Optimal molecular crowding accelerates group II intron folding and maximizes catalysis.

Unlike in vivo conditions, group II intron ribozymes are known to require high magnesium(II) concentrations ([Mg2+]) and high temperatures (42 °C) for folding and catalysis in vitro. A possible explanation for this difference is the highly crowded cellular environment, which can be mimicked in vitro by macromolecular crowding agents. Here, we combined bulk activity assays and single-molecule Förster Resonance Energy Transfer (smFRET) to study the influence of polyethylene glycol (PEG) on catalysis and folding of the ribozyme. Our activity studies reveal that PEG reduces the [Mg2+] required, and we found an "optimum" [PEG] that yields maximum activity. smFRET experiments show that the most compact state population, the putative active state, increases with increasing [PEG]. Dynamic transitions between folded states also increase. Therefore, this study shows that optimal molecular crowding concentrations help the ribozyme not only to reach the native fold but also to increase its in vitro activity to approach that in physiological conditions.

Real-time elastography for the detection of fibrotic and inflammatory tissue in patients with stricturing Crohn's disease.

PURPOSE: The distinction between active inflammation and fibrosis of the bowel wall is essential for therapeutic decisions in stricturing Crohn's disease. We aimed to assess whether real-time elastography (RTE) with strain ratio measurement could be useful in differentiating fibrotic from inflamed bowel strictures and to evaluate the possible relationship between US techniques and the histology of the stenotic bowel wall. MATERIALS AND METHODS: Bowel ultrasonography (including RTE, color-Doppler and CEUS examination) was prospectively evaluated in 26 patients with symptomatic stricturing Crohn's disease, before surgery. RTE was adopted to evaluate bowel stiffness: five loops of 20 RTE frames were recorded for each stenotic segment and the mean strain ratio (MSR) was obtained. Histology scoring systems both for inflammation and fibrosis were established for surgical specimens. RESULTS: No significant correlation was found between MSR and fibrosis score (P = 0.877). Color-Doppler score was significantly related to gut wall and submucosal thicknesses (P = 0.006 and P = 0.032, respectively). There was no significant correlation between the number of vessels counted at histology and color-Doppler and CEUS examinations (P = 0.170 and P = 0.302, respectively). CONCLUSION: MSR detection was not able to distinguish fibrotic from inflammatory tissue in our selected population. This result could be influenced by the presence of the superimposed inflammation. Larger cohort of patients, further analysis with shear wave elastography, and validated histopathology classification systems for fibrosis and inflammation are necessary to assess if intestinal fibrosis could be reliably detected on the basis of bowel elastic properties.

Accuracy of elastography point quantification and steatosis influence on assessing liver fibrosis in patients with chronic hepatitis C.

BACKGROUND & AIMS: Elastography point quantification is a novel non-invasive method for the assessment of liver fibrosis by measuring liver stiffness. The aim of this study was to evaluate the accuracy of elastography point quantification for the diagnosis of liver fibrosis and to assess impact of steatosis on liver stiffness measurement, in a cohort of patients with chronic hepatitis C. METHODS: In this single-centre cross-sectional study, 211 consecutive patients with chronic hepatitis C, scheduled for liver biopsy, were examined with the elastography point quantification technology. On the same day, all patients underwent clinical examination, laboratory tests and abdominal ultrasound. RESULTS: The best cut-offs of liver stiffness measurement were 6.16 kPa for the diagnosis of significant fibrosis (≥S3) and 6.79 kPa for advanced fibrosis (≥S4). Areas under the receiver operating characteristic curve were 0.831 (CI: 0.773-0.880) for significant fibrosis, and 0.954 (CI: 0.916-0.978) for advanced fibrosis. Among patients within the same fibrosis stages (S0-S2 and S3-S6; S0-S3 and S4-S6), mean liver stiffness measurement values were similar in patients with steatosis (≥10% at liver biopsy or detected by ultrasound) compared to those without. Discordance between elastography point quantification and histology were affected by the presence of BMI>30 kg/m2 (P=.047, CI: 0.136-0.988 and P=.020, CI: 0.083-0.812 respectively). CONCLUSIONS: In patients with chronic hepatitis C, elastography point quantification is an accurate non-invasive method for the diagnosis of significant and advanced fibrosis. The presence of obesity is a risk factor for misclassification of significant and advanced liver fibrosis.

Contrast enhancement ultrasound application in focal liver lesions characterization: a retrospective study about guidelines application (SOCEUS-CEUS survey).

INTRODUCTION: The SOCEUS survey aims to evaluate how contrast-enhanced ultrasound (CEUS) is effectively used in the focal liver lesions characterization. MATERIALS AND METHODS: In the survey were involved Verona, Brescia and Trieste Radiological Centers and Arezzo and Bologna Non-radiological Centers. Inclusion criteria were liver focal lesion detection at conventional ultrasound and studied by means of CEUS, with or without CT or MRI examinations, done previous or subsequent to CEUS. RESULTS: 1069 forms were collected. Patients with benign lesions, who did not undergo any other studies, were 255/561 (45.5 %). Among patients with diagnosis of hemangioma at CEUS, those who had no other investigations were 129/267 (48.3 %). Patients with malignant lesions who had studies pre-CEUS (CT and/or MRI) were 328/508 (65 %), whereas those who had examinations post-CEUS (CT and/or MRI) were 218/508 (42.9 %). Concordance rate between CEUS and CT investigations pre- and post-CEUS was, respectively, 66 and 89 %. Concordance rate between CEUS and MRI studies pre- and post-CEUS was, respectively, 87.5 and 81.5 %. CONCLUSION: This study proves contrast-enhanced ultrasound correct application in the involved centers.

Mimicking the in vivo Environment--The Effect of Crowding on RNA and Biomacromolecular Folding and Activity.

In vitro studies on macromolecules, like proteins and nucleic acids, are mostly carried out in highly diluted systems where the molecules are studied under artificial conditions. These experimental conditions are optimized for both the system under investigation and the technique used. However, these conditions often do not reflect the in vivo situation and are therefore inappropriate for a reliable prediction of the native behavior of the molecules and their interactions under in vivo conditions. The intracellular environment is packed with cosolutes (macromolecules, metabolites, etc.) that create 'macromolecular crowding'. The addition of natural or synthetic macromolecules to the sample solution enables crowding to be mimicked. In this surrounding most of the studied biomolecules show a more compact structure, an increased activity, and a decrease of salt requirement for structure formation and function. Herein, we refer to a collection of examples for proteins and nucleic acids and their interactions in crowding environments and present in detail the effect of cosolutes on RNA folding and activity using a group II intron ribozyme as an example.

BOBA FRET: bootstrap-based analysis of single-molecule FRET data.

Time-binned single-molecule Förster resonance energy transfer (smFRET) experiments with surface-tethered nucleic acids or proteins permit to follow folding and catalysis of single molecules in real-time. Due to the intrinsically low signal-to-noise ratio (SNR) in smFRET time traces, research over the past years has focused on the development of new methods to extract discrete states (conformations) from noisy data. However, limited observation time typically leads to pronounced cross-sample variability, i.e., single molecules display differences in the relative population of states and the corresponding conversion rates. Quantification of cross-sample variability is necessary to perform statistical testing in order to assess whether changes observed in response to an experimental parameter (metal ion concentration, the presence of a ligand, etc.) are significant. However, such hypothesis testing has been disregarded to date, precluding robust biological interpretation. Here, we address this problem by a bootstrap-based approach to estimate the experimental variability. Simulated time traces are presented to assess the robustness of the algorithm in conjunction with approaches commonly used in thermodynamic and kinetic analysis of time-binned smFRET data. Furthermore, a pair of functionally important sequences derived from the self-cleaving group II intron Sc.ai5γ (d3'EBS1/IBS1) is used as a model system. Through statistical hypothesis testing, divalent metal ions are shown to have a statistically significant effect on both thermodynamic and kinetic aspects of their interaction. The Matlab source code used for analysis (bootstrap-based analysis of smFRET data, BOBA FRET), as well as a graphical user interface, is available via http://www.aci.uzh.ch/rna/.

Serological tests in gluten sensitivity (nonceliac gluten intolerance).

GOALS: To characterize the serological pattern of gluten sensitivity (GS) and to compare it with that found in celiac disease. BACKGROUND: GS has recently been identified as a new clinical entity included in the spectrum of gluten-related disorders, but it is still lacking of diagnostic markers. STUDY: Sera from 78 patients with GS and 80 patients with celiac disease were retrospectively assessed for immunoglobulin (Ig)G/IgA antigliadin antibodies (AGA), IgG deamidated gliadin peptide antibodies (DGP-AGA), IgA tissue transglutaminase antibodies (tTGA), and IgA endomysial antibodies (EmA). RESULTS: IgG AGA were positive in 56.4% of GS patients and in 81.2% of celiac patients, with high antibody titers in both groups. IgA AGA were detected in 7.7% of GS patients and in 75% of celiac patients, showing lower enzyme-linked immunosorbent assay activities in GS than those found in celiac disease. Only 1 of the 78 patients with GS was positive for IgG DGP-AGA (detected in 88.7% of patients with celiac disease). IgA tTGA and IgA EmA were negative in all GS patients, whereas their positivity in celiac patients was 98.7% and 95%, respectively. Patients with GS displayed a variegated clinical picture with intestinal and extraintestinal symptoms (abdominal pain, bloating, diarrhea, constipation, foggy mind, tiredness, eczema/skin rash, headache, joint/muscle pain, numbness of legs/arms, depression, and anemia) together with normal or mildly abnormal small intestinal mucosa. CONCLUSIONS: The serological pattern of GS is characterized by IgG AGA positivity in more than half of cases associated to IgA AGA in a few patients, but without EmA, tTGA, and DGP-AGA, which are the specific markers of celiac disease.

Old and new serological tests for celiac disease screening.

Evaluation of: Lewis NR, Scott BB. Meta-analysis: deamidated gliadin peptide (DGP) antibody and tissue transglutaminase (tTG) antibody compared as screening test for celiac disease. Aliment. Pharmacol. Ther. 31(1), 73-81 (2010). In celiac disease (CD), deamidation of gliadin peptides, induced by tissue transglutaminase (tTG), generates novel antigenic epitopes evoking a specific immune response. Serological tests based on the detection of antibodies to deamidated gliadin peptides (DGP) have been developed with very promising results in terms of sensitivity and specificity for CD screening. In the present study, a meta-analysis of studies published from 1998 to 2008 was designed to compare the performance of DGP antibodies with that of tTG antibodies, the validated and routinely employed test for CD screening. The authors have limited their analysis to IgA class antibodies underlining that most of the considered studies had methodological imperfections, especially ascertainment bias. The results of this meta-analysis indicated that the pooled sensitivities for DGP and tTG antibodies were 87.8% (95% CI: 85.6-89.9) and 93% (95% CI: 91.2-94.5), respectively, and the pooled specificities were 94.1% (95%CI: 92.5-95.5) and 96.5% (95% CI: 95.2-97.5), respectively. In summary, although both tests represent a very good tool for identifying celiac patients, tTG antibodies display a higher predictive value than DGP antibodies, and must still be considered the best serological test for CD screening.

Deamidated gliadin peptide antibodies as a routine test for celiac disease: a prospective analysis.

GOALS: This study was designed to establish whether deamidated gliadin peptide antibodies (DGP-AGA) could improve the serologic workup for celiac disease (CD). BACKGROUND: The best serologic approach for CD screening is currently based on the combined detection of tissue transglutaminase (tTGA), endomysial (EmA), and gliadin antibodies (AGA). STUDY: One hundred forty-four consecutive patients with gastrointestinal and extraintestinal signs suggestive for CD were investigated using serologic tests, that is, IgG and IgA DGP-AGA, IgA tTGA, IgA EmA, and duodenal biopsy. RESULTS: Forty-eight out of 144 patients (33%) had CD with different severity of villous atrophy. IgA tTGA showed 93.7% sensitivity compared with 91.6% for IgA EmA, 84.3% for IgA DGP-AGA, and 82.3% for IgG DGP-AGA. Of the 3 cases negative for IgA tTGA, IgA EmA, and IgA DGP-AGA, 2 had total IgA deficiency, although both were positive for IgG DGP-AGA. IgG DGP-AGA showed a very high specificity for CD (98.9%), not only superior to IgA DGP-AGA (79.8%), but also to IgA tTGA (96.6%) and very close to IgA EmA (100%). CONCLUSIONS: Our prospective study shows that the combined search for IgA tTGA and IgG DGP-AGA provides the best diagnostic accuracy for CD, allowing the identification of all CD cases---except one---with a very high specificity. The serologic workup for CD screening could be significantly improved by the routine introduction of IgG DGP-AGA together with IgA tTGA, thus reducing the number of tests and with an obvious advantage in terms of cost-efficacy.

Sensorineural hearing loss and celiac disease: a coincidental finding.

BACKGROUND: Celiac disease (CD) can be associated with a variety of extraintestinal manifestations, including neurological diseases. A new neurological correlation has been found between CD and sensorineural hearing loss (SNHL). OBJECTIVE: To verify the association between SNHL and CD, and to establish whether the neurological hearing impairment in CD is related to nonorgan-specific and antineuronal antibodies, as well as the presence of autoimmune disorders. METHODS: A sample of 59 consecutive biopsy- and serologically proven CD patients were studied. Among CD patients, 11 were newly diagnosed and 48 were on a gluten-free diet. Hearing function was assessed by audiometric analysis in all CD patients as well as in 59 age- and sex-matched controls. Patients were tested for a panel of immune markers including nonorgan-specific autoantibodies and antineuronal antibodies. RESULTS: SNHL was detected in five CD patients (8.5%) and in two controls (3.4%). In one patient, the SNHL was bilateral, whereas the remaining four had a monolateral impairment. The prevalence of SNHL was not significantly different between CD patients and controls. At least one of the antibodies tested for was positive in two of the five CD patients with SNHL and in 12 of the 54 CD patients without SNHL. Antineuronal antibodies to central nervous system antigens were consistently negative in the five CD patients with SNHL. Only one of the five CD patients with SNHL had Hashimoto thyroiditis. CONCLUSIONS: SNHL and CD occur coincidentally. Hearing function should be assessed only in CD patients with clinical signs of hearing deficiency.

Prevalence of celiac disease in children with type 1 diabetes mellitus increased in the mid-1990 s: an 18-year longitudinal study based on anti-endomysial antibodies.

Between 1987 and 2004, 331 consecutive children, all newly diagnosed with type 1 diabetes mellitus in our pediatric clinic, underwent repeated serological screening for celiac disease (CD) by means of anti-endomysial antibodies, measured prospectively between 1994 and 2004, and retrospectively, using frozen banked serum, between 1987 and 1993. There were 22 cases (6.6%) of biopsy-proven CD among the 331 diabetic children. The prevalence of CD was significantly (P = 0.015) higher after 1994 (10.6%) than before 1994 (3.3%). The rapid change in the risk of CD among Italian diabetic children that occurred in the mid-1990 s could be related to changes in environmental factors, namely, eating habits and viral infections.

Usefulness of antibodies to deamidated gliadin peptides in celiac disease diagnosis and follow-up.

The prevalence of the recently described deamidated gliadin peptide antibodies was compared with that of the routinely used antigliadin, antiendomysial, and tissue transglutaminase antibodies in the sera of 128 untreated celiac patients and 134 controls. Sensitivity and specificity for celiac disease were 83.6 and 90.3% for IgA and 84.4 and 98.5% for IgG antibodies to deamidated gliadin peptides. The new test displayed higher diagnostic accuracy than antigliadin antibodies and, although less sensitive than antiendomysial and tissue transglutaminase antibodies, showed significantly higher specificity than tissue transglutaminase antibodies (P < 0.001). Persistence of peptide antibodies after gluten withdrawal was an expression of low compliance with the diet and of the lack of improvement of the intestinal mucosa. The combined use of tissue transglutaminase and deamidated gliadin peptide antibodies seems to be a very useful tool for celiac disease diagnosis. Moreover, antibodies to deamidated gliadin peptides can be helpful in disease follow-up.

Plasma citrulline concentration: a reliable marker of small bowel absorptive capacity independent of intestinal inflammation.

OBJECTIVES: Postabsorptive plasma citrulline concentration has been proposed as a reliable marker of small bowel absorptive capacity in short bowel patients. The aim of this study was to address the potentially confounding impact of intestinal inflammation. METHODS: Fifty-five patients were selected according to diagnosis, small bowel length, and degree of bowel inflammation. (a) Crohn's disease (CD) with massive small bowel resection leaving 220) (N = 7), (d) CD without resection or active inflammation (normal CRP and CDAI <150) (N = 9), (e) mesenteric infarction (MI) with resection leaving