Role of water in protein aggregation and amyloid polymorphism.

A variety of neurodegenerative diseases are associated with amyloid plaques, which begin as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding of this process underscores the need to decipher the principles governing protein aggregation. Mechanisms of in vivo amyloid formation involve a number of coconspirators and complex interactions with membranes.

Individual learning curve reduces the clinical value of urinary cytology.

Unlabelled: The aim of the study was to define the learning curve of a single cytologist as a limitation of urinary cytology. A total of 1034 cytologic and histologic findings of patients undergoing transurethral resection of the bladder for suspicion of bladder cancer were reviewed, and cytologic evaluations of a single cytologist from the beginning of his learning period were compared with the results of a cytologist at a national reference center. Our results showed that the individual learning curve has a significant impact on the quality of urine cytology.

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide.

Understanding the influence of macromolecular crowding and nanoparticles on the formation of in-register β-sheets, the primary structural component of amyloid fibrils, is a first step towards describing in vivo protein aggregation and interactions between synthetic materials and proteins. Using all atom molecular simulations in implicit solvent we illustrate the effects of nanoparticle size, shape, and volume fraction on oligomer formation of an amyloidogenic peptide from the transthyretin protein. Surprisingly, we find that inert spherical crowding particles destabilize in-register β-sheets formed by dimers while stabilizing β-sheets comprised of trimers and tetramers.

Similar efficacy of thalidomide- and bortezomib-based regimens for first relapse of multiple myeloma.

Many regimens containing novel drugs have been developed for multiple myeloma (MM). It is not yet clear whether some of the novel agents are better than others. In a retrospective study, we have analyzed the outcomes of patients with first relapse of MM treated with thalidomide-based (T) regimens (n=105) or bortezomib-based (B) regimens (n=106).

Protein folding in a reverse micelle environment: the role of confinement and dehydration.

Characterization of the molecular interactions that stabilize the folded state of proteins including hydrogen bond formation, solvation, molecular crowding, and interaction with membrane environments is a fundamental goal of theoretical biophysics. Inspired by recent experimental studies by Gai and co-workers, we have used molecular dynamics simulations to explore the structure and dynamics of the alanine-rich AKA(2) peptide in bulk solution and in a reverse micelle environment. The simulated structure of the reverse micelle shows substantial deviations from a spherical geometry.

Factors governing fibrillogenesis of polypeptide chains revealed by lattice models.

Using lattice models we explore the factors that determine the tendencies of polypeptide chains to aggregate by exhaustively sampling the sequence and conformational space. The morphologies of the fibril-like structures and the time scales (τ(fib)) for their formation depend on a balance between hydrophobic and Coulomb interactions. The extent of population of an ensemble of N* structures, which are fibril-prone structures in the spectrum of conformations of an isolated protein, is the major determinant of τ(fib).

Toward a molecular theory of early and late events in monomer to amyloid fibril formation.

Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of transition from monomers to fibrils is needed to obtain insights into the growth of amyloid fibrils and more generally self-assembly multisubunit protein complexes. Significant advances using computations of protein aggregation in a number of systems have established generic and sequence-specific aspects of the early steps in oligomer formation. Theoretical considerations, which view oligomer and fibril growth as diffusion in a complex energy landscape, and computational studies, involving minimal lattice and coarse-grained models, have revealed general principles governing the transition from monomeric protein to ordered fibrillar aggregates.

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires.

Amyloid-like fibrils from a number of small peptides that are unrelated by sequence adopt a cross-β-spine in which the two sheets fully interdigitate to create a dry interface. Formation of such a dry interface is usually associated with self-assembly of extended hydrophobic surfaces. Here we investigate how a dry interface is created in the process of protofilament formation in vastly different sequences using two amyloidogenic peptides, one a polar sequence from the N terminus of the yeast prion Sup35 and the other a predominantly hydrophobic sequence from the C terminus of Aβ-peptide.

Generalized simulated tempering for exploring strong phase transitions.

An extension of the simulation tempering algorithm is proposed. It is shown to be particularly suited to the exploration of first-order phase transition systems characterized by the backbending or S-loop in the statistical temperature or a microcanonical caloric curve. A guided Markov process in an auxiliary parameter space systematically combines a set of parametrized Tsallis-weight ensemble simulations, which are targeted to transform unstable or metastable energy states of canonical ensembles into stable ones and smoothly join ordered and disordered phases across phase transition regions via a succession of unimodal energy distributions.

Retrospective analysis of the results of high-dose chemotherapy with the support of autologous blood stem cells in patients with multiple myeloma. The experience of a single centre.

Despite new medical products introduced in multiple myeloma therapy, autologous stem cell transplant (ASCT) remains a standard procedure in younger patients with symptomatic disease. We analyzed a group of 190 patients who underwent ASCT at our clinic for multiple myeloma as primary therapy in years 1995-2008. The total number of transplants performed in this group was 291.

Efficacy and safety of a new intravenous immunoglobulin 10% formulation (octagam® 10%) in patients with immune thrombocytopenia.

Intravenous immunoglobulin (IVIg) has an established role in the treatment of immune thrombocytopenia (ITP). The safety and efficacy of a new ready-to-use IVIg 10% formulation (octagam(®) 10%) were investigated in a prospective phase III study in 116 adult patients with ITP (platelet count ≤20×10(9)/l). Sixty-six patients had chronic ITP and 49 were newly diagnosed.

The archaeal Lsm protein binds to small RNAs.

Proteins of the Lsm family, including eukaryotic Sm proteins and bacterial Hfq, are key players in RNA metabolism. Little is known about the archaeal homologues of these proteins. Therefore, we characterized the Lsm protein from the haloarchaeon Haloferax volcanii using in vitro and in vivo approaches.

Generalized replica exchange method.

We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weight and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters.

Urinary cytology in era of fluorescence endoscopy: redefining the role of an established method with a new reference standard.

Objectives: To assess whether the use of fluorescence endoscopy (FE) decreases the clinical value of urinary cytology compared with the use of white light endoscopy (WLE).

Methods: The endoscopic, cytologic, and histologic findings of patients who had undergone transurethral resection of the bladder with or without FE were reviewed. The number and characteristics of the tumors that had been overlooked by WLE or FE but detected by cytology were analyzed.

Influence of clinical information on the interpretation of urinary cytology in bladder cancer: how suggestible is a cytologist?

Objective: to determine the influence of the knowledge of the endoscopic findings and the influence of the patient's history on the cytologist's judgement, as urinary cytology is known to be subjective and has several limitations, in particular a high inter- and intra-observer variability.

Patients And Methods: we analysed the cytological and histological findings of patients who underwent transurethral resection of a bladder tumour, and determined whether the cytologist was aware of the endoscopic findings or not. The sensitivity and specificity of cytology were calculated with or without this knowledge, and that of the patients' bladder cancer history.

Principles governing oligomer formation in amyloidogenic peptides.

Identifying the principles that describe the formation of protein oligomers and fibrils with distinct morphologies is a daunting problem. Here we summarize general principles of oligomer formation gleaned from molecular dynamics simulations of Abeta-peptides. The spectra of high free energy structures sampled by the monomer provide insights into the plausible fibril structures, providing a rationale for the 'strain phenomenon.

Structures of beta-amyloid peptide 1-40, 1-42, and 1-55-the 672-726 fragment of APP-in a membrane environment with implications for interactions with gamma-secretase.

Aggregation of Amyloid beta (Abeta) peptide has been linked to the neurodegenerative Alzheimer's Disease and implicated in other amyloid diseases including cerebral amyloid angiopathy. Abeta peptide is generated by cleavage of the amyloid precursor protein (APP) by transmembrane proteases. It is crucial to determine the structures of beta-amyloid peptides in a membrane to provide a molecular basis for the cleavage mechanism.

Combined environmental risk assessment for 5-fluorouracil and capecitabine in Europe.

An environmental risk assessment (ERA) was made for the old cytostatic active pharmaceutical ingredient 5-fluorouracil (5-FU) and for capecitabine (CAP), which is a prodrug of 5-FU. This ERA is based on published and company internal data as well as new test results for physicochemical, human metabolism, biodegradability, environmental partitioning and fate, and acute and chronic ecotoxicity properties of the active substance 5-FU as well as on use sales data for 5-FU and CAP in Europe. Predicted environmental concentrations (PECs) were extrapolated following the EMEA 2006 Guideline on ERA for human pharmaceuticals and the European Union 2003 Technical Guidance Document (TGD) for risk assessment as well as the TGD-based application EUSES v2.

Recommendations on the environmental risk assessment of pharmaceuticals: Effect characterization.

The effects testing of pharmaceuticals consists of a tiered investigation of ecotoxicological endpoints. However, effects testing has to be performed only when the predicted environmental concentrations (PECs) of pharmaceuticals are above certain action limits. To study the appropriateness of these action limits, a literature search was performed for pharmaceuticals with predicted no-effect concentrations (PNECs) close to or below the action limits.

Mixture toxicity of the antiviral drug Tamiflu((R)) (oseltamivir ethylester) and its active metabolite oseltamivir acid.

Tamiflu (oseltamivir ethylester) is an antiviral agent for the treatment of influenza A and B. The pro-drug Tamiflu is converted in the human body to the pharmacologically active metabolite, oseltamivir acid, with a yield of 75%. Oseltamivir acid is indirectly photodegradable and slowly biodegradable in sewage works and sediment/water systems.

Local land-use planning to conserve biodiversity: planners' perspectives on what works.

Because habitat loss due to urbanization is a primary threat to biodiversity, and land-use decisions in urbanizing areas are mainly made at the local level, land-use planning by municipal planning departments has a potentially important--but largely unrealized--role in conserving biodiversity. To understand planners' perspectives on the factors that facilitate and impede biodiversity conservation in local planning, we interviewed directors of 17 municipal planning departments in the greater Seattle (Washington, U.S.

Structure-guided design of potent and selective pyrimidylpyrrole inhibitors of extracellular signal-regulated kinase (ERK) using conformational control.

The Ras/Raf/MEK/ERK signal transduction, an oncogenic pathway implicated in a variety of human cancers, is a key target in anticancer drug design. A novel series of pyrimidylpyrrole ERK inhibitors has been identified. Discovery of a conformational change for lead compound 2, when bound to ERK2 relative to antitarget GSK3, enabled structure-guided selectivity optimization, which led to the discovery of 11e, a potent, selective, and orally bioavailable inhibitor of ERK.

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

The mechanism of addition of a soluble unstructured monomer to a preformed ordered amyloid fibril is a complex process. On the basis of the kinetics of monomer disassociation of Abeta(1-40) from the amyloid fibril, it has been suggested that deposition is a multistep process involving a rapid reversible association of the unstructured monomer to the fibril surface (docking) followed by a slower conformational rearrangement leading to the incorporation onto the underlying fibril lattice (locking). By exploiting the vast time scale separation between the dock and lock processes and using molecular dynamics simulation of deposition of the disordered peptide fragment (35)MVGGVV(40) from the Abeta peptide onto the fibril with known crystal structure, we provide a thermodynamic basis for the dock-lock mechanism of fibril growth.

Identification and validation of the methylated TWIST1 and NID2 genes through real-time methylation-specific polymerase chain reaction assays for the noninvasive detection of primary bladder cancer in urine samples.

Background: Accumulating evidence suggests that DNA methylation markers could serve as sensitive and specific cancer biomarkers.

Objective: To determine whether a panel of methylated genes would have the potential to identify primary bladder cancer (BCa) in voided urine samples.

Design, Setting, And Participants: A pharmacologic unmasking reexpression analysis in BCa cell lines was initially undertaken to unveil candidate methylated genes, which were then evaluated in methylation-specific polymerase chain reaction (MSP) assays performed on DNA extracted from noncancerous and cancerous bladder tissues.

Dynamics of locking of peptides onto growing amyloid fibrils.

Sequence-dependent variations in the growth mechanism and stability of amyloid fibrils, which are implicated in a number of neurodegenerative diseases, are poorly understood. We have carried out extensive all-atom molecular dynamics simulations to monitor the structural changes that occur upon addition of random coil (RC) monomer fragments from the yeast prion Sup35 and Abeta-peptide onto a preformed fibril. Using the atomic resolution structures of the microcrystals as the starting points, we show that the RC --> beta-strand transition for the Sup35 fragment occurs abruptly over a very narrow time interval, whereas the acquisition of strand content is less dramatic for the hydrophobic-rich Abeta-peptide.