Investigating the mechanism of peptide aggregation: insights from mixed monte carlo-molecular dynamics simulations

The early stages of peptide aggregation are currently not accessible by experimental techniques at atomic resolution. In this article, we address this problem through the application of a mixed simulation scheme in which a preliminary coarse-grained Monte Carlo analysis of the free-energy landscape is used to identify representative conformations of the aggregates and subsequent all-atom molecular dynamics simulations are used to analyze in detail possible pathways for the stabilization of oligomers. This protocol was applied to systems consisting of multiple copies of the model peptide GNNQQNY, whose detailed structures in the aggregated state have been recently solved in another study. The analysis of the various trajectories provides dynamical and structural insight into the details of aggregation. In particular, the simulations suggest a hierarchical mechanism characterized by the initial formation of stable parallel β-sheet dimers and identify the formation of the polar zipper motif as a fundamental feature for the stabilization of initial oligomers. Simulation results are consistent with experimentally derived observations and provide an atomically detailed view of the putative initial stages of fibril formation.     

Novel integrated microdialysis-amperometric system for in vitro detection of dopamine secreted from PC12 cells: design, construction, and validation

A novel dual channel in vitro apparatus, derived from a previously described design, has been coupled with dopamine (DA) microsensors for the flow-through detection of DA secreted from PC12 cells. The device, including two independent microdialysis capillaries, was loaded with a solution containing PC12 cells while a constant phosphate-buffered saline (PBS) medium perfusion was carried out using a dual channel miniaturized peristaltic pump. One capillary was perfused with normal PBS, whereas extracellular calcium was removed from extracellular fluid of the second capillary. After a first period of stabilization and DA baseline recording, KCl (75 mM) was added to the perfusion fluid of both capillaries. In this manner, a simultaneous “treatment–control” experimental design was performed to detect K⁺-evoked calcium-dependent DA secretion. For this purpose, self-referencing DA microsensors were developed, and procedures for making, testing, and calibrating them are described in detail. The electronic circuitry was derived from previously published schematics and optimized for dual sensor constant potential amperometry applications. The microdialysis system was tested and validated in vitro under different experimental conditions, and DA secretion was confirmed by high-performance liquid chromatography with electrochemical detection (HPLC–EC). PC12 cell viability was quantified before and after each experiment. The proposed apparatus serves as a reliable model for studying the effects of different drugs on DA secretion through the direct comparison of extracellular DA increase in treatment–control experiments performed on the same initial PC12 cell population.     

Chaperonins: The hunt for the Group II mechanism

Chaperonins are multi-subunit complexes that enhance the efficiency of protein-folding reactions by capturing protein substrates in their central cavities. They occur in all prokaryotic and eukaryotic cell types and, alone amongst molecular chaperones, chaperonin knockouts are always lethal. Chaperonins come in two forms; the Group I are found in bacteria, mitochondria and plastids [W.A. Fenton, A.L. Horwich, Q. Rev. Biophys. 36 (2003) 229-256, [1]] and the Group II in the eukaryotic cytoplasm and in archaea [N.J. Cowan, S.A. Lewis, Adv. Protein Chem. 59 (2001) 73-104, [2]]. Both use energy derived from ATP binding and hydrolysis to drive a series of structural rearrangements that enable them to capture, engulf and then release polypeptide chains that have either not yet acquired the native, biologically active state or have been denatured in the cell.     

Molecular characteristics of small intestinal and renal brush border thiamin transporters in rats.

The molecular characteristics of thiamin (T) transport were studied in the small intestinal and renal brush border membrane vesicles of rats, using [(3)H]T at high specific activity. The effects of various chemical modifiers (amino acid blockers) on T uptake were examined and their specificity assessed. Treatment with the carboxylic specific blockers 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, (1-ethyl-3-[3-(dimethylamino)propyl]-carbodiimide hydrochloride and N-ethyl-5-phenylisoaxolium-3'-sulfonate (Woodward's Reagent K) and with the sulfhydryl specific blocker p-chloromercuribenzene sulfonate inhibited T transport in both types of vesicles. Phenylglyoxal, but not ninhydrin, both reagents for arginine residues, and diethylpyrocarbonate, a reagent for histidine residues, specifically decreased T transport only in renal and small intestinal vesicles respectively. Similarly 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole reacted, but not N-acetylimidazole, both of which are reagents for tyrosine residues. However, 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole inhibition was aspecific. Acetylsalicylic acid, a reagent for lysine and serine residues, decreased T transport, but the lysine effect was aspecific. Acetylsalicylic acid serine blockage also eliminated T/H(+) exchange in small intestinal vesicles. Taken together, these results suggest that for T transport carboxylic and sulfhydryl groups and serine residues are essential in both renal and small intestinal brush border membrane vesicles. In addition, arginine and histidine residues are also essential respectively for renal and small intestinal transporters. Serine was essential for the T/H(+) antiport mechanism.     

Selective enzymatic hydrolysis of aromatic diesters using esterase from Brevibacterium imperiale B222

Summary A practical procedure has been developed for the chemoselective microbial hydrolysis of aromatic dicarboxylic esters to give the corresponding monoesters, using cellular lysate and whole cell of Brevibacterium imperiale B222. The produced monoesters can be transformed into hydroxyacids, useful intermediates in the synthesis of polyesters.     

Restriction of the T-cell receptor V delta gene repertoire is due to preferential rearrangement and is independent of antigen selection

To determine whether the limited V gene usage by the T-cell receptor delta (TCRD) chain is dictated by preferential rearrangement or by antigen selection, we characterized and compared the TCRDV gene repertoire of the productive with that of the unprotective allele in 80 human TCRG/TCRD clones. Six different V genes were found on the expressed allele; two of them, provisionally named DV7 and DV8, have not been described before on the surface of TCRG/TCRD T cells. Overall, six V genes and six non-V elements were isolated from the unproductive allele. Interestingly, the same set of genes was rearranged both in the productive and in the unproductive chromosome. These findings seem to suggest that antigen-independent mechanisms play a major role in the restriction of the TCRDV gene repertoire.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide database and have been assigned the accession numbers Z46643 (DV7-E2), Z46644 (DV8-E6), Z46645 (DV8-M1), Z46641 (AV12-E4), Z46642 (AV29-E5), Z46652 (DREC-E13), Z46637 (TCR-d), Z46638 (TCR-n), Z46639 (TCR-r), Z46653 (PSI-DVu), and Z46640 (TCR-w)     

Phenotypic Changes Across a Geographic Gradient: The Case of Three Sympatric Dolphin Species

Phenotypic changes in the mammalian mandible can occur at different spatial and temporal scales. We investigated mandibular size and shape variation in three extant closely related dolphins (Cetacea, Odontoceti): Tursiops truncatus, Stenella coeruleoalba and Delphinus delphis in order to test the hypothesis that similar phenotypic changes occur across the same geographical gradient. Our data included 219 specimens representative of the following geographic locations: the Mediterranean Sea, the eastern north Atlantic and the North Sea. Each mandibula was photographed laterally and spatial positioning of eight homologous 2D landmarks was recorded. After applying generalised Procrustes analysis (GPA), intraspecific variation was first investigated between sexes and among populations to allow further pooling of samples. Size and shape differences among populations and species were investigated through multivariate ordination techniques (PCA), Procrustes ANOVA and allometric analyses. In all three species, Mediterranean populations clearly differed in mandible shape from the extra-Mediterranean ones. Among the three, the direction of geographic phenotypic changes was significantly similar in the striped and common dolphin, while the bottlenose dolphin was the most divergent species, differing both in size and allometric trajectory. Shape variation of the two former species highlighted a morphological convergence in the Atlantic, and a phenotypic divergence in the Mediterranean. Shape differences among the three dolphin species were interpreted in the light of different prey preferences, feeding strategies and habitat partitioning to avoid direct competition.     

Perioperative surgery- and anaesthesia-related risks of laparoscopic Roux-en-Y gastric bypass - a single centre,retrospective data analysis

Background

Conservative obesity treatment often leads to limited results. Bariatric surgery is highly efficient, but the candidates are at risk of developing perioperative complications. Bariatric outcomes have been well described in the past, but there are only few reports of perioperative outcomes.The aim of this study was to evaluate the incidence of anaesthetic and surgical complications of Roux-en-Y bypass.

Methods

Data of all adult patients, who underwent primary Roux-en-Y gastric bypass surgery between 1/2006 and 12/2013 at the University Hospital Zurich were analysed. Using our clinical database, anaesthetic and surgical complications during the first 30?days after surgery were analysed and risk factors determined by multivariate analysis.

Results

Seven hundred eleven patients (72% female, median age 40?years) were analysed. Overall, surgical complications occurred in 34% patient, while complications attributable to anaesthesia occurred in 37%. Post-operative nausea and vomiting (PONV) were observed in 34%, intubation-related complications in 4%, and delayed extubation in 2% of our patients. Within the first 30?days after surgery, 22% of the patients presented with an infection. Gastrointestinal complications were found in 8%, and bleeding complications in 3%. Anaesthesia complications were less common in older patients and in patients anaesthetized with a volatile anaesthetic. Severe complications were more common in patients with a lower body mass index (BMI) and with longer surgery. The risk to develop a postoperative infection was higher in diabetic patients.

Conclusion

Roux-en-Y bariatric surgery has few anaesthetic complications, the most common is PONV. PONV is more common in younger patients and not more common with volatile anaesthetics. Major complications are overall rare and occur in patients with lower BMI and longer surgery, likely reflecting more difficult procedures.

     

A case of malignant insulinoma responsive to somatostatin analogs treatment

Background

Insulinoma is a rare tumour representing 1–2% of all pancreatic neoplasms and it is malignant in only 10% of cases. Locoregional invasion or metastases define malignancy, whereas the dimension (>?2?cm), CK19 status, the tumor staging and grading (Ki67?>?2%), and the age of onset (>?50?years) can be considered elements of suspect.

Case presentation

We describe the case of a 68-year-old man presenting symptoms compatible with hypoglycemia. The symptoms regressed with food intake. These episodes initially occurred during physical activity, later also during fasting. The fasting test was performed and the laboratory results showed endogenous hyperinsulinemia compatible with insulinoma. The patient appeared responsive to somatostatin analogs and so he was treated with short acting octreotide, obtaining a good control of glycemia. Imaging investigations showed the presence of a lesion of the uncinate pancreatic process of about 4?cm with a high sst2 receptor density. The patient underwent exploratory laparotomy and duodenocephalopancreasectomy after one month.The definitive histological examination revealed an insulinoma (T3N1MO, AGCC VII G1) with a low replicative index (Ki67: 2%).

Conclusions

This report describes a case of malignant insulinoma responsive to octreotide analogs administered pre-operatively in order to try to prevent hypoglycemia. The response to octreotide analogs is not predictable and should be initially assessed under strict clinical surveillance.

     

A stereodynamic fluorescent probe for amino acids. Circular dichroism and circularly polarized luminescence analysis

The use of stereodynamic probes is becoming one of the leading strategies for the fast and effective determination of enantiomeric excess. Recently, we reported a series of novel molecular architectures based on a modified tris(2‐pyridylmethyl)amine complex (TPMA), which are able to amplify the electronic CD, in the case of Zn(II) assemblies and vibrational CD, in the case of Co(II) assemblies. Herein, we report a structural modification of the ligand with the purpose to obtain a fluorescent chiral probe. The study deals with the synthesis of the novel ligand, the formation of the self‐assembly system with amino acids, and the study of the electronic CD and circularly polarized luminescence.