bluuebunny/crossref_metadata_2025 huggingface dataset:
Building a protein name dictionary from full text: a machine learning term extraction approach
Authors: Shi Lei , Campagne Fabien
Published: April 2005

Background

The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature.

Results

We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text.

Conclusion

This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.
A method for aligning RNA secondary structures and its application to RNA motif detection
Authors: Liu Jianghui , Wang Jason TL , Hu Jun , Tian Bin
Published: April 2005

Background

Alignment of RNA secondary structures is important in studying functional RNA motifs. In recent years, much progress has been made in RNA motif finding and structure alignment. However, existing tools either require a large number of prealigned structures or suffer from high time complexities. This makes it difficult for the tools to process RNAs whose prealigned structures are unavailable or process very large RNA structure databases.

Results

We present here an efficient tool called RSmatch for aligning RNA secondary structures and for motif detection. Motivated by widely used algorithms for RNA folding, we decompose an RNA secondary structure into a set of atomic structure components that are further organized by a tree model to capture the structural particularities. RSmatch can find the optimal global or local alignment between two RNA secondary structures using two scoring matrices, one for single-stranded regions and the other for double-stranded regions. The time complexity of RSmatch is O(mn) where m is the size of the query structure and n that of the subject structure. When applied to searching a structure database, RSmatch can find similar RNA substructures, and is capable of conducting multiple structure alignment and iterative database search. Therefore it can be used to identify functional RNA motifs. The accuracy of RSmatch is tested by experiments using a number of known RNA structures, including simple stem-loops and complex structures containing junctions.

Conclusion

With respect to computing efficiency and accuracy, RSmatch compares favorably with other tools for RNA structure alignment and motif detection. This tool shall be useful to researchers interested in comparing RNA structures obtained from wet lab experiments or RNA folding programs, particularly when the size of the structure dataset is large.
Valine 738 and lysine 735 in the fifth transmembrane domain of rTas1r3 mediate insensitivity towards lactisole of the rat sweet taste receptor
Authors: Winnig Marcel , Bufe Bernd , Meyerhof Wolfgang
Published: April 2005

Background

The sweet taste inhibitor lactisole acts on the human sweet taste receptor heteromer TAS1R2-TAS1R3 but not on its rodent counterpart. Recently, it was shown that the lactisole sensitivity of the human sweet taste receptor involves the part of TAS1R3 encompassing the seven transmembrane regions but not the huge N-terminal domain. Using mutational analysis we investigated which amino acid residues distinguish lactisole insensitive rat from sensitive human T1R3 receptors.

Results

The functional analysis of specific receptor mutants in HEK293T cells revealed that the exchange of valine 738 in the fifth transmembrane domain of rTas1r3 by an alanine is sufficient to confer lactisole sensitivity to the rat sweet taste receptor. The sensitivity of this receptor mutant is ~2 fold lower than the sensitivity of the human sweet taste receptor. Additional substitution of lysine 735 by phenylalanine in rTas1r3 results in a rat sweet taste receptor that is as sensitive to lactisole as its human counterpart. The exchange of valine 738 to alanine was accompanied by a ~50% reduction in receptor efficacy. This effect was seen with all six different sweet compounds examined.

Conclusion

The lactisole insensitivity of rat sweet taste receptor is caused by only two amino acids in transmembrane region five, which is critical for the interaction of lactisole with the sweet taste receptor. The observation that the mutant receptor simultaneously displays a generally reduced sensitivity towards all agonists suggests that the lactisole insensitivity of the rodent receptor might be more likely caused by the inaccessibility of the lactisole binding site rather then by its direct disruption.
Diseased muscles that lack dystrophin or laminin-α2 have altered compositions and proliferation of mononuclear cell populations
Authors: Girgenrath Mahasweta , Kostek Christine A , Miller Jeffrey Boone
Published: April 2005

Background

Multiple types of mononucleate cells reside among the multinucleate myofibers in skeletal muscles and these mononucleate cells function in muscle maintenance and repair. How neuromuscular disease might affect different types of muscle mononucleate cells had not been determined. In this study, therefore, we examined how two neuromuscular diseases, dystrophin-deficiency and laminin-α2-deficiency, altered the proliferation and composition of different subsets of muscle-derived mononucleate cells.

Methods

We used fluorescence-activated cell sorting combined with bromodeoxyuridine labeling to examine proliferation rates and compositions of mononuclear cells in diseased and healthy mouse skeletal muscle. We prepared mononucleate cells from muscles of mdx (dystrophin-deficient) or Lama2-/- (laminin-α2-deficient) mice and compared them to cells from healthy control muscles. We enumerated subsets of resident muscle cells based on Sca-1 and CD45 expression patterns and determined the proliferation of each cell subset in vivo by BrdU incorporation.

Results

We found that the proliferation and composition of the mononucleate cells in dystrophin-deficient and laminin-α2-deficient diseased muscles are different than in healthy muscle. The mdx and Lama2-/- muscles showed similar significant increases in CD45+ cells compared to healthy muscle. Changes in proliferation, however, differed between the two diseases with proliferation increased in mdx and decreased in Lama2-/- muscles compared to healthy muscles. In particular, the most abundant Sca-1-/CD45- subset, which contains muscle precursor cells, had increased proliferation in mdx muscle but decreased proliferation in Lama2-/- muscles.

Conclusion

The similar increases in CD45+ cells, but opposite changes in proliferation of muscle precursor cells, may underlie aspects of the distinct pathologies in the two diseases.
Add-on topiramate reduces weight in overweight patients with affective disorders: a clinical case series
Authors: Kirov George , Tredget John
Published: April 2005

Background

The weight-gain caused by many psychotropic drugs is a major cause for poor compliance with such medications and could also increase cardio-vascular morbidity among psychiatric patients. Recent reports have shown that the anticonvulsant topiramate causes weight loss in various patient groups. The drug has also shown effectiveness in open trials as a mood stabilizer in patients with affective disorders, but not in controlled trials in the acute treatment of mania. We used topiramate to treat 12 patients with affective disorders who had a body-mass index >30 kg/m2.

Methods

Topiramate was prescribed as part of our routine clinical practice, as an add-on medication, or as a replacement of a mood stabilizer. Patients' weight was recorded in 1 to 2 monthly intervals. Patients were followed up for between 6 and 12 months. The final dose of topiramate varied from 200 to 600 mg/day.

Results

Topiramate was effective in reducing the weight in 10 out of the 12 patients. At six months the 12 patients had lost a mean of 7.75 kg (SD = 6.9 kg, p < 0.001) and at 12 months 9 patients had lost a mean of 9.61 kg (SD = 6.7 kg, p = 0.003). Three patients stopped the treatment: one due to side effects, one due to possible side effects, and one suffered a manic relapse and showed no sustained weight loss. There were no other clear changes in the course of illness of the patients.

Conclusion

The evidence of a strong weight-reducing potential of topiramate is indisputable and clinically significant. Topiramate could be considered in the treatment of bipolar patients who are overweight, or whose concerns about weight gain compromise their compliance with long-term prophylactic medication. So far there is no evidence that topiramate has anti-manic effect and it should not be used as monotherapy.
Enhanced levels of Hsulf-1 interfere with heparin-binding growth factor signaling in pancreatic cancer
Authors: Li Junsheng , Kleeff Jörg , Abiatari Ivane , Kayed Hany , Giese Nathalia A , Felix Klaus , Giese Thomas , Büchler Markus W , Friess Helmut
Published: April 2005

Hsulf-1 is a newly identified enzyme, which has the ability to decrease the growth of hepatocellular, ovarian, and head and neck squamous cell carcinoma cells by interfering with heparin-binding growth factor signaling. Since pancreatic cancers over-express a number of heparin-binding growth factors and their receptors, the expression and function of this enzyme in pancreatic cancer was analyzed.

Results

Pancreatic cancer samples expressed significantly (22.5-fold) increased Hsulf-1 mRNA levels compared to normal controls, and Hsulf-1 mRNA was localized in the cancer cells themselves as well as in peritumoral fibroblasts. 4 out of 8 examined pancreatic cancer cell lines expressed Hsulf-1, whereas its expression was below the level of detection in the other cell lines. Stable transfection of the Hsulf-1 negative Panc-1 pancreatic cancer cell line with a full length Hsulf-1 expression vector resulted in increased sulfatase activity and decreased cell-surface heparan-sulfate proteoglycan (HSPG) sulfation. Hsulf-1 expression reduced both anchorage-dependent and -independent cell growth and decreased FGF-2 mediated cell growth and invasion in this cell line.

Conclusion

High expression of Hsulf-1 occurs in the stromal elements as well as in the tumor cells in pancreatic cancer and interferes with heparin-binding growth factor signaling.
Combination of qualitative and quantitative methods for developing a new Health Related Quality of Life measure for patients with anogenital warts
Authors: Badia Xavier , Colombo Jose Antonio , Lara Nuria , Llorens M Angels , Olmos Luis , de los Terreros Miguel Sainz , Varela Jose Antonio , Vilata Juan Jose
Published: April 2005

Background

Anogenital warts are the most easily recognized sign of genital Human Papilloma Virus infection. The objective was to develop a short, valid and reliable questionnaire to measure Health Related Quality of Life (HRQL) in patients with anogenital warts.

Methods

First a literature review was performed to identify relevant papers describing the impact of anogenital warts in HRQL; second the main domains were identified by some experts in a focus group, and third in-depth-semi-structured interviews were conducted in patients with anogenital warts to identify the initial set of items. A qualitative reduction of the initial set of items was performed based on the mean scoring of the experts for the three scales: clarity, frequency and importance. The initial questionnaire was pilot tested in 135 patients. Rasch analysis was performed with the results of the questionnaire in order to refine the instrument. Spearman's correlation was calculated between the initial questionnaire and the reduced version. Additionally the measurement properties (validity and reliability) of the resulting final questionnaire were tested and compared using standard procedures (Cronbach's Alpha and item-total correlation).

Results

the main domains identified as affected in patient's life were: sexual, colleagues and partner relationships. After a proper qualitative reduction the initial set of 134 items was reduced to 22. The questionnaire was pilot tested in 135 patients and two dimensions were identified after the multifactorial analysis: emotional dimension and sexual activity dimension. As a result of the Rasch analysis the questionnaire was reduced to 10 items. High correlation was found between the initial and the reduced version for the two dimensions. Cronbach's alpha values were acceptable (0.86).

Conclusion

The initial 22 items questionnaire was reduced by Rasch analysis to a version of 10 items, with two dimensions: emotional and sexual. The results suggest the adequacy of the 10 items to evaluate HRQL of patients with anogenital warts in a valid and reliable way.
Acute phase reactants add little to composite disease activity indices for rheumatoid arthritis: validation of a clinical activity score
Authors: Aletaha Daniel , Nell Valerie PK , Stamm Tanja , Uffmann Martin , Pflugbeil Stephan , Machold Klaus , Smolen Josef S
Published: April 2005

Introduction

Frequent assessments of rheumatoid arthritis (RA) disease activity allow timely adaptation of therapy, which is essential in preventing disease progression. However, values of acute phase reactants (APRs) are needed to calculate current composite activity indices, such as the Disease Activity Score (DAS)28, the DAS28-CRP (i.e. the DAS28 using C-reactive protein instead of erythrocyte sedimentation rate) and the Simplified Disease Activity Index (SDAI). We hypothesized that APRs make limited contribution to the SDAI, and that an SDAI-modification eliminating APRs – termed the Clinical Disease Activity Index (CDAI; i.e. the sum of tender and swollen joint counts [28 joints] and patient and physician global assessments [in cm]) – would have comparable validity in clinical cohorts.

Method

Data sources comprised an observational cohort of 767 RA patients (average disease duration 8.1 ± 10.6 years), and an independent inception cohort of 106 patients (disease duration 11.5 ± 12.5 weeks) who were followed prospectively.

Results

Our clinically based hypothesis was statistically supported: APRs accounted only for 15% of the DAS28, and for 5% of the SDAI and the DAS28-CRP. In both cohorts the CDAI correlated strongly with DAS28 (R = 0.89–0.90) and comparably to the correlation of SDAI with DAS28 (R = 0.90–0.91). In additional analyses, the CDAI when compared to the SDAI and the DAS28 agreed with a weighted kappa of 0.70 and 0.79, respectively, and comparably to the agreement between DAS28 and DAS28-CRP. All three scores correlated similarly with Health Assessment Questionnaire (HAQ) scores (R = 0.45–0.47). The average changes in all scores were greater in patients with better American College of Rheumatology response (P < 0.0001, analysis of variance; discriminant validity). All scores exhibited similar correlations with radiological progression (construct validity) over 3 years (R = 0.54–0.58; P < 0.0001).

Conclusion

APRs add little information on top (and independent) of the combination of clinical variables included in the SDAI. A purely clinical score is a valid measure of disease activity and will have its greatest merits in clinical practice rather than research, where APRs are usually always available. The CDAI may facilitate immediate and consistent treatment decisions and help to improve patient outcomes in the longer term.
Augmented IL-10 production and redox-dependent signaling pathways in glucose-6-phosphate dehydrogenase-deficient mouse peritoneal macrophages
Authors: Wilmanski Jeanette , Siddiqi Muhammad , Deitch Edwin A , Spolarics Zoltán
Published: April 2005

Glucose-6-phosphate dehydrogenase (G6PD) supports cellular antioxidant pathways. G6PD deficiency is associated with malaria protection but was shown to worsen the clinical course to injury. This study tested whether G6PD deficiency manifests in altered cytokine responses using peritoneal macrophages from a G6PD-deficient mouse model with a degree of defect similar to the common type A– human G6PD deficiency. Lipopolysaccharide (LPS)-induced interleukin (IL)-10 and IL-12 production was doubled in G6PD-deficient macrophages compared with wild-type (WT). Protein kinase C (PKC) activation by phorbol-ester prior to LPS resulted in a fivefold greater IL-10 production in G6PD-deficient macrophages compared with WT. Interferon-γ treatment prior to LPS augmented IL-12 production in G6PD-deficient and WT macrophages and partially inhibited IL-10 production by G6PD-deficient macrophages. The antioxidants (N-acetyl-L-cysteine and glutathione ethyl-ester) blunted IL-10 and IL-12 production, indicating a role for oxidative stress in the observed response differences between deficient and WT macrophages. LPS-induced activation of nuclear factor-κB, cyclic adenosine monophosphate response element-binding protein, and specificity protein 3 was augmented in G6PD-deficient cells compared with WT. The PKCδ inhibitor Rottlerin inhibited IL-10 and IL-12 production at different 50% effective-dose concentrations between deficient and WT macrophages, indicating elevated PKCδ activity in deficient cells. This study reveals that activated G6PD-deficient macrophages display an augmented production of cytokines with a prominent impact on IL-10 production. The altered cytokine responses are associated with augmented activation of redox-dependent transcription factors and PKCδ. Alterations in signaling pathways and associated changes in cytokine production may play a role in modulating the inflammatory responses following bacterial or malarial infections in G6PD deficiency.
Leukocyte apoptosis and its significance in sepsis and shock
Authors: Wesche Doreen E , Lomas-Neira Joanne L , Perl Mario , Chung Chun-Shiang , Ayala Alfred
Published: April 2005

Sepsis and multiple organ failure continue to be significant problems among trauma, burn, and the critically ill patient population. Thus, a number of laboratories have focused on understanding the role of altered apoptotic cell death in contributing to immune and organ dysfunction seen in sepsis and shock. Immune cells that undergo altered apoptotic changes include neutrophils, macrophages, dendritic cells, as well as various lymphocyte populations. Evidence of epithelial as well as endothelial cell apoptotic changes has also been reported. Although mediators such as steroids, tumor necrosis factor, nitric oxide, C5a, and Fas ligand (FasL) appear to contribute to the apoptotic changes, their effects are tissue- and cell population-selective. As inhibiting Fas-FasL signaling (e.g., gene deficiency, Fas fusion protein, or Fas short interfering RNA administration), caspase inhibition (caspase mimetic peptides), and/or the overexpression of downstream antiapoptotic molecules (e.g., Bcl-2, Akt) improve survival of septic mice, it not only demonstrates the pathological significance of this process but points to novel targets for the treatment of sepsis.
T cells from paroxysmal nocturnal haemoglobinuria (PNH) patients show an altered CD40-dependent pathway
Authors: Terrazzano Giuseppe , Sica Michela , Becchimanzi Cristina , Costantini Silvia , Rotoli Bruno , Zappacosta Serafino , Alfinito Fiorella , Ruggiero Giuseppina
Published: April 2005

Paroxysmal nocturnal haemoglobinuria (PNH) is a haematopoiesis disorder characterized by the expansion of a stem cell bearing a somatic mutation in the phosphatidylinositol glycan-A (PIG-A) gene, which is involved in the biosynthesis of the glycosylphosphatidylinositol (GPI) anchor. A number of data suggest the inability of the PIG-A mutation to account alone for the clonal dominance of the GPI-defective clone and for the development of PNH. In this context, additional immune-mediated mechanisms have been hypothesized. We focused on the analysis of T lymphocytes in three PNH patients bearing a mixed GPI+ and GPI– T cell population and showing a marked cytopenia. To analyze the biological mechanisms underlying the control of T cell homeostasis in PNH, we addressed the study of CD40-dependent pathways, suggested to be of crucial relevance for the control of autoreactive T cell clones. Our data revealed significant, functional alterations in GPI+ and GPI– T cell compartments. In the GPI– T cells, severe defects in T cell receptor-dependent proliferation, interferon-γ production, CD25, CD54, and human leukocyte antigen-DR surface expression were observed. By contrast, GPI+ T lymphocytes showed a significant increase of all these parameters, and the analysis of CD40-dependent pathways revealed a functional persistence of CD154 expression on the CD48+CD4+ lymphocytes. The alterations of the GPI+ T cell subset could be involved in the biological mechanisms underlying PNH pathogenesis.
Fas-mediated death and sensory adaptation limit the pathogenic potential of autoreactive T cells after strong antigenic stimulation
Authors: Ryan Kelli R , McCue David , Anderton Stephen M
Published: April 2005

The ability of autoreactive T cells to induce autoimmune pathology is dependent on their ability to respond to the level of autoantigen presented in the target organ. Emerging evidence suggests that at the population level, T cell sensitivity for self can be reduced by deletion of those cells bearing high-affinity T cell receptors (TCRs) or by sensory adaptation of individual cells. Here, we have investigated the mechanisms that prevent the induction of experimental autoimmune encephalomyelitis (EAE) when myelin basic protein (MBP)-reactive T cells are exposed to a strong, antigenic stimulus. Stimulation of MBP-reactive TCR transgenic T cells with a superagonist peptide led to extensive activation-induced cell death (AICD) through Fas signaling. Using T cells lacking Fas, we found that disruption of this deletional mechanism only partially increased EAE in response to superagonist, failing to restore susceptibility to the level found in response to the wild-type MBP peptide. A significant fraction of the MBP-reactive T cells was able to avoid AICD in response to superagonist, but these cells had a reduced sensitivity for an antigen that correlated with elevated levels of CD5. Therefore, when TCR affinity is fixed, autoreactive T cell sensitivity can be shifted to below a threshold for harm by a combination of AICD and sensory adaptation.
Asymmetrical protein kinase A activity establishes neutrophil cytoskeletal polarity and enables chemotaxis
Authors: Jones Samuel L , Sharief Yousuf
Published: April 2005

Neutrophil chemotaxis requires precise spatial organization of the actin cytoskeleton and integrin activation to polarize the cell and enable migration. Protein kinase A (PKA) activity regulates integrin activation and actin cytoskeletal organization, suggesting that PKA is a key element in the mechanism regulating neutrophil chemotaxis. Our hypothesis is that asymmetrical PKA activity is critical for establishing neutrophil adhesive and cytoskeletal polarity required for migration during chemotaxis. To test this hypothesis, we first determined that global treatment with the PKA inhibitor KT5720 decreased formylated Met-Leu-Phe (fMLF)-induced migration. The ability of PKA inhibitors to reduce migration correlated with increased overall β2 integrin cell-surface expression, affinity activation, and cellular adhesion. We next determined whether asymmetrical PKA activity was sufficient to induce migration. Exposure to gradient of the PKA inhibitors KT5720 or H-89 or a stearated, cell-permeant peptide (St-Ht31), which inhibits PKA binding to anchorage proteins, stimulated neutrophil migration in a chemotaxis chamber. Global treatment with KT5720 abolished the ability of fMLF to polarize the neutrophil actin cytoskeleton. In contrast to global treatment with KT5720, a point source of KT5720 was sufficient to polarize the actin cytoskeleton. The ability of KT5720 and St-Ht31 to stimulate migration was abolished by pretreatment with the phosphatidylinositol-3 kinase (PI-3K) inhibitors wortmannin and LY294002. These data suggest that asymmetrical PKA activity is necessary and sufficient for actin cytoskeletal polarization and migration during neutrophil chemotaxis. In addition, our data suggest PI-3K is an effector of PKA during chemotaxis.
Minocycline attenuates T cell and microglia activity to impair cytokine production in T cell-microglia interaction
Authors: Giuliani Fabrizio , Hader Walter , Yong V Wee
Published: April 2005

Minocycline, a tetracycline with anti-inflammatory properties, has been reported to down-regulate the activity of microglia, whose activation occurs in inflammatory and degenerative diseases of the central nervous system, such as multiple sclerosis and Alzheimer's disease. In these disorders, a T cell component is also evident, and we have demonstrated previously that the interaction of activated T cells with microglia led to the substantial increase in tumor necrosis factor α (TNF-α) levels. Here, we report that minocycline decreases TNF-α levels produced in human T cell-microglia interaction. This effect is mediated by a direct action of minocycline on the activated T cells and on microglia, which resulted in the decreased ability of T cells to contact microglia. In correspondence, minocycline decreased the expression on T cells of the CD40 ligand (CD40L), a key molecule regulating the contact-mediated interaction of T cells with microglia. These results demonstrate that the mechanism of action of minocycline involves not only microglia but also T cells and their subsequent activation of microglia. The capacity of minocycline to down-regulate CD40L on T cells may provide a new means to target the CD40-CD40L pathway, which regulates several inflammatory processes.
Angiotensin II increases human monocyte matrix metalloproteinase-1 through the AT2 receptor and prostaglandin E2: implications for atherosclerotic plaque rupture
Authors: Kim Min P , Zhou Min , Wahl Larry M
Published: April 2005

Angiotensin II (Ang II)-mediated hypertension increases the risk for acute coronary syndrome, a consequence of atherosclerotic plaque rupture, which may be caused by matrix metalloproteinases (MMPs). Here, we show that human primary monocytes stimulated with tumor necrosis factor α (TNF-α) and granulocyte macrophage-colony stimulating factor (GM-CSF) release Ang II, which is an integral component of the signal transduction pathway that leads to MMP-1 production. An Ang II-mediated increase in MMP-1 synthesis occurred only in conjunction with cytokine stimulation. Moreover, Ang II mediated its effect through the Ang II type 2 (AT2) receptor, as demonstrated by enhancement of MMP-1 production by an AT2 agonist, CGP-42112A, and inhibition of MMP-1 production by PD1233319, an AT2 antagonist. Additionally, exogenous Ang II caused a significant enhancement in MMP-1 production by cytokine-stimulated monocytes, and the most effective enhancement occurrred when Ang II was added 6 h after stimulation. Furthermore, Ang II and the AT2 agonist increased prostaglandin E2 (PGE2), which in turn mediated the increase in MMP-1, as shown by the inhibition of MMP-1 by indomethacin or aspirin. In contrast, the AT2 antagonist inhibited the PGE2 production induced by TNF-α and GM-CSF. Ang II, through its interaction with the AT2 receptor, has a central role in mediating the PGE2-dependent production of MMP-1 by monocytes stimulated with TNF-α and GM-CSF. These observations provide insight into the association between hypertension and acute coronary syndrome and a possible mechanism by which Ang-converting enzyme inhibitor and aspirin may reduce the risk for heart attacks.
Antiobesity Effect of a Melanin-Concentrating Hormone 1 Receptor Antagonist in Diet-Induced Obese Mice
Authors: Mashiko Satoshi , Ishihara Akane , Gomori Akira , Moriya Ryuichi , Ito Makoto , Iwaasa Hisashi , Matsuda Masao , Feng Yue , Shen Zhu , Marsh Donald J. , Bednarek Maria A. , MacNeil Douglas J. , Kanatani Akio
Published: April 2005

Melanin-concentrating hormone (MCH) is a cyclic orexigenic peptide expressed in the lateral hypothalamus, which plays an important role in regulating energy balance. To elucidate the physiological role of MCH in obesity development, the present study examined the effect of a selective MCH1 receptor (MCH1R) antagonist in the diet-induced obesity mouse model. The MCH1R antagonist has high affinity and selectivity for MCH-1R and potently inhibits intracerebroventricularly injected MCH-induced food intake in Sprague Dawley rats. Chronic intracerebroventricular infusion of the MCH1R antagonist (7.5 μg/d) completely suppressed body weight gain in diet-induced obese mice during the treatment periods and significantly decreased cumulative food intake, by 14%. Carcass analysis showed that the MCH1R antagonist resulted in a selective decrease of body fat in the diet-induced obese mice. In addition, the MCH1R antagonist ameliorated the obesity-related hypercholesterolemia, hyperinsulinemia, hyperglycemia, and hyperleptinemia. These results indicate that MCH has a major role in the development of diet-induced obesity in mice and that a MCH1R antagonist might be a useful candidate as an antiobesity agent.
Potential Role for Human Cytochrome P450 3A4 in Estradiol Homeostasis
Authors: Yu Ai-Ming , Fukamachi Katsumi , Krausz Kristopher W. , Cheung Connie , Gonzalez Frank J.
Published: April 2005

Previously, a human CYP3A4-transgenic (Tg-CYP3A4) mouse line was reported to exhibit enhanced metabolism of midazolam by cytochrome P450 3A4 (CYP3A4) expressed in small intestine. Here we show that expression of CYP3A4 and murine cyp3a and cyp2b was both age and sex dependent. CYP3A4 was expressed in the livers of male and female Tg-CYP3A4 mice at 2 and 4 wk of age. Since 6 wk, CYP3A4 was undetectable in male livers, whereas it was constitutively expressed in female livers at decreased levels (3- to 5-fold). Pregnenolone 16α-carbonitrile markedly induced hepatic CYP3A4 expression, and the level was higher in females than males. Induction of intrinsic murine cyp3a and cyp2b was also sex dependent. Tg-CYP3A4 females were found to be deficient in lactation, leading to a markedly lower pup survival. The mammary glands of the Tg-CYP3A4 lactating mothers had underdeveloped alveoli with low milk content. Furthermore, β-casein and whey acidic protein mRNAs were expressed at markedly lower levels in Tg-CYP3A4 pregnant and nursing mouse mammary glands compared with wild-type mice. This impaired lactation phenotype was associated with significantly reduced serum estradiol levels in Tg-CYP3A4 mice. A pharmacokinetic study revealed that the clearance of iv administrated [3H]estradiol was markedly enhanced in Tg-CYP3A4 mice compared with wild-type mice. These results suggest that CYP3A4 may play an important role in estradiol homeostasis. This may be of concern for treatment of pregnant and lactating women because CYP3A4 gene expression and enzymatic activity can be potentially modified by CYP3A4 inhibitors or inducers in medications, supplements, beverages, and diet.
Human Growth Hormone-Releasing Factor (hGRF)1–29-Albumin Bioconjugates Activate the GRF Receptor on the Anterior Pituitary in Rats: Identification of CJC-1295 as a Long-Lasting GRF Analog
Authors: Jetté Lucie , Léger Roger , Thibaudeau Karen , Benquet Corinne , Robitaille Martin , Pellerin Isabelle , Paradis Véronique , van Wyk Pieter , Pham Khan , Bridon Dominique P.
Published: April 2005

In vivo bioconjugation to the free thiol on Cys34 of serum albumin by a strategically placed reactive group on a bioactive peptide is a useful tool to extend plasma half-life. Three maleimido derivates of human GH-releasing factor (hGRF)1–29 were synthesized and bioconjugated to human serum albumin ex vivo. All three human serum albumin conjugates showed enhanced in vitro stability against dipeptidylpeptidase-IV and were bioactive in a GH secretion assay in cultured rat anterior pituitary cells. When the maleimido derivatives were individually administered sc to normal male Sprague Dawley rats, an acute secretion of GH was measured in plasma. The best compound, CJC-1295, showed a 4-fold increase in GH area under the curve over a 2-h period compared with hGRF1–29. CJC-1295, a tetrasubstituted form of hGRF1–29 with an added Nε-3-maleimidopropionamide derivative of lysine at the C terminus, was selected for further pharmacokinetic evaluation, where it was found to be present in plasma beyond 72 h. A Western blot analysis of the plasma of a rat injected with CJC-1295 showed the presence of a CJC-1295 immunoreactive species on the band corresponding to serum albumin, appearing after 15 min and remaining in circulation beyond 24 h. These results led to the identification of CJC-1295 as a stable and active hGRF1–29 analog with an extended plasma half-life.
Estrogen Can Act via Estrogen Receptor α and β to Protect Hippocampal Neurons against Global Ischemia-Induced Cell Death
Authors: Miller Nora R. , Jover Teresa , Cohen Hillel W. , Zukin R. Suzanne , Etgen Anne M.
Published: April 2005

Estradiol at physiological concentrations intervenes in apoptotic death cascades and ameliorates neuronal death in experimental models of focal and global ischemia. The cellular targets that mediate estradiol protection of hippocampal neurons in global ischemia are, however, unclear. The present study examined the hypothesis that estradiol protects hippocampal neurons in ovariectomized rats via estrogen receptor (ER)α and/or β. Estradiol (14 d pretreatment) afforded robust protection of CA1 neurons against global ischemia-induced death. The broad-spectrum ER antagonist ICI 182,780 (intracerebroventricularly, 0 and 12 h after ischemia) abolished estrogen protection, consistent with a role for ERs. To evaluate the potential roles of ERα vs. ERβ in estrogen protection, we administered subtype-selective agonists for 14 d before and 7 d after ischemia. The ERα-selective agonist propyl pyrazole triol (PPT, 10 mg/kg) and ERβ-selective agonist WAY 200070–3 (1 mg/kg) produced nearly complete protection of CA1 neurons in approximately 50% of the animals. PPT, but not WAY 200070–3, at doses used for protection, elicited lordosis, induced negative feedback inhibition of LH release, and reduced weight gain. These findings establish the efficacy of the PPT dose in neuroendocrine assays and specificity of WAY 200070–3 for ERβ. We also examined the ability of estradiol and neuronal injury to regulate ERα and ERβ expression. Both estradiol and global ischemia markedly increased ERα, but not ERβ, protein in CA1. These data indicate that estradiol can act via ERα and ERβ to protect CA1 neurons from global ischemia-induced death and that both estradiol and global ischemia modulate ERα expression in hippocampal CA1.
p38 Mitogen-Activated Protein Kinase (MAPK) Is a Key Mediator in Glucocorticoid-Induced Apoptosis of Lymphoid Cells: Correlation between p38 MAPK Activation and Site-Specific Phosphorylation of the Human Glucocorticoid Receptor at Serine 211
Authors: Miller Aaron L. , Webb M. Scott , Copik Alicja J. , Wang Yongxin , Johnson Betty H. , Kumar Raj , Thompson E. Brad
Published: April 2005

Glucocorticoids (GCs) induce apoptosis in lymphoid cells through activation of the GC receptor (GR). We have evaluated the role of p38, a MAPK, in lymphoid cell apoptosis upon treatment with the synthetic GCs dexamethasone (Dex) or deacylcortivazol (DAC). The highly conserved phosphoprotein p38 MAPK is activated by specific phosphorylation of its threonine180 and tyrosine182 residues. We show that Dex and DAC stimulate p38 MAPK phosphorylation and increase the mRNA of MAPK kinase 3, a specific immediate upstream activator of p38 MAPK. Enzymatic assays confirmed elevated activity of p38 MAPK. Pharmacological inhibition of p38 MAPK activity was protective against GC-driven apoptosis in human and mouse lymphoid cells. In contrast, inhibition of the MAPKs, ERK and cJun N-terminal kinase, enhanced apoptosis. Activated p38 MAPK phosphorylates specific downstream targets. Because phosphorylation of the GR is affected by MAPKs, we examined its phosphorylation state in our system. We found serine 211 of the human GR to be a substrate for p38 MAPK both in vitro and intracellularly. Mutation of this site to alanine greatly diminished GR-driven gene transcription and apoptosis. Our results clearly demonstrate a role for p38 MAPK signaling in the pathway of GC-induced apoptosis of lymphoid cells.
Involvement of the Diels–Alderases in the Biosynthesis of Natural Products
Authors: Oikawa Hideaki
Published: April 2005

Recent studies on a novel C–C bond formation enzyme, Diels–Alderase, show that this unusual enzyme is involved in the biosynthesis of secondary metabolites. In this account, I describe studies related to Diels–Alderases including biomimetic synthesis, the biological utilization of the Diels–Alder reaction, and natural Diels–Alderases. The function and catalytic mechanism of natural Diels–Alderases, such as solanapyrone synthase, lovastatin nonaketide synthase, and macrophomate synthase, are of great interest due to the diversity of molecular skeletons in natural Diels–Alder adducts. The first structure analysis of macrophomate synthase provided information on detailed mechanisms regarding active site organization among the substrates, metal and amino acid residues, and regarding how to avoid product inhibition.
Construction and Control of Self-Assembly of Amyloid and Fibrous Peptides
Authors: Mihara Hisakazu , Matsumura Sachiko , Takahashi Tsuyoshi
Published: April 2005

The aggregation of peptides and proteins into amyloid fibrils is most commonly associated with a variety of serious diseases such as Alzheimer’s disease and the transmissible spongiform encephalopathies (prion diseases). Amyloid-like fibrils are undesirable states for proteins as biomolecules, however, these are fascinating nanoconstructs because of their highly ordered tertiary structure in which numerous β-stranded polypeptide chains align regularly. These kinds of fibrous peptides have the potential to be engineered into ones revealing basic insights into amyloid formation and protein folding, as well as developing novel peptidyl nanoscale materials. We have demonstrated that de novo designed peptides undergo self-initiated structural transition and fibril formation, showing representative properties of amyloid. Cofibril formation from two, three, or four peptide species with well-designed amino acid sequences was achieved, so that the charged residues within the β-strands were complementary to each other. This homologous recognition mechanism can be applied for the inhibition of the fibril formation. Meanwhile, cofibril formation indicates a possibility of functionalizing the fibrils by co-assembling of peptides with various elements to develop a fibrous peptide material as a well-ordered nanoconstruct. Another designing approach demonstrated the production of unique straight nanofibers with defined widths. The fibrils may make a nanoscaffold onto which a variety of functional groups can be arranged. The studies on engineering fibrous peptides will afford insight into desease-related amyloid formation and will help to develop nanoscale fibrous constructs.
14 Step-15 Electron Reversible Redox Behavior of Tetrameric Oligomer of Oxo-Bridged Triruthenium Cluster
Authors: Hamaguchi Tomohiko , Nagino Haruko , Hoki Katsunori , Kido Hiroaki , Yamaguchi Tadashi , Breedlove Brian K , Ito Tasuku
Published: April 2005

Pyrazine-bridged trimeric and tetrameric oligomers of triruthenium clusters, [{Ru3O(CH3CO2)6(CO)(py)}-(μ-pz)-{Ru3O(CH3CO2)6(CO)}-(μ-pz)-{Ru3O(CH3CO2)6(py)2}]+ (1) and [{Ru3O(CH3CO2)6(CO)(py)}-(μ-pz)-{Ru3O(CH3CO2)6(CO)}-(μ-pz)-{Ru3O(CH3CO2)6(py)}-(μ-pz)-{Ru3O(CH3CO2)6(dmap)2}]2+ (2), were prepared (pz = pyrazine, py = pyridine, dmap = 4-dimethylaminopyridine). Trimer 1 and tetramer 2 show closely spaced 11 step-12 electron and 14 step-15 electron reversible redox waves, respectively, in their cyclic voltammograms in CH3CN. These compounds were designed specifically to incorporate the above-mentioned electrochemical behavior, using the unique redox properties characteristic of triruthenium clusters: (i) each Ru3 cluster unit generally exhibits four reversible single electron waves from Ru3IV,III,III to Ru3II,II,II state; (ii) the redox potentials of the cluster units strongly depend on the basicity of the ancillary ligand; (iii) redox potentials of the Ru3 cluster units vary by 300–500 mV depending on the presence or the absence of a carbonyl ligand on the cluster unit; (iv) in the negative potential region, electronic interaction through the bridging pyrazine between adjacent Ru3 units containing a carbonyl ligand makes the difference in redox potential of each unit larger. 1 and 2 were synthesized by linking Ru3 cluster units with the desired ancillary ligand set in the appropriate order.
Kinetic Study of the Mechanism of Free-Radical Scavenging Action in Curcumin: Effects of Solvent and pH
Authors: Ohara Keishi , Mizukami Wataru , Tokunaga Aiko , Nagaoka Shin-ichi , Uno Hidemitsu , Mukai Kazuo
Published: April 2005

A kinetic study was performed for the free-radical scavenging actions of curcumin and half-curcumin, which has a half-structure of curcumin, in order to clarify the mechanism of free-radical-scavenging in curcumin. The second-order rate constants for radical-scavenging reactions of curcumin and half-curcumin were measured by a stopped-flow spectrophotometer in several organic solvents (methanol, ethanol, acetonitrile, chloroform, and benzene) and in aqueous Triton X-100 (5.0 wt %) micelle solutions at various pH. The difference in the rate constant and solvent dependence between curcumin and half-curcumin suggests that the enol structure with the intramolecular hydrogen-bond of curcumin strongly enhances the radical-scavenging activity. Furthermore, notable pH dependences were observed for the rate constants of curcumin and half-curcumin in micelle solutions, suggesting that the acid–base dissociation equilibrium of phenol-protons in curcumin and half-curcumin affects their radical-scavenging activities.
Biohydrogen Production from Sucrose Using the Light-Harvesting Function of Zinc Chlorophyll-a
Authors: Takeuchi Yumi , Amao Yutaka
Published: April 2005

A biohydrogen production system, has been developed that couples sucrose hydrolysis by invertase and glucose dehydrogenase (GDH) and hydrogen production with a platinum colloid as a catalyst. The system uses the visible light-harvesting function of artificial Zn chlorophyll-a (Zn Chl-a), prepared from Mg Chl-a (obtained from Spilurina). When a sample solution containing sucrose, invertase, nicotinamide adenine dinucreotide (NAD+), Zn Chl-a, methylviologen (MV2+, an electron carrier), and platinum colloid was irradiated, continuous hydrogen production was observed with the irradiation time. The amount of hydrogen production was about 10.5 μmol after 4 h of irradiation under the optimum condition.
In Situ Ore Formation Experiment: Amino Acids and Amino Sugars Trapped in Artificial Chimneys on Deep-Sea Hydrothermal Systems at Suiyo Seamount, Izu-Bonin Arc, Pacific Ocean
Authors: Takano Yoshinori , Marumo Katsumi , Ebashi Toshiomi , Gupta Lallan P , Kawahata Hodaka , Kobayashi Kensei , Yamagishi Akihiko , Kuwabara Tomohiko
Published: April 2005

The present study reports on the bio-organic composition of a deep-sea venting hydrothermal system originating from arc volcanism; the origin of the particulates in hydrothermal fluids from the Suiyo Seamount in the southern Izu-Bonin (Ogasawara) Arc is discussed with regard to amino compounds. Chimney samples on deep-sea hydrothermal systems and core samples at Suiyo Seamount were determined for amino acids, and occasionally amino sugars. Two types of chimney samples were obtained from active hydrothermal systems by submersible vehicles: one was natural chimney (NC) on a hydrothermal natural vent; the other was artificial chimneys (AC), mainly formed by the growth and deposition of sulfide-rich particulate components in a Kuwabara-type in situ incubator (KI incubator). Total hydrolyzed amino acids (THAA) and hydrolyzed hexosamines (HA) in AC ranged from 10.7 nmol/g to 64.0 nmol/g and from 0 nmol/g to 8.1 nmol/g, respectively, while THAA in hydrothermally altered core samples ranged from 26.0 nmol/g to 107.4 nmol/g-rock. The THAA was thus of the same order of magnitude in AC and core samples. The representative biochemical indicator ratios of β-alanine/aspartic acid and γ-aminobutyric acid/glutamic acid were low. This is consistent with a large microbial population and labile subterranean biogenic organic compounds. A micro energy dispersive X-ray spectrometer (μEDX) was used to show that the formation of massive pyrite- and chalcopyrite-ores, the major matrixes of the natural chimney structures, were processed during hydrothermal activity. These data suggest that labile particulate organic matter (POM) and/or dissolved organic matter (DOM) from hydrothermal fluid were continuously trapped to form concentrated organic matter in a sulfide-rich matrix.
Anomalous Salting-Out Effect of Sodium Perchlorate on fac-Tris(glycinato)cobalt(III)
Authors: Yoshimura Yasuki
Published: April 2005

The effect of NaClO4 on fac- and mer-isomers of tris(amino acidato)cobalt(III) ([Co(aa)3]) was examined by determining their solubilities in aqueous NaClO4 solutions. An addition of NaClO4 increased the solubilities of both the isomers of [Co(aa)3] except for tris(glycinato)cobalt(III) ([Co(gly)3]). While the solubility of mer-[Co(gly)3] was also increased by the addition of NaClO4, NaClO4 brought about abnormally large decrease in the solubility of fac-[Co(gly)3]. The addition of NaClO4 also produced a decrease in the solubility of tris(acetylacetonato)cobalt(III) ([Co(acac)3]). The salting-out effect of NaClO4 on fac-[Co(gly)3] was compared with that on [Co(acac)3]. While both the enthalpy (ΔtrH°) and entropy of transfer (ΔtrS°) from water to aqueous NaClO4 solutions for [Co(acac)3] were positive, those for fac-[Co(gly)3] were generally negative. On the basis of these results, an origin for the salting-out effect of NaClO4 on fac-[Co(gly)3] is discussed.
Novel Assembly of Resorcin[4]arene to Form a Self-Dimer Directly Linked via O–H···π Interaction in the Solid State
Authors: Aoki Katsuyuki , Shimizu Chiharu , Fujisawa Ikuhide
Published: April 2005

When tetraethylresorcin[4]arene is crystallized from dioxane, it forms a “head-to-head” arranged self-dimer directly connected by non-conventional O–H···π interaction. The resorcinarene molecule adopts the unusual flattened-cone conformation, where two of the four intramolecular hydrogen bonds are broken.
Magnetic Alignment of Fiber-Shaped Pseudoisocyanine J Aggregates in a Gelated Solution
Authors: Kitahama Yasutaka , Kimura Yasuyuki , Takazawa Ken , Kido Giyuu
Published: April 2005

An aqueous solution of 1,1′-diethyl-2,2′-quinocyanine bromide (PIC-Br) containing highly concentrated counter ions provided by NaCl was prepared by heating the solution at 90 °C. Upon cooling the solution to room temperature, it transformed into a gel-like state. Optical microscopy revealed that fiber-shaped J aggregates formed a network structure in the gelated solution. By cooling the solution in a magnetic field of 10 T, highly oriented J aggregates were obtained in the gel. Without any additional treatment, the alignment of the fibers was preserved after the gelated solution was removed from the magnetic field. The absorption spectra of the gelated solution showed a strongly polarized J-band, reflecting the high degree of orientation of the magnetically aligned J aggregates.