UniProt and Mass Spectrometry-Based Proteomics-A 2-Way Working Relationship

The human proteome comprises of all of the proteins produced by the sequences translated from the human genome with additional modifications in both sequence and function caused by nonsynonymous variants and posttranslational modifications including cleavage of the initial transcript into smaller peptides and polypeptides. The UniProtKB database (www.uniprot.org) is the world's leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information and presents a summary of experimentally verified, or computationally predicted, functional information added by our expert biocuration team for each protein in the proteome. Researchers in the field of mass spectrometry-based proteomics both consume and add to the body of data available in UniProtKB, and this review highlights the information we provide to this community and the knowledge we in turn obtain from groups via deposition of large-scale datasets in public domain databases.

Genetics and Epigenetics of Nasal Polyposis: A Systematic Review

Chronic rhinosinusitis (CRS) is an inflammatory disease of the nose and paranasal sinuses that is often associated with nasal polyposis (CRSwNP) in the most severe cases. As in other complex diseases, genetic factors are thought to play an important role in the risk and development of the disease. Environment may also modulate the epigenetic signature in affected patients. In the present systematic review, we aimed to compile all published data on genetic and epigenetic variations in CRSwNP since 2000. We found 104 articles, 24 of which were related to epigenetic studies. We identified more than 150 genetic variants in 99 genes involved in the pathogenesis of nasal polyposis. These were clustered into 8 main networks, linking genes involved in inflammation and immune response (eg, MHC), cytokine genes (eg, TNF), leukotriene metabolism, and the extracellular matrix. A total of 89 miRNAs were also identified; these are associated mainly with biological functions such as the cell cycle, inflammation, and the immune response. We propose a potential relationship between genes and the miRNAs identified that may open new lines of investigation. An in-depth knowledge of gene variants and epigenetic traits could help us to design more tailored treatment for patients with CRSwNP.

Survival of Critically Ill Oncologic Patients Requiring Invasive Ventilatory Support: A Prospective Comparative Cohort Study With Nononcologic Patients

PURPOSE

Cancer is in the process of changing to become a chronic disease; therefore, an increasing number of oncologic patients (OPs) are being admitted to intensive care units (ICUs) for supportive care of disease or therapy-related complications. We compare the short- and long-term outcomes of critically ill mechanically ventilated OPs with those of their nononcologic counterparts.

PATIENTS AND METHODS

We performed a prospective study of patients admitted to our ICU between October 2017 and February 2019. Demographic, physiologic, laboratory, clinical, and treatment data were obtained. The primary outcome was survival at 28 days and at the end of the follow-up period. Secondary outcomes were survival according to acute severity scoring (Acute Physiology and Chronic Health Evaluation II score), Eastern Cooperative Oncology Group (ECOG) performance status, and Charlson comorbidity index.

RESULTS

A total of 1,490 patients were admitted during the study period; 358 patients (24%) were OPs, and 100 of these OPs were supported with mechanical ventilation. Seventy-three percent of OPs had an ECOG performances status of 0 or 1, and 90% had solid tumors. Reason for admission to the ICU was postoperative admission in 44 patients and neutropenic infection in 10 patients. The follow-up period was 148 days (range, 42 to 363 days). Survival at 28 days was similar between OPs and nononcologic patients and associated with the Acute Physiology and Chronic Health Evaluation II score. However, long-term survival was lower in OPs compared with nononcologic patients (52% v 76%, respectively; P < .001) and associated with poor ECOG performance status.

CONCLUSION

Short-term survival of critically ill, mechanically ventilated OPs is similar to that of their nononcologic counterparts and is determined by the severity of the critical illness.

Using the Gene Ontology to Annotate Key Players in Parkinson's Disease

The Gene Ontology (GO) is widely recognised as the gold standard bioinformatics resource for summarizing functional knowledge of gene products in a consistent and computable, information-rich language. GO describes cellular and organismal processes across all species, yet until now there has been a considerable gene annotation deficit within the neurological and immunological domains, both of which are relevant to Parkinson’s disease. Here we introduce the Parkinson’s disease GO Annotation Project, funded by Parkinson’s UK and supported by the GO Consortium, which is addressing this deficit by providing GO annotation to Parkinson’s-relevant human gene products, principally through expert literature curation. We discuss the steps taken to prioritise proteins, publications and cellular processes for annotation, examples of how GO annotations capture Parkinson’s-relevant information, and the advantages that a topic-focused annotation approach offers to users. Building on the existing GO resource, this project collates a vast amount of Parkinson’s-relevant literature into a set of high-quality annotations to be utilized by the research community.

Experimental Observation of Convective Cell Formation due to a Fast Wave Antenna in the Large Plasma Device

An experiment in a linear device, the Large Plasma Device, is used to study sheaths caused by an actively powered radio frequency (rf) antenna. The rf antenna used in the experiment consists of a single current strap recessed inside a copper box enclosure without a Faraday screen. A large increase in the plasma potential was observed along magnetic field lines that connect to the antenna limiter. The electric field from the spatial variation of the rectified plasma potential generated E[over →]×B[over →]_{0} flows, often referred to as convective cells. The presence of the flows generated by these potentials is confirmed by Mach probes. The observed convective cell flows are seen to cause the plasma in front of the antenna to flow away and cause a density modification near the antenna edge. These can cause hot spots and damage to the antenna and can result in a decrease in the ion cyclotron range of frequencies antenna coupling.

An update on the Enzyme Portal: an integrative approach for exploring enzyme knowledge

Enzymes are a key part of life processes and are increasingly important for various areas of research such as medicine, biotechnology, bioprocessing and drug research. The goal of the Enzyme Portal is to provide an interface to all European Bioinformatics Institute (EMBL-EBI) data about enzymes (de Matos, P., et al., (2013), BMC Bioinformatics, 14 (1), 103). These data include enzyme function, sequence features and family classification, protein structure, reactions, pathways, small molecules, diseases and the associated literature. The sources of enzyme data are: the UniProt Knowledgebase (UniProtKB) (UniProt Consortium, 2015), the Protein Data Bank in Europe (PDBe), (Valenkar, S., et al., Nucleic Acids Res.2016; 44, D385–D395) Rhea—a database of enzyme-catalysed reactions (Morgat, A., et al., Nucleic Acids Res. 2015; 43, D459-D464), Reactome—a database of biochemical pathways (Fabregat, A., et al., Nucleic Acids Res. 2016; 44, D481–D487), IntEnz—a resource with enzyme nomenclature information (Fleischmann, A., et al., Nucleic Acids Res. 2004 32, D434–D437) and ChEBI (Hastings, J., et al., Nucleic Acids Res. 2013) and ChEMBL (Bento, A. P., et al., Nucleic Acids Res. 201442, 1083–1090)—resources which contain information about small-molecule chemistry and bioactivity. This article describes the redesign of Enzyme Portal and the increased functionality added to maximise integration and interpretation of these data. Use case examples of the Enzyme Portal and the versatile workflows its supports are illustrated. We welcome the suggestion of new resources for integration.

Resolution of single and double Holliday junction recombination intermediates by GEN1

Genetic recombination provides an important mechanism for the repair of DNA double-strand breaks. Homologous pairing and strand exchange lead to the formation of DNA intermediates, in which sister chromatids or homologous chromosomes are covalently linked by four-way Holliday junctions (HJs). Depending on the type of recombination reaction that takes place, intermediates may have single or double HJs, and their resolution is essential for proper chromosome segregation. In mitotic cells, double HJs are primarily dissolved by the BLM helicase-TopoisomeraseIIIα-RMI1-RMI2 (BTR) complex, whereas single HJs (and double HJs that have escaped the attention of BTR) are resolved by structure-selective endonucleases known as HJ resolvases. These enzymes are ubiquitous in nature, because they are present in bacteriophage, bacteria, archaea, and simple and complex eukaryotes. The human HJ resolvase GEN1 is a member of the XPG/Rad2 family of 5'-flap endonucleases. Biochemical studies of GEN1 revealed that it cleaves synthetic DNA substrates containing a single HJ by a mechanism similar to that shown by the prototypic HJ resolvase, Escherichia coli RuvC protein, but it is unclear whether these substrates fully recapitulate the properties of recombination intermediates that arise within a physiological context. Here, we show that GEN1 efficiently cleaves both single and double HJs contained within large recombination intermediates. Moreover, we find that GEN1 exhibits a weak sequence preference for incision between two G residues that reside in a T-rich region of DNA. These results contrast with those obtained with RuvC, which exhibits a strict requirement for the consensus sequence 5'-A/TTTG/C-3'.

Assessment of a rapid liquid-based cytology method for measuring sputum cell counts

Differential sputum cell counting is not widely available despite proven clinical utility in the management of asthma. We compared eosinophil counts obtained using liquid-based cytology (LBC), a routine histopathological processing method, and the current standard method. Eosinophil counts obtained using LBC were a strong predictor of sputum eosinophilia (≥3%) determined by the standard method suggesting LBC could be used in the management of asthma.

Thermodynamic temperature assignment to the point of inflection of the melting curve of high-temperature fixed points

The thermodynamic temperature of the point of inflection of the melting transition of Re-C, Pt-C and Co-C eutectics has been determined to be 2747.84 ± 0.35 K, 2011.43 ± 0.18 K and 1597.39 ± 0.13 K, respectively, and the thermodynamic temperature of the freezing transition of Cu has been determined to be 1357.80 ± 0.08 K, where the ± symbol represents 95% coverage. These results are the best consensus estimates obtained from measurements made using various spectroradiometric primary thermometry techniques by nine different national metrology institutes. The good agreement between the institutes suggests that spectroradiometric thermometry techniques are sufficiently mature (at least in those institutes) to allow the direct realization of thermodynamic temperature above 1234 K (rather than the use of a temperature scale) and that metal-carbon eutectics can be used as high-temperature fixed points for thermodynamic temperature dissemination. The results directly support the developing mise en pratique for the definition of the kelvin to include direct measurement of thermodynamic temperature.

Dissemination of thermodynamic temperature above the freezing point of silver

The mise-en-pratique for the definition of the kelvin at high temperatures will formally allow dissemination of thermodynamic temperature either directly or mediated through high-temperature fixed points (HTFPs). In this paper, these two distinct dissemination methods are evaluated, namely source-based and detector-based. This was achieved by performing two distinct dissemination trials: one based on HTFPs, the other based on absolutely calibrated radiation thermometers or filter radiometers. These trials involved six national metrology institutes in Europe in the frame of the European Metrology Research Programme joint project 'Implementing the new kelvin' (InK). The results have shown that both dissemination routes are possible, with similar standard uncertainties of 1-2 K, over the range 1273-2773 K, showing that, depending on the facilities available in the laboratory, it will soon be possible to disseminate thermodynamic temperatures above 1273 K to users by either of the two methods with uncertainties comparable to the current temperature scale.

Evaluation of a fibrate, specific stimulant of PPARα, as a therapeutic alternative to the treatment of clinical ovine pregnancy toxaemia

Ovine pregnancy toxaemia is a metabolic disorder affecting sheep in their last 6 weeks of pregnancy as a result of their inability to maintain adequate energy homoeostasis. Different alternative treatments are available with variable results. The aim of this research was to evaluate a peroxisome proliferator-activated receptor alpha (PPARα) stimulant as an alternative to treat clinical pregnancy toxaemia. Thirty-three adult sheep, with known gestation date and carrying a single foetus, were fasted from day 130 of gestation until animals showed clinical disease. From that moment onwards, sheep were treated during 6 days with three different therapeutic alternatives: 10 mg/kg of 2-methyl-2-phenoxy-propionic acid; 10 mg/kg of 2-methyl-2-phenoxy-propionic acid + 100 mL of propylene glycol oral; or 100 mL of propylene glycol oral. Glycaemia and serum β-hydroxybutyrate (BHOB) were determined daily. Liver biopsies were taken at day 130 of gestation, at the beginning and end of treatments and at 5 days postpartum, evaluating the extent and degree of the steatosis lesion. Even though in sheep treated with 2-methyl-2-phenoxy-propionic acid, serum concentrations of glucose and BHOB recovered more slowly, we conclude that 2-methyl-2-phenoxy-propionic acid alone or combined with propylene glycol can be used as an alternative to effectively treat fatty liver, and therefore pregnancy toxaemia.

The utility of exhaled nitric oxide in patients with suspected asthma

The value of FENO measurements in patients with symptoms suggestive of asthma is unclear. We performed an observational study to assess the ability of FENO to diagnose asthma and to predict response to inhaled corticosteroids (ICS). Our findings suggest FENO is not useful for asthma diagnosis but is accurate at predicting ICS response.

A resistively heated CeB6 emissive probe

The plasma potential, V(p), is a key quantity in experimental plasma physics. Its spatial gradients directly yield the electrostatic field present. Emissive probes operating under space-charge limited emission conditions float close to V(p) even under time-varying conditions. Throughout their long history in plasma physics, they have mostly been constructed with resistively heated tungsten wire filaments. In high density plasmas (>10(12) cm(-3)), hexaboride emitters are required because tungsten filaments cannot be heated to sufficient emission without component failure. A resistively heated emissive probe with a cerium hexaboride, CeB6, emitter has been developed to work in plasma densities up to 10(13) cm(-3). To show functionality, three spatial profiles of V(p) are compared using the emissive probe, a cold floating probe, and a swept probe inside a plasma containing regions with and without current. The swept probe and emissive probe agree well across the profile while the floating cold probe fails in the current carrying region.

Contemporary wars and their contributions to vascular injury management

INTRODUCTION

Man's inhumanity for man still knows no boundaries, as we continue as a species as a whole to engage in war. According to Kohn's Dictionary of Wars [1], of over 3,700 years of recorded history, there have been a total of 3,010 wars. One is hard pressed to actually find a period of time in which here has not been an active conflict in the globe. The world has experienced two world wars: WWI (1914-1918) and WWII (1939-1945). The total number of military casualties in WWI was over 37 million, while WWII so far, has been the deadliest military conflict in history with over 60 million people killed accounting for slightly over 2.5% of the world's population.

MATERIAL AND METHODS

The purpose of this study is to review contemporary wars and their contributions to vascular injury management. It is precisely wartime contributions that have led to the more precise identification and management of these injuries resulting in countless lives and extremities saved. However, surgeons dealing with vascular injuries have faced a tough and arduous road. Their journey was initiated by surgical mavericks which undaunted, pressed on against all odds guided by William Stewart Halsted's classic statement in 1912: "One of the chief fascinations in surgery is the management of wounded vessels."

CONCLUSION

Contemporary wars of the XX-XXI centuries gave birth, defined and advanced the field of vascular injury management.

Decision-making during NHEJ: a network of interactions in human Polμ implicated in substrate recognition and end-bridging

Human Polμ is a DNA polymerase belonging to the X family that has been implicated in the non-homologous end-joining (NHEJ) pathway during repair of double-strand breaks in DNA. Loop1 is a flexible piece of Polμ which has a critical role during terminal transferase and end-joining activities: it acts as a pseudo-template when the template strand is discontinuous or unavailable, whilst diffusing away if present to avoid steric clashes. Mutational analysis and inspection of the 3D structures available allowed us to identify a network of residues in charge of sensing the presence or absence of discontinuities in the template strand, which will in turn determine the final position adopted by Loop1. This network is formed by the previously uncharacterized thumb mini-loop (NSH motif) and the positively charged helix N, which contribute to the correct positioning of Loop1 and to juxtapose the discontinuous template strand during NHEJ of incompatible ends. Accordingly, single mutation of specific conserved residues in these motifs, whilst irrelevant in most of the cases for gap filling, largely affected terminal transferase and end-joining activities. Other point mutations in the ‘hinges’ of Loop1, such as residues Phe³⁸⁵ or Phe³⁸⁹, corroborated the flexibility requirements of this motif.

Atom-light interactions in photonic crystals

The integration of nanophotonics and atomic physics has been a long-sought goal that would open new frontiers for optical physics, including novel quantum transport and many-body phenomena with photon-mediated atomic interactions. Reaching this goal requires surmounting diverse challenges in nanofabrication and atomic manipulation. Here we report the development of a novel integrated optical circuit with a photonic crystal capable of both localizing and interfacing atoms with guided photons. Optical bands of a photonic crystal waveguide are aligned with selected atomic transitions. From reflection spectra measured with average atom number N=1.1+/-0.4, we infer that atoms are localized within the waveguide by optical dipole forces. The fraction of single-atom radiative decay into the waveguide is Γ1D/Γ'≃(0.32±0.08), where Γ1D is the rate of emission into the guided mode and Γ' is the decay rate into all other channels. Γ1D/Γ' is unprecedented in all current atom-photon interfaces.

Reduction of residual amplitude modulation to 1 × 10⁻⁶ for frequency modulation and laser stabilization

Active control and cancellation of residual amplitude modulation (RAM) in phase modulation of an optical carrier is one of the key technologies for achieving the ultimate stability of a laser locked to an ultrastable optical cavity. Furthermore, such techniques are versatile tools in various frequency modulation-based spectroscopy applications. In this Letter we report a simple and robust approach to actively stabilize RAM in an optical phase modulation process. We employ a waveguide-based electro-optic modulator (EOM) to provide phase modulation and implement an active servo with both DC electric field and temperature feedback onto the EOM to cancel both the in-phase and quadrature components of the RAM. This technique allows RAM control on the parts-per-million level where RAM-induced frequency instability is comparable to or lower than the fundamental thermal noise limit of the best available optical cavities.

Optical spectrum analyzer with quantum-limited noise floor

Interactions between atoms and lasers provide the potential for unprecedented control of quantum states. Fulfilling this potential requires detailed knowledge of frequency noise in optical oscillators with state-of-the-art stability. We demonstrate a technique that precisely measures the noise spectrum of an ultrastable laser using optical lattice-trapped 87Sr atoms as a quantum projection noise-limited reference. We determine the laser noise spectrum from near dc to 100 Hz via the measured fluctuations in atomic excitation, guided by a simple and robust theory model. The noise spectrum yields a 26(4) mHz linewidth at a central frequency of 429 THz, corresponding to an optical quality factor of 1.6×10(16). This approach improves upon optical heterodyne beats between two similar laser systems by providing information unique to a single laser and complements the traditionally used Allan deviation which evaluates laser performance at relatively long time scales. We use this technique to verify the reduction of resonant noise in our ultrastable laser via feedback from an optical heterodyne beat. Finally, we show that knowledge of our laser's spectrum allows us to accurately predict the laser-limited stability for optical atomic clocks.

A specific N-terminal extension of the 8 kDa domain is required for DNA end-bridging by human Polμ and Polλ

Human DNA polymerases mu (Polµ) and lambda (Polλ) are X family members involved in the repair of double-strand breaks in DNA during non-homologous end joining. Crucial abilities of these enzymes include bridging of the two 3′ single-stranded overhangs and trans-polymerization using one 3′ end as primer and the other as template, to minimize sequence loss. In this context, we have studied the importance of a previously uncharacterised sequence (‘brooch’), located at the N-terminal boundary of the Polß-like polymerase core, and formed by Tyr¹⁴¹, Ala¹⁴², Cys¹⁴³, Gln¹⁴⁴ and Arg¹⁴⁵ in Polµ, and by Trp²³⁹, Val²⁴⁰, Cys²⁴¹, Ala²⁴² and Gln²⁴³ in Polλ. The brooch is potentially implicated in the maintenance of a closed conformation throughout the catalytic cycle, and our studies indicate that it could be a target of Cdk phosphorylation in Polµ. The brooch is irrelevant for 1 nt gap filling, but of specific importance during end joining: single mutations in the conserved residues reduced the formation of two ended synapses and strongly diminished the ability of Polµ and polymerase lambda to perform non-homologous end joining reactions in vitro.

Ribonucleotides and manganese ions improve non-homologous end joining by human Polμ

Human DNA polymerase mu (Polμ), a family X member involved in DNA repair, has both template-directed and terminal transferase (template-independent) activities. In addition to their ability to incorporate untemplated nucleotides, another similarity between Polµ and terminal deoxynucleotidyl transferase (TdT) is their promiscuity in using ribonucleotides (NTPs), whose physiological significance is presently unknown. As shown here, Polµ can use NTPs instead of deoxynucleotides (dNTPs) during non-homologous end joining (NHEJ) of non-complementary ends, a Polµ-specific task. Moreover, a physiological concentration of Mn²⁺ ions did benefit Polµ-mediated NHEJ by improving the efficiency and accuracy of nucleotide insertion. Analysis of different mutations in the ‘steric gate’ of the active site indicated that Polµ is taking advantage of an open active site, valid for selecting alternative activating metal ions and nucleotides as substrates. This versatility would allow ad hoc selection of the most appropriate nucleotide/metal ion combination for individual NHEJ events to gain efficiency without a cost in terms of fidelity, thus widening the spectrum of available solutions to position a discontinuous template strand in proper register for connection.

Comparison of two independent Sr optical clocks with 1×10(-17) stability at 10(3) s

Many-particle optical lattice clocks have the potential for unprecedented measurement precision and stability due to their low quantum projection noise. However, this potential has so far never been realized because clock stability has been limited by frequency noise of optical local oscillators. By synchronously probing two ^{87}Sr lattice systems using a laser with a thermal noise floor of 1×10(-15), we remove classically correlated laser noise from the intercomparison, but this does not demonstrate independent clock performance. With an improved optical oscillator that has a 1×10(-16) thermal noise floor, we demonstrate an order of magnitude improvement over the best reported stability of any independent clock, achieving a fractional instability of 1×10(-17) in 1000 s of averaging time for synchronous or asynchronous comparisons. This result is within a factor of 2 of the combined quantum projection noise limit for a 160 ms probe time with ~10(3) atoms in each clock. We further demonstrate that even at this high precision, the overall systematic uncertainty of our clock is not limited by atomic interactions. For the second Sr clock, which has a cavity-enhanced lattice, the atomic-density-dependent frequency shift is evaluated to be -3.11×10(-17) with an uncertainty of 8.2×10(-19).

DNA expansions generated by human Polμ on iterative sequences

Polµ is the only DNA polymerase equipped with template-directed and terminal transferase activities. Polµ is also able to accept distortions in both primer and template strands, resulting in misinsertions and extension of realigned mismatched primer terminus. In this study, we propose a model for human Polµ-mediated dinucleotide expansion as a function of the sequence context. In this model, Polµ requires an initial dislocation, that must be subsequently stabilized, to generate large sequence expansions at different 5′-P-containing DNA substrates, including those that mimic non-homologous end-joining (NHEJ) intermediates. Our mechanistic studies point at human Polµ residues His³²⁹ and Arg³⁸⁷ as responsible for regulating nucleotide expansions occurring during DNA repair transactions, either promoting or blocking, respectively, iterative polymerization. This is reminiscent of the role of both residues in the mechanism of terminal transferase activity. The iterative synthesis performed by Polµ at various contexts may lead to frameshift mutations producing DNA damage and instability, which may end in different human disorders, including cancer or congenital abnormalities.

DNA-binding determinants promoting NHEJ by human Polμ

Non-homologous end-joining (NHEJ), the preferred pathway to repair double-strand breaks (DSBs) in higher eukaryotes, relies on a collection of molecular tools to process the broken ends, including specific DNA polymerases. Among them, Polµ is unique as it can catalyze DNA synthesis upon connection of two non-complementary ends. Here, we demonstrate that this capacity is intrinsic to Polµ, not conferred by other NHEJ factors. To understand the molecular determinants of its specific function in NHEJ, the interaction of human Polµ with DNA has been directly visualized by electromobility shift assay and footprinting assays. Stable interaction with a DNA gap requires the presence of a recessive 5′-P, thus orienting the catalytic domain for primer and nucleotide binding. Accordingly, recognition of the 5′-P is crucial to align the two DNA substrates of the NHEJ reaction. Site-directed mutagenesis demonstrates the relevance of three specific residues (Lys²⁴⁹, Arg²⁵³ and Arg⁴¹⁶) in stabilizing the primer strand during end synapsis, allowing a range of microhomology-induced distortions beneficial for NHEJ. Moreover, our results suggest that the Polµ BRCT domain, thought to be exclusively involved in interaction with NHEJ core factors, has a direct role in binding the DNA region neighbor to the 5′-P, thus boosting Polµ-mediated NHEJ reactions.

Full phase stabilization of a Yb:fiber femtosecond frequency comb via high-bandwidth transducers

We present full phase stabilization of an amplified Yb:fiber femtosecond frequency comb using an intracavity electro-optic modulator and an acousto-optic modulator. These transducers provide high servo bandwidths of 580 kHz and 250 kHz for f(rep) and f(ceo), producing a robust and low phase noise fiber frequency comb. The comb was self-referenced with an f-2f interferometer and phase locked to an ultrastable optical reference used for the JILA Sr optical clock at 698 nm, exhibiting 0.21 rad and 0.47 rad of integrated phase errors (over 1 mHz-1 MHz), respectively. Alternatively, the comb was locked to two optical references at 698 nm and 1064 nm, obtaining 0.43 rad and 0.14 rad of integrated phase errors, respectively.

A tripartite complex composed of ETV6-NTRK3, IRS1 and IGF1R is required for ETV6-NTRK3-mediated membrane localization and transformation

ETV6-NTRK3 (EN), a chimeric tyrosine kinase generated by t(12;15) translocations, is a dominantly acting oncoprotein in diverse tumor types. We previously showed that insulin-like growth factor 1 receptor (IGF1R) is essential for EN-mediated oncogenesis and that insulin receptor substrate 1 (IRS1) is constitutively tyrosine phosphorylated and bound by EN in transformed cells. Given that IRS1 is also an adapter for IGF1R, we hypothesized that IRS1 might localize EN to IGF1R at the membrane to activate phosphatidylinositol 3-kinase (PI3K)-Akt, which is critical for EN oncogenesis. In this study, we examined EN/IRS1/IGF1R complexes in detail. We find that both IRS1 and kinase active IGF1R are required for EN transformation, that tyrosine phosphorylated IRS1 is present in high molecular weight complexes with EN and IGF1R, and that EN colocalizes with IGF1R at the plasma membrane. Both IGF1R kinase activity and an intact cytoplasmic Y950 residue, the IRS1-docking site of IGF1R, are required, confirming the importance of the IGF1R/IRS1 interaction for EN oncogenesis. The dual specificity IGF1R and insulin receptor (INSR) inhibitor, BMS-536924, blocks EN transformation activity, cell survival and its interaction with IRS proteins, and induces a striking shift of EN proteins to smaller sized molecular complexes. We conclude that a tripartite complex of EN, IRS1 and IGF1R localizes EN to the membrane and that this is essential for EN-mediated transformation. These findings provide an explanation for the observed IGF1R dependency of EN transformation. Blocking IGF1R kinase activity may, therefore, provide a tractable therapeutic strategy for the many tumor types driven by the EN oncoprotein.

Gastric anti-ulcer activity of silymarin, a lipoxygenase inhibitor, in rats

Oral treatment with silymarin was found to be effective in the prevention of gastric ulceration induced by cold-restraint stress, in rats. Statistically significant ulcer index values with respect to the control group, were observed. In 6 h pyloric-ligated animals silymarin showed a significant reduction in the number and severity of the ulcers; however, it did not alter the gastric secretion volume or acidity although histamine concentration was significantly decreased. In absolute ethanol-induced ulcers, treatment with silymarin 1 or 2 h before the anti-ulcerogenic agent, did not prevent the formation of gastric lesions. Furthermore, the hexosamine content was decreased significantly, but the total protein output was enhanced, showing similar values to those with the standard drug, carbenoxolone. These results suggest that the anti-ulcerogenic effect of silymarin could be related to its inhibitory mechanism of enzymatic peroxidation by the lipoxygenase pathway, avoiding leukotriene synthesis.

Abstract P5-10-17: Bevacizumab (Bev) in Combination with Docetaxel (T) and Cyclophosphamide (C) as Adjuvant Treatment (AdjRx) for Patients (pts) with Early Stage (ES) Breast Cancer (BrCa) and Normal HER-2 Status. A Pilot Evaluation

In random assignment trials, the combination of Bev+ chemotherapy has been shown to produce superior response rates and progression free survival compared to chemotherapy alone, providing a rationale for the study of Bev in the AdjRx of pts with ESBrCa. As a principal side effect of Bev is hypertension (HTN), anthracycline-containing (Anth) AdjRx may pose additional cardiovascular risks. The role of Anth in Her2 normal ESBC is uncertain. TC is a standard non-Anth AdjRx. We performed a single arm pilot study to evaluate the feasibility and toxicity of TC+Bev in pts with ESBC in preparation for participation in a random assignment trial. Methods: Eligibility criteria included: ESBC which was HER-2 normal, node-positive or &gt;2 cm and receptor negative, or &gt;3 cm and receptor positive, normal cardiac ejection fraction (EF), no active or uncontrolled cardiovascular disease, normal organ and marrow function. Treatment consisted of four 3 weekly cycles of docetaxel 75 mg/m2 together with cyclophosphamide 600 mg/m2. Patients commenced bevacizumab 15 mg/kg i.v. on day 1, and q 3 weeks to a total of 19 treatments. Pts were monitored clinically, with echocardiograms and with serial estimations of BNP and troponin.

Results: A total of 105 female pts were accrued in 9 ICORG sites between Dec 2008 and June 2010. Ages ranged from 26-86 (median 55). At June 2010, 33 have completed all phases of therapy, 54 are still on treatment. Eighteen pts have been removed from study due to: HTN -7, intestinal perforation -2, withdrew consent-4, proteinuia-1, anaphylaxis-1, infection-3. The perforations occurred at cycles 9 and 19. Neither pt. with perforation had prior abdominal surgery. The median number of cycles achieved by the discontinued pts was 9. HTN requiring Rx occurred in 25 pts. Among 12 with HTN who have completed Bev, 2 are off HTN meds, and 9 are on reducing doses. The median EF at base line was 67%, at 13 cycles (42 pts) 63%, 18 cycles (27 pts) 66%. Six pts had EF drop &gt;10%, in 3 of these EF fell below 50% as last recorded value. There were no episodes of clinical cardiac failure. Troponin and BNP levels were normal in all 57 pts with serial measurements. Thirteen pts required treatment for neutropenia-related infection or for abscess.

Conclusions: The spectrum and frequency of bevacizumab toxicity in our population of healthy adjuvant pts is similar to that reported for pts with metastatic BC and other malignancies. Hypertension is the principal cause of treatment discontinuation, but cardiac toxicity appears to be limited, with this non-anth chemotherapy +Bev. Intestinal perforation can also occur in pts with ESBC. These toxicities can occur in the post chemotherapy phase of Bev therapy. Pts enrolled on random assignment trials of Bev containing AdjRx require careful monitoring for toxicity.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P5-10-17.

Apnoeic and obstructive nonapnoeic sleep respiratory events

Obstructive nonapnoeic event (ONE) scoring is shrouded in confusion. This is important in patients with mild disease, in whom precision is crucial. The aims of the present study were: 1) to identify ONEs using oesophageal pressure (OP) (OP-ONEs) and a noninvasive (NI) method (NI-ONEs); 2) to compare both methods of scoring; and 3) to determine the contribution of ONE definitions to clinical findings. Patients with suspected sleep apnoeas (respiratory disturbance index <or=10) during a first polysomnography were subjected to a second with an OP measurement. OP-ONEs and NI-ONEs were defined as an increase in OP or discernible reduction in the amplitude of thoracoabdominal bands with both desaturation and/or arousal. Bland-Altman analysis established agreement. Comparisons were made between OP-ONEs, NI-ONEs and clinical findings. In our sample (n = 90), the addition of an arousal to the NI-ONEs or OP-ONEs with only desaturation increased the number of NI-ONEs by 329 and 362%, respectively. NI-ONEs with arousal and/or desaturation detected 91% of OP-ONEs. The association with sleepiness depended on the incorporation of arousal into the definition of ONEs. In patients with mild disease, the addition of an arousal to ONEs, with only desaturation, markedly increased respiratory disturbance index, with probable therapeutic implications. Scoring respiratory events as apnoea and ONEs is easier and sufficiently accurate.

Removal of odour-causing compounds using carbonaceous adsorbents/catalysts prepared from sewage sludge

This paper discusses H(2)S, NH(3) and VOCs removal by sewage-sludge-derived materials with outstanding chemical and textural properties. These materials were obtained from different precursors using different chemical and thermal treatments. Results show that the H(2)S removal process entailed a catalytic conversion of H(2)S to S or SO(4) (2-) species. On the other hand, adsorption is the main mechanism governing the performance of sludge-based materials for NH(3) and VOCs. Retention capacities (x/M values) obtained for some of the sludge-based adsorbents/catalysts are similar to those obtained with commercial activated carbons selected as reference materials.

Sr lattice clock at 1 x 10(-16) fractional uncertainty by remote optical evaluation with a Ca clock

Optical atomic clocks promise timekeeping at the highest precision and accuracy, owing to their high operating frequencies. Rigorous evaluations of these clocks require direct comparisons between them. We have realized a high-performance remote comparison of optical clocks over kilometer-scale urban distances, a key step for development, dissemination, and application of these optical standards. Through this remote comparison and a proper design of lattice-confined neutral atoms for clock operation, we evaluate the uncertainty of a strontium (Sr) optical lattice clock at the 1 x 10(-16) fractional level, surpassing the current best evaluations of cesium (Cs) primary standards. We also report on the observation of density-dependent effects in the spin-polarized fermionic sample and discuss the current limiting effect of blackbody radiation-induced frequency shifts.

A novel mathematical model identifies potential factors regulating bone apposition

The development of pharmaceutical treatments for bone disease can be enhanced by mathematical models that predict their effects on matrix apposition during cancellous bone remodelling. Therefore, a mathematical model was constructed to simulate the rate of focal bone formation from the number of osteoid-forming osteoblasts at one microsite and their rate of activity. The number of mature osteoid-forming cells was simulated from a relationship describing the proliferation of preosteoblasts. Osteoblast activity was described by Michaelis-Menten enzyme kinetic equations adapted to describe cellular activity. The model incorporates the negative feedback effects on the rates of bone apposition due to the reduction in size of mature osteoblasts with continuing differentiation and the reduction in number of osteoid-forming cells with apoptosis and osteocyte formation. In addition, the rate of mineralisation is limited according to osteoid substrate availability. Results of sensitivity analysis revealed the amount of bone formed at one microsite to be more sensitive to changes in factors that controlled cell growth during proliferation and the number of mature osteoid-forming osteoblasts than to those that determined cellular activity. Matrix and osteocyte signalling were shown to have potentially important roles in controlling rates of osteoid apposition in normal, healthy bone. This simple model supports the critical role of controlled mitotic growth in normal bone apposition. It can also help to explain how the homeostatic processes of bone resorption and apposition during remodelling can be disrupted by growth factors that affect the mitotic fraction and division time of proliferative preosteoblast cells.

Sensitivity analysis of a novel mathematical model identifies factors determining bone resorption rates

The development of pharmaceutical treatments for bone disease can be enhanced by computational models that predict their effects on resorption and rates of remodeling. Therefore, a simple mathematical model was formulated to simulate erosion depth and duration of resorption, using Michaelis-Menten (M-M) equations to describe changing rates of cellular activity during the two phases of bone resorption. The model was based on histomorphometric data and cellular interactions that occur in the bone microenvironment cited from the literature. Availability of bone substrate for osteoclastic activity during Phase I was assumed to be limited by the ratio of RANKL (ligand for receptor activator for nuclear factor kappaB) to osteoprotegerin (OPG) ('effective RANKL'). The required presence of marrow stromal cell produced macrophage-colony stimulating factor (M-CSF) for osteoclast action was represented as a factor equal to 1 for healthy bone. Growth factors released from the matrix during Phase I were assumed to cause two negative feedback effects: (1) the inhibitory effect of transforming growth factor-beta1 (TGFbeta1)-induced production of OPG by marrow osteoblast stromal cells, reducing effective RANKL; (2) the apoptosis of osteoclast nuclei assumed to occur at high concentrations of TGFbeta. This signaled the end of Phase I. During Phase II, cellular activity to remove the collagen fibrils left behind by osteoclasts was also simulated by Michaelis-Menten kinetic equations. Results of sensitivity analysis revealed variation in resorption depth and duration to fluctuate within 6% and 7% of the baseline value for changes in most input parameters. However, resorption depth was reduced and the duration of resorption lengthened by both a decrease in matrix TGFbeta and an increase the apoptotic threshold. Furthermore, the duration of resorption, but not erosion depth, was sensitive to changes in the maximum rate of cellular activity during removal of collagen fibrils. This mathematical model, which simulates the changing rates of cellular activity, has identified factors that reduce the duration and depth of resorption. It also suggests new targets for modeling therapeutic intervention to slow the rate of bone remodeling.

A prospective randomized multi-center study for the treatment of lumbar spinal stenosis with the X STOP interspinous implant: 1-year results

Patients suffering from neurogenic intermittent claudication secondary to lumbar spinal stenosis have historically been limited to a choice between a decompressive laminectomy with or without fusion or a regimen of non-operative therapies. The X STOP Interspinous Process Distraction System (St. Francis Medical Technologies, Concord, Calif.), a new interspinous implant for patients whose symptoms are exacerbated in extension and relieved in flexion, has been available in Europe since June 2002. This study reports the results from a prospective, randomized trial of the X STOP conducted at nine centers in the U.S. Two hundred patients were enrolled in the study and 191 were treated; 100 received the X STOP and 91 received non-operative therapy (NON OP) as a control. The Zurich Claudication Questionnaire (ZCQ) was the primary outcomes measurement. Validated for lumbar spinal stenosis patients, the ZCQ measures physical function, symptom severity, and patient satisfaction. Patients completed the ZCQ upon enrollment and at follow-up periods of 6 weeks, 6 months, and 1 year. Using the ZCQ criteria, at 6 weeks the success rate was 52% for X STOP patients and 10% for NON OP patients. At 6 months, the success rates were 52 and 9%, respectively, and at 1 year, 59 and 12%. The results of this prospective study indicate that the X STOP offers a significant improvement over non-operative therapies at 1 year with a success rate comparable to published reports for decompressive laminectomy, but with considerably lower morbidity.

Quantitation of PGE9509924, a novel, nonfluorinated quinolone, in rat plasma using liquid chromatography electrospray-tandem mass spectrometry following solid-phase extraction sample clean-up in a 96-well format

PGE9509924, a novel nonfluorinated quinolone, is a potent antibacterial agent with a broad spectrum of activity. A semi-automated method using 96-well format, solid-phase extraction has been developed for quantitating PGE9509924 in rat plasma. The Waters Oasis HLB extraction plate containing a polymeric packing material was found to give the best overall recoveries. All liquid transfer steps other than aliquoting the plasma are accomplished using a 96-channel pipettor. Reverse-phase HPLC with electrospray/MS/MS detection using selective reaction monitoring is used to quantitate the samples. Stable isotopically labeled PGE9509924 is used as the internal standard. The assay is linear over the range from 0.01 to 10 ug/ml. Excellent precision is obtained within a single run and between multiple runs performed on different days. CVs of <6% were observed. The combination of the semi-automated, 96-well parallel sample processing and the short runtime on the LC/MS/MS results in a high throughput assay with reduced operator interaction.

Development of a chiral assay for a novel, nonfluorinated quinolone, PGE-9509924, in dog plasma using high performance liquid chromatography with electrospray tandem mass spectrometry or fluorescence detection

PGE-9509924 is a nonfluorinated quinolone and is active against a variety of susceptible and drug resistant bacteria in vitro and in animal infection models. A method for determining both enantiomers of PGE-9509924 in dog plasma has been developed. The enantiomers are derivatized with a chiral derivatizing agent, (-)-1-(9-fluorenyl)ethyl chloroformate (FLEC) and the resulting diastereomers are separated by reverse phase chromatography. Plasma samples are prepared via solid phase extraction (SPE) in a 96-well format prior to being derivatized. Samples are then analyzed by electrospray-LC/MS/MS with multiple reaction monitoring or by HPLC with fluorescence detection. Results of a side-by-side validation of the method with LC/MS/MS and HPLC/Fl detection are presented. Over the range selected for validation (0.025-10 micro g/ml), both methods give similar results with identical limits of quantitation. Due to the selectivity of LC/MS/MS and the use of a stable-isotopically labeled internal standard, significantly shorter chromatographic runtimes are achieved with LC/MS/MS, making it the method of choice for sample analysis.

Preoperative evaluation of chronic alcoholics assessed for surgery of the upper digestive tract

BACKGROUND

Alcoholics are at risk of developing major complications in the postoperative period. Adequate prophylactic treatment, as well as preoperative abstinence, can significantly decrease the rate of complications. However, the preoperative diagnosis of alcoholism is difficult to establish. The purpose of this study was to assess whether three preoperative visits, an alcohol-related questionnaire (CAGE), and the laboratory markers carbohydrate-deficient transferrin (CDT) and gamma-glutamyltransferase (GGT) would increase the rate of detection of chronic alcoholics.

METHODS

The study included the Departments of ENT, Facial and Maxillofacial Surgery, and General Surgery of a university hospital; 705 male patients were assessed for tumor surgery of the upper digestive tract and were allocated to 5 different groups. All patients were seen three times, and five different strategies were used to detect chronic alcoholics. The gold standard was the diagnosis of alcohol misuse made by an experienced (blinded) investigator according to the DSM-III-R. The main outcome measurements were the detection rates of the different test strategies.

RESULTS

By clinical routine alone, only 16% were detected during the first visit and 34% after three visits. If the CAGE questionnaire was added, sensitivity increased to 64%. The further addition of GGT or CDT led to 80 and 85% detections, respectively. A combination of all tests had a sensitivity of 91%.

CONCLUSIONS

To detect more alcoholic patients at risk for major complications, patients should be seen more often, and additional diagnostic tools such as the CAGE, CDT, and GGT should be used before surgery.

Total colonic manometry as a guide for surgical management of functional colonic obstruction: Preliminary results

BACKGROUND/PURPOSE

Functional colonic obstruction (pseudo-obstruction) encompasses a broad group of motility disorders. Medical management of colonic pseudo-obstruction is complex and often fails, leading to surgical referral. In most cases (excepting Hirschsprung's disease) the surgeon is unable to precisely localize the area of functional obstruction. Total colonic manometry can directly measure intraluminal pressures and contractile function along the entire length of the colon. The authors propose that total colonic manometry can be used by the pediatric surgeon to guide the timing and extent of surgical therapy in refractory functional colonic obstruction.

METHODS

Four patients were evaluated for functional colonic obstruction. All underwent barium enema and rectal biopsy with a diagnosis of Hirschsprung's disease in one patient. All patients underwent colonoscopy and total colonic manometry. Manometric tracings were obtained while fasting, after feeding, and after pharmacologic stimulation both preoperatively (n = 4) and postoperatively (n = 3).

RESULTS

Total colonic manometry identified an abrupt end of normal peristalsis in 2 of the non-Hirschsprung's patients (one in the proximal colon and one in the transverse colon). Medical therapy failed in both of these patients, and they underwent diverting ostomy proximal to the loss of normal peristalsis. The third non-Hirschsprung's patient essentially had normal manometry and was able to have her colon decompressed successfully on a laxative regimen. Repeat manometry after colonic decompression showed return of normal peristalsis in 2 of these patients and continued abnormal peristaltic activity in the third. Definitive surgical intervention based on the results of total colonic manometry was performed on the latter. All 3 patients achieved normal continence. A fourth patient had Hirschsprung's disease confirmed by rectal biopsy and underwent a 1-stage neonatal modified Duhamel procedure, which was complicated by postoperative functional obstruction. Manometry showed a lack of peristaltic function beginning in the right colon. An ileostomy was performed, and timing of ileostomy closure was guided by the return of normal colonic peristalsis seen on manometry.

CONCLUSIONS

These initial cases show the utility of total colonic manometry in the management of colonic pseudo-obstruction syndromes. In addition to its diagnostic utility, direct measurement of colonic motor activity can be valuable in deciding the need for and timing of diversion, the extent of resection, and the suitability of the patient for restoring bowel continuity. In Hirschsprung's disease, total colonic manometry can potentially be used to determine suitability for primary neonatal pull-through versus a staged approach. J Pediatr Surg 36:1757-1763.

Issues in system boundary definition for substance flow analysis: the case of nitrogen cycle management in Catalonia

The great complexity of the nitrogen cycle, including anthropogenic contributions, makes it necessary to carry out local studies, which allow us to identify the specific cause-effect links in a particular society. Models of local societies that are based on methods such as Substance Flow Analysis (SFA), which study and characterise the performance of metabolic exchanges between human society and the environment, are a useful tools for directing local policy towards sustainable management of the nitrogen cycle. In this paper, the selection of geographical boundaries for SFA application is discussed. Data availability and accuracy, and the possibility of linking the results with instructions for decision making, are critical aspects for proper scale selection. The experience obtained in the construction of the model for Catalonia is used to draw attention to the difficulties found in regional studies.

A human CD46 transgenic pig model system for the study of discordant xenotransplantation

BACKGROUND

The chronic shortage in the supply of human organs available for allotransplantation has turned attention toward the use of animals as potential donors, with pigs as the most likely species under consideration. Hyperacute rejection, the initial and immediate barrier to a pig-to-primate xenograft, has been addressed by generation of transgenic pigs that express the human membrane-bound complement-regulatory proteins CD59 and/or CD55. Difficulty has been encountered in generation of transgenic animals that express a third membrane-bound complement-regulatory protein, CD46.

METHODS

We have generated transgenic animals by using a large genomic construct that encompasses the entire human CD46 gene.

RESULTS

We report the first description of transgenic mice and pigs that express high levels of human CD46 in a cell and tissue type-specific manner, resembling patterns of endogenous CD46 expression observed in human tissues. Furthermore, when human CD46 transgenic porcine hearts were transplanted into baboons, the grafts did not succumb to hyperacute rejection, and survival extended for up to 23 days. Under the same conditions, nontransgenic grafts underwent hyperacute rejection within 90 min.

CONCLUSIONS

This is the first report to describe generation of transgenic pigs that express human CD46, and the first in vivo demonstration of the ability of human CD46 expressed on pig organs to regulate complement activation and overcome hyperacute rejection upon transplantation of a vascularized organ into nonhuman primates.

Simulating the growth response of aspen to elevated ozone: a mechanistic approach to scaling a leaf-level model of ozone effects on photosynthesis to a complex canopy architecture

Predicting ozone-induced reduction of carbon sequestration of forests under elevated tropospheric ozone concentrations requires robust mechanistic leaf-level models, scaled up to whole tree and stand level. As ozone effects depend on genotype, the ability to predict these effects on forest carbon cycling via competitive response between genotypes will also be required. This study tests a process-based model that predicts the relative effects of ozone on the photosynthetic rate and growth of an ozone-sensitive aspen clone, as a first step in simulating the competitive response of genotypes to atmospheric and climate change. The resulting composite model simulated the relative above ground growth response of ozone-sensitive aspen clone 259 exposed to square wave variation in ozone concentration. This included a greater effect on stem diameter than on stem height, earlier leaf abscission, and reduced stem and leaf dry matter production at the end of the growing season. Further development of the model to reduce predictive uncertainty is discussed.

Melatonin profiles and sleep characteristics in boys with fragile X syndrome: a preliminary study

Sleep patterns and endogenous melatonin profiles in 13 fragile X boys between the age of 4.7 and 11.0 years were compared to those of 8 age-matched, normal control boys. Parents recorded sleep patterns on a Sleep Diary Chart for 14 consecutive days. Twelve saliva samples were obtained from 8 fragile X participants and all of the controls over 48 hours for the assessment of salivary melatonin profiles. The results showed greater variability in total sleep time and difficulty in sleep maintenance in fragile X boys compared with the control participants. Nocturnal melatonin production, expressed as both peak level and area under the concentration-time curve between 20:00 h and 08:00 h, were found to be significantly larger in fragile X boys than in controls. Additionally, the mean of the minimum daytime melatonin levels recorded was significantly higher for the fragile X group. Elevated levels in some fragile X boys relative to the range seen in controls, occurring either during the day or at night, or in both segments of the secretory profile for some individuals, may be due in part to overactivity of the sympathetic nervous system. Alternative molecular mechanisms leading to changes in melatonin profiles in fragile X are also discussed.

Development of in vivo-matured porcine oocytes following intracytoplasmic sperm injection

The objective of this study was to assess the development of porcine ova fertilized by intracytoplasmic sperm injection (ICSI). Allyl trenbolone (Regumate) was used to synchronize estrus in 13 postpuberal gilts. Gilts were superovulated with pregnant mare serum gonadotropin and hCG. Ova were aspirated from 5- to 8-mm follicles at 36 h after hCG. Cumulus cells were removed by blunt dissection and pipetting in Beltsville embryo culture medium (BECM) supplemented with 0.1% hyaluronidase. Sperm were washed and resuspended in BECM + 8% polyvinylpyrrolidone. Ova (n = 237) that exhibited a polar body were centrifuged at 15 000 x g for 6 min and injected with a single spermatozoon. One hundred fifty-four ova were cultured in NCSU-23 medium in a 5% CO(2) in air environment for 168 h. Ova were fixed in acetic acid/ethanol and stained with 1% orcein. Sixty-nine ICSI ova were cultured for 24 h and transferred (mean = 23) to three recipients. Eighty-one ova (69%) that survived ICSI cleaved within 48 h. Thirty-eight percent (31/81) of these ova became blastocysts (mean +/- SEM = 24.7 +/- 1.1 cells). One recipient gave birth to three pigs. These results demonstrate that porcine embryos derived from ICSI can develop into live pigs.

CD46 transgene expression in pig peripheral blood mononuclear cells does not alter their susceptibility to measles virus or their capacity to downregulate endogenous and transgenic CD46

CD46 (or membrane cofactor protein) protects autologous cells from complement-mediated lysis and has been expressed as a transgene in pigs to overcome complement-mediated hyperacute rejection of porcine organs upon transplantation into primates. Since CD46 has been identified as a receptor for measles virus (MV), the susceptibility of CD46-transgenic (tg) pig peripheral blood mononuclear cells (PBMC) to infection with MV strains which do and do not use CD46 as receptor was investigated. Surprisingly, it was found that MV vaccine strains (e.g. Edmonston) bound to tg as well as non-tg pig PBMC. Phytohaemagglutinin-stimulated CD46-tg and non-tg pig PBMC were equally well infected with MV vaccine strains irrespective of CD46 expression. Upon infection, tg CD46 was downregulated from the cell surface. In contrast, the binding capacity for MV wild-type strains to pig and human PBMC was low, irrespective of CD46 expression. These MV strains did not infect tg or non-tg pig cells. Expression of endogenous pig CD46 was detected with polyclonal sera against human CD46. After infection of pig PBMC with MV strain Edmonston, endogenous pig CD46 was also downregulated. This suggests an interaction between MV Edmonston and pig CD46. However, polyclonal CD46 sera did not inhibit infection with MV Edmonston indicating that CD46 may not exclusively act as a receptor for MV on these cells. Interestingly, similar results were observed using human PBMC. Data suggest that CD46 downregulation after interaction with MV may also occur in porcine organs which express endogenous and/or human CD46 as a means of protection against complement-mediated damage.

The role SWISS-PROT and TrEMBL play in the genome research environment

SWISS-PROT, a curated protein sequence data bank, contains not only sequence data but also annotation relevant to a particular sequence. The annotation added to each entry is done by a team of biologists and comes, primarily, from articles in journals reporting the actual sequencing and sometimes characterisation. Review articles and collaboration with external experts also play a role along with the use of secondary databases like PROSITE and Pfam in addition to a variety of feature prediction methods. Annotation added by these methods is checked for relevance and likelihood to a particular sequence. The onset of genome sequencing has led to a dramatic increase in sequence data to be included in SWISS-PROT. This has led to the production of TrEMBL (Translation of the EMBL database). TrEMBL consists of entries in a SWISS-PROT format that are derived from the translation of all coding sequences in the EMBL nucleotide sequence database, that are not in SWISS-PROT. Unlike SWISS-PROT entries those in TrEMBL are awaiting manual annotation. However, rather than just representing basic sequence and source information, steps have been taken to add features and annotation automatically. In taking these steps it is hoped that TrEMBL entries are enhanced with some indication as to what a protein is, could or may be.

Metabolism of antisense oligonucleotides in rat liver homogenates

Phosphorothioate antisense oligodeoxynucleotides are novel therapeutic agents designed to selectively and specifically inhibit production of various disease-related gene products. In vivo pharmacokinetic experiments indicate that these molecules are widely distributed in many species, with the majority of oligomers accumulating within liver and kidney. To better understand the metabolism of these agents, we studied the stability of several phosphorothioate oligodeoxynucleotides, their congeners, and second generation oligomer chemistries in rat liver homogenates. To examine metabolism, background nuclease activity was characterized in whole liver homogenates by using ISIS 1049, a 21-mer phosphodiester oligodeoxynucleotide. Nuclease activity could readily be detected in liver homogenates. Under optimized conditions, the predominant enzymatic activity was 3'-exonucleolytic and could be influenced by pH and ionic conditions. However, in addition to 3' exonucleases, 5' exo- and endonuclease activities were also observed. Our data indicate that metabolism of phosphorothioate oligodeoxynucleotides was more complex than that of phosphodiesters for many reasons, including phosphorothioate oligodeoxynucleotide inhibition of nucleases and the presence of R(p) and S(p) stereoisomers. The rate of phosphorothioate metabolism also appeared to be influenced by sequence, with pyrimidine-rich compounds being metabolized to a greater extent than purine-rich oligomers. Other factors affecting stability included oligomer chemistry and length. Concomitant experiments performed in rats dosed systemically with the same compounds mimic the activities seen in vitro and suggest that this liver homogenate system is a valuable model with which to study the mechanism of metabolism of antisense oligonucleotides.

13C-urea breath test for the diagnosis of Helicobacter pylori infection before treatment: is citric acid necessary?

AIM

13C-urea breath test is one of the best methods for the diagnosis of Helicobacter pylori infection. Although a citric acid solution is generally used prior to urea intake, the superiority of this strategy has not been sufficiently demonstrated. Thus, our aim was to compare 13C-urea breath test with and without citric acid solution, to evaluate whether 13C-urea breath test can also achieve favourable results when the test meal is omitted.

METHODS

13C-urea breath test with and without citric acid were compared prospectively in 53 subjects without prior Helicobacter pylori eradication therapy prescription. Basal samples and at 15', 30', and 45' after taking 100 mg of 13C-urea were obtained. The gold standard for Helicobacter pylori diagnosis was the 13C-urea breath test result with citric acid at 30', and "Delta Over Baseline" values >5 at that time were considered positive.

RESULTS

The prevalence of Helicobacter pylori infection was 68%. Mean Delta Over Baseline values with citric acid at 15', 30' and 45' were: 29.6+/-39, 30.8+/-37 and 24.6+/-27; whereas respective values without citric acid were lower: 14.9+/-22, 12.2+/-17 and 10D+/-13 (p<O. 001 for all comparisons, Wilcoxon test for paired data). Thus, the area under the curve (constructed with Delta Over Baseline values at different times) with citric acid was 85+/- 102, and 37+/-50 without citric acid [p<0.001). Correlation coefficient between Delta Over Baseline values with and without citric acid at 30' was 0.73 (p<0.0001). The percentage of subjects achieving the highest Delta Over Baseline value at 15', 30' and 45' with citric acid was 51%, 30% and 19%, whereas without citric acid it was 51%, 26% and 23% (non-significant differences). The area under receiver operating characteristic curve for 13C-urea breath test without citric acid was: 0.98 at 15', 1 at 30' and 0.97 at 45'. The best cut-off point for 13C-urea breath test without citric acid at 30' was anywhere between 3. 3 and 3.9 (that is, a lower value than that usually considered with citric acid), with 100% (95% confidence interval, 90-100%) sensitivity and 100% [82-100%) specificity

CONCLUSIONS

13C-urea breath test values with citric acid are higher than those obtained without citric acid, although this difference does not imply a diagnostic superiority in untreated patients when considering 13C-urea breath test without citric acid at 30'. Therefore, for the diagnosis of Helicobacter pylori infection in untreated patients, citric acid solution in 13C-urea breath test protocol can be omitted.

Angiogenic cytokines in mesothelioma: a study of VEGF, FGF-1 and -2, and TGF beta expression

Vascular endothelial growth factor (VEGF), acidic and basic fibroblast growth factors (FGF-1 and -2), and transforming growth factor beta (TGFbeta) are potent angiogenic cytokines. Malignant mesothelioma of the pleura presents with a high intra-tumoural microvascular density (IMD) which also has prognostic relevance. This study was designed to verify the immunohistochemical expression of the angiogenic cytokines in mesothelioma as well as in non-neoplastic human mesothelial cells and to study the individual as well as the combined expression of these cytokines in mesothelioma in relation to both IMD and prognosis. In addition, four mesothelioma cell lines were studied by ELISA for the secretion of VEGF and FGF-2 in their supernatants and were shown to contain high levels of both of these cytokines. Immunohistochemically, VEGF, FGF-1 and -2, and TGFbeta immunoreactivity was present in 81, 67, 92 and 96 per cent of mesotheliomas, and in 20, 50, 40, and 10 per cent of samples of the non-neoplastic mesothelium, respectively. Co-ordinate expression of the cytokines was observed whereby mesotheliomas expressed more than one cytokine. The combined immunohistochemical expression levels for all four cytokines correlated significantly with both IMD (p=0.01) and prognosis (p=0. 0013). When studied individually, high FGF-2 expression correlated best with more tumour aggressiveness and worse prognosis for mesothelioma (p=0.0011). There was no significant correlation between prognosis and immunoexpression of VEGF (p=0.07), FGF-1 (p=0.3), or TGFbeta (p=0.1), or between IMD and any of the cytokines studied individually. These data support the assertion that selective angiogenic cytokines might contribute to the progressive changes of mesothelioma by tumour angiogenesis.

Return of the internal jugular vein--development of collateral drainage following neonatal ligation of the vein

The development of collateral venous drainage in the neck of a child, who as a neonate had undergone ligation and cannulation of the right internal jugular vein, is described. The resultant vessels were of sufficient calibre to be considered as potential sites for vascular access, although it is possible that their course in the thorax may preclude correct placement of a central venous catheter. Nevertheless, we feel that this case further illustrates the benefit of hand-held ultrasonography in visualizing the vascular structures of the neck. Moreover, ligation of a vein in the neonatal period should not be a contraindication to subsequent assessment of that site for vascular access.