Characterization of an intronless human calmodulin-like pseudogene

We report the isolation and characterization of a human genomic clone encoding a calmodulin-like pseudogene. It contains an open reading frame of 444 nucleotides, not interrupted by introns. The nucleotide sequence of the open reading frame shows 80%, 71% and 69% identity to the previously reported human calmodulin cDNAs lambda ht6 [17], hCWP [22], and lambda hCE1 [23], respectively. The derived amino acid sequence has only 85% identity to vertebrate calmodulin, but shows four potentially functional Ca2+-binding loops. In the human tissues tested, this pseudogene is not expressed, though gene structure including promoter elements and a putative polyadenylation site seems to be intact.     

Cleavage of CXCR1 on neutrophils disables bacterial killing in cystic fibrosis lung disease

Interleukin-8 (IL-8) activates neutrophils via the chemokine receptors CXCR1 and CXCR2. However, the airways of individuals with cystic fibrosis are frequently colonized by bacterial pathogens, despite the presence of large numbers of neutrophils and IL-8. Here we show that IL-8 promotes bacterial killing by neutrophils through CXCR1 but not CXCR2. Unopposed proteolytic activity in the airways of individuals with cystic fibrosis cleaved CXCR1 on neutrophils and disabled their bacterial-killing capacity. These effects were protease concentration-dependent and also occurred to a lesser extent in individuals with chronic obstructive pulmonary disease. Receptor cleavage induced the release of glycosylated CXCR1 fragments that were capable of stimulating IL-8 production in bronchial epithelial cells via Toll-like receptor 2. In vivo inhibition of proteases by inhalation of alpha1-antitrypsin restored CXCR1 expression and improved bacterial killing in individuals with cystic fibrosis. The cleavage of CXCR1, the functional consequences of its cleavage, and the identification of soluble CXCR1 fragments that behave as bioactive components represent a new pathophysiologic mechanism in cystic fibrosis and other chronic lung diseases.     

InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our predictions with binding sites in Protein Data Bank and found significantly more binding events occur at sites we predicted. Several regions containing disease-causing mutations or cancer polymorphisms in human are predicted to be binding for protein pairs related to the disease, which suggests novel mechanistic hypotheses for several diseases.     

A colorimetric-based amplification system for proteinases including MMP2 and ADAM8

We have developed a new amplification system for proteinases that is sensitive, simple, and inexpensive to run, exemplified by a horseradish peroxidase (HRP)-conjugated, dual MMP2 (matrix metalloproteinase 2) and ADAM8 (a disintegrin and metalloproteinase 8) peptide substrate assay presented herein. The HRP-conjugated substrate is attached to beads through a 6× histidine tag and then incubated with the target enzyme, cleaving the HRP reporter. This product is subsequently removed from the unreacted bound portions of the substrate by magnetic deposition of the beads. The amount of product is then quantified using a standard HRP color development assay employing 3,3′,5,5′-tetramethylbenzidine (TMB) and hydrogen peroxide (H₂O₂). This HRP amplification system represents a new approach to proteinase assays and could be applied to other enzymes, such as lipases, esterases, and kinases, as long as the unreacted substrate can be physically separated from the product and catalysis by the enzyme to be quantified is not impaired dramatically by steric hindrance from the HRP entity.     

A Novel Link between Fic (Filamentation Induced by cAMP)-mediated Adenylylation/AMPylation and the Unfolded Protein Response

The maintenance of endoplasmic reticulum (ER) homeostasis is a critical aspect of determining cell fate and requires a properly functioning unfolded protein response (UPR). We have discovered a previously unknown role of a post-translational modification termed adenylylation/AMPylation in regulating signal transduction events during UPR induction. A family of enzymes, defined by the presence of a Fic (filamentation induced by cAMP) domain, catalyzes this adenylylation reaction. The human genome encodes a single Fic protein, called HYPE (Huntingtin yeast interacting protein E), with adenylyltransferase activity but unknown physiological target(s). Here, we demonstrate that HYPE localizes to the lumen of the endoplasmic reticulum via its hydrophobic N terminus and adenylylates the ER molecular chaperone, BiP, at Ser-365 and Thr-366. BiP functions as a sentinel for protein misfolding and maintains ER homeostasis. We found that adenylylation enhances BiP''s ATPase activity, which is required for refolding misfolded proteins while coping with ER stress. Accordingly, HYPE expression levels increase upon stress. Furthermore, siRNA-mediated knockdown of HYPE prevents the induction of an unfolded protein response. Thus, we identify HYPE as a new UPR regulator and provide the first functional data for Fic-mediated adenylylation in mammalian signaling.     

San Francisco Syncope Rule to predict short-term serious outcomes: a systematic review

Background:

The San Francisco Syncope Rule has been proposed as a clinical decision rule for risk stratification of patients presenting to the emergency department with syncope. It has been validated across various populations and settings. We undertook a systematic review of its accuracy in predicting short-term serious outcomes.

Methods:

We identified studies by means of systematic searches in seven electronic databases from inception to January 2011. We extracted study data in duplicate and used a bivariate random-effects model to assess the predictive accuracy and test characteristics.

Results:

We included 12 studies with a total of 5316 patients, of whom 596 (11%) experienced a serious outcome. The prevalence of serious outcomes across the studies varied between 5% and 26%. The pooled estimate of sensitivity of the San Francisco Syncope Rule was 0.87 (95% confidence interval [CI] 0.79–0.93), and the pooled estimate of specificity was 0.52 (95% CI 0.43–0.62). There was substantial between-study heterogeneity (resulting in a 95% prediction interval for sensitivity of 0.55–0.98). The probability of a serious outcome given a negative score with the San Francisco Syncope Rule was 5% or lower, and the probability was 2% or lower when the rule was applied only to patients for whom no cause of syncope was identified after initial evaluation in the emergency department. The most common cause of false-negative classification for a serious outcome was cardiac arrhythmia.

Interpretation:

The San Francisco Syncope Rule should be applied only for patients in whom no cause of syncope is evident after initial evaluation in the emergency department. Consideration of all available electrocardiograms, as well as arrhythmia monitoring, should be included in application of the San Francisco Syncope Rule. Between-study heterogeneity was likely due to inconsistent classification of arrhythmia.Syncope is defined as sudden, transient loss of consciousness with the inability to maintain postural tone, followed by spontaneous recovery and return to pre-existing neurologic function.^1–5 It represents a common clinical problem, accounting for 1%–3% of visits to the emergency department and up to 6% of admissions to acute care hospitals.^6,7Assessment of syncope in patients presenting to the emergency department is challenging because of the heterogeneity of underlying pathophysiologic processes and diseases. Although many underlying causes of syncope are benign, others are associated with substantial morbidity or mortality, including cardiac arrhythmia, myocardial infarction, pulmonary embolism and occult hemorrhage.^4,8–10 Consequently, a considerable proportion of patients with benign causes of syncope are admitted for inpatient evaluation.^11,12 Therefore, risk stratification that allows for the safe discharge of patients at low risk of a serious outcome is important for efficient management of patients in emergency departments and for reduction of costs associated with unnecessary diagnostic workup.^12,13In recent years, various prediction rules based on the probability of an adverse outcome after an episode of syncope have been proposed.^3,14–16 However, the San Francisco Syncope Rule, derived by Quinn and colleagues in 2004,³ is the only prediction rule for serious outcomes that has been validated in a variety of populations and settings. This simple, five-step clinical decision rule is intended to identify patients at low risk of short-term serious outcomes^3,17 (Box 1).

Box 1:

San Francisco Syncope Rule³

AimPrediction of short-term (within 30 days) serious outcomes in patients presenting to the emergency department with syncope.DefinitionsSyncope: Transient loss of consciousness with return to baseline neurologic function. Trauma-associated and alcohol- or drug-related loss of consciousness excluded, as is definite seizure or altered mental status.Serious outcome: Death, myocardial infarction, arrhythmia, pulmonary embolism, stroke, subarachnoid hemorrhage, significant hemorrhage or any condition causing or likely to cause a return visit to the emergency department and admission to hospital for a related event.Selection of predictors in multivariable analysis: Fifty predictor variables were evaluated for significant associations with a serious outcome and combined to create a minimal set of predictors that are highly sensitive and specific for prediction of a serious outcome.Clinical decision ruleFive risk factors, indicated by the mnemonic “CHESS,” were identified to predict patients at high risk of a serious outcome:

• C – History of congestive heart failure
• H – Hematocrit < 30%
• E – Abnormal findings on 12-lead ECG or cardiac monitoring¹⁷ (new changes or nonsinus rhythm)
• S – History of shortness of breath
• S – Systolic blood pressure < 90 mm Hg at triage

Note: ECG = electrocardiogram.The aim of this study was to conduct a systematic review and meta-analysis of the accuracy of the San Francisco Syncope Rule in predicting short-term serious outcome for patients presenting to the emergency department with syncope.