Next-generation sequencing of a combinatorial peptide phage library screened against ubiquitin identifies peptide aptamers that can inhibit the in vitro ubiquitin transfer cascade

Defining dynamic protein-protein interactions in the ubiquitin conjugation reaction is a challenging research area. Generating peptide aptamers that target components such as ubiquitin itself, E1, E2, or E3 could provide tools to dissect novel features of the enzymatic cascade. Next-generation deep sequencing platforms were used to identify peptide sequences isolated from phage-peptide libraries screened against Ubiquitin and its ortholog NEDD8. In over three rounds of selection under differing wash criteria, over 13,000 peptides were acquired targeting ubiquitin, while over 10,000 peptides were selected against NEDD8. The overlap in peptides against these two proteins was less than 5% suggesting a high degree in specificity of Ubiquitin or NEDD8 toward linear peptide motifs. Two of these ubiquitin-binding peptides were identified that inhibit both E3 ubiquitin ligases MDM2 and CHIP. NMR analysis highlighted distinct modes of binding of the two different peptide aptamers. These data highlight the utility of using next-generation sequencing of combinatorial phage-peptide libraries to isolate peptide aptamers toward a protein target that can be used as a chemical tool in a complex multi-enzyme reaction.

Rearrangement of mitochondrial pyruvate dehydrogenase subunit dihydrolipoamide dehydrogenase protein-protein interactions by the MDM2 ligand nutlin-3

Drugs targeting MDM2's hydrophobic pocket activate p53. However, these agents act allosterically and have agonist effects on MDM2's protein interaction landscape. Dominant p53‐independent MDM2‐drug responsive‐binding proteins have not been stratified. We used as a variable the differential expression of MDM2 protein as a function of cell density to identify Nutlin‐3 responsive MDM2‐binding proteins that are perturbed independent of cell density using SWATH‐MS. Dihydrolipoamide dehydrogenase, the E3 subunit of the mitochondrial pyruvate dehydrogenase complex, was one of two Nutlin‐3 perturbed proteins identified fours hour posttreatment at two cell densities. Immunoblotting confirmed that dihydrolipoamide dehydrogenase was induced by Nutlin‐3. Depletion of MDM2 using siRNA also elevated dihydrolipoamide dehydrogenase in Nutlin‐3 treated cells. Mitotracker confirmed that Nutlin‐3 inhibits mitochondrial activity. Enrichment of mitochondria using TOM22+ immunobeads and TMT labeling defined key changes in the mitochondrial proteome after Nutlin‐3 treatment. Proximity ligation identified rearrangements of cellular protein–protein complexes in situ. In response to Nutlin‐3, a reduction of dihydrolipoamide dehydrogenase/dihydrolipoamide acetyltransferase protein complexes highlighted a disruption of the pyruvate dehydrogenase complex. This coincides with an increase in MDM2/dihydrolipoamide dehydrogenase complexes in the nucleus that was further enhanced by the nuclear export inhibitor Leptomycin B. The data suggest one therapeutic impact of MDM2 drugs might be on the early perturbation of specific protein–protein interactions within the mitochondria. This methodology forms a blueprint for biomarker discovery that can identify rearrangements of MDM2 protein–protein complexes in drug‐treated cells.

A systems wide mass spectrometric based linear motif screen to identify dominant in-vivo interacting proteins for the ubiquitin ligase MDM2

Linear motifs mediate protein-protein interactions (PPI) that allow expansion of a target protein interactome at a systems level. This study uses a proteomics approach and linear motif sub-stratifications to expand on PPIs of MDM2. MDM2 is a multi-functional protein with over one hundred known binding partners not stratified by hierarchy or function. A new linear motif based on a MDM2 interaction consensus is used to select novel MDM2 interactors based on Nutlin-3 responsiveness in a cell-based proteomics screen. MDM2 binds a subset of peptide motifs corresponding to real proteins with a range of allosteric responses to MDM2 ligands. We validate cyclophilin B as a novel protein with a consensus MDM2 binding motif that is stabilised by Nutlin-3 in vivo, thus identifying one of the few known interactors of MDM2 that is stabilised by Nutlin-3. These data invoke two modes of peptide binding at the MDM2 N-terminus that rely on a consensus core motif to control the equilibrium between MDM2 binding proteins. This approach stratifies MDM2 interacting proteins based on the linear motif feature and provides a new biomarker assay to define clinically relevant Nutlin-3 responsive MDM2 interactors.

Measuring three-dimensional strain distribution in tendon

Tendons are tough fibrous tissues that facilitate skeletal movement by transferring muscular force to bone. Studies into the effects of mechanical stress on tendons have shown that these can either accelerate healing or cause tendon injuries depending on the load applied. It is known that local strain magnitude and direction play an important role in tendon remodelling and also failure, and different techniques to study strain distribution have been proposed. Image registration and processing techniques are among the recently employed methods. In this study, a novel three-dimensional image processing technique using the Sheffield Image Registration Toolkit is introduced to study local strain and displacement distribution in tendon. The results show that the local normal strain values in the loading axis are smaller than the global applied load, and fibre sliding was detected as a dominant mechanism for transferring the applied load within tendon. However, results from different samples suggest three distinct modes of deformation during loading, as some show only parallel sliding of fibres in respect to the loading axis, whereas others are twisted or deflected in directions transverse to the loading axis. The proposed 3D image registration method is essential for analysing this out-of-plane movement, which cannot be detected using a standard 2D method.

Assessing a virtual reality surgical skills simulator

The Institute for Defense Analyses (IDA) was contracted to perform a military standard task analysis of laparoscopic cholecystectomy, and to study the effectiveness of a virtual reality surgical skills simulator as a tool for surgical training and as a method for recording psychomotor behavior. This report describes the purpose of the study, its design, initial results, and implications for the field of medical education.

Substance abuse and clozapine treatment

Among 118 patients with DSM-III-R diagnoses of schizophrenia or schizoaffective disorder who received treatment with clozapine, 29 patients had an antecedent or current history of substance abuse. Substance abusers and nonabusers showed similar improvements on measures of psychopathology and psychosocial functioning after 6 months of clozapine therapy. The implications of this finding are discussed.

Substance abuse among patients with treatment-resistant schizophrenia: characteristics and implications for clozapine therapy

OBJECTIVE

The goals of this study were 1) to determine the extent of substance abuse in patients with treatment-resistant schizophrenia and 2) to assess the relevance of such abuse to subsequent response to treatment with clozapine.

METHOD

The subjects were 118 treatment-resistant patients with DSM-III-R diagnoses of schizophrenia or schizoaffective disorder who underwent detailed demographic, clinical, and psychopathological evaluations before commencing treatment with clozapine. Lifetime and current histories of substance abuse were also systematically evaluated and characterized according to the Research Diagnostic Criteria and DSM-III-R. Response to clozapine treatment at 6 months was determined with measures of psychopathology and psychosocial function.

RESULTS

An antecedent or current history of substance abuse was determined for 29 patients. Although predominantly male, the abusers did not differ from the nonabusers on other demographic features. The substance abusers actually showed less psychopathology (negative and disorganization symptoms) and better psychosocial functioning at baseline; however, both groups attained similar improvements on these measures after 6 months of clozapine therapy.

CONCLUSIONS

A modest extent of previous or current substance abuse was observed among neuroleptic-resistant schizophrenic patients who subsequently received treatment with clozapine. This antecedent history of substance abuse did not appear to negatively influence subsequent response to clozapine treatment.

Cost effectiveness of clozapine in neuroleptic-resistant schizophrenia

OBJECTIVE

The goal of this study was to determine whether clozapine is a cost-effective treatment for treatment-resistant schizophrenia.

METHOD

Data were collected on 96 treatment-resistant patients with schizophrenia for 2 years before they entered a clozapine treatment study and for at least 2 years after they entered the study. Information about the cost of inpatient and outpatient treatment, housing costs, other costs, and family burden through direct interview or questionnaire of these patients and their families were available for 47 of the 96 patients. Data on lost income and Social Security disability insurance were also obtained. Outcome measures included psychopathology, quality of life, global functioning, work function, and rehospitalization.

RESULTS

The cost of treatment was significantly decreased in the patients who continued clozapine treatment for at least 2 years. This was primarily due to a dramatic decrease in the frequency and cost of rehospitalization. Costs were nonsignificantly lower in patients who dropped out of treatment. The estimated total 2-year cost for the 59 patients who continued clozapine treatment, the 34 patients who dropped out, and the three who interrupted treatment decreased from $7,390,206 to $5,719,463, a savings of $8,702/year per patient. There was a decrease in total costs of $22,936/year for the 37 patients who continued clozapine treatment for whom cost data were available. There were no significant changes in lost income or Social Security disability insurance payments in either group. Clozapine produced a marked improvement in Brief Psychiatric Rating Scale total scores as well as positive negative symptom scores, Global Assessment Scale scores, Quality of Life Scale scores, work functioning, capacity for independent living, and rehospitalization rates.

CONCLUSIONS

Clozapine is a cost-effective treatment for treatment-resistant schizophrenic patients. Cost savings result almost exclusively from the reduced cost of hospitalization.

Thoracoscopic esophageal myotomy in the treatment of achalasia

We treated 24 patients with achalasia using thoracoscopic (22 patients) or laparoscopic (2 patients) esophagomyotomy. The only operative complications were mucosal lacerations, which occurred in 3 patients and required conversion to an open procedure in 2. Twenty-two (91%) patients were eating by the second postoperative day. Analgesics were only required for the management of pain from the chest tube, which remained in place for a median time of 24 hours. The median postoperative hospital stay was 3 days (range, 20 to 14 days). The myotomy proved to be incomplete in the first 3 patients, who required a second myotomy; this was done laparoscopically in 2. One patient had a paraesophageal hernia repaired 6 months after the myotomy, and 1 patient required an esophagectomy 1 year after the myotomy for a large nonfunctioning esophagus. Late follow-up showed that swallowing was excellent in 17 (71%) and fair to good in 4 (17%). Sixteen (66%) of these 24 patients have regained their original weight. Thus, excellent to good results were ultimately obtained in nearly 90% of the patients. These results suggest that esophageal myotomy performed using minimally invasive techniques appears to be the treatment of choice for achalasia.

Thoracoscopic esophagomyotomy. Initial experience with a new approach for the treatment of achalasia

The authors treated 17 patients with achalasia by a thoracoscopic (15 patients) or laparoscopic (2 patients) Heller myotomy. All patients had dysphagia and an upper gastrointestinal series demonstrating a dilated esophagus with a bird-beak deformity at the cardia. Manometry showed a mean lower esophageal sphincter (LES) pressure of 32 +/- 4 mmHg, incomplete sphincter relaxation on swallowing, and no primary esophageal peristalsis. After operation, mean LES pressure was 10 +/- 2 mmHg. Fifteen patients were fed on the second postoperative day. The average hospital stay was 3 days, and there were no deaths or major complications. In three early patients, the myotomy was not carried far enough onto the stomach, and dysphagia persisted until a second myotomy was performed (laparoscopically in two patients). The authors found that having an endoscope in the esophagus during the operation facilitated exposure and was vital to determine the appropriate length of the myotomy. With regard to dysphagia, final results were excellent in 12 patients (70%), good in two patients (12%), fair in two patients (12%), and poor in one patient (6%). Heller myotomy can be safely and reliably performed with minimally invasive techniques. Dysphagia is relieved, postoperative pain is minimal, hospital stay is short, and the patient can return quickly to normal activity.

Sexual self-disclosure among university women

Although there has been considerable research about self-disclosure, there has been a lack of research regarding disclosure of sexual topics. In order to increase our understanding of sexual self-disclosure (SSD), a scale was developed to measure SSD, and 10 variables were tested as predictors of SSD. The subjects were 203 unmarried university females aged 18-22. SSD was measured separately for each of the target groups of mother, father, close friend, and dating partner. Correlation and multiple regression analyses were performed separately for virgin and non-virgin subjects. The one variable which was significant for each of the target groups in each of the analyses was sexual comfort level of the target person. The variables of sex guilt and target person's sexual attitudes were significant for disclosure to each of the target groups among the nonvirgin subjects but to only some of the target groups among the virgin subjects. The remaining seven predictor variables were significant for at least one of the target groups. In the multiple regression models, the proportion of variance explained ranged from 28% to 58%. The results indicate the value of controlling for both target group and virginity status when analyzing the relationship of predictor variables to SSD.

Variations in concentrating function of the gallbladder in the conscious monkey

Hepatic bile is concentrated in the gallbladder by absorption of water and electrolytes. The rate of water absorption can be influenced in vitro and in vivo by gastrointestinal hormones and neurogenic transmitters. Recent studies have demonstrated that besides its absorbing activity, the gallbladder has the ability to secrete fluid into its lumen. In the present experiments, we studied the rate of net water absorption in the gallbladders of pig-tailed monkeys sitting in restraining chairs. Bile from the common bile duct and the gallbladder was led out through cannulas to a stream splitter, samples were obtained, and bile was returned to the duodenum. By measuring outflow from the gallbladder and the concentration of bile acids in hepatic bile and bile that had passed through the gallbladder, net water absorption from the gallbladder bile could be calculated. The results demonstrate that during daytime fasting there was a net absorption corresponding to 30% of the fasting gallbladder volume per hour, and after feeding there was a net secretion of fluid into the gallbladder lumen. Compared with the awake fasting state, net water absorption from the gallbladder decreased at night while the animal was fasting and asleep. Physiologically, secretion of fluid after a meal could help to empty the gallbladder, and changes in net water absorption by the gallbladder could influence the kinetics of the enterohepatic circulation of bile acids.

Computed tomography and nuclear magnetic resonance imaging of pancreatic islet cell tumors

Eleven patients with pancreatic islet cell tumors smaller than 2.5 cm were examined by use of computed tomography (CT) and new scanning protocol. Seven of 11 tumors were localized and CT accurately assessed multiple lesions, retroperitoneal invasion, or liver metastases when present. CT is now the initial imaging procedure of choice for diagnosis and staging of islet cell tumors. Nuclear magnetic resonance can distinguish islet cell tumors from normal retroperitoneal structures and appears to be a promising new pancreatic imaging modality.

Sludge is calcium bilirubinate associated with bile stasis

Biliary sludge is a frequent finding on abdominal sonography. It is most often found after prolonged stasis of gallbladder bile associated with other illness or mechanical obstruction of the common duct, and seldom indicates primary gallbladder disease. In most cases, sludge is a suspension of pigment precipitates in bile, and is at least in part calcium bilirubinate. Sludge may disappear with the return of normal gallbladder contractility. The ease with which this precipitate forms during stasis of gallbladder bile suggests a role for this process in the pathogenesis of cholelithiasis.

Increased production of triglyceride-rich lipoproteins after partial biliary diversion in the rhesus monkey

An interrelationship between bile acid and triglyceride metabolism is suggested by observations in patients with endogenous hypertriglyceridemia and in subjects treated with bile acid-binding resins or chenodeoxycholic acid. We investigated this possible interrelationship in the rhesus monkey. The effect of 14 days of partial bile diversion on plasma concentration and secretion rates of triglyceride-rich lipoproteins was studied by means of a stream-splitting device that permitted controlled interruption of the enterohepatic circulation. Diversion of 25% of the enterohepatic circulation resulted in increased bile acid synthesis and decreased bile acid secretion and pool size, and was associated with a 75% increase in fasting serum triglyceride concentration and a twofold increase in the rate of secretion of triglyceride-rich lipoproteins into plasma. Intraduodenal replacemtn of cholic acid during the period of bile diversion completely prevented the increase in lipoprotein secretion and partially prevented the increase in fasting plasma triglycerides, suggesting that these changes resulted from loss of bile acid rather than other components of bile. These studies show that partial removal of bile acids from the enterohepatic circulation augments the secretion of triglyceride-rich lipoprotein into plasma in the rhesus monkey. Elucidation of the mechanism of this effect may provide important new information concerning the control of hepatic lipoprotein secretion.

Ulcer disease, metabolic alkalosis and hyperparathyroidism: A mechanism of interrelationship?

In both normal volunteers and in patients with primary hyperparathyroidism, the induction of a metabolic alkalosis by infusion of sodium bicarbonate results in a decrease in serum calcium ion and in an increase of circulating parathyroid hormone concentrations. Bicarbonate infusion may serve in man as a new provocative test for release of parathyroid hormone. Furthermore, we speculate that the metabolic alkalosis which is found at times in patients with the Zollinger-Ellison syndrome and severe peptic ulcer disease may result in parathyroid gland stimulation.