bluuebunny/crossref_metadata_2025 huggingface dataset:
The Max homodimeric b‐HLH‐LZ significantly interferes with the specific heterodimerization between the c‐Myc and Max b‐HLH‐LZ in absence of DNA: a quantitative analysis
Authors: McDuff François‐Olivier , Naud Jean‐François , Montagne Martin , Sauvé Simon , Lavigne Pierre
Published: February 2009

Specific heterodimerization plays a crucial role in the regulation of the biology of the cell. For example, the specific heterodimerization between the b‐HLH‐LZ transcription factors c‐Myc and Max is a prerequisite for c‐Myc transcriptional activity that leads to cell growth, proliferation and tumorigenesis. On the other hand, the Mad proteins can compete with c‐Myc for Max. The Mad/Max heterodimer antagonizes the effect of the c‐Myc/Max heterodimer. In this contribution, we have focused on the specific heterodimerization between the b‐HLH‐LZ domains of c‐Myc and Max using CD and NMR. While the c‐Myc and Max b‐HLH‐LZ domains are found to preferentially form a heterodimer; we demonstrate for the first time that a significant population of the Max homodimeric b‐HLH‐LZ can also form and hence interferes significantly with the specific heterodimerization. This indicates that the Max/Max homodimer can also interfere with c‐Myc/Max functions, therefore adding to the complexity of the regulation of transcription by the Myc/Max/Mad network. The demonstration of the existence of the homodimeric population was made possible by the application of numerical routines that enable the simulation of composite spectroscopic signal (e.g. CD) as a function of temperature and total concentration of proteins. From a systems biology perspective, our routines may be of general interest as they offer the opportunity to treat many competing equilibriums in order to predict the probability of existence of protein complexes. Copyright © 2009 John Wiley & Sons, Ltd.
Spatial variation of intestinal skatole production and microbial community in Jinhua and Landrace pigs
Authors: Li Cai‐Yan , Wu Chao , Liu Jian‐Xin , Wang Yi‐Zhen , Wang Jia‐Kun
Published: February 2009

BACKGROUND: An excessive accumulation of skatole in pigs is a major contributor to boar taint. Intestinal skatole concentrations may vary among different pig segments and breeds. The objective of this study was to evaluate the spatial variation of intestinal skatole production and the microbial community in local Jinhua and exotic Landrace pigs.

RESULTS: For both breeds, skatole concentration increased towards the rectum and segment had a significant effect on skatole (P < 0.001). The caecal skatole concentration in Landrace was significantly lower than proximal, distal colonic and rectal skatole levels (P < 0.05). Compared with Jinhua pigs, the rectal skatole and proximal and distal colonic indole levels were significantly higher in Landrace pigs (P < 0.05). Volatile fatty acids were significantly affected by breed except for isobutyrate and isovalerate (P < 0.05), with higher butyrate level and lower pH in Landrace pigs (P < 0.05). There were no significant differences in mitosis and apoptosis for the two breeds. The denaturing gradient gel electrophoresis profile showed differences between breeds and segments within one breed, though some bands were common to all samples.

CONCLUSION: The higher skatole levels in Landrace pigs may be not associated with higher intestinal apoptosis. The results suggested that pig genotype plays a role in the establishment of the host‐specific microbiota and that the variations in fermentation patterns are more likely to explain differences in intestinal skatole production. Copyright © 2009 Society of Chemical Industry
Implications of spatial and temporal changes in concentration of pyruvate and glucose in onion (Allium cepa L.) bulbs during controlled atmosphere storage
Authors: Abayomi Louise A , Terry Leon A
Published: February 2009

BACKGROUND: Pungency and perceived sweetness are important quality assurance parameters for onion producers; however, there is still a paucity of information describing the spatial changes within the bulb of some taste‐related compounds during storage. Accordingly, onion bulbs of cultivars (cvs.), SS1 (low pungency, low dry matter) and Renate (pungent, high dry matter) bulbs, were divided into 12 sections and both spatial and temporal variations of pyruvate and glucose were recorded during standard controlled atmosphere storage.

RESULTS: Pyruvate within cv. SS1 bulbs reached 8.3 µmol g−1 fresh weight (FW) from pre‐storage levels of less than 3.4 µmol g−1 FW, whilst pyruvate changes in cv. Renate remained in the ‘pungent’ category, between 12 µmol g−1 FW and 15 µmol g−1 FW; thus having fewer implications for marketing and quality assurance. Glucose concentrations were significantly higher for both cvs. in the neck region as compared to basal tissue. Higher glucose levels were recorded in the core of the bulb than in outer scales of cv. Renate. The opposite was found for cv. SS1. There was an inverse correlation of − 0.69 and − 0.87 between glucose and pyruvate for cvs. SS1 and Renate, respectively.

CONCLUSION: In order to measure overall bulb flavour, it is recommended that sampling procedures, particularly for routine pungency determination, be carried out on bulb quarters or wedges rather than equatorial sections. Copyright © 2009 Society of Chemical Industry
Structure elucidation of three diphenyl ether derivatives from the mangrove endophytic fungus SBE‐14 from the South China Sea
Authors: Liu Fan , Li Qing , Yang Hong , Cai Xiao‐Ling , Xia Xue‐Kui , Chen Sheng‐Ping , Li Meng‐Feng , She Zhi‐Gang , Lin Yong‐Cheng
Published: February 2009

Two new natural products, tenelate A (1) and B (2), together with the known compound, tenellic acid C (3), were isolated from the mangrove endophytic fungus Talaromyces sp. (SBE‐14), from the South China Sea. Their structures were elucidated by spectroscopic methods, mainly 1D and 2D NMR techniques. Copyright © 2009 John Wiley & Sons, Ltd.
Fast acquisition scheme for achieving high‐resolution MRS with J‐scaling under inhomogeneous fields
Authors: Chen Xi , Lin Meijin , Chen Zhong , Zhong Jianhui
Published: February 2009

Intermolecular multiple‐quantum coherences (iMQCs) can refocus the phase dispersion caused by magnetic field inhomogeneities while preserving the chemical shift, so they have been applied to achieve high‐resolution MR spectroscopy free of line broadening caused by susceptibility gradients. However, previous iMQC high‐resolution methods all require two‐dimensional spectra sampling of the full range of chemical shifts of solute evolutions in both F1 and F2 dimensions, resulting in a prolonged scanning time for data acquisition. In this work, sparse sampling in the t1 dimension and subsequent fold‐over correction are used to speed up the intermolecular zero‐quantum coherence spectroscopy by up to 50 times on high‐field MR systems. Furthermore, three types of spectra with homo‐decoupling, original J‐coupling constants, and doubled J‐coupling constants respectively are obtained with manipulation of the t1 period. The water suppression is also improved by the combined use of intermolecular double‐quantum filter and excitation sculpting. The feasibilities of this group of new sequences are demonstrated by experiments using an agar gel phantom with an air bubble, in vitro pig brain tissues and an intact postmortem mudskipper. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Postmortem MRI of human brain hemispheres: T2 relaxation times during formaldehyde fixation
Authors: Dawe Robert J. , Bennett David A. , Schneider Julie A. , Vasireddi Sunil K. , Arfanakis Konstantinos
Published: February 2009

Unlike in vivo imaging, postmortem MRI allows for invasive examination of the tissue specimen immediately after the MR scan. However, natural tissue decomposition and chemical fixation cause the postmortem tissue's MRI properties to be different from those found in vivo. Moreover, these properties change as postmortem fixation time elapses. The goal of this study was to characterize the T2 relaxation changes that occur over time in cadaveric human brain hemispheres during fixation. Five hemispheres immersed in formaldehyde solution were scanned on a weekly basis for 3 months postmortem, and once again at 6 months postmortem. The T2 relaxation times were measured throughout the hemispheres. Over time, T2 values near the edges of the hemispheres decreased rapidly after death, while T2 values of deep tissue decreased more slowly. This difference is likely due to the relatively large distance from the hemisphere surface, and other barriers limiting diffusion of formaldehyde molecules to deep tissues. In addition, T2 values in deep tissue did not continuously decay to a plateau, but instead reached a minimum and then increased to a plateau. This final increase may be due to the effects of prolonged tissue decomposition, a hypothesis that is supported by numerical simulations of the fixation process. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Multicomponent T2 relaxation analysis in cartilage
Authors: Reiter David A. , Lin Ping‐Chang , Fishbein Kenneth W. , Spencer Richard G.
Published: February 2009

MR techniques are sensitive to the early stages of osteoarthritis, characterized by disruption of collagen and loss of proteoglycan (PG), but are of limited specificity. Here, water compartments in normal and trypsin‐degraded bovine nasal cartilage were identified using a nonnegative least squares multiexponential analysis of T2 relaxation. Three components were detected: T2,1 = 2.3 ms, T2,2 = 25.2 ms, and T2,3 = 96.3 ms, with fractions w1 = 6.2%, w2 = 14.5%, and w3 = 79.3%, respectively. Trypsinization resulted in increased (P < 0.01) values of T2,2 = 64.2 ms and T2,3 = 149.4 ms, supporting their assignment to water compartments that are bound and loosely associated with PG, respectively. The T2 of the rapidly relaxing component was not altered by digestion, supporting assignment to relatively immobile collagen‐bound water. Relaxation data were simulated for a range of TE, number of echoes, and SNR to guide selection of acquisition parameters and assess the accuracy and precision of experimental results. Based on this, the expected experimental accuracy of measured T2s and associated weights was within 2% and 4% respectively, with precision within 1% and 3%. These results demonstrate the potential of multiexponential T2 analysis to increase the specificity of MR characterization of cartilage. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
High‐order doubly asymptotic open boundaries for scalar wave equation
Authors: Prempramote Suriyon , Song Chongmin , Tin‐Loi Francis , Lin Gao
Published: February 2009

High‐order doubly asymptotic open boundaries are developed for transient analyses of scalar waves propagating in a semi‐infinite layer with a constant depth and a circular cavity in a full‐plane. The open boundaries are derived in the frequency domain as doubly asymptotic continued fraction solutions of the dynamic stiffness of the unbounded domains. Each term of the continued fraction is a linear function of the excitation frequency. The constants of the continued fraction solutions are determined recursively. The continued fraction solution is expressed in the time domain as ordinary differential equations, which can be solved by standard time‐stepping schemes. No parameters other than the orders of the low‐ and high‐frequency expansions need to be selected by users. Numerical experiments demonstrate that evanescent waves and long‐time (low‐frequency) responses are simulated accurately. In comparison with singly asymptotic open boundaries, significant gain in accuracy is achieved at no additional computational cost. Copyright © 2009 John Wiley & Sons, Ltd.
Type 2 diabetes in pregnancy: more to come?
Authors: Coulthard T , Hawthorne G
Published: February 2009

The objective of this study was to determine the rate of increase in pregnancies complicated by type 2 diabetes in the former UK Northern health region between 1996 and 2006.

Since 1993, all data for women with pregnancies complicated by pre‐existing type 1 and type 2 diabetes have been prospectively collected by the Northern Diabetes Pregnancy Survey. The annual incidence of women with type 2 diabetes was collected and further analysed for associations with age, body mass index and ethnicity, perinatal mortality and stillbirth rates.

There was an approximate four‐fold increase in type 2 diabetes in pregnancy (r2 = 0.85) during the 11 years. The majority (80.8%) of the women were white, although ethnic minorities were over‐represented; 88.2% women were overweight or obese. Stillbirth and perinatal mortality rates were four to five times higher than the national average.

The number of pregnancies in women with type 2 diabetes is increasing. This has important implications for primary care and maternity service provision as these pregnancies are high risk. Women with type 2 diabetes will need targeted preconception care and maternity units may need to expand their diabetes service provision if a rise in perinatal mortality is to be prevented. Copyright © 2008 John Wiley & Sons.
The prevalence of risk factors for foot ulceration in Egyptian diabetic patients
Authors: El‐Nahas MR , Gawish HMS , Tarshoby MM , State OI , Boulton AJM
Published: February 2009

The effect of ethnicity on diabetic foot ulceration (DFU), neuropathy and peripheral arterial disease (PAD) remains controversial, with few previous studies from Egypt. The aim of this study was to examine the prevalence of DFU and its risk factors in a cohort of patients presented to the outpatient diabetes clinic at Mansoura University Specialized Medical Hospital.

Over a period of 12 months, 1220 diabetic patients were screened for DFU, neuropathy, PAD, foot deformities, and skin and nail abnormalities.

The mean age was 50.5 ± 10.9 years and 36.8% were male. Diabetes duration was 7.9 ± 5.9 years and BMI 34.5 ± 6.7. The prevalence of active or past foot ulceration was 1.2% and 5.7% respectively. Monofilament insensitivity was found in 124 patients (10.2%). Only 38 patients (3.1%) had absent foot pulses. We found dry skin in 544 patients (44.6%), calluses in 69 (5.7%), tinea pedis in 532 (43.6%) and thick nails in 215 (17.6%); 61.6% of our patients used inappropriate footwear and 93.8% received no prior foot education.

It was concluded that, despite the low prevalence of neuropathy and PAD in our diabetic patients, the prevalence of DFU is still high. The lack of knowledge regarding diabetic foot problems, inappropriate footwear and the high prevalence of skin and nail pathology in Egypt could explain this paradox. It is suggested that regional differences in the risk factors for DFU should be considered when preventative strategies are planned. Copyright © 2008 John Wiley & Sons.
Paediatric obesity and type 2 diabetes: strategies for prevention and treatment
Authors: Aschemeier B , Kordonouri O , Danne T , Lange K
Published: February 2009

The rising pandemic of obesity has caused an increase in the prevalence of type 2 diabetes in children and adolescents worldwide. Between 8% and 43% of children with newly‐diagnosed diabetes have type 2 diabetes in the USA, while in Europe currently only 0.5% of the newly‐diagnosed cases are classified as type 2. Ethnic factors, pubertal insulin resistance and female gender play a major role. Accelerated weight gain in infants may not only lead to type 2 diabetes later in life, but has also been implicated in the pathogenesis of type 1 diabetes. Therefore, preventive approaches against childhood obesity and type 2 diabetes need to start in the preschool age group. Age‐appropriate education programmes for paediatric type 2 diabetes should include elements of programmes for paediatric diabetes as well as those for weight management. Thus, they need to be delivered by a multidisciplinary team.

Psychological approaches focusing on training in flexible control of eating and lifestyle behaviour appear to be more successful than rigid treatment regimens. Oral agents and insulin are frequently needed to reach the glycaemic goals. Most of the therapeutic and educational approaches are not well established in the paediatric age group as studies with sufficient power are lacking. Furthermore, many adolescents with type 2 diabetes have been reported to be lost to follow up from continuous paediatric diabetes care after short disease duration. Copyright ©2008 John Wiley & Sons.
Aprotinin and the risk of death and renal dysfunction in patients undergoing cardiac surgery: a meta‐analysis of epidemiologic studies
Authors: Gagne Joshua J. , Griesdale Donald E. G. , Schneeweiss Sebastian
Published: February 2009

Purpose

Observational studies have reported conflicting results regarding aprotinin's risk of renal dysfunction and death. A meta‐analysis was conducted to summarize results and explain variation of published epidemiologic studies on risks of renal dysfunction and death associated with aprotinin.

Methods

MEDLINE and EMBASE were systematically searched for non‐experimental studies that reported risk of renal dysfunction or death with aprotinin use during cardiac surgery in adults. Random‐effects meta‐analyses were used to pool results across studies for each outcome. Stratified and meta‐regression analyses were used to identify sources of heterogeneity.

Results

Eleven relevant studies were identified and included in the analysis, including 10 that reported renal dysfunction and seven that reported death. Aprotinin was associated with renal dysfunction (risk ratio (RR), 1.42; 95%CI 1.13–1.79) and long‐term mortality (hazard ratio (HR) 1.22; 95%CI 1.08–1.39). Pooled estimates were lower for short‐term mortality (RR 1.16; 95%CI 0.84–1.58) and renal failure requiring dialysis (RR 1.17; 95%CI 0.99–1.38). Cardiopulmonary bypass (CPB) time, which may be on the causal pathway, was a significant source of heterogeneity, with a 29% increased risk of renal dysfunction for every 10 minute increase in CPB time (p = 0.03).

Conclusions

Despite some studies that reported no association between aprotinin and renal outcomes during cardiac surgery, the totality of epidemiologic evidence indicates an increased risk that cannot be fully explained by need for transfused red blood cells (RBCs). Epidemiologic studies also suggest an increased risk of long‐term mortality associated with aprotinin as compared to various comparators used in these studies, although residual confounding cannot be ruled out. Copyright © 2009 John Wiley & Sons, Ltd.
Religious beliefs, social support, self‐efficacy and adjustment to cancer
Authors: Howsepian Barbara A. , Merluzzi Thomas V.
Published: February 2009

Purpose: Religious beliefs have received relatively little attention in research on coping with cancer. In this study, the relationship of religious beliefs and perceived social support with adjustment to cancer was studied in a coping model that included self‐efficacy for coping as a mediator. Of particular interest was the relationship between religious beliefs and social support.

Method: Data were collected from 164 in‐treatment cancer patients. They completed measures of religious beliefs, social support, physical functioning, self‐efficacy for coping, and adjustment. A model comparison approach was used to assess the fit of models that included or excluded the contribution of religious beliefs while testing the relationship between religious beliefs and social support.

Results: Religious beliefs were more strongly connected to perceived social support than with other constructs. Importantly, a coping model that included religious beliefs fit the data significantly better than a model without paths related to religious beliefs. Self‐efficacy partially mediated the relation of age, physical functioning, and perceived support to adjustment, but not religious beliefs.

Discussion: Religious beliefs may not directly affect self‐efficacy and adjustment; however, cancer patients who have religious beliefs may experience an enhanced sense of social support from a community with whom they share those beliefs. Copyright © 2009 John Wiley & Sons, Ltd.
The Distress Thermometer assessed in women at risk of developing hereditary breast cancer
Authors: van Dooren S. , Duivenvoorden H. J. , Passchier J. , Bannink M. , Tan M. B. M. , Oldenmenger W. H. , Seynaeve C. , van der Rijt C. C. D.
Published: February 2009

Objectives: The Distress Thermometer (DT) is a promising instrument to get insight into distress experienced by cancer patients. At our Family Cancer Clinic the DT, including an adapted problem list, was completed by 100 women at increased risk of developing hereditary breast cancer (mean age 45.2 years; SD: 10.5). Additionally, the women filled in either the Hospital Anxiety and Depression Scale as psychological component (n=48) or the somatic subscale of the Symptom Checklist‐90 as somatic component (n=50) to identify associations with the DT‐score. Further, the women filled in an evaluation form.

Results: The median score on the DT was 2 (range: 0–9). With regression analysis adjusted for age, the contribution of mood and somatic complaints, respectively, was investigated. The standardized regression coefficient for anxiety was 0.32 (ns), for depression 0.14 (ns) and for the somatic subscale 0.49 (p<0.001). The explained variance for anxiety and depression was 16%, and for somatic complaints 24%. The differences between the coefficients were not significant. Evaluation forms were returned by 73 women. In 50% of the cases, the physician had discussed the DT/problem list, which was appreciated by the majority of these women (80%). Sixty‐two percent of the women would recommend the use of the DT for other patients.

Conclusion: The use of the DT/problem list seems promising for the current population, and was appreciated by the majority of the women. As mood and somatic complaints did not differ significantly in explaining the experienced distress, other candidate factors need to be examined. Copyright © 2009 John Wiley & Sons, Ltd.
IQ in late adolescence/early adulthood, risk factors in middle age, and later cancer mortality in men: the Vietnam Experience Study
Authors: Batty G. David , Mortensen Laust H. , Gale Catharine R. , Shipley Martin J. , Roberts Beverly A. , Deary Ian J.
Published: February 2009

Objectives: (i) examine the relation, if any, of pre‐morbid IQ scores at 20 years of age with the risk of later cancer mortality; and (ii) explore the role, if any, of potential mediating factors (e.g. smoking, obesity), assessed in middle age, in explaining the IQ–cancer relation.

Methods: Cohort study of 14, 491 male, Vietnam‐era, former US army personnel with IQ test scores at around 20 years of age (1965‐71), who participated in a risk factor survey at around age 38 years of age (1985‐6), who were then followed up for mortality experience for 15 years.

Results: There were 176 cancer deaths during mortality surveillance. We found an inverse association of IQ with later mortality from all cancers combined (age‐adjusted HRper one SD decrease in IQ; 95% confidence interval: 1.27; 1.10, 1.46) and smoking‐related malignancies (1.37; 1.14, 1.64). There was some attenuation following control for mediating variables, particularly smoking and income, but the gradients generally held at conventional levels of statistical significance.

Conclusions: Higher scores on pre‐morbid IQ tests are associated with lower risk of later cancer morality. The strength of the relation was partially mediated by established risk factors. Copyright © 2009 John Wiley & Sons, Ltd.
Personality traits and psychosocial stress: quality of life over 2 years following breast cancer diagnosis and psychological impact factors
Authors: Härtl Kristin , Engel Jutta , Herschbach Peter , Reinecker Hans , Sommer Harald , Friese Klaus
Published: February 2009

Objective: The aim of this study was to investigate changes in the quality of life (QoL) and body image among breast cancer patients over 2 years and to examine different predictive factors for QoL 2 years after the primary operation.

Methods: A total of 203 women with a primary diagnosis of breast cancer completed the questionnaires 2 weeks and 6, 12, 18, and 24 months after surgery. Quality of Life Questionnaire (QLQ‐C30), Breast Cancer Specific Quality of Life Questionnaire Module (QLQ‐BR23), Questionnaire on Stress in Cancer Patients (QSC‐R23), Freiburg Personality Inventory (FPI‐R), Life Orientation Test (LOT) were used as standardized measures.

Results: The overall QoL and most functional and symptom scales improved during the 2‐year period. However, cognitive functioning, body image, and the three symptom scales of insomnia, constipation, and diarrhea did not change. Age was only capable of predicting physical functioning, whereas tumor size, axillary surgery, and adjuvant chemotherapy were not predictive of the long‐term QoL functional scores. Initial distress was the most potent predictive factor for long‐term QoL. Baseline functioning predicted functional QoL scores 2 years later. And higher scores for neuroticism were associated with a poorer QoL. However, optimism was not capable of predicting the QoL 2 years later.

Conclusion: Screening measures should be implemented at the time when breast cancer is diagnosed, in order to identify psychologically vulnerable patients and offer them professional psycho‐oncological help. Copyright © 2009 John Wiley & Sons, Ltd.
Marital adjustment, satisfaction and dissolution among hematopoietic stem cell transplant patients and spouses: a prospective, five‐year longitudinal investigation
Authors: Langer Shelby L. , Yi Jean C. , Storer Barry E. , Syrjala Karen L.
Published: February 2009

Objective: To examine the trajectory of marital adjustment, satisfaction and dissolution among 121 hematopoietic stem cell transplant (HSCT) couples—as a function of role (patient or spouse) and gender.

Methods: Prospective, longitudinal design. Participants completed the Dyadic Adjustment Scale at six time points: pre‐transplant (4–7 days after beginning medical workup prior to starting transplant), 6 months post‐transplant, and 1, 2, 3 and 5 years post‐transplant. They also reported on marital status over time.

Results: Participants ranged in age from 23–68 (52% female patients and 48% female spouses). Ninety‐eight patients received an allogeneic transplant; 23 received an autologous transplant. Marital dissolution was uncommon (four divorces since the transplant among 55 participating 5‐year survivors, 7%). Dyadic satisfaction was stable over time for both male and female patients and male spouses, but not for female spouses who reported reductions in satisfaction at all time points relative to baseline.

Conclusion: Couples were by and large resilient. However, caregiver‐specific gender differences indicate an increased risk for relationship maladjustment and dissatisfaction among female spouses and ultimately, female spouse/male patient couples. Copyright © 2009 John Wiley & Sons, Ltd.
Low stroma androgen receptor level in normal and tumor prostate tissue is related to poor outcome in prostate cancer patients
Authors: Wikström Pernilla , Marusic Josip , Stattin Pär , Bergh Anders
Published: February 2009

BACKGROUND

The role of androgen receptors (ARs) in the prostate tumor cell environment is largely unknown.

METHODS

AR immunostaining was evaluated in relation to stroma morphology, expression of AR co‐activator ARA55, tumor characteristics and clinical outcome in normal and prostate cancer (PCa) tissue obtained at transurethral resection in men treated with expectancy, and in diagnostic transrectal core biopsies in men treated with surgical castration. Stroma composition was studied by Masson‐trichrome and desmin staining. Levels of AR and ARA55 mRNA were quantified by laser micro‐dissection and RT‐PCR.

RESULTS

The percentage of cells with positive nuclear AR immunostaining in the tumor and normal stroma was inversely related to Gleason score, tumor size, tumor stage, metastasis, response to castration therapy, and cancer‐specific survival. The AR staining in the normal stroma provided independent prognostic information in Cox multiple linear regression analysis. Loss of stroma AR staining was linked to low expression of ARA55 in stroma smooth muscle cells, and in tumors also to gradual disappearance of this cell type.

CONCLUSIONS

PCa aggressiveness and efficacy of castration therapy are related to AR levels in the tumor stroma and importantly to AR levels in the surrounding normal prostate tissue stroma. Prostate 69: 799–809, 2009. © 2009 Wiley‐Liss, Inc.
Vasoactive intestinal peptide behaves as a pro‐metastatic factor in human prostate cancer cells
Authors: Fernández‐Martínez Ana B. , Bajo Ana M. , Sánchez‐Chapado Manuel , Prieto Juan C. , Carmena María J.
Published: February 2009

BACKGROUND

There is little known on the involvement of vasoactive intestinal peptide (VIP) in the metastatic cascade of human prostate cancer, that is, cell proliferation, cell–cell adhesion, extracellular‐matrix degradation, and migration/invasion. Here we evaluated the expression of related biomarker proteins (cyclin D1, metalloproteinases MMP‐2 and MMP‐9, and E‐cadherin) in human androgen‐dependent (LNCaP) and independent (PC3) prostate cancer cells.

METHODS

Reverse transcriptase (RT)‐polymerase chain reaction (PCR), gelatin zymography, Western blotting, confocal immunofluorescence microscopy, and assays on cell proliferation, adhesion, wound‐healing, migration and random homing were performed.

RESULTS

VIP increased cell proliferation and cyclin D1 expression whereas it decreased cell adhesion and E‐cadherin expression in LNCaP and PC3 cells. VIP enhanced the gelatinolytic activity of MMP‐2 and MMP‐9. Semiquantitative RT‐PCR assays showed that VIP stimulated mRNA levels of these MMPs and suppressed mRNA levels of its inhibitory protein RECK. VIP promoted cell invasion and migration, and the responses were faster according to the most aggressive status in cancer progression (androgen‐independence). The involvement of nuclear factor‐κB (NF‐κB) was demonstrated since the anti‐inflammatory agent curcumin blocked VIP effects on the above biomarkers in both cell lines.

CONCLUSIONS

Taken together, these results and the presence of κB sites on gene promoter of cyclin D1, MMPs and, possibly, E‐cadherin suggest that VIP may act as a cytokine in an early metastatic stage of human prostate cancer through the NF‐κB/MMPs‐RECK/E‐cadherin system. Our findings may help to define novel targets and agents with potential usefulness in prostate cancer therapy. Prostate 69: 774–786, 2009. © 2009 Wiley‐Liss, Inc.
Oleanane Triterpenoid CDDO‐Me inhibits growth and induces apoptosis in prostate cancer cells by independently targeting pro‐survival Akt and mTOR
Authors: Deeb Dorrah , Gao Xiaohua , Jiang Hao , Dulchavsky Scott A. , Gautam Subhash C.
Published: February 2009

BACKGROUND

Synthetic triterpenoids are potent anticancer agents, but their therapeutic efficacy or mechanism of action for prostate cancer has not been investigated. The goal of this study was to determine the antitumor activity and the mechanism of action of methyl‐2‐cyano‐3,12‐dioxooleana‐1,9(11)‐dien‐28‐oate (CDDO‐Me), a oleanane‐derived synthetic triterpenoid for human prostate cancer cells.

METHODS

The antitumor activity of CDDO‐Me for hormone‐refractory PC‐3 (AR−) and C4‐2 (AR+) prostate cancer cell lines was determined by effects on cell growth and induction of apoptosis, identification of molecular targets, and therapeutic efficacy in vivo in PC‐3 xenograft model.

RESULTS

CDDO‐Me inhibited the growth and induced apoptosis in PC‐3 and C4‐2 cells at extremely low concentrations. The antitumor activity of CDDO‐Me was associated with the inhibition of p‐Akt, mammalian target of rapamycin (mTOR), and nuclear factor kappa B (NF‐κB) signaling proteins and their downstream targets such as p‐Bad and p‐Foxo3a (Akt); p‐S6K1, p‐eIF‐4E and p‐4E‐BP1 (mTOR); and COX‐2, VEGF and cyclin D1(NF‐κB). Silencing of Akt sensitized the PC‐3 cells to CDDO‐Me, whereas overexpression of Akt induced resistance to CDDO‐Me. Targeted silencing of Akt showed that Akt does not regulate mTOR activation in PC‐3 cells, but targeted silencing of mTOR sensitized PC‐3 cells to CDDO‐Me mediated growth inhibition. Further, treatment with CDDO‐Me inhibited the growth of PC‐3 xenografts in nude mice.

CONCLUSIONS

This study demonstrated potent antitumor activity of CDDO‐Me against prostate cancer cells both in vitro and in vivo. Data also identified Akt and mTOR as molecular targets of CDDO‐Me in prostate cancer cells. Prostate 69: 851–860, 2009. © 2009 Wiley‐Liss, Inc.
Order propensity of an intrinsically disordered protein, the cyclin‐dependent‐kinase inhibitor Sic1
Authors: Brocca Stefania , Šamalíková Mária , Uversky Vladimir N. , Lotti Marina , Vanoni Marco , Alberghina Lilia , Grandori Rita
Published: February 2009

Intrinsically disordered proteins (IDPs) carry out important biological functions and offer an instructive model system for folding and binding studies. However, their structural characterization in the absence of interactors is hindered by their highly dynamic conformation. The cyclin‐dependent‐kinase inhibitor (Cki) Sic1 from Saccharomyces cerevisiae is a key regulator of the yeast cell cycle, which controls entrance into S phase and coordination between cell growth and proliferation. Its last 70 out of 284 residues display functional and structural homology to the inhibitory domain of mammalian p21 and p27. Sic1 has escaped systematic structural characterization until now. Here, complementary biophysical methods are applied to the study of conformational properties of pure Sic1 in solution. Based on sequence analysis, gel filtration, circular dichroism (CD), electrospray‐ionization mass spectrometry (ESI‐MS), and limited proteolysis, it can be concluded that the whole molecule exists in a highly disordered state and can, therefore, be classified as an IDP. However, the results of these experiments indicate, at the same time, that the protein displays some content in secondary and tertiary structure, having properties similar to those of molten globules or premolten globules. Proteolysis‐hypersensitive sites cluster at the N‐terminus and in the middle of the molecule, whereas the most structured region resides at the C‐terminus, including part of the inhibitory domain and the casein‐kinase‐2 (CK2) phosphorylation target S201. The mutations S201A and S201E, which are known to affect Sic1 function, do not have significant effects on the conformational properties of the pure protein. Proteins 2009;76:731–746. © 2009 Wiley‐Liss, Inc.
Normal‐mode‐based modeling of allosteric couplings that underlie cyclic conformational transition in F1 ATPase
Authors: Zheng Wenjun
Published: February 2009

F1 ATPase, a rotary motor comprised of a central stalk (γ subunit) enclosed by three α and β subunits alternately arranged in a hexamer, features highly cooperative binding and hydrolysis of ATP. Despite steady progress in biophysical, biochemical, and computational studies of this fascinating motor, the structural basis for cooperative ATPase involving its three catalytic sites remains not fully understood. To illuminate this key mechanistic puzzle, we have employed a coarse‐grained elastic network model to probe the allosteric couplings underlying the cyclic conformational transition in F1 ATPase at a residue level of detail. We will elucidate how ATP binding and product (ADP and phosphate) release at two catalytic sites are coupled with the rotation of γ subunit via various domain motions in α3β3 hexamer (including intrasubunit hinge‐bending motions in β subunits and intersubunit rigid‐body rotations between adjacent α and β subunits). To this end, we have used a normal‐mode‐based correlation analysis to quantify the allosteric couplings of these domain motions to local motions at catalytic sites and the rotation of γ subunit. We have then identified key amino acid residues involved in the above couplings, some of which have been validated against past studies of mutated and γ‐truncated F1 ATPase. Our finding strongly supports a binding change mechanism where ATP binding to the empty catalytic site triggers a series of intra‐ and intersubunit domain motions leading to ATP hydrolysis and product release at the other two closed catalytic sites. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Effect of D to E mutation of the RGD motif in rhodostomin on its activity, structure, and dynamics: Importance of the interactions between the D residue and integrin
Authors: Chen Chiu‐Yueh , Shiu Jia‐Hau , Hsieh Yao‐Husn , Liu Yu‐Chen , Chen Yen‐Chin , Chen Yi‐Chun , Jeng Wen‐Yih , Tang Ming‐Jer , Lo Szecheng J. , Chuang Woei‐Jer
Published: February 2009

Rhodostomin (Rho) is a snake venom protein containing an RGD motif that specifically inhibits the integrin‐binding function. Rho produced in Pichia pastoris inhibits platelet aggregation with a KI of 78 nM as potent as native Rho. In contrast, its D51E mutant inhibits platelet aggregation with a KI of 49 μM. Structural analysis of Rho and its D51E mutant showed that they have the same tertiary fold with three two‐stranded antiparallel β‐sheets. There are no structural backbone differences between the RG[D/E] loop which extends outward from the protein core and the RG[D/E] sequence at its apex in a four‐residue RG[D/E]M type I turn. Two minor differences between Rho and its D51E mutant were only found from their backbone dynamics and 3D structures. The R2 value of E51 is 13% higher than that of the D51 residue. A difference in the charge separation of 1.76 Å was found between the sidechains of positive (R49) and negative residues (D51 or E51).The docking of Rho into integrin αvβ3 showed that the backbone amide and carbonyl groups of the D51 residue of Rho were formed hydrogen bonds with the integrin residues R216 and R214, respectively. In contrast, these hydrogen bonds were absent in the D51E mutant‐integrin complex. Our findings suggest that the interactions between both the sidechain and backbone of the D residue of RGD‐containing ligands and integrin are important for their binding. Proteins 2009. © 2009 Wiley‐Liss, Inc.
A coarse‐grained potential for fold recognition and molecular dynamics simulations of proteins
Authors: Májek Peter , Elber Ron
Published: February 2009

A coarse‐grained potential for protein simulations and fold ranking is presented. The potential is based on a two‐point model of individual amino acids and a specific implementation of hydrogen bonding. Parameters are determined for distance dependent pair interactions, pseudo bonds, angles, and torsions. A scaling factor for a hydrogen bonding term is also determined. Iterative sampling for 4867 proteins reproduces distributions of internal coordinates and distances observed in the Protein Data Bank. The adjustment of the potential and resampling are in the spirit of the generalized ensemble approach. No native structure information (e.g., secondary structure) is used in the calculation of the potential or in the simulation of a particular protein. The potential is subject to two tests as follows: (i) simulations of 956 globular proteins in the neighborhood of their native folds (these proteins were not used in the training set) and (ii) discrimination between native and decoy structures for 2470 proteins with 305,000 decoys and the “Decoys ‘R’ Us” dataset. In the first test, 58% of tested proteins stay within 5 Å from the native fold in Molecular Dynamics simulations of more than 20 nanoseconds using the new potential. The potential is also useful in differentiating between correct and approximate folds providing significant signal for structure prediction algorithms. Sampling with the potential consistently regenerates the distribution of distances and internal coordinates it learned. Nevertheless, during Molecular Dynamics simulations structures are found that reproduce the learned distributions but are far from the native fold. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Multiscale characterization of protein conformational ensembles
Authors: Shehu Amarda , Kavraki Lydia E. , Clementi Cecilia
Published: February 2009

We propose a multiscale exploration method to characterize the conformational space populated by a protein at equilibrium. The method efficiently obtains a large set of equilibrium conformations in two stages: first exploring the entire space at a coarse‐grained level of detail, then narrowing a refined exploration to selected low‐energy regions. The coarse‐grained exploration periodically adds all‐atom detail to selected conformations to ensure that the search leads to regions which maintain low energies in all‐atom detail. The second stage reconstructs selected low‐energy coarse‐grained conformations in all‐atom detail. A low‐dimensional energy landscape associated with all‐atom conformations allows focusing the exploration to energy minima and their conformational ensembles. The lowest energy ensembles are enriched with additional all‐atom conformations through further multiscale exploration. The lowest energy ensembles obtained from the application of the method to three different proteins correctly capture the known functional states of the considered systems. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Membrane insertion of the FYVE domain is modulated by pH
Authors: He Ju , Vora Mohsin , Haney Rachel M. , Filonov Grigory S. , Musselman Catherine A. , Burd Christopher G. , Kutateladze Andrei G. , Verkhusha Vladislav V. , Stahelin Robert V. , Kutateladze Tatiana G.
Published: February 2009

The FYVE domain associates with phosphatidylinositol 3‐phosphate [PtdIns(3)P] in membranes of early endosomes and penetrates bilayers. Here, we detail principles of membrane anchoring and show that the FYVE domain insertion into PtdIns(3)P‐enriched membranes and membrane‐mimetics is substantially increased in acidic conditions. The EEA1 FYVE domain binds to POPC/POPE/PtdIns(3)P vesicles with a Kd of 49 nM at pH 6.0, however associates ∼24 fold weaker at pH 8.0. The decrease in the affinity is primarily due to much faster dissociation of the protein from the bilayers in basic media. Lowering the pH enhances the interaction of the Hrs, RUFY1, Vps27p and WDFY1 FYVE domains with PtdIns(3)P‐containing membranes in vitro and in vivo, indicating that pH‐dependency is a general function of the FYVE finger family. The PtdIns(3)P binding and membrane insertion of the FYVE domain is modulated by the two adjacent His residues of the R(R/K)HHCRXCG signature motif. Mutation of either His residue abolishes the pH‐sensitivity. Both protonation of the His residues and nonspecific electrostatic contacts stabilize the FYVE domain in the lipid‐bound form, promoting its penetration and increasing the membrane residence time. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Multiple solvent crystal structures of ribonuclease A: An assessment of the method
Authors: Dechene Michelle , Wink Glenna , Smith Mychal , Swartz Paul , Mattos Carla
Published: February 2009

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6‐hexanediol, 70% isopropanol, 50% R,S,R‐bisfuran alcohol, 70% t‐butanol, 50% trifluoroethanol, or 1.0M trimethylamine‐N‐oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) and with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor‐bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot‐spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Graphical models of protein–protein interaction specificity from correlated mutations and interaction data
Authors: Thomas John , Ramakrishnan Naren , Bailey‐Kellogg Chris
Published: February 2009

Protein–protein interactions are mediated by complementary amino acids defining complementary surfaces. Typically not all members of a family of related proteins interact equally well with all members of a partner family; thus analysis of the sequence record can reveal the complementary amino acid partners that confer interaction specificity. This article develops methods for learning and using probabilistic graphical models of such residue “cross‐coupling” constraints between interacting protein families, based on multiple sequence alignments and information about which pairs of proteins are known to interact. Our models generalize traditional consensus sequence binding motifs, and provide a probabilistic semantics enabling sound evaluation of the plausibility of new possible interactions. Furthermore, predictions made by the models can be explained in terms of the underlying residue interactions. Our approach supports different levels of prior knowledge regarding interactions, including both one‐to‐one (e.g., pairs of proteins from the same organism) and many‐to‐many (e.g., experimentally identified interactions), and we present a technique to account for possible bias in the represented interactions. We apply our approach in studies of PDZ domains and their ligands, fundamental building blocks in a number of protein assemblies. Our algorithms are able to identify biologically interesting cross‐coupling constraints, to successfully identify known interactions, and to make explainable predictions about novel interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.
Inverse‐electron‐demand Diels‐Alder reaction as a highly efficient chemoselective ligation procedure: Synthesis and function of a BioShuttle for temozolomide transport into prostate cancer cells
Authors: Pipkorn Rüdiger , Waldeck Waldemar , Didinger Bernd , Koch Mario , Mueller Gabriele , Wiessler Manfred , Braun Klaus
Published: February 2009

Hormone‐refractory prostate cancer (HRPC), insensitive to most cytostatic interventions, features low response rates and bad prognosis. Studies with HRPC treated with temozolomide (TMZ) showed a poor response and the results were discouraging. Therefore, TMZ has been considered to be ineffective for the treatment of patients with symptomatic and progressive HRPC. A solution to this problem is demonstrated in this study by combining proper solid‐phase peptide synthesis and a chemoselective new ‘click’ chemistry based on the Diels–Alder reaction with ‘inverse‐electron‐demand’ (DARinv) for the construction of a highly efficient TMZ‐BioShuttle in which TMZ is ligated to transporter and subcellular address molecules. The transport to the targeted nuclei resulted in much higher efficiency and better pharmacological effects. The reformulation of TMZ to TMZ‐BioShuttle achieved higher in vitro killing of prostate cancer cells. Accordingly, the potential of TMZ for the treatment of prostate tumors was dramatically enhanced even in a tenfold lower concentration than applied normally. This TMZ‐BioShuttle may be well suited for combining chemotherapy with other cytostatic agents or radiation therapy. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.