bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteomic Analysis of Seed Filling in Brassica napus. Developmental Characterization of Metabolic Isozymes Using High-Resolution Two-Dimensional Gel Electrophoresis
Authors: Hajduch Martin , Casteel Jill E. , Hurrelmeyer Katherine E. , Song Zhao , Agrawal Ganesh Kumar , Thelen Jay J. 
Published: March 2006

Abstract
Brassica napus (cultivar Reston) seed proteins were analyzed at 2, 3, 4, 5, and 6 weeks after flowering in biological quadruplicate using two-dimensional gel electrophoresis. Developmental expression profiles for 794 protein spot groups were established and hierarchical cluster analysis revealed 12 different expression trends. Tryptic peptides from each spot group were analyzed in duplicate using matrix-assisted laser desorption ionization time-of-flight mass spectrometry and liquid chromatography-tandem mass spectrometry. The identity of 517 spot groups was determined, representing 289 nonredundant proteins. These proteins were classified into 14 functional categories based upon the Arabidopsis (Arabidopsisthaliana) genome classification scheme. Energy and metabolism related proteins were highly represented in developing seed, accounting for 24.3% and 16.8% of the total proteins, respectively. Analysis of subclasses within the metabolism group revealed coordinated expression during seed filling. The influence of prominently expressed seed storage proteins on relative quantification data is discussed and an in silico subtraction method is presented. The preponderance of energy and metabolic proteins detected in this study provides an in-depth proteomic view on carbon assimilation in B. napus seed. These data suggest that sugar mobilization from glucose to coenzyme A and its acyl derivative is a collaboration between the cytosol and plastids and that temporal control of enzymes and pathways extends beyond transcription. This study provides a systematic analysis of metabolic processes operating in developing B. napus seed from the perspective of protein expression. Data generated from this study have been deposited into a web database (http://oilseedproteomics.missouri.edu) that is accessible to the public domain.
Recruitment of Novel Calcium-Binding Proteins for Root Nodule Symbiosis in Medicago truncatula
Authors: Liu Junqi , Miller Susan S. , Graham Michelle , Bucciarelli Bruna , Catalano Christina M. , Sherrier D. Janine , Samac Deborah A. , Ivashuta Sergey , Fedorova Maria , Matsumoto Peter , Gantt J. Stephen , Vance Carroll P. 
Published: March 2006

Abstract
Legume rhizobia symbiotic nitrogen (N2) fixation plays a critical role in sustainable nitrogen management in agriculture and in the Earth's nitrogen cycle. Signaling between rhizobia and legumes initiates development of a unique plant organ, the root nodule, where bacteria undergo endocytosis and become surrounded by a plant membrane to form a symbiosome. Between this membrane and the encased bacteria exists a matrix-filled space (the symbiosome space) that is thought to contain a mixture of plant- and bacteria-derived proteins. Maintenance of the symbiosis state requires continuous communication between the plant and bacterial partners. Here, we show in the model legume Medicago truncatula that a novel family of six calmodulin-like proteins (CaMLs), expressed specifically in root nodules, are localized within the symbiosome space. All six nodule-specific CaML genes are clustered in the M. truncatula genome, along with two other nodule-specific genes, nodulin-22 and nodulin-25. Sequence comparisons and phylogenetic analysis suggest that an unequal recombination event occurred between nodulin-25 and a nearby calmodulin, which gave rise to the first CaML, and the gene family evolved by tandem duplication and divergence. The data provide striking evidence for the recruitment of a ubiquitous Ca2+-binding gene for symbiotic purposes.
Carbonic Anhydrase and Its Influence on Carbon Isotope Discrimination during C4 Photosynthesis. Insights from Antisense RNA in Flaveria bidentis
Authors: Cousins Asaph B. , Badger Murray R. , von Caemmerer Susanne 
Published: March 2006

Abstract
In C4 plants, carbonic anhydrase (CA) facilitates both the chemical and isotopic equilibration of atmospheric CO2 and bicarbonate (HCO3−) in the mesophyll cytoplasm. The CA-catalyzed reaction is essential for C4 photosynthesis, and the model of carbon isotope discrimination (Δ13C) in C4 plants predicts that changes in CA activity will influence Δ13C. However, experimentally, the influence of CA on Δ13C has not been demonstrated in C4 plants. Here, we compared measurements of Δ13C during C4 photosynthesis in Flaveria bidentis wild-type plants with F. bidentis plants with reduced levels of CA due to the expression of antisense constructs targeted to a putative mesophyll cytosolic CA. Plants with reduced CA activity had greater Δ13C, which was also evident in the leaf dry matter carbon isotope composition (δ13C). Contrary to the isotope measurements, photosynthetic rates were not affected until CA activity was less than 20% of wild type. Measurements of Δ13C, δ13C of leaf dry matter, and rates of net CO2 assimilation were all dramatically altered when CA activity was less than 5% of wild type. CA activity in wild-type F. bidentis is sufficient to maintain net CO2 assimilation; however, reducing leaf CA activity has a relatively large influence on Δ13C, often without changes in net CO2 assimilation. Our data indicate that the extent of CA activity in C4 leaves needs to be taken into account when using Δ13C and/or δ13C to model the response of C4 photosynthesis to changing environmental conditions.
CYP707A1 and CYP707A2, Which Encode Abscisic Acid 8′-Hydroxylases, Are Indispensable for Proper Control of Seed Dormancy and Germination in Arabidopsis
Authors: Okamoto Masanori , Kuwahara Ayuko , Seo Mistunori , Kushiro Tetsuo , Asami Tadao , Hirai Nobuhiro , Kamiya Yuji , Koshiba Tomokazu , Nambara Eiji 
Published: March 2006

Abstract
Endogenous abscisic acid (ABA) levels are regulated by both biosynthesis and catabolism of the hormone. ABA 8′-hydroxylase is considered to be the key catabolic enzyme in many physiological processes. We have previously identified that four members of the Arabidopsis (Arabidopsis thaliana) CYP707A gene family (CYP707A1 to CYP707A4) encode ABA 8′-hydroxylases, and that the cyp707a2 mutants showed an increase in ABA levels in dry and imbibed seeds. In this study, we showed that the cyp707a1 mutant accumulated ABA to higher levels in dry seeds than the cyp707a2 mutant. Expression analysis showed that the CYP707A1 was expressed predominantly during mid-maturation and was down-regulated during late-maturation. Concomitantly, the CYP707A2 transcript levels increased from late-maturation to mature dry seed. Phenotypic analysis of single and double cyp707a mutants indicates that the CYP707A1 is important for reducing ABA levels during mid-maturation. On the other hand, CYP707A2 is responsible for the regulation of ABA levels from late-maturation to germination. Moreover, CYP707A1 and CYP707A3 were also shown to be involved in postgermination growth. Spatial expression analysis suggests that CYP707A1 was expressed predominantly in embryo during mid-maturation, whereas CYP707A2 expression was detected in both embryo and endosperm from late-maturation to germination. Our results demonstrate that each CYP707A gene plays a distinct role during seed development and postgermination growth.
Personal view: the paradox of runaway competitions in gastroenterology
Authors: SONNENBERG A. 
Published: March 2006

SummaryOccasionally, gastroenterologists harbour reservations about the appropriateness of various procedures and management options, yet find themselves drawn into a competition and forced by outside exigencies to provide such services. The aim of the present analysis was to describe patterns of runaway competitions and factors that influence their occurrence in gastroenterology. The interactions between two physicians or physician and patient are modelled as non‐zero‐sum games of two players.The outcomes associated with two behavioural strategies of two players are arranged in a two‐by‐two game matrix. Many scenarios of clinical gastroenterology and social interactions among gastroenterologists are characterized by the underlying game of prisoner's dilemma, where two players can choose to co‐operate or compete with each other. Although from their joint perspective co‐operation results in a higher joint utility, the perspective of each individual favours competition.Following the inescapable logic of their individual perspective, the players end up with a worse outcome than through co‐operation. A runaway competition ensues if the game is played repeatedly with players successively increasing their stakes. Ultimately, each player tries to outdo the opponent while heading in the wrong direction. Recognizing the hallmarks of the game of prisoner's dilemma may help gastroenterologists to avoid such competitions.
Effect of lactulose and Saccharomyces boulardii administration on the colonic urea‐nitrogen metabolism and the bifidobacteria concentration in healthy human subjects
Authors: DE PRETER V. , VANHOUTTE T. , HUYS G. , SWINGS J. , RUTGEERTS P. , VERBEKE K. 
Published: March 2006

SummaryBackground  Protein fermentation products, especially ammonia, are implicated in the pathogenesis of certain diseases.Aim  To investigate the influence of lactulose and Saccharomyces boulardii cells on the composition of the intestinal microbiota and on the metabolic fate of ammonia by means of lactose‐[15N, 15N]‐ureide.Methods  An at random, placebo‐controlled, crossover study was performed in 43 healthy volunteers to evaluate the influence of lactulose and/or S. boulardii cells either administered as a single dose or after a 4‐week intake period. Urine and faeces were collected. All samples were analysed for 15N‐content by combustion‐isotope ratio mass spectrometry. Real‐time polymerase chain reaction was applied to determine the composition of the predominant faecal microbiota.Results  A single administration of lactulose significantly decreased urinary 15N‐excretion in a dose‐dependent way. After long‐term administration of lactulose, a significant reduction of the urinary 15N‐excretion was observed, which was accompanied with a significant increase in the faecal 15N‐output, more specifically more 15N was found in the bacterial fraction. A significant rise in the Bifidobacterium population was found after lactulose intake. No significant effects were observed after S. boulardii intake.Conclusion  Dietary addition of lactulose can exert a bifidogenic effect accompanied by a favourable effect on the colonic NH3‐metabolism.
Altered levels of biochemical indices of bone turnover and bone‐related vitamins in patients with Crohn's disease and ulcerative colitis
Authors: GILMAN J. , SHANAHAN F. , CASHMAN K. D. 
Published: March 2006

SummaryBackground  The pathogenesis of inflammatory bowel disease‐associated osteopenia may be related to pathological rates of bone turnover; however, the literature shows mixed results.Aim  To compare bone biomarkers in inflammatory bowel disease patients (Crohn's disease: n = 68, and ulcerative colitis: n = 32, separately) with age‐ and sex‐matched healthy controls.Subjects  Patients and controls were recruited from Cork University Hospital and Cork City area, respectively.Results  Relative to that in their respective controls, Crohn's disease (n = 47) and ulcerative colitis (n = 26) patients (i.e. excluding supplement users) had significantly (P < 0.05–0.001) higher serum undercarboxylated osteocalcin (by 27% and 63%, respectively) and bone‐specific alkaline phosphatase (by 15% and 21%, respectively) and urinary Type I collagen cross‐linked N‐telopeptides concentrations (by 87% and 112%, respectively). Relative to that in their respective controls, Crohn's disease and ulcerative colitis patients had significantly (P < 0.01) lower serum total osteocalcin (by 20% and 42%, respectively) and 25‐hydroxyvitamin D (by 37% and 42%, respectively), while serum parathyroid hormone levels were similar. In the combined patient group (n = 100), undercarboxylated osteocalcin was positively associated with bone markers.Conclusions  Both Crohn's disease and ulcerative colitis patients have altered bone turnover relative to that in healthy controls.
Biliary lipids, cholesterol and bile synthesis: different adaptive mechanisms to dietary cholesterol in lean and obese subjects
Authors: KLASS D. M. , BÜHRMANN K. , SAUTER G. , DEL PUPPO M. , SCHEIBNER J. , FUCHS M. , STANGE E. F. 
Published: March 2006

SummaryBackground  Increased biliary cholesterol secretion together with elevated cholesterol synthesis may predispose obese subjects to cholesterol gallstone formation.Aim  To investigate whether processing of dietary cholesterol is altered in obesity, we enrolled eight lean and seven obese subjects in a double‐blind crossover study.Methods  Cholesterol consumption was 300 mg/day on low and 1300 mg/day on high cholesterol diet. After 3 weeks on either diet, hepatic bile was collected to determine biliary lipid secretion, and bile salt composition by high‐performance liquid chromatography and cholesterol saturation index was calculated. Cholesterol synthesis was measured employing mass isotopomer distribution analysis. Bile acid synthesis via neutral and acidic pathway was assessed by serum levels of 7α‐hydroxy‐4‐cholesten‐3‐one and 27‐hydroxycholesterol.Results  Cholesterol synthesis was increased in obese compared with lean and feedback inhibited only in obese. On low cholesterol diet, cholesterol secretion was doubled in obese but bile acid composition and synthesis was similar between the two groups. After high cholesterol diet, cholesterol saturation index and bile secretion were unchanged. In contrast to obese, lean increased bile acid synthesis only via the acidic pathway.Conclusions  Dietary cholesterol appears to preferentially induce bile acid synthesis via the acidic pathway in lean, whereas cholesterol synthesis was inhibited in obese. Thus, stable cholesterol saturation index may be achieved by different mechanisms.
Personal view: adequate relief as a primary endpoint in irritable bowel syndrome
Authors: MANGEL A. W. 
Published: March 2006

SummaryThe success of a clinical trial is judged by achieving statistical and clinical significance on the primary endpoint. This is particularly relevant in those trials that are initiated to achieve regulatory approval of a new therapeutic agent. Selection of an endpoint for which statistical significance will be too difficult to achieve can result in clinical trial data that fails to meet regulatory requirements for product approval.Over the past decade, significant progress has been made in development and refinement of the study design for evaluating new therapeutic agents targeted for the treatment of irritable bowel syndrome. One aspect of trial design that has been advanced is recognition of the endpoint of ‘Adequate Relief.’ Adequate relief has been used as a primary endpoint in treatment trials with alosetron, cilansetron and dextofisopam. With each of these agents, statistically significant benefit was seen when compared to placebo.As an endpoint, adequate relief is responsive, reproducible and moves in the same direction as other meaningful measures, and, therefore, displays properties of a validated endpoint. Adequate relief should be considered an acceptable primary endpoint by regulatory agencies for use in clinical trials of novel therapeutic agents for irritable bowel syndrome.
Unawareness of gastrointestinal symptomatology in adult coeliac patients with unexplained iron‐deficiency anaemia presentation
Authors: BACCINI F. , ALOE SPIRITI M. A. , VANNELLA L. , MONARCA B. , DELLE FAVE G. , ANNIBALE B. 
Published: March 2006

SummaryBackground  Most adults with coeliac disease have a subclinical form of the disease and iron‐deficiency anaemia may be the sole presenting symptom.Aim  To evaluate demographic, clinical and biochemical characteristics of adult coeliac disease patients presenting with iron‐deficiency anaemia.Patients  A total of 108 iron‐deficiency anaemia patients in whom coeliac disease has been diagnosed were studied. As a control group 108 non‐coeliac iron‐deficiency anaemia patients, comparable for sex and age, were studied.Results  Of the 108 coeliac disease patients, 95 (88%) were female (mean age 34 years, range 19–72) and 13 (12%) were male (mean age 33 years, range 15–65). The median duration of iron‐deficiency anaemia before diagnosis was 66 months in coeliac disease patients and 14 months in the iron‐deficiency anaemia control group (P = 0.0001). The occurrence of at least one gastrointestinal symptom, not spontaneously reported, was observed in 92 (85%) patients with coeliac disease and in 67 (62%) patients in the control group (P = 0.001). The concomitant presence of diarrhoea, abdominal pain and abdominal bloating was detected in 14% patients with coeliac disease with respect to 3% in the control group (P = 0.005).Conclusions  The vast majority of coeliac disease patients with iron‐deficiency anaemia presentation were unaware of the gastrointestinal symptoms and this relationship is useful for diet compliance.
Gastroenterologists utilize the referral for EGD to enhance colon cancer screening more effectively than primary care physicians
Authors: MENEES S. B. , SCHEIMAN J. , CARLOS R. , MULDER A. , FENDRICK A. M. 
Published: March 2006

SummaryBackground  Colorectal cancer screening rates among patients with upper gastrointestinal symptoms undergoing oesophagogastroduodenoscopy have not been previously established. We hypothesize that gastroenterologists seize this opportunity more frequently than primary care providers.Aims  To assess colorectal cancer screening rates at the time of direct access oesophagogastroduodenoscopy and gastrointestinal clinic evaluation for upper gastrointestinal symptoms. To compare rates in the 6 months following the oesophagogastroduodenoscopy in both cohorts of patients.Methods  Retrospective review. primary care physician group: direct access oesophagogastroduodenoscopy (n = 247) vs. gastrointestinal group (n = 278). Multivariable regression analysis utilized to assess predictors of screening outcome.Results  Colorectal cancer screening at the time of referral was 54%. Among the 243 unscreened patients, an additional 29% in the primary care physician group vs. 59% in the gastrointestinal group completed colorectal cancer screening in 6 months of follow‐up. Nearly 60% patients evaluated in gastrointestinal clinic for upper symptoms had documented discussion, and 99% of those patients underwent colonoscopy (P < 0.001). Gastrointestinal consultation increased the probability of colorectal cancer screening completion eightfold (95% CI 3.69–18.96).Conclusions  At the time of evaluation for upper symptoms, half of patients were not current with colorectal cancer screening recommendations. Referrals for the direct access oesophagogastroduodenoscopy and, more importantly, the gastroenterology consult represent key opportunities for colorectal cancer screening education and improved compliance.
Predictors of the placebo response in functional dyspepsia
Authors: TALLEY N. J. , LOCKE G. R. , LAHR B. D. , ZINSMEISTER A. R. , COHARD‐RADICE M. , D'ELIA T. V. , TACK J. , EARNEST D. L. 
Published: March 2006

SummaryBackground  Trials in functional dyspepsia report placebo response rates of 30% to 40%.Aim  We aimed to identify predictors of the placebo response.Methods  Patients from primary, secondary and tertiary practices with functional dyspepsia defined by Rome II criteria were enrolled into one of four clinical trials; 220 patients were randomized to receive placebo. Scintigraphic assessment of gastric emptying at baseline was repeated at the end of the treatment in those with delayed emptying. After a 2 week run‐in period, patients were followed for 8 weeks on placebo. Response was assessed on a weekly basis and a responder was defined as satisfactory relief of meal‐related symptoms on at least 50% of weeks.Results  The mean age was 44 years (range 18–82) and 74% were female; 76 (35%) were placebo responders. The predominant symptom was an unstable measure over the trial. Independent predictors of a lower placebo response were lower body mass index and a more consistent predominant symptom pattern (both P < 0.05). No association was seen with age, gender, centre type, baseline symptom score, baseline or change in gastric emptying, or baseline quality of life.Conclusion  In functional dyspepsia, a consistent predominant symptom pattern and lower body mass index may be associated with a lower placebo response rate.
The effects of esomeprazole combined with aspirin or rofecoxib on prostaglandin E2 production in patients with Barrett's oesophagus
Authors: TRIADAFILOPOULOS G. , KAUR B. , SOOD S. , TRAXLER B. , LEVINE D. , WESTON A. 
Published: March 2006

SummaryBackground  Reducing mucosal cyclo‐oxygenase‐2 and prostaglandin E2 production and suppressing intraoesophageal acid may be effective chemopreventive strategies in patients with Barrett's oesophagus.Aim  To compare the effects of aspirin and rofecoxib when administered with esomeprazole on prostaglandin E2 production, cyclo‐oxygenase‐2 expression and proliferating cell nuclear antigen expression in patients with Barrett's oesophagus.Methods  This exploratory, multicentre, randomized, open‐label, four‐way crossover study in 45 patients with Barrett's oesophagus evaluated prostaglandin E2 content, proliferating cell nuclear antigen expression, and cyclo‐oxygenase‐2 expression after 10 days of sequential treatments with: esomeprazole 40 mg twice daily plus aspirin 325 mg once daily (E40 b.d. + A325); E40 b.d. plus rofecoxib 25 mg once daily (E40 b.d. + R25); E40 b.d.; and rofecoxib 25 mg once daily (R25).Results  Prostaglandin E2 content reduction in Barrett's oesophagus tissue was significantly greater with E40 b.d. + A325 compared with E40 b.d. + R25, E40 b.d. or R25 (P < 0.05). All treatments containing E40 b.d. significantly decreased proliferating cell nuclear antigen expression from baseline (P < 0.05). None of the treatments significantly reduced cyclo‐oxygenase‐2 expression.Conclusions  The combined treatment of esomeprazole 40 mg b.d. and aspirin 325 mg significantly decreased mucosal prostaglandin E2 content and all treatments containing esomeprazole significantly reduced proliferating cell nuclear antigen expression in patients with Barrett's oesophagus.
Dose–response evaluation of the antisecretory effect of continuous infusion intravenous lansoprazole regimens over 48 h
Authors: HOWDEN C. W. , METZ D. C. , HUNT B. , VAKILY M. , KUKULKA M. , AMER F. , SAMRA N. 
Published: March 2006

SummaryBackground  Attainment of intragastric pH < 6.0 may require high‐dose continuously infused proton pump therapy.Aim  To assess the pharmacokinetic and pharmacodynamic dose–responses of continuous infusion regimens of lansoprazole.Methods  Healthy adult subjects were assigned to lansoprazole 60‐mg intravenous bolus, followed by 6‐mg/h continuous infusion; a 90‐mg intravenous bolus followed by 6‐, 7.5‐, or 9‐mg/h continuous infusion; or placebo.Results  Mean intragastric pH values for lansoprazole regimens ranged from 4.8 to 5.2 (0–24 h), 5.5 to 6.0 (>24 to 48 h) and 5.2 to 5.6 (0–48 h). Within these three intervals, the percentages of time intragastric pH exceeded 4, 5 and 6 ranged from 65% to 96%, 54% to 88% and 30% to 61% respectively. Pharmacokinetic parameters were dose‐independent with steady‐state plasma concentrations achieved within 6–12 h postdose and maintained over 48 h. The mean systemic clearance of lansoprazole was lower in CYP2C19 heterozygous metabolizers than in homozygous extensive metabolizers (9.2 vs. 16.5 L/h), with substantial variability resulting in overlapping ranges of clearance values for both subpopulations. All lansoprazole regimens were well‐tolerated.Conclusions  Lansoprazole administered as a 60‐mg intravenous bolus followed by 6‐mg/h continuous infusion produced intragastric pH effects comparable with those of higher dosage regimens.