Pancreatic cystic lesions: clinical predictors of malignancy in patients undergoing surgery.

BACKGROUND: Despite advances in cross-sectional imaging and the use of molecular markers, distinguishing between benign and malignant cysts remains a clinical challenge. AIMS: To identify both preoperative clinical and cyst characteristics at the time of EUS that predict malignancy. METHODS: A retrospective analysis was performed on consecutive patients with pancreatic cysts who underwent endoscopic ultrasound (EUS) and surgical resection from May 1996 to December 2007 at a tertiary centre. Clinical history, EUS characteristics, cytology, tumour markers and surgical histology were collected. Predictors of malignancy were determined by univariate and multivariate analysis using logistic regression. RESULTS: A total of 153 patients underwent a EUS and subsequent surgical intervention.Of the 153 patients, 57 (37%) had a histological diagnosis of malignancy. On univariate analysis, older age (P < 0.001), male gender (P = 0.010), jaundice (P = 0.039), history of other malignancy (P = 0.036), associated mass in cyst (P = 0.004) and malignant cytology (P < 0.001) were found to be associated with malignancy. History of pancreatitis (P = 0.008) and endoscopist impression of pseudocyst (P = 0.001) were found to be associated with benign cysts. Multivariate analysis found that only older age [Odds ratio (OR), 1.04; 95% confidence interval (CI), 1.01-1.08], male gender (OR, 2.26; 95% CI, 1.08-4.73) and malignant cytology (OR, 6.60; 95% CI, 2.02-21.58) were independent predictors of malignancy. CONCLUSIONS: Older age, male gender and malignant cytology from EUS predict malignancy at surgical resection. These characteristics may be used to estimate the probability of malignancy in a cyst and aid in management.

Endoscopic pH monitoring for patients with suspected or refractory gastroesophageal reflux disease.

BACKGROUND: Wireless pH studies can offer prolonged pH monitoring, which may potentially facilitate the diagnosis and management of patients with gastroesophageal reflux disease (GERD). The aim of the present study was to evaluate the detection rate of abnormal esophageal acid exposure using prolonged pH monitoring in patients with suspected or refractory GERD symptoms. METHODS: Patients undergoing prolonged ambulatory pH studies for the evaluation of GERD-related symptoms were assessed. Patients with a known diagnosis of GERD were tested on medical therapy, while patients with suspected GERD were tested off therapy. The wireless pH capsules were placed during upper endoscopy 6 cm above the squamocolumnar junction. RESULTS: One hundred ninety-one patients underwent a total of 198 pH studies. Fifty ambulatory pH studies (25%) were excluded from the analysis: 27 patients (14%) had insufficient data capture (less than 18 h on at least one day of monitoring), 15 patients had premature capsule release (7%), seven were repeat studies (3.5%) and one had intolerable pain requiring capsule removal (0.5%). There were 115 patients undergoing pH studies who were off medication, and 33 patients were on therapy. For the two groups of patients, results were as follows: 32 (28%) and 22 (67%) patients with normal studies on both days; 58 (50%) and five (15%) patients with abnormal studies on both days; 18 (16%) and three (9%) patients with abnormal studies on day 1 only; and seven (6%) and three (9%) patients with abnormal studies on day 2 only, respectively. CONCLUSIONS: Prolonged 48 h pH monitoring can detect more abnormal esophageal acid exposure but is associated with a significant rate of incomplete studies.

Watershed monitoring and modelling and USA regulatory compliance.

The aim of the Columbus program was to implement a comprehensive watershed monitoring-network including water chemistry, aquatic biology and alternative sensors to establish water environment health and methods for determining future restoration progress and early warning for protection of drinking water supplies. The program was implemented to comply with USA regulatory requirements including Total Maximum Daily Load (TMDL) rules of the Clean Water Act (CWA) and Source Water Assessment and Protection (SWAP) rules under the Safe Drinking Water Act (SDWA). The USEPA Office of Research and Development and the Water Environment Research Foundation provided quality assurance oversight. The results obtained demonstrated that significant wet weather data is necessary to establish relationships between land use, water chemistry, aquatic biology and sensor data. These measurements and relationships formed the basis for calibrating the US EPA BASINS Model, prioritizing watershed health and determination of compliance with water quality standards. Conclusions specify priorities of cost-effective drainage system controls that attenuate stormwater flows and capture flushed pollutants. A network of permanent long-term real-time monitoring using combination of continuous sensor measurements, water column sampling and aquatic biology surveys and a regional organization is prescribed to protect drinking water supplies and measure progress towards water quality targets.

Production and clinical development of a Hansenula polymorpha-derived PEGylated hirudin.

This article describes the expression of the hirudin gene heterologously in the methylotrophic yeast Hansenula polymorpha, the establishment of an industrial-scale production process and the subsequent clinical development of polyethylene glycol (PEG)-hirudin. PEGylation increases the molecular weight of hirudin, thereby reducing its kidney filtration rate and immunogenicity and increasing its half-life in the circulation.

Structural biology of HIV.

The human immunodeficiency virus (HIV) genome encodes a total of three structural proteins, two envelope proteins, three enzymes, and six accessory proteins. Studies over the past ten years have provided high-resolution three-dimensional structural information for all of the viral enzymes, structural proteins and envelope proteins, as well as for three of the accessory proteins. In some cases it has been possible to solve the structures of the intact, native proteins, but in most cases structural data were obtained for isolated protein domains, peptidic fragments, or mutants. Peptide complexes with two regulatory RNA fragments and a protein complex with an RNA recognition/encapsidation element have also been structurally characterized. This article summarizes the high-resolution structural information that is currently available for HIV proteins and reviews current structure-function and structure-biological relationships.

Dynamical behavior of the HIV-1 nucleocapsid protein.

The HIV-1 nucleocapsid protein (NC) contains two CCHC-type zinc knuckle domains that are essential for genome recognition, packaging and infectivity. The solution structure of the protein has been determined independently by three groups. Although the structures of the individual zinc knuckle domains are similar, two of the studies indicated that the knuckles behave as independently folded, non-interacting domains connected by a flexible tether, whereas one study revealed the presence of interknuckle NOE cross-peaks, which were interpreted in terms of a more compact structure in which the knuckles are in close proximity. We have collected multidimensional NMR data for the recombinant, isotopically labeled HIV-1 NC protein, and confirmed the presence of weak interknuckle NOEs. However, the NOE data are not consistent with a single protein conformation. 15N NMR relaxation studies reveal that the two zinc knuckle domains possess different effective rotational correlation times, indicating that the knuckles are not tumbling as a single globular domain. In addition, the 1H NMR chemical shifts of isolated zinc knuckle peptides are very similar to those of the intact protein. The combined results indicate that the interknuckle interactions, which involve the close approach of the side-chains of Phe16 and Trp37, are transitory. The solution behavior of NC may be best considered as a rapid equilibrium between conformations with weakly interacting and non-interacting knuckle domains. This inherent conformational flexibility may be functionally important, enabling adaptive binding of NC to different recognition elements within the HIV-1 psi-RNA packaging signal.

Three-dimensional structure of the HTLV-II matrix protein and comparative analysis of matrix proteins from the different classes of pathogenic human retroviruses.

The matrix protein performs similar roles in all retroviruses, initially directing membrane localization of the assembling viral particle and subsequently forming a stable structural shell associated with the inner surface of the mature viral membrane. Although conserved structural elements are likely to perform these functions in all retroviral matrix proteins, invariant motifs are not evident at the primary sequence level and three-dimensional structures have been available for only the primate lentiviral matrix proteins. We have therefore used NMR spectroscopy to determine the structure of the matrix protein from human T-cell leukemia virus type II (HTLV-II), a member of the human oncovirus subclass of retroviruses. A total of 577 distance restraints were used to build 20 refined models that superimpose with an rmsd of 0.71 A for the backbone atoms of the structured regions. The globular HTLV-II matrix structure is composed of four alpha-helices and a 3(10) helix. Exposed basic residues near the C terminus of helix II form a putative membrane binding surface which could act in concert with the N-terminal myristoyl group to anchor the protein on the viral membrane surface. Clear structural similarities between the HTLV-II and HIV-1 matrix proteins suggest that the topology and exposed cationic membrane binding surface are likely to be conserved features of retroviral matrix proteins.

Optimization of pro-urokinase secretion from recombinant Saccharomyces cerevisiae.

Secretion of a nonglycosylated form of human pro-urokinase, also known as single-chain urinary plasminogen activator (scu-PA), from Saccharomyces cerevisiae is described. A "supersecreting" yeast strain harboring multiple copies of integrated plasmids was grown batchwise and at constant respiratory quotient (RQ) in 20-L fermenters. Because the promoters used to drive expression of the pro-urokinase genes are not tightly regulated, secretion into the culture supernatant was growth associated. Although the final cell density achieved in the perturbed-batch fermentation (45 g dry wt/L) was less than that observed in the RQ-controlled culture (77 g dry wt/L), the scu-PA titer in the perturbed-batch fermentation (1863 IU/mL) was nearly twice that attained at constant RQ (1108 IU/mL). The effects on cell growth and scu-PA titer of other process variables (pH, temperature, phosphate concentration, and medium composition) are also discussed.

Characterization of a nonglycosylated single chain urinary plasminogen activator secreted from yeast.

Using site-directed mutagenesis, we have changed the asparagine in human single-chain urinary plasminogen activator (u-PA) at position 302 to an alanine. This alteration removes the only known amino acid residue glycosylated in the protein. The single-chain u-PA containing an alanine residue at position 302 instead of asparagine (scu-PA(N302A] cDNA gene was expressed in the yeast Saccharomyces cerevisiae. Secretion of the protein product into the culture broth was achieved by replacing the human secretion signal codons with those from yeast invertase, adding a yeast promoter from the constitutively expressed glycolytic genes triosephosphate isomerase or phosphoglycerate kinase, and integrating multiple copies of these transcriptional units into the genome of yeast strains carrying the "supersecreting" mutation ssc1. When fermented in a fed-batch mode, these recombinant baker's yeast strains secreted scu-PA(N302A) in a strongly growth-associated manner. Greater than 90% of the u-PA found in the culture broth was in the single-chain form. Scu-PA(N302A) was purified to homogeneity using two chromatography steps. The purified protein had a molecular weight of 47,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and lacked any detectable N-linked glycosylation. The in vitro fibrinolytic properties of scu-PA(N302A) were found to be essentially equivalent to those of natural single-chain u-PA derived from the human kidney cell line TCL-598. Since scu-PA(N302A) lacks the immunogenic N-linked carbohydrate pattern of yeast, it may be a useful therapeutic agent which can be produced economically by yeast fermentation.

Cybernetic modeling of bacteriol cultures at low growth rates: single-substrate systems.

The cybernetic framework developed by Ramkrishna and co-workers has been expanded to include the effects of cellular maintenance energy requirements on biomass levels in slow-growing, carbon-substrate-limited cultures. A simple structured model, based on the existence of distinct key enzymes for growth and maintenance functions, is presented. Comparisons of the model with experimental data for the growth of Klebsiella oxytoca in constant fed-batch culture on glucose, fructose, arabinose, and xylose show good agreement. In addition, perturbed fed-batch culture experiments indicate that slow-growing cultures respond less rapidly to a removal of the growth limitation than do faster-growing ones. The possibility of a growth-rate dependent "critical resource" is discussed.

Cybernetic modeling of bacterial cultures at low growth rates: Mixed-substrate systems.

A cybernetic model to predict the low-growth-rate behavior of bacteria in mixed-substrate environment is presented. Using only growth and maintenance parameters from single-substrate experiments, the model accurately predicts the simultaneous substrate utilization and maintenance energy effects in constant fed-batch cultures of Klebsiella oxytoca. The robustness of the model was examined more rigorously by perturbing glucose-limited fed-batch cultures with additions of arabinose, xylose, and fructose. In all cases, reasonable agreement of the model prediction with the experimental data was observed.

Revised enzyme synthesis rate expression in cybernetic models of bacterial growth.

A revised enzyme synthesis rate expression for cybernetic models of bacterial growth is presented. The rate expression, which is comprised of inducible and constitutive contributions, provides for a basal enzyme level that is necessary to predict certain types of commonly observed continuous culture transients. The response of a continuous culture to a step change in feed stream composition is simulated using both the old and new formulations, and the ramifications for the "matching-law" formulation are discussed.