bluuebunny/crossref_metadata_2025 huggingface dataset:
A Polydiacetylene Supramolecular System That Emits Red, Green, and Blue Fluorescence
Authors: Park Eun Young , Kim Jun Woo , Ahn Dong June , Kim Jong‐Man
Published: January 2007

A polymer system based on polydiacetylene (PDA) supramolecules that emits red, green, and blue fluorescence has been constructed. The three‐color emitting system is comprised of red‐fluorescent PDA vesicles in which green‐fluorescent fluorescein molecules are encapsulated. Finally, the blue‐fluorescence component is introduced by reacting terminal amine groups on the PDA vesicle surfaces with fluorescamine. Thin PDA‐polymer‐containing poly(vinyl alcohol) films formed by using this strategy display red, green, and blue fluorescence upon excitation with light at specific wavelengths.

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Cover Picture: Macromol. Rapid Commun. 1/2007
Authors: Komp Ansgar , Finkelmann Heino
Published: January 2007

Cover: Smectic‐A Liquid Single Crystal Elastomers exhibiting optical transparency and spontaneous shape change are presented on the cover. Additionally, a simple model of the liquid crystalline phase is presented. The background shows a beautiful SA texture of the monomer taken between crossed polarizers. Further details can be found in the article by A. Komp, and H. Finkelmann* on page 55.
Theory of Multiple‐Detection Size‐Exclusion Chromatography of Complex Branched Polymers
Authors: Gaborieau Marianne , Gilbert Robert G. , Gray‐Weale Angus , Hernandez Javier M. , Castignolles Patrice
Published: January 2007

SEC separates complex branched polymers by hydrodynamic volume, rather than by molecular weight or branching characteristics. Equations relating the response of different types of detectors are derived including band broadening, by defining a distribution function N′(M,Vh), the number of chains with molecular weight M and hydrodynamic volume Vh. While the true molecular weight distribution of complex polymers cannot be determined by SEC, irrespective of the detector used, the formalism enables multiple detection SEC data to be processed to both analyze the polymer sample and reveal mechanistic information about polymer synthesis. The formalism also shows how the true weight‐ and number‐average molecular weight, $\overline M _{\rm w}$ and $\overline M _{\rm n}$, can be obtained from correct processing of the hydrodynamic volume distributions.

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Monte‐Carlo Study of Triblock Copolymer/Homopolymer Blend Films
Authors: Huang Yongmin , Xia Han , Liu Honglai , Hu Ying
Published: January 2007

The morphologies of triblock copolymer/homopolymer blend films confined between two neutral hard walls were studied via MC simulations on a simple cubic lattice. For ABA/A and ABA/B blend films, the effects of φh (the volume fraction of the homopolymer) and Mh/Mb (the ratio of the molecular mass of the homopolymer to that of the corresponding blocks) on the morphologies were investigated in detail. For both ABA/A and ABA/B blend films, a higher φh or Mh/Mb would result in stronger macrophase separation between the triblock copolymer and homopolymer. For ABA/C blend films, Mh/Mb hardly influences the morphologies of homopolymer domains regardless of whether the homopolymer C is more compatible with block A or with block B. Compared to AB/A and AB/C blend films, the morphologies of ABA/A (or ABA/B) and ABA/C blend films are much more irregular. The simulated results in this work show good consistency with experiments and other simulations.

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Brownian Dynamics Simulation of Self‐Consistently Coarse‐Grained Dilute Aggregated Polymer Suspensions
Authors: Shie Sheng C. , Hua Chi C. , Chen Show A.
Published: January 2007

We propose a self‐consistent coarse‐graining procedure for realistic Brownian dynamics simulations of dilute solutions consisting of van der Waals force‐driven aggregated polymer chains. A specific application investigated here concerns mesoscale aggregation properties in dilute conjugated polymer solutions, knowledge of which has proven crucial for controlling the electrical‐conduction and light‐emitting behaviors of the solution‐cast polymer films. Beginning with a bead‐rod/bead‐spring chain, the interaction between two non‐bonded beads, currently parameterized through a Lennard‐Jones potential, is constructed so that the single chain geometry matches that in the real polymer solution. At the second stage of coarse‐graining, the mother bead‐rod/bead‐spring chain is further mapped onto a dumbbell, with the potential function constructed so as to reproduce the pair interchain potential obtained on the basis of the previously constructed chain models. Without additional adjustable parameters, the simulation may, in principle, be utilized to investigate specific dilute polymer solutions in which the supramolecular aggregation structure is primarily controlled through van der Waals attraction and excluded‐volume repulsion. Simulation results are examined in detail for a widely studied semiconducting, semiflexible polymer in two distinct solvents (aromatic or aliphatic), as well as for a usual flexible, basically non‐aggregated polymer solution for contrasting purpose. Despite a significant degree of coarse‐graining associated with the dumbbell model, the simulation can, in general, clearly distinguish between aggregated and non‐aggregated polymer solutions and, in particular, successfully capture the underlying aggregation features of the target polymer solutions as implied by recent experimental observations. In the meantime, detailed insight is gained into the essential physics governing supramolecular aggregation of semiflexible chains in dilute solution.

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Dynamic Optimization of Molecular Weight Distribution Using Orthogonal Collocation on Finite Elements and Fixed Pivot Methods: An Experimental and Theoretical Investigation
Authors: Saliakas Vassilis , Chatzidoukas Christos , Krallis Apostolos , Meimaroglou Dimitris , Kiparissides Costas
Published: January 2007

In the present study, two numerical methods, namely the orthogonal collocation on finite elements and the fixed pivot technique, are employed to calculate the MWD in an MMA free‐radical batch suspension polymerization reactor operating up to very high conversions (e.g., ≥95%). The theoretical MWD predictions are directly compared with experimentally measured MWDs, obtained from a pilot‐scale batch MMA suspension polymerization reactor. It is shown that there is a very good agreement between model predictions and experimental measurements on both monomer conversion and MWD. Subsequently, two different time‐optimal temperature trajectories are calculated to obtain a polymer having either a narrow or a bimodal MWD in minimum batch time. The calculated time optimal trajectories are then applied, as set point temperature changes, to a pilot plant batch polymerization reactor. It is shown that the measured MWDs are in very good agreement with the off‐line calculated optimal MWDs.

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Combining standardized time series area and Cramér–von Mises variance estimators
Authors: Goldsman David , Kang Keebom , Kim Seong‐Hee , Seila Andrew F. , Tokol Gamze
Published: January 2007

We propose three related estimators for the variance parameter arising from a steady‐state simulation process. All are based on combinations of standardized‐time‐series area and Cramér–von Mises (CvM) estimators. The first is a straightforward linear combination of the area and CvM estimators; the second resembles a Durbin–Watson statistic; and the third is related to a jackknifed version of the first. The main derivations yield analytical expressions for the bias and variance of the new estimators. These results show that the new estimators often perform better than the pure area, pure CvM, and benchmark nonoverlapping and overlapping batch means estimators, especially in terms of variance and mean squared error. We also give exact and Monte Carlo examples illustrating our findings.© 2007 Wiley Periodicals, Inc. Naval Research Logistics, 2007
Measuring nurses' practice environments with the revised nursing work index: Evidence from registered nurses in the veterans health administration
Authors: Li Yu‐Fang , Lake Eileen T. , Sales Anne E. , Sharp Nancy D. , Greiner Gwendolyn T. , Lowy Elliott , Liu Chuan‐Fen , Mitchell Pamela H. , Sochalski Julie A.
Published: January 2007

The Revised Nursing Work Index (NWI‐R) is a widely used instrument for evaluating registered nurses' (RNs) practice environments. The existence of multiple subscale sets from the NWI‐R raises questions about its generalizability. We tested the validity of the one‐, three‐, and five‐subscale sets from the NWI‐R and derived a short‐form subscale set using a sample of RNs from the Veterans Health Administration (VHA). The prior sets do not have an excellent fit to these data. Results of exploratory factor analyses suggested a four‐factor model with Opportunity for Advancement, Collegial Nurse‐Physician Relations, Staffing Adequacy, and Nurse Manager Leadership as the most salient and parsimonious solution. Additional research is needed to corroborate these findings in other nurse samples and settings. © 2007 Wiley Periodicals, Inc. Res Nurs Health 30: 31–44, 2007
Psychometric characteristics of the spiritual perspective scale in pregnant African‐American women
Authors: Dailey Dawn E. , Stewart Anita L.
Published: January 2007

In health disparities research, studying the vulnerabilities of African Americans should be balanced by research on resources and strengths that influence health. One resource is spirituality, yet few tools have been developed and tested in diverse populations. This study evaluated the psychometric characteristics of the Spiritual Perspective Scale (SPS) in 102 pregnant African American women. Internal consistency reliability was high and evidence of construct validity was provided. The SPS correlated as hypothesized with church attendance, religiosity, and self‐reported spirituality. In addition, the SPS correlated negatively with depression, anxiety, and stress. Factor analysis revealed a two‐factor solution. The SPS performed well suggesting that it is an appropriate tool to use as a measure of spirituality in pregnant African American women. © 2007 Wiley Periodicals, Inc. Res Nurs Health 30: 61–71, 2007
The effect of a multi‐component smoking cessation intervention in African American women residing in public housing
Authors: Andrews Jeannette O. , Felton Gwen , Ellen Wewers Mary , Waller Jennifer , Tingen Martha
Published: January 2007

The purpose of this study was to test the effectiveness of a multi‐component smoking cessation intervention in African American women residing in public housing. The intervention consisted of: (a) nurse led behavioral/empowerment counseling; (b) nicotine replacement therapy; and, (c) community health workers to enhance smoking self‐efficacy, social support, and spiritual well‐being. The results showed a 6‐month continuous smoking abstinence of 27.5% and 5.7% in the intervention and comparison groups. Changes in social support and smoking self‐efficacy over time predicted smoking abstinence, and self‐efficacy mediated 6‐month smoking abstinence outcomes. Spiritual well‐being did not predict or mediate smoking abstinence outcomes. These findings support the use of a nurse/community health worker model to deliver culturally tailored behavioral interventions with marginalized communities. © 2007 Wiley Periodicals, Inc. Res Nurs Health 30: 45–60, 2007
The influence of maternal and child characteristics and paternal support on interactions of mothers and their medically fragile infants
Authors: Lee Tzu‐Ying , Holditch‐Davis Diane , Miles Margaret Shandor
Published: January 2007

The influences of maternal characteristics, infant characteristics, and paternal support on maternal positive involvement and developmental stimulation were examined over time in 59 mothers and their medically fragile infants using an ecological framework. Higher maternal education was associated with greater maternal positive involvement. More maternal depressive symptoms, more infant technological dependence, and lower birthweights were associated with less maternal positive involvement at 6 months but greater involvement at 12 months. Higher paternal helpfulness facilitated positive involvement in mothers with low depressive symptoms but not in those with elevated symptoms. Higher maternal education and more depressive symptoms were associated with more developmental stimulation. Thus, maternal interactive behaviors are affected by maternal, infant, and environment factors, and these effects change over time. © 2007 Wiley Periodicals, Inc. Res Nurs Health 30: 17–30, 2007
Subsequent malignant neoplasms in survivors of childhood cancer: Childhood Cancer Survivor Study (CCSS) studies
Authors: Davies Stella M.
Published: January 2007

Survival of children diagnosed with cancer has improved markedly, because of improvements in chemotherapy and radiation treatment protocols, better diagnosis, and risk classification and improved supportive care. Significant numbers of survivors are now entering their 30s and 40s, and data indicate that excess mortality continues in this group at least as long as 25 to 30 years after treatment. The Childhood Cancer Survivor Study (CCSS) is a large cohort study of 14,054 childhood cancer survivors who have been followed for over 13 years, with a median time from diagnosis now approaching 20 years. This cohort offers an extraordinary opportunity to study therapy‐associated subsequent malignant neoplasms, and has allowed improved definition of incidence and risk factors for subsequent breast and thyroid cancer. The collection of genetic samples from members of the cohort has allowed the inclusion of studies of genetic susceptibility to subsequent malignant neoplasms in this population with a uniquely well‐defined carcinogenic exposure. The planned formation of a new CCSS cohort, treated with more modern therapy, will allow the extension of these studies to younger populations and will define their experience of subsequent malignant neoplasms. Pediatr Blood Cancer 2007;48:727–730. © 2007 Wiley‐Liss, Inc.
Iodine‐131‐metaiodobenzylguanidine therapy with reduced‐intensity allogeneic stem cell transplantation in recurrent neuroblastoma
Authors: Takahashi Hiroka , Manabe Atsushi , Aoyama Chiaki , Kamiya Takahiro , Kato Itaru , Takusagawa Ayako , Ogawa Chitose , Ozawa Miwa , Hosoya Ryota , Yokoyama Kunihiko
Published: January 2007

Neuroblastoma is the most common extracranial solid tumor of childhood, and iodine‐131‐metaiodobenzylguanidine (MIBG) therapy is a new approach for grade IV neuroblastoma. We describe the case history of a 3‐year‐old girl with recurrent neuroblastoma who received MIBG therapy with reduced‐intensity allogeneic stem cell transplantation (RIST) because of an extensive bone marrow involvement. The post‐transplant course was uneventful and complete chimerism was obtained. Neither acute nor chronic graft‐versus‐host disease (GVHD) was observed. The patient remained in remission for 3 months after RIST until the second relapse. MIBG therapy combined with RIST warrants further trials. Pediatr Blood Cancer 2008;50:676–678. © 2007 Wiley‐Liss, Inc.
Attention dysfunction and parent reporting in children with brain tumors
Authors: Patel Sunita K. , Lai‐Yates Judy J. , Anderson Jonathan W. , Katz Ernest R.
Published: January 2007

Background

The IQ declines observed in children treated for brain tumor emerge as “late effects” and are conceptualized as secondary to changes in underlying mental processes, such as attention. Early identification of the underlying changes might help minimize the long‐term adverse outcomes. We evaluated the validity of a time‐efficient, standardized parent‐report measure in identifying attention dysfunction in childhood brain tumor survivors.

Procedure

Seventy survivors between ages 6 and 16 who met eligibility criteria and who had completed a standard neuropsychological evaluation were classified into an attention dysfunction group and a non‐attention dysfunction group, based on their performance on objective measures of attention. Analysis of covariance was used to evaluate group differences on the widely used, parent report Child Behavioral Checklist (CBCL).

Results

Survivors in the attention dysfunction group were reported by their parents as having significantly more attention problems relative to the group without attention dysfunction on objective testing. Furthermore, survivors categorized as having attention dysfunction based on their neuropsychological test scores were reported on the CBCL by their parents as having significantly more social problems compared to the non‐attention dysfunction group.

Conclusions

Standardized parent reporting of attention problems shows promise as a screening tool to detect attention dysfunction among survivors of childhood brain tumors. Findings include a strong association of decreased social functioning with attention dysfunction in brain tumor survivors. Furthermore, exploratory data suggest that the behavioral presentation of attention dysfunction in this group may be different from other clinical groups. Pediatr Blood Cancer 2007;49:970–974. © 2007 Wiley‐Liss, Inc.
High incidence of meningioma in cranial irradiated survivors of childhood acute lymphoblastic leukemia
Authors: Goshen Yacov , Stark Batia , Kornreich Liora , Michowiz Shalom , Feinmesser Meora , Yaniv Isaac
Published: January 2007

Background

Most survivors of childhood acute lymphoblastic leukemia (ALL) and T‐cell lymphoma (T‐NHL) treated before 1990 received cranial radiation. This study assessed the occurrence of second tumors in irradiated and non‐irradiated survivors.

Methods

Two hundred and ten survivors of ALL and T‐NHL were treated between 1974 and 1997 by several protocols. Imaging (MRI, CT) was performed every 3–6 years in 76/88 irradiated and 74/122 non‐irradiated patients for the last 20 years.

Results

From January 1998 through 2004, meningiomas were detected in 16 survivors (8 female, 8 male) at age 20–39 years (median 28.7); 15 were asymptomatic. Cranial imaging done 2–8 years previously in 11 revealed no abnormalities. Fifteen had been diagnosed with ALL or T‐NHL 10–29 years earlier (median 21) and received cranial irradiation (24 Gy in 14) at age 2–14 years (median 7.6). Fifteen tumors arose in the convexity. Three patients had multiple lesions. Complete resection was performed in 12 patients, with one complication. One patient had a recurrence, and four with small tumors are under surveillance. Only one low‐grade glioma and two basal‐cell carcinomas were found. Only one of the 74 non‐irradiated patients (median follow‐up 14 years) developed meningioma. The Kaplan‐Meier estimate of incidence of meningioma was 14.8 ± 7.6 at 20 years.

Conclusions

Survivors of childhood ALL treated with cranial radiation require prolonged surveillance because of a high incidence of late meningiomas. Early detection, when the tumor is still small, facilitates resection and may reduce complications. Pediatr Blood Cancer 2007;49:294–297. © 2007 Wiley‐Liss, Inc.
Ovarian dysgerminoma and Apert syndrome
Authors: Rouzier Cécile , Soler Christine , Hofman Paul , Brennetot Caroline , Bieth Eric , Pedeutour Florence
Published: January 2007

Apert syndrome is an autosomal dominant disorder that results from gain‐of‐function mutations in the FGFR2 gene. FGFR2 also has been shown to be amplified in stomach and breast cancers. We report the case of a 13‐year‐old female with Apert syndrome who developed an ovarian dysgerminoma. The FGFR2 exon 7 sequencing showed the classical Apert syndrome c.758C > G transversion (p.Pro253Arg). The genomic analyses of the tumor cells showed low level gains and losses of several chromosomes. This is the second report of the association of Apert syndrome with cancer. Our observation raises the hypothesis of a role for FGFR2 mutations in tumorigenesis. Pediatr Blood Cancer 2008;50:696–698. © 2007 Wiley‐Liss, Inc.
Prenatal diagnosis in the Netherlands, 1991–2000: number of invasive procedures, indications, abnormal results and terminations of pregnancy
Authors: Nagel H. T. C. , Knegt A. C. , Kloosterman M. D. , Wildschut H. I. J. , Leschot N. J. , Vandenbussche F. P. H. A.
Published: January 2007

Objective

To provide an overview of invasive prenatal diagnosis in the Netherlands and to analyse trends.

Methods

Annual results from all centres for invasive prenatal diagnosis in the Netherlands over the period 1991–2000 were combined and described, with particular emphasis on indications, abnormal results, type of invasive procedures, and terminations of pregnancy.

Results

The percentage of invasive prenatal diagnosis increased from 5% of births in 1991 to 6% in 1996 and subsequently remained at that level. During the study period, the number of pregnant women aged 36 and older increased by 70%, but the number of procedures performed because of maternal age remained stable. The detection rate for abnormal results was 2–3% for maternal age and rose from 9 to 13% for other indications. Other trends during the study period included a relative decrease in cordocentesis (−82%) and chorionic villi biopsy (−18%) in favour of amniocentesis (+48%), and a strong decrease in the number of amniocentesis procedures for increased risk of neural tube defect. In 71% of the cases with abnormal results, the pregnancy was terminated.

Conclusion

There was a significant decrease in the percentage of pregnant women aged 36 or older who underwent invasive prenatal diagnosis without previous screening. Copyright © 2007 John Wiley & Sons, Ltd.
Cover Picture: Plasma Process. Polym. 1/2007
Authors: Masutani Yasushi , Nagai Nodoka , Fujita Shiro , Hayashi Masushi , Kogoma Masuhiro , Tanaka Kunihito
Published: January 2007

Cover: The combination of atmospheric pressure glow plasma fluorination and surface roughening is effective in the formation of highly releasing surfaces. A 180° peel test with an acrylic pressure‐sensitive adhesive tape presents this evidence. Further details can be found in the article by Y. Masutani,* N. Nagai, S. Fujita, M. Hayashi, M. Kogoma, and K. Tanaka on page 41.
Comparison of two‐dimensional gel electrophoresis based and shotgun strategies in the study of plasma membrane proteome
Authors: He Jintang , Liu Yashu , He Sizhi , Wang Qingsong , Pu Hai , Tong Yuanpeng , Ji Jianguo
Published: January 2007

Membrane proteins play important roles in various plasma membrane (PM) activities such as signal transduction and cell recognition. However, a comprehensive proteomic study of membrane proteins remains difficult. Different strategies have been employed to study PM proteome, but little effort has been made to systematically evaluate them. In the present work, liver PM was prepared by subcellular fractionation and an aliquot was washed by sodium carbonate. After evaluation of the PM fraction by electron microscopy and Western blotting, proteins in both original and carbonate washed PM were identified by either 2‐DE coupled MALDI‐TOF‐MS or shotgun strategies. Then protein characteristics such as molecular weight, pI, grand average hydrophobicity, subcellular location, and transmembrane domains were systematically compared. The comparative analysis showed that shotgun strategies were more suitable to identify membrane proteins, while 2‐DE‐based strategies may serve as a complement. Furthermore, carbonate washing obviously enriched the integral membrane proteins. All the results suggested that the strategy combining carbonate washing and shotgun identification was the optimum strategy to study human liver PM proteome. Using this strategy, 260 high‐confidence proteins were identified, wherein 139 were integral membrane proteins which had 1–17 transmembrane domains.
Searching for potential biomarkers of cisplatin resistance in human ovarian cancer using a label‐free LC/MS‐based protein quantification method
Authors: Fitzpatrick Dawn P. G. , You Jin‐Sam , Bemis Kerry G. , Wery Jean‐Pierre , Ludwig James R. , Wang Mu
Published: January 2007

Platinum‐based chemotherapy, such as cisplatin, is the primary treatment for ovarian cancer. However, drug resistance has become a major impediment to the successful treatment of ovarian cancer. To date, the molecular mechanisms of resistance to platinum‐based chemotherapy remain unclear. In this study, we applied an LC/MS‐based protein quantification method to examine the global protein expression of two pairs of ovarian cancer cell lines, A2780/A2780‐CP (cisplatin‐sensitive/cisplatin‐resistant) and 2008/2008‐C13*5.25 (cisplatin‐sensitive/cisplatin‐resistant). We identified and quantified over 2000 proteins from these cell lines and 760 proteins showed significant expression changes with a false discovery rate of less than 5% between paired groups. Based on the results we obtained, we suggest several potential pathways that may be involved in cisplatin resistance in human ovarian cancer. This study provides not only a new proteomic platform for large‐scale quantitative protein analysis, but also important information for discovery of potential biomarkers of cisplatin resistance in ovarian cancer. Furthermore, these results may be clinically relevant for diagnostics, prognostics, and therapeutic improvement for ovarian cancer treatment.
Structural characterization of the functional regions in the archaeal protein Sso7d
Authors: Renzone Giovanni , Vitale Rosa M. , Scaloni Andrea , Rossi Mosè , Amodeo Pietro , Guagliardi Annamaria
Published: January 2007

Sso7d from the extreme thermophilic crenarchaeon Sulfolobus solfataricus is a multifunctional protein in in vitro assays, whose in vivo role is still puzzling. Crystals of Sso7d in complex with DNA elucidated the protein surface involved in the binding to the nucleic acid, whereas the locations of the Sso7d regions responsible for a chaperone activity in renaturing protein aggregates (i.e., the protein‐binding surface and the site of ATPase activity) are still unknown. We identified the regions of Sso7d involved in protein‐binding by limited proteolysis experiments associated to advanced mass spectrometric procedures performed on isolated Sso7d and Sso7d in complex with the peptide melittin. By affinity labeling of Sso7d with the ATP analogue 5′‐p‐fluorosulfonylbenzoyl adenosine and characterization of the labeled tryptic peptides by tandem mass spectrometry, we found that Y7 and K39 are residues involved in ATP binding/hydrolysis. Insights into the positions of the ligands melittin and ATP were achieved by a molecular modeling study; the models obtained were in agreement with most experimental data. A comparison among the complexes of Sso7d with DNA, with melittin, and with ATP showed that the DNA‐binding surface and the protein‐binding surface overlap, whereas the ATPase site is mostly independent of the binding sites for the nucleic acid and melittin. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Structural basis of allele variation of human thiopurine‐S‐methyltransferase
Authors: Wu Hong , Horton John R. , Battaile Kevin , Allali‐Hassani Abdellah , Martin Fernando , Zeng Hong , Loppnau Peter , Vedadi Masoud , Bochkarev Alexey , Plotnikov Alexander N. , Cheng Xiaodong
Published: January 2007

Human thiopurine S‐methyltransferase (TPMT) exhibits considerable person‐to‐person variation in activity to thiopurine drugs. We have produced an N‐terminal truncation of human TPMT protein, crystallized the protein in complex with the methyl donor product S‐adenosyl‐L‐homocysteine, and determined the atomic structure to the resolution of 1.58 and 1.89 Å, respectively, for the seleno‐methionine incorporated and wild type proteins. The structure of TPMT indicates that the naturally occurring amino acid polymorphisms scatter throughout the structure, and that the amino acids whose alteration have the most influence on function are those that form intra‐molecular stabilizing interactions (mainly van der Waals contacts). Furthermore, we have produced four TPMT mutant proteins containing variant alleles of TPMT*2, *3A, *3B, and *3C and examined the structure‐function relationship of the mutant proteins based on their expression and solubility in bacteria and their thermostability profile. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Indel‐based targeting of essential proteins in human pathogens that have close host orthologue(s): Discovery of selective inhibitors forLeishmania donovanielongation factor‐1α
Authors: Nandan Devki , Lopez Martin , Ban Fuqiang , Huang Meilan , Li Yvonne , Reiner Neil E. , Cherkasov Artem
Published: January 2007

We propose a novel strategy for selective targeting of essential pathogen proteins that contain sizable indels (insertions/deletions) in their sequences compared with their host orthologues. This approach has been tested on elongation factor‐1α (EF‐1α) from the protozoan pathogenLeishmania donovani. Leishmania EF‐1α is 82% identical to the corresponding human orthologue, but possesses a 12 aminoacid sequence deletion compared with human EF‐1α. We used this indel‐differentiated region to design small molecules that selectively bind to leishmania EF‐1α and not to the human protein. Three unrelated molecules were identified with the capacity to inhibit protein synthesis in leishmania by up to 75% while exhibiting no effect on human protein translation. These candidates may serve as prototypes for future development of antiprotozoan therapeutics. More generally, these findings provide a basis for a novel drug design platform. This platform targets essential pathogen proteins that are highly conserved across species, and consequently would not typically be considered to be conventional drug targets. We anticipate that such indel‐directed targeting of essential proteins in microbial pathogens may help address the growing problem of antibiotic resistance. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Chaperone‐mediated inhibition of tubulin self‐assembly
Authors: Mitra Gopa , Saha Abhik , Gupta Twishasri Das , Poddar Asim , Das Kali P. , Das Gupta Sujoy K. , Bhattacharyya Bhabatarak
Published: January 2007

Molecular chaperones are known to play an important role in facilitating the proper folding of many newly synthesized proteins. Here, we have shown that chaperone proteins exhibit another unique property to inhibit tubulin self‐assembly efficiently. Chaperones tested include α‐crystallin from bovine eye lenses, HSP16.3, HSP70 from Mycobacterium tuberculosis and α s‐casein from milk. All of them inhibit polymerization in a dose‐dependent manner independent of assembly inducers used. The critical concentration of MTP polymerization increases with increasing concentration of HSP16.3. Increase in chaperone concentration lowers the extent of polymerization and increases the lag time of self‐assembly reaction. Although the addition of a chaperone at the early stage of elongation phase shows no effect on polymerization, the same concentration of chaperone inhibits polymerization completely when added before the initiation of polymerization. Bindings of HSP16.3 and α s‐casein to tubulin have been confirmed using isothermal titration calorimetry. Affinity constants of tubulin are 5.3 ×× 104 and 9.8 ×× 105 M−1 for HSP16.3 and α s‐casein, respectively. Thermodynamic parameters indicate favourable entropy and enthalpy changes for both chaperones‐tubulin interactions. Positive entropy change suggests that the interaction is hydrophobic in nature and desolvation occurring during formation of tubulin‐chaperone complex. On the basis of thermodynamic data and observations made upon addition of chaperone at early elongation phase or before the initiation of polymerization, we hypothesize that chaperones bind tubulin at the protein‐protein interaction site involved in the nucleation phase of self‐assembly. Proteins 2007. © 2007 Wiley‐Liss, Inc.
A protein‐specifically adapted scoring function for the reranking of docking solutions
Authors: Müller Wolfgang , Sticht Heinrich
Published: January 2007

In this work, we developed a protein‐specifically adapted scoring function and applied it to the reranking of protein–protein docking solutions generated with a conventional docking program. The approach was validated using experimentally determined structures of the bacterial HPr–protein in complex with four structurally nonhomologous binding partners as an example. A sufficiently large data basis for the generation of protein‐specifically adapted pair potentials was generated by modeling all orthologous complexes for each type of interaction resulting in a total of 224 complexes. The parameters for potential generation were systematically varied and resulted in a total of 66,132 different scoring functions that were tested for their ability of successful reranking of 1000 docking solutions generated from modeled structures of the unbound binding partners. Parameters that proved critical for the generation of good scoring functions were the distance cutoff used for the generation of the pair potential, and an additional cutoff that allows a proper weighting of conserved and nonconserved contacts in the interface. Compared to the original scoring function, application of this novel type of scoring functions resulted in a significant accumulation of acceptable docking solutions within the first 10 ranks. Depending on the type of complex investigated one to five acceptable complex geometries are found among the 10 highest‐ranked solutions and for three of the four systems tested, an acceptable solution was placed on the first rank. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Characterization and identification of diarylheptanoids in ginger (Zingiber officinale Rosc.) using high‐performance liquid chromatography/electrospray ionization mass spectrometry
Authors: Jiang Hongliang , Timmermann Barbara N. , Gang David R.
Published: January 2007

In our continuing investigation of diarylheptanoids in Zingiberaceae plants using liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS/MS), 26 diarylheptanoids were identified from fresh ginger rhizome. Of the 26 compounds, 15 diarylheptanoids appear to be new compounds. In addition, the majority of these compounds (18) were acetylated, which is different from our investigation of diarylheptanoids from turmeric, another member of the Zingiberaceae, which did not possess any acetylated diarylheptanoids. In all, five distinct groups (homologous series) of diarylheptanoids were found in extracts from ginger rhizome. These groups were differentiated by structural differences on the heptane skeletons, whereas homologs within each group differed by substitution patterns on the aromatic rings. Diagnostic fragmentation behavior in (+)‐ and (−)ESI‐MS/MS analyses for each group of homologs, as well as information regarding polarity obtained from retention time data, allowed us to classify compounds by group and identify them based on key structural features. Copyright © 2007 John Wiley & Sons, Ltd.
Estimating risk of breast cancer in carriers of BRCA1 and BRCA2 mutations: a meta‐analytic approach
Authors: Fu Rongwei , Harris Emily L. , Helfand Mark , Nelson Heidi D.
Published: January 2007

Estimates of penetrance (or risk) of breast cancer among BRCA mutation carriers in published studies are heterogeneous, prohibiting direct combined estimates. Estimates of prevalence of BRCA mutations are more homogeneous and could allow combined estimates of prevalence. We propose a combined estimator of penetrance from combined estimates of the prevalence of BRCA mutations in women with and without breast cancer and from the probability of breast cancer by using Bayes' Theorem. The relative risk of having breast cancer with positive family history and the prevalence of positive family history contribute to the combined estimate of penetrance if family history is present. The combined estimate incorporates variation in estimates from different resources. The method is illustrated by using data from Ashkenazi Jewish women unselected for family history and for those with family history. Risks of breast cancer conferred by BRCA1 and BRCA2 mutations are estimated to be 8.39 per cent (6.56, 10.68 per cent) and 2.66 per cent (1.85, 3.82 per cent) by 40 years old, and 47.45 per cent (37.39, 57.72 per cent) and 31.85 per cent (23.72, 41.26 per cent) by 75 years old, respectively. For those with family history, risks of breast cancer conferred by BRCA mutations appear to be higher. Copyright © 2007 John Wiley & Sons, Ltd.
Enhanced neural differentiation of neural stem cells and neurite growth by amniotic epithelial cell co‐culture
Authors: Meng Xiao‐ting , Chen Dong , Dong Zhi‐yong , Liu Jia‐mei
Published: January 2007

Amniotic epithelial cells (AECs) were reported to show a neuroprotective effect on neurons, but there was no direct evidence for a functional relationship between neural stem cells (NSCs) and AECs. The aim of this study was to determine whether AECs could stimulate differentiation and expand neurogenesis of NSCs, and whether the roles were due to a diffusible factor or required direct cell‐cell contact. AECs were isolated from rat amnion on E14–16 and NSCs were isolated from neocortical tissue. The growth and differentiation of NSCs were compared under different conditions. The results showed that NSCs cultured with FGF‐2 proliferated and formed floating neurospheres while those grown in B27 without FGF‐2 failed to thrive. Those grown either with AEC conditioned medium or in transwells showed significantly improved survival. Moreover, the neural differentiation and length of neurite were greater in exogenous FGF groups when NSCs were allowed direct contact with AECs. Western blotting, immunocytochemistry and RT‐PCR indicated that rat AECs could secrete NT‐3 and BDNF. Furthermore, the presence of FGF‐2 enhanced the function of AECs. These findings identified that AECs may be regarded as a critical component of NSCs niche and suggested that direct cell‐to‐cell contact may provide additional and independent support. Such information would circumvent the need for AECs‐NSCs co‐culture and could potentially facilitate the production of neurons for future clinical applications.
Enrichment of epidermal stem cells by rapid adherence and analysis of the reciprocal interaction of epidermal stem cells with neighboring cells using an organotypic system
Authors: Dong Rui , Liu Xiaoliang , Liu Yuan , Deng Zhihong , Nie Xin , Wang Xinwen , Jin Yan
Published: January 2007

Keratinocytes have the ability to adhere to extracellular matrix rapidly. With this in mind, in this study we isolated keratinocytes known as rapidly adhering (RA) cells. To compare epidermal regenerative abilities, skin substitutes were reconstructed by adding keratinocytes or RA cells to two groups of bioengineered dermis made by fibroblasts and hair follicle dermal cells respectively. After transplantation, the results illustrated that the skin substitutes including RA cells were integrated into the host tissue. Furthermore, with hair follicle dermal cells’ influences, the RA cells could form structures very similar to normal hair follicles. These results indicate that RA cells are predominately comprised of epidermal stem cells. The results also demonstrated that besides the reciprocal interaction of epidermal stem cells with dermal cells, the interaction of epidermal stem cells with keratinocytes were critical in epidermis morphogenesis and self‐renewal, and application of RA cells could optimize engineering of skin substitutes.
Detection of potassium currents and regulation of multidrug resistance by potassium channels in human gastric cancer cells
Authors: Han Ying , Shi Yongquan , Han Zheyi , Sun Li , Fan Daiming
Published: January 2007

The present study aimed to investigate the potassium currents and further explore the role of potassium channels in drug response of gastric cancer cells. By patch‐clamp technique, potassium currents of human gastric cancer cell SGC7901 were recorded in the mode of voltage clamp. Both 4‐aminopyridine (4‐AP) and tetraethylammonium (TEA) could almost completely block this current. The chemotherapeutic drugs, adriamycin or 5‐fluorouracil could significantly increase the K+ current density on SGC7901 cells in a dose‐dependent manner. 4‐AP or TEA was found to restrain adriamycin‐induced apoptosis and enhance multidrug‐resistant phenotype of SGC7901 cells. Up‐regulation of Kv1.5, which has been found widely expressed in gastric cancer cells including SGC7901, increased the K+ current density and sensitivity of SGC7901 cells to multiple chemotherapeutic drugs, whereas down‐regulation of Kv1.5 enhanced the drug‐resistant phenotype of SGC7901 cells. In conclusion, potassium channels may exert regulatory effects on multidrug resistance by regulating drug‐induced apoptosis in gastric cancer cells.
Long interstitial (TTAGGG)n arrays do not colocalize with repressive chromatin modifications in Chinese hamster cells
Authors: Svetlova M.P. , Solovjeva L.V. , Smirnova A.N. , Tomilin N.V.
Published: January 2007

Interstitial tandem (TTAGGG)n repeats (ITRs) in Chinese hamster (CH) cells are mostly arranged into the long (>100 kb) continuous pericentric arrays which do not contain HindIII sites (Faravelli M, Azzalin CM, Bertoni L, Chernova O, Attolini C, Mondello C, et al. Molecular organization of internal telomeric sequences in Chinese hamster chromosomes, Gene 2002;283,11–16), are free of protein‐coding genes, and can formally be classified as heterochromatin. ITRs dynamically interact with (TTAGGG)n‐binding protein TRF1 and can be visualized using Green Fluorescent Protein (GFP)‐tagged TRF1. Here we examined whether mobility of GFP‐TRF1 associated with ITRs in CH cells is affected by inhibitors of transcription and whether ITRs colocalize with known repressive chromatin modifications hallmarked by histone H3 trimethylated at lysine‐9 (H3K9m3) or lysine‐27 (H3K27m3). We found that GFP‐TRF1 bodies do not colocalize in the nuclei of V79 cells with H3K9m3 or H3K27m3 indicating that ITRs do not represent typical constitutive or facultative heterochromatin. Mobility of ITR‐bound GFP‐TRF1 is suppressed by inhibitors of transcription consistent with the view that TRF1 is exchanged during transcription of ITRs. However, GFP‐TRF1 bodies do not colocalize with nuclear hubs of intensive transcription detected through in vivo incorporation of 5‐bromouridine triphosphate. Using real‐time PCR, we also examined transcription of unique sequences adjacent to (TTAGGG)n arrays in CH genome and found that they are transcribed, indicating that these arrays do not generally inhibit transcription in cis. Together, our results suggest that ITRs represent a special kind of moderately transcribed heterochromatin which possible function remains to be established.
Changes in composition and activities of 26S proteasomes under the action of doxorubicin—apoptosis inductor of erythroleukemic K562 cells
Authors: Tsimokha Anna S. , Mittenberg Alexey G. , Kulichkova Valentina A. , Kozhukharova Irina V. , Gause Larisa N. , Konstantinova Irina M.
Published: January 2007

Changes in the subunit composition, phosphorylation of the subunits, and regulation of the activities of 26S proteasomes in proliferating cells undergoing programmed cell death have not been studied so far. Moreover, there are no reports on phosphorylation of proteasome subunits both in normal and in neoplastic cells during apoptosis. The data of the present study show for the first time that apoptosis inductor doxorubicin regulates subunit composition, enzymatic activities, and phosphorylation state of 26S proteasomes in neoplastic (proerythroleukemic K562) cells or, in other words, induces reprogramming of proteasome population. Furthermore, the phosphorylation state of proteasomes is found to be the mechanism controlling specificity of proteasomal proteolytic and endoribonuclease activities.
Phosphoinositide 3‐kinase inhibitor LY294002 but not serum withdrawal suppresses proliferation of murine embryonic stem cells
Authors: Lianguzova Maria S. , Chuykin Ilia A. , Nordheim Alfred , Pospelov Valery A.
Published: January 2007

Mouse embryonic stem (mES) cells have short duration of their cell cycle and are capable of proliferating in the absence of growth factors. To find out which signaling pathways contribute to the regulation of the mES cell cycle, we used pharmacological inhibitors of MAP and PI3 kinase cascades. The MAP kinase inhibitors as well as serum withdrawal did not affect mES cell cycle distribution, whereas the inhibitor of PI3K activity, LY294002, induced accumulation of cells in G1 phase followed by apoptotic cell death. Serum withdrawal also causes apoptosis, but it does not change the content and activity of cell cycle regulators. In contrast, in mES cells treated with LY294002, the activities of Cdk2 and E2F were significantly decreased. Interestingly, LY294002 had a much stronger effect on cell cycle distribution in low serum conditions, implying that serum can promote G1 → S transition of mES cells by a LY294002‐resistant mechanism. Thus, proliferation of mES cells is maintained by at least two separate mechanisms: a LY294002‐sensitive pathway, which is active even in the absence of serum, and LY294002‐resistant, but serum‐dependent, pathway.
Extra‐cellular matrix proteins induce re‐distribution of α‐actinin‐1 and α‐actinin‐4 in A431 cells
Authors: Bolshakova Anastasia , Petukhova Olga , Turoverova Lidia , Tentler Dmitri , Babakov Vladimir , Magnusson Karl‐Eric , Pinaev George
Published: January 2007

Alpha‐actinins are actin‐binding proteins of non‐muscle cells, which can participate in the regulation of transcription factor activity. We describe the distribution of α‐actinin‐1 and −4 depending on different actin cytoskeleton formed as a result of cell adhesion to extracellular matrix proteins, such as fibronectin and laminin 2/4. Immunofluorescent studies show a difference in the distribution of α‐actinin and −4. Both isoforms localise along stress‐fibres, but α‐actinin‐1 localises in the perinuclear region more abundantly than α‐actinin‐4. Western blot analysis demonstrated existence of truncated forms of both isoforms. Truncated α‐actinin‐1 appears in cells spread on fibronectin or laminin. Cell spreading also correlated with more tight association of α‐actinin‐4 with chromatin. Basing on our previous finding of an interaction of α‐actinin‐4 with p65 subunit of the NF‐κB, we checked the possible influence of immobilised ligands on its redistribution in nuclear complexes containing p65. α‐Actinin‐4 seems to be present in some but not all nuclear complexes containing p65. Immobilised ligands may affect the interaction of α‐actinin‐4/p65 complexes with chromatin. The data suggest that adhesion to extra‐cellular matrix may interfere in cellular reactions mediated by α‐actinin‐1 and −4.
Different disturbances—one pathway of protein unfolding. Actin folding‐unfolding and misfolding
Authors: Povarova Olga I. , Kuznetsova Irina M. , Turoverov Konstantin K.
Published: January 2007

This review summarizes the results of our investigations of actin unfolding‐refolding and presents the notion that protein unfolding pathway, the number and the appearance order of intermediate states do not dependent on denaturing agents. To place our concept in the context of current knowledge of protein folding, we review in brief the development of general ideas of protein folding mechanisms, paying special attention to some key points of this process. Thus we focus on the characteristics of amino acid sequences that provide the existence of protein native structure, and on the interactions that compensate the increase of free energy due to the decrease of entropy on the way from multitude unfolded conformations to unique native state. In particular, we emphasize that ordered structures can arise both due to intramolecular and intermolecular interactions which lead to the formation of native and misfolded (associates, amorphous aggregates amyloid and amyloid‐like fibrils) states, respectively.