to show an upregulation of ERβ gene expression in laser microdissected prostate cancer specimens.CONCLUSIONSIn concert with recent studies the findings suggest differential production of ERβ splice variants, which may play important roles in the genesis of prostate cancer. Prostate 69: 810–819, 2009. © 2009 Wiley‐Liss, Inc.
Significance of preoperative HbA1c level in patients with diabetes mellitus and clinically localized prostate cancer
Authors: Hong Sung Kyu , Lee Seung Tae , Kim Sung Soo , Min Kyung Eun , Byun Seok‐Soo , Cho Sung Yong , Choe Gheeyoung , Lee Sang Eun 
Published: February 2009

AbstractINTRODUCTIONWe investigated potential relationships of history of diabetes mellitus (DM) and glycemic control, represented by hemoglobin A1c (HbA1c) level, with characteristics of tumor among patients who received radical prostatectomy (RP) for clinically localized prostate cancer.METHODSWe reviewed data of 740 patients who underwent RP for clinically localized prostate cancer between 2004 and 2008 without receiving preoperative radiation or hormonal treatment. Univariate and multivariate logistic regression analyses addressed the associations of history of DM and HbA1c level with known prognostic variables of prostate cancer.RESULTSNo significant differences were observed in various preoperative and pathological parameters between those with (n = 89) and without DM (n = 651). When only the subjects with DM were divided into two groups (group 1 and 2) according to HbA1c level (<6.5% vs. ≥6.5%), group 2 demonstrated significantly higher rate of extraprostatic extension of tumor (P = 0.043) and high (≥7) pathological Gleason score (P = 0.005) than group 1. Also among those with DM, HbA1c level was observed to be an independent predictor for high pathologic Gleason score (P = 0.010) and extraprostatic extension of tumor (P = 0.035), respectively in multivariate analyses.CONCLUSIONAlthough simple history of having DM may not be a significant factor regarding aggressiveness of clinically localized prostate cancer, the glycemic control, as represented by HbA1c level, may be a useful preoperative predictor of aggressive tumor profile among patients with DM who are also diagnosed with clinically localized prostate cancer. Prostate 69: 820–826, 2009. © 2009 Wiley‐Liss, Inc.
Structural comparison of chromosomal and exogenous dihydrofolate reductase from Staphylococcus aureus in complex with the potent inhibitor trimethoprim
Authors: Heaslet Holly , Harris Melissa , Fahnoe Kelly , Sarver Ronald , Putz Henry , Chang Jeanne , Subramanyam Chakrapani , Barreiro Gabriela , Miller J. Richard 
Published: February 2009

AbstractDihydrofolate reductase (DHFR) is the enzyme responsible for the NADPH‐dependent reduction of 5,6‐dihydrofolate to 5,6,7,8‐tetrahydrofolate, an essential cofactor in the synthesis of purines, thymidylate, methionine, and other key metabolites. Because of its importance in multiple cellular functions, DHFR has been the subject of much research targeting the enzyme with anticancer, antibacterial, and antimicrobial agents. Clinically used compounds targeting DHFR include methotrexate for the treatment of cancer and diaminopyrimidines (DAPs) such as trimethoprim (TMP) for the treatment of bacterial infections. DAP inhibitors of DHFR have been used clinically for >30 years and resistance to these agents has become widespread. Methicillin‐resistant Staphylococcus aureus (MRSA), the causative agent of many serious nosocomial and community acquired infections, and other gram‐positive organisms can show resistance to DAPs through mutation of the chromosomal gene or acquisition of an alternative DHFR termed “S1 DHFR.” To develop new therapies for health threats such as MRSA, it is important to understand the molecular basis of DAP resistance. Here, we report the crystal structure of the wild‐type chromosomal DHFR from S. aureus in complex with NADPH and TMP. We have also solved the structure of the exogenous, TMP resistant S1 DHFR, apo and in complex with TMP. The structural and thermodynamic data point to important molecular differences between the two enzymes that lead to dramatically reduced affinity of DAPs to S1 DHFR. These differences in enzyme binding affinity translate into reduced antibacterial activity against strains of S. aureus that express S1 DHFR. Proteins 2009. © 2009 Wiley‐Liss, Inc.
An all‐atom knowledge‐based energy function for protein‐DNA threading, docking decoy discrimination, and prediction of transcription‐factor binding profiles
Authors: Xu Beisi , Yang Yuedong , Liang Haojun , Zhou Yaoqi 
Published: February 2009

AbstractHow to make an accurate representation of protein‐DNA interaction by an energy function is a long‐standing unsolved problem in structural biology. Here, we modified a statistical potential based on the distance‐scaled, finite ideal‐gas reference state so that it is optimized for protein‐DNA interactions. The changes include a volume‐fraction correction to account for unmixable atom types in proteins and DNA in addition to the usage of a low‐count correction, residue/base‐specific atom types, and a shorter cutoff distance for protein‐DNA interactions. The new statistical energy functions are tested in threading and docking decoy discriminations and prediction of protein‐DNA binding affinities and transcription‐factor binding profiles. The results indicate that new proposed energy functions are among the best in existing energy functions for protein‐DNA interactions. The new energy functions are available as a web‐server called DDNA 2.0 at http://sparks.informatics.iupui.edu. The server version was trained by the entire 212 protein‐DNA complexes. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry
Authors: Sharma Seema , Zheng Haiyan , Huang Yuanpeng J. , Ertekin Asli , Hamuro Yoshitomo , Rossi Paolo , Tejero Roberto , Acton Thomas B. , Xiao Rong , Jiang Mei , Zhao Li , Ma Li‐Chung , Swapna G. V. T. , Aramini James M. , Montelione Gaetano T. 
Published: February 2009

AbstractDisordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of 1H/2H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using 1H‐15N HSQC and 1H‐15N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.
The molecular evolution of HIV‐1 protease simulated at atomic detail
Authors: Tiana G. , Broglia R. A. 
Published: February 2009

AbstractProgress in understanding protein folding allows to simulate, with atomic detail, the evolution of amino‐acid sequences folding to a given native conformation. A particularly attractive example is the HIV‐1 protease, main target of therapies to fight AIDS, which under drug pressure is able to develop resistance within few months from the starting of therapy. By comparing the results of simulations of the evolution of the protease with the corresponding proteomic data, one can approximately determine the value of the associated evolution pressure under which the enzyme has become and, as a consequence, map out the energy landscape in sequence space of the HIV‐1 protease. It is found that there are several families of sequences folding to the native conformations of the enzyme. Each of these families are characterized by different sets of highly conserved (“hot”) amino acids which play a critical role in the folding and stability of the protease. There are two main possibilities for the virus to move from one family to a different one: (a) in a single generation, through the concerted mutations of the hot amino acids, a highly unlikely event, (b) through a folding path (if it exists), again a very improbable event. In fact, the number of generations needed by the virus to change stepwise its sequence from one family to another is astronomically large. These results point to the “hot” segments of the protease as promising targets for a nonconventional inhibition strategy, likely not to create resistance. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Molecular dynamics studies of the P pilus rod subunit PapA
Authors: Vitagliano Luigi , Ruggiero Alessia , Pedone Carlo , Berisio Rita 
Published: February 2009

AbstractAdhesion of uropathogenic Escherichia coli to host tissues is mediated by pili, which extend from the outer cell membrane of the bacterium. Here we report molecular dynamics (MD) characterizations of the major constituent of P pili from the uropathogenic E. coli, PapA, in unliganded state and in complex with the G1 strand of the chaperone PapD. To mimic the PapA response to the gradual dissociation of the PapD G1 strand and to evaluate the role of PapA chaperone recognition sites, we also carried out MD simulations of complexes of PapA with fragments of PapD G1 strand, that leave either the P4 or both P3 and P4 sites unoccupied. Data on the unbound form of PapA indicate that, upon release of the chaperone, PapA evolves toward compact states that are likely not prone to subunit–subunit association. In line with recent experimental reports, this finding implies that chaperone release and subunit–subunit association must be concerted. Our data also indicated that the gradual unbinding of the chaperone from the PapA groove has increasingly strong structural consequences. Indeed, the release of the chaperone from the site P4, which is closest to the initiation site (P5), does not have dramatic effects on the domain structure, whereas its release from both the P4 and the adjacent P3 sites induces a quick structural transition toward a collapsed state, where the subunit groove is obstructed. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
N‐(ureidoethyl)amides of cyclic enkephalin analogs
Authors: Ciszewska Małgorzata , Kwasiborska Maria , Nowakowski Michał , Oleszczuk Marta , Wójcik Jacek , Chung Nga N. , Schiller Peter W. , Izdebski Jan 
Published: February 2009

AbstractNovel N‐(ureidoethyl)amides of cyclic enkephalin analogs have been synthesized. The p‐nitrophenyl carbamate of 1‐Boc‐1,2‐diaminoethane was coupled with 4‐methylbenzhydrylamine (MBHA) resin. The Boc group was removed by treatment with HCl/dioxane, and the peptide chain was assembled using Boc strategy. For deprotection of amino function, HCl/dioxane was used. D‐Lys or D‐Orn were incorporated in position 2, and the side chains of Lys, Orn, Dab, or Dap in position 5 were protected with Fmoc group. Side chain protection was removed by treatment with 55% piperidine in DMF, and cyclization was achieved by treatment with bis‐(4‐nitrophenyl)carbonate to form a urea bridge. The peptide was cleaved from the resin by treatment with 45% TFA in DCM. The peptides were tested in the guinea‐pig ileum (GPI) and mouse vas deferens (MVD) assays. Divers opioid activities were observed, depending on the size of the ring. In comparison with [Leu5]enkephalin, all peptides were more active in the GPI assay (between 125 and 12 times), and some of them were also more potent in the MVD assay. The conformational propensities of each peptide were determined using the EDMC method in conjunction with NMR experiments. This approach allows treating the dynamical behavior of small peptides properly. The results were compared with those obtained previously for corresponding nonsubstituted amides and are in agreement with the biologically active conformation proposed by us earlier. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Antiestrogenic and anticancer activities of peptides derived from the active site of alpha‐fetoprotein
Authors: Joseph Leroy C. , Bennett James A. , Kirschner Karl N. , Shields George C. , Hughes John , Lostritto Nicole , Jacobson Herbert I. , Andersen Thomas T. 
Published: February 2009

AbstractCyclo[EKTOVNOGN] (AFPep), a cyclic 9‐amino acid peptide derived from the active site of alpha‐fetoprotein, has been shown to prevent carcinogen‐induced mammary cancer in rats and inhibit the growth of ER+ human breast cancer xenografts in mice. Recently, studies using replica exchange molecular dynamics predicted that the TOVN region of AFPep might form a dynamically stable putative Type I beta‐turn, and thus be biologically active without additional amino acids. The studies presented in this paper were performed to determine whether TOVN and other small analogs of AFPep would inhibit estrogen‐stimulated cancer growth and exhibit a broad effective‐dose range. These peptides contained nine or fewer amino acids, and were designed to bracket or include the putative pharmacophoric region (TOVN) of AFPep. Biological activities of these peptides were evaluated using an immature mouse uterine growth inhibition assay, a T47D breast cancer cell proliferation assay, and an MCF‐7 breast cancer xenograft assay. TOVN had very weak antiestrogenic activity in comparison to AFPep's activity, whereas TOVNO had antiestrogenic and anticancer activities similar to AFPep. OVNO, which does not form a putative Type I beta‐turn, had virtually no antiestrogenic and anticancer activities. A putative proteolytic cleavage product of AFPep, TOVNOGNEK, significantly inhibited E2‐stimulated growth in vivo and in vitro over a wider dose range than AFPep or TOVNO. We conclude that TOVNO has anticancer potential, that TOVNOGNEK is as effective as AFPep in suppressing growth of human breast cancer cells, and that it does so over a broader effective‐dose range. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Thermodynamics of partitioning of substance P in isotropic bicelles
Authors: Kim Chul , Baek Seung Bin , Kim Do Hun , Lim Sung Chul , Lee Hyeong Ju , Lee Hee Cheon 
Published: February 2009

AbstractThe temperature dependence of the partition of a neuropeptide, substance P (SP), in isotropic (q = 0.5) bicelles was investigated by using pulsed field gradient NMR diffusion technique. The partition coefficient decreases as the temperature is increased from 295 to 325 K, indicating a favorable (negative) enthalpy change upon partitioning of the peptide. Thermodynamic analysis of the data shows that the partitioning of SP at 300 K is driven by the enthalpic term (ΔH) with the value of − 4.03 kcal mol−1, while it is opposed by the entropic term (−TΔS) by approximately 1.28 kcal mol−1 with a small negative change in heat capacity (ΔCp). The enthalpy‐driven process for the partition of SP in bicelles is the same as in dodecylphosphocholine (DPC) micelles, however, the negative entropy change in bicelles of flat bilayer surface is in sharp contrast with the positive entropy change in DPC micelles of highly curved surface, indicating that the curvature of the membrane surface might play a significant role in the partitioning of peptides. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Synthetic diamond films as a platform material for label‐free protein sensors
Authors: Bijnens Nathalie , Vermeeren Veronique , Daenen Michaël , Grieten Lars , Haenen Ken , Wenmackers Sylvia , Williams Oliver A. , Ameloot Marcel , vandeVen Martin , Michiels Luc , Wagner Patrick 
Published: February 2009

AbstractIn the framework of developing a fast and label‐free immunosensor for C‐reactive protein (CRP) detection, H‐terminated nanocrystalline diamond (NCD) was functionalised with anti‐CRP antibodies that were physically adsorbed to the surface. Impedance spectroscopy was used to electronically detect real‐time CRP recognition. Different impedance behaviours were observed after CRP addition as compared to after FITC‐labelled ssDNA addition at low (100 Hz) as well as at high frequencies (1 MHz). Physical interpretations of the observed impedance changes were obtained by fitting the data to an equivalent electrical circuit. Concentrations of 1 μM CRP were recognised with a reaction time of 30 minutes. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
8 W single‐emitter InGaN laser in pulsed operation
Authors: Brüninghoff Stefanie , Eichler Christoph , Tautz Sönke , Lell Alfred , Sabathil Matthias , Lutgen Stephan , Strauß Uwe 
Published: February 2009

AbstractWe present the investigation of an optimized epitaxial layer structure in order to reach high optical output powers of several watts. The influence of an interlayer, which is located between the multiple quantum well layers and the electron blocking layer, is analysed carefully. For high current densities the leakage current density increases with increasing interlayer thickness. Correlating the leakage current density with the injection efficiency it is found that by decreasing the interlayer thickness constant injection efficiency for high current regions can be reached. This is essential for a linear laser characteristic up to high optical output power levels. Further enhancement can be achieved by enlarging the total waveguiding layer structure. As a result the optical power density in the resonator was decreased. With these improvements threshold current density and slope efficiency of 2.7 kA/cm2 and 2.1 W/A can be achieved. The optical output power is increased to 8.7 W for a 20 μm broad single‐emitter ridge‐waveguide laser in pulsed operation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Carbonization of porous silicon optical gas sensors for enhanced stability and sensitivity
Authors: Torres‐Costa V. , Salonen J. , Jalkanen T. M. , Lehto V.‐P. , Martín‐Palma R. J. , Martínez‐Duart J. M. 
Published: February 2009

AbstractNanostructured porous silicon (PS) optical filters have been widely proposed for their use in biological and chemical sensing applications. Porous silicon, however, presents a reactive surface that must be adequately passivated in order to achieve the required chemical stability mandatory for sensing applications. In the present work, thermal carbonization by acetylene decomposition (TCAD) is shown to provide effective passivation of PS internal surface, as well as an enhancement of the device's sensitivity to certain species. Moreover, it is shown that the TCAD process, as opposed to more common oxidation treatments, has only minor effects on the optical properties of PS. Thus, the optical performance of PS interference filters is preserved after the carbonization process. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Terahertz transmission through p+ porous silicon membranes
Authors: Lo Shu‐Zee A. , Rossi Andrea M. , Murphy Thomas E. 
Published: February 2009

AbstractWe report an experimental measurement of far infrared dielectric properties of p+‐doped free‐standing porous silicon membranes, characterized using terahertz time‐domain spectroscopy. Freshly fabricated hydrogen‐terminated porous silicon samples exhibited significant absorption in the terahertz regime, and the absorption was observed to slowly drift in response to the surrounding environment and the duration of illumination. Samples that are partially oxidized, either by age or through thermal oxidation in an oven, become almost transparent in the terahertz spectral regime, and the dielectric properties stabilize to a constant value. The partially‐oxidized porous silicon samples are observed to have an absorption coefficient of approximately 2 cm–1 over the range of 0–2 THz, which corresponds to an effective resistivity of 35 ± 9 Ω cm, approximately four orders of magnitude higher than that of the crystalline silicon from which they were formed. Spectral transmission measurements further confirm that p+ porous silicon has no significant absorption peaks or other spectral variation in the 0–2 THz regime. These findings suggest that p+ porous silicon could be a useful material for fabricating future THz devices. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Biomagnetic field detection using very high sensitivity magnetoimpedance sensors for medical applications
Authors: Uchiyama Tsuyoshi , Nakayama Shinsuke , Mohri Kaneo , Bushida Kenichi 
Published: February 2009

AbstractThis paper demonstrates the performance of magnetoimpedance (MI) sensors for biomagnetic field recording. The rms noise of an amorphous wire MI sensor with 600 turns of pick‐up coil was estimated as approximately 3 pT/Hz1/2 at 1 Hz. Here, we demonstrate that this sensitivity is enough to clearly detect magnetic cardiogram signals. We also measured the biomagnetic field around a smooth muscle tissue sample taken from a guinea‐pig. We discovered that the magnetic‐field waveform of a small tissue sample is similar to the voltage waveform measured by a microelectrode array in a smooth muscle sheet sample. The results suggest that the localized biomagnetic field generated by smooth muscle cells can be detected by an MI sensor. We concluded that the MI sensor is a promising device for use as a noninvasive tool to test cell activity or function through magnetic‐field measurement. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)