Ornithokinin (avian bradykinin) from the skin of the Chinese bamboo odorous frog, Odorrana versabilis

One of the most widespread and abundant families of pharmacologically active peptides in amphibian defensive skin secretions is the bradykinins and related peptides. Despite retaining certain primary structural attributes that assign them to this peptide family, bradykinins and related peptides are unique among amphibian skin peptides in that they exhibit a wide range of primary structural variations, post-translational modifications and/or N-terminal or C-terminal extensions. Initially it was believed that their high degree of primary structural heterogeneity was reflective of random gene mutations within species, but latterly, there is an increasing body of evidence that the spectrum of structural modifications found within this peptide family is reflective of the vertebrate predator spectrum of individual species. Here we report the discovery of ornithokinin (avian bradykinin – Thr6, Leu8-bradykinin) in the skin secretion of the Chinese bamboo odorous frog, Odorrana versabilis. Molecular cloning of its biosynthetic precursor-encoding cDNA from a skin secretion-derived cDNA library revealed a deduced open-reading frame of 86 amino acid residues, encoding a single copy of ornithokinin towards its C-terminus. The domain architecture of this ornithokinin precursor protein was consistent with that of a typical amphibian skin peptide and quite different to that of the ornithokininogen from chicken plasma. Ornithokinin was reported to induce hypotension in the chicken and to contract the chicken oviduct but to have no obvious effect on the rat uterus. However, in this study, synthetic ornithokinin was found to contract the rat ileum (EC50 = 539 nM) and to increase contraction frequency in the rat uterus (EC50 = 1.87 μM).

Fibroblast growth factor receptor 4 (FGFR4): a targetable regulator of drug resistance in colorectal cancer

The discovery of underlying mechanisms of drug resistance, and the development of novel agents to target these pathways, is a priority for patients with advanced colorectal cancer (CRC). We previously undertook a systems biology approach to design a functional genomic screen and identified fibroblast growth factor receptor 4 (FGFR4) as a potential mediator of drug resistance. The aim of this study was to examine the role of FGFR4 in drug resistance using RNAi and the small-molecule inhibitor BGJ398 (Novartis). We found that FGFR4 is highly expressed at the RNA and protein levels in colon cancer tumour tissue compared with normal colonic mucosa and other tumours. Silencing of FGFR4 reduced cell viability in a panel of colon cancer cell lines and increased caspase-dependent apoptosis. A synergistic interaction was also observed between FGFR4 silencing and 5-fluorouracil (5-FU) and oxaliplatin chemotherapy in colon cancer cell lines. Mechanistically, FGFR4 silencing decreased activity of the pro-survival STAT3 transcription factor and expression of the anti-apoptotic protein c-FLIP. Furthermore, silencing of STAT3 resulted in downregulation of c-FLIP protein expression, suggesting that FGFR4 may regulate c-FLIP expression via STAT3. A similar phenotype and downstream pathway changes were observed following FGFR4 silencing in cell lines resistant to 5-FU, oxaliplatin and SN38 and upon exposure of parental cells to the FGFR small-molecule inhibitor BGJ398. Our results indicate that FGFR4 is a targetable regulator of chemo-resistance in CRC, and hence inhibiting FGFR4 in combination with 5-FU and oxaliplatin is a potential therapeutic strategy for this disease.

Distal volcanic ash layers in the Lateglacial Interstadial (GI-1): problems of stratigraphic discrimination

A new Icelandic ash layer has been detected in mid-Interstadial sediments in a number of Scottish Lateglacial sequences and has been named the Penifiler Tephra. It is rhyolitic in composition and possesses a chemistry, which is similar to the Borrobol Tephra of early Lateglacial Interstadial age, which also occurs in a number of these same sequences. Where the Borrobol Tephra has been identified in these sequences it consistently exhibits a diffuse distribution accompanied in some cases by stratigraphic bimodality. A number of sedimentological and taphonomic factors are considered in order to account for this distribution. One possibility is that these distributions are produced by taphonomic factors. Another possibility is that the Borrobol Tephra may not be the product of a single Icelandic eruption, but of two events closely spaced in time. In at least two of the sequences investigated in this study, basaltic shards were found in association with the Penifiler and Borrobol tephras, suggesting either a basaltic phase associated with these eruptions, or coincident eruptions from a separate basaltic volcanic centre. The discovery of the new Penifiler Tephra makes a contribution to the regional tephrostratigraphic framework, and provides an additional isochron for assessing the synchroneity of palaeoenvironmental changes during the Interstadial. The true stratigraphic nature and age of the Borrobol Tephra, however, remains unresolved and, therefore, its use as an isochron is more problematic. The possible occurrence of basaltic populations may strengthen correlations with basaltic tephras recently detected in the NGRIP ice-core.

Detection of Lateglacial distal tephra layers in the Netherlands

Three distal tephra layers or cryptotephras have been detected within a sedimentary sequence from the Netherlands that spans the last glacial-interglacial transition. Geochemical analyses identify one as the Vedde Ash, which represents the southernmost discovery of this mid-Younger Dryas tephra so far. This tephra was found as a distinct horizon in three different cores sampled within the basin. The remaining two tephras have not been geochemically ‘fingerprinted’, partly due to low concentrations and uneven distributions of shards within the sequences sampled. Nevertheless, there is the potential for tracing these tephra layers throughout the Netherlands and into other parts of continental Europe. Accordingly, the possibilities for precise correlation of Dutch palaeoenvironmental records with other continental, marine and ice-core records from the North Atlantic region are highlighted.

Similarity between Positronium-Atom and Electron-Atom Scattering

We employ the impulse approximation for a description of positronium-atom scattering. Our analysis and calculations of Ps-Kr and Ps-Ar collisions provide a theoretical explanation of the similarity between the cross sections for positronium scattering and electron scattering for a range of atomic and molecular targets observed by S. J. Brawley et al. [Science 330, 789 (2010)].

Discovering subgroups of patients from DNA copy number data using NMF on compacted matrices

In the study of complex genetic diseases, the identification of subgroups of patients sharing similar genetic characteristics represents a challenging task, for example, to improve treatment decision. One type of genetic lesion, frequently investigated in such disorders, is the change of the DNA copy number (CN) at specific genomic traits. Non-negative Matrix Factorization (NMF) is a standard technique to reduce the dimensionality of a data set and to cluster data samples, while keeping its most relevant information in meaningful components. Thus, it can be used to discover subgroups of patients from CN profiles. It is however computationally impractical for very high dimensional data, such as CN microarray data. Deciding the most suitable number of subgroups is also a challenging problem. The aim of this work is to derive a procedure to compact high dimensional data, in order to improve NMF applicability without compromising the quality of the clustering. This is particularly important for analyzing high-resolution microarray data. Many commonly used quality measures, as well as our own measures, are employed to decide the number of subgroups and to assess the quality of the results. Our measures are based on the idea of identifying robust subgroups, inspired by biologically/clinically relevance instead of simply aiming at well-separated clusters. We evaluate our procedure using four real independent data sets. In these data sets, our method was able to find accurate subgroups with individual molecular and clinical features and outperformed the standard NMF in terms of accuracy in the factorization fitness function. Hence, it can be useful for the discovery of subgroups of patients with similar CN profiles in the study of heterogeneous diseases.

Price Discovery in the Dual-Platform US Treasury Market

Inter-dealer trading in US Treasury securities is almost equally divided between two electronic trading platforms that have only slight differences in terms of their relative liquidity and transparency. BrokerTec is more active in the trading of 2-, 5-, and 10-year T-notes while eSpeed has more active trading in the 30-year bond. Over the period studied, eSpeed provides a more pre-trade transparent platform than BrokerTec. We examine the contribution to ‘price discovery’ of activity in the two platforms using high frequency data. We find that price discovery does not derive equally from the two platforms and that the shares vary across term to maturity. This can be traced to differential trading activities and transparency of the two platforms.

FoodCAP: acid-labile protein adducts of heterocyclic amines in human blood are not viable biomarkers of HCA dietary exposure

Intake of heterocyclic amines (HCAs, carcinogens produced during cooking of meat/fish, the most abundant being PhIP, DiMeIQx and MeIQx) is influenced by many factors including type/thickness of meat and cooking method/temperature/duration. Thus, assessment of HCA dietary exposure is difficult. Protein adducts of HCAs have been proposed as potential medium-term biomarkers of exposure, e.g. PhIP adducted to serum albumin or haemoglobin. However, evidence is still lacking that HCA adducts are viable biomarkers in humans consuming normal diets. The FoodCAP project, supported by World Cancer Research Fund, developed a highly sensitive mass spectrometric method for hydrolysis, extraction and detection of acid-labile HCAs in blood and assessed their validity as biomarkers of exposure. Multiple acid/alkaline hydrolysis conditions were assessed, followed by liquid-liquid extraction, clean-up by cation-exchange SPE and quantification by UPLC-ESI-MS/ MS. Blood was analysed from volunteers who completed food diaries to estimate HCA intake based on the US National Cancer Institute’s CHARRED database. Standard HCAs were recovered quantitatively from fortified blood. In addition, PhIP/MeIQx adducts bound to albumin and haemoglobin prepared in vitro using a human liver microsome system were also detectable in blood fortified at low ppt concentrations. However, except for one sample (5pg/ml PhIP), acid-labile PhIP, 7,8-DiMeIQx, 4,8-DiMeIQx and MeIQx were not observed above the 2pg/ml limit of detection in plasma (n=35), or in serum, whole blood or purified albumin, even in volunteers with high meat consumption (nominal HCA intake >2µg/day). It is concluded that HCA blood protein adducts are not viable biomarkers of exposure. Untargeted metabolomic analyses may facilitate discovery of suitable markers.

Optical Spectroscopy of Unbound Asteroid Pairs

The recently discovered unbound asteroid pairs have been suggested to be the result of the decoupling of binary asteroids formed either through collision processes or, more likely, rotational fission of a rubble-pile asteroid after spin-up (Vokrouhlicky et al. 2008, AJ 136, 280; Pravec et al., 2010, Nature, 466, 1085). Much of the evidence for linkage of the asteroids in each pair relies solely on the backwards integrations of their orbits. We report new results from our continuing spectroscopic survey of the unbound asteroid pairs, including the youngest known pair, (6070) Rhineland - (54827) 2001 NQ8. The survey goal is to determine whether the asteroids in each unbound pair have similar spectra and therefore composition, expected if they have formed from a common parent body. Low-resolution spectroscopy covering the range 0.4-0.95 microns was conducted using the 3.6m ESO NTT+EFOSC2 during 2011-2012 and the 4.2m WHT+ACAM. We have attempted to maintain a high level of consistency between the observations of the components in each pair to ensure that differences in the asteroid spectra are not the result of the observing method or data reduction, but purely caused by compositional differences. Our WHT data indicates that the asteroids of unbound pair 17198 - 229056 exhibit different spectra and have been assigned different taxonomies, A and R respectively. Initial analysis of our data from the NTT suggests that the asteroids in unbound pairs 6070 - 54827 and 38707 - 32957 are likely silicate-dominated asteroids. The components of pair 23998 - 205383 are potentially X-type asteroids. We present final taxonomic classifications and the likelihood of spectral similarity in each pair.

Molecular diagnostics of myeloproliferative neoplasms

Since the discovery of the JAK2 V617F mutation in the majority of the myeloproliferative neoplasms (MPN) of polycythemia vera, essential thrombocythemia and primary myelofibrosis ten years ago, further MPN-specific mutational events, notably in JAK2 exon 12, MPL exon 10 and CALR exon 9 have been identified. These discoveries have been rapidly incorporated into evolving molecular diagnostic algorithms. While many of these mutations appear to have prognostic implications, establishing MPN diagnosis is of immediate clinical importance with selection, implementation and the continual evaluation of the appropriate laboratory methodology to achieve this diagnosis similarly vital. The advantages and limitations of these approaches in identifying and quantitating the common MPN-associated mutations is considered herein with particular regard to their clinical utility. The evolution of molecular diagnostic applications and platforms has occurred in parallel with the discovery of MPN-associated mutations and it therefore appears likely that emerging technologies such as next-generation sequencing and digital PCR will in the future, play an increasing role in the molecular diagnosis of MPN. 

The molecular basis of galactosemia - Past, present and future

Galactosemia, an inborn error of galactose metabolism, was first described in the 1900s by von Ruess. The subsequent 100years has seen considerable progress in understanding the underlying genetics and biochemistry of this condition. Initial studies concentrated on increasing the understanding of the clinical manifestations of the disease. However, Leloir's discovery of the pathway of galactose catabolism in the 1940s and 1950s enabled other scientists, notably Kalckar, to link the disease to a specific enzymatic step in the pathway. Kalckar's work established that defects in galactose 1-phosphate uridylyltransferase (GALT) were responsible for the majority of cases of galactosemia. However, over the next three decades it became clear that there were two other forms of galactosemia: type II resulting from deficiencies in galactokinase (GALK1) and type III where the affected enzyme is UDP-galactose 4'-epimerase (GALE). From the 1970s, molecular biology approaches were applied to galactosemia. The chromosomal locations and DNA sequences of the three genes were determined. These studies enabled modern biochemical studies. Structures of the proteins have been determined and biochemical studies have shown that enzymatic impairment often results from misfolding and consequent protein instability. Cellular and model organism studies have demonstrated that reduced GALT or GALE activity results in increased oxidative stress. Thus, after a century of progress, it is possible to conceive of improved therapies including drugs to manipulate the pathway to reduce potentially toxic intermediates, antioxidants to reduce the oxidative stress of cells or use of "pharmacological chaperones" to stabilise the affected proteins.

Navigating Grounded Theory:A critical and reflective response to the challenges of using grounded theory in an education PhD

This paper offers a critical reflection upon the use of a grounded theory approach within a doctoral study. As well as providing an outline of grounded theory, it begins by noting the existence of some powerful critiques of a grounded theory approach, in particular around the key concepts of ‘theory’, ‘discovery’ and ‘ground’. It is argued that, in some cases, grounded theory struggles to counter these challenges, especially in its ‘purist’ forms. However, with reference to research carried out as part of a PhD study of sharing education in Northern Ireland which employed a grounded theory approach, a case is made for an open and critical grounded theory based upon three principles: pragmatism; research as practice; and reflexivity. It is concluded that a reasonable case can be made for grounded theory where: grounded theory researchers maintain a balance between belonging to and critique of the grounded theory community; where there is an emphasis upon theorizing rather than the discovery of theory; and where the strengths of grounded theory as 'practice' and 'craft' are maximised.

King David’s City at Khirbet Qeiyafa: Results of the Second Radiocarbon Dating Project

Fifteen samples of burnt olive pits discovered inside a jar in the destruction layer of the Iron Age city of Khirbet Qeiyafa were analyzed by accelerator mass spectrometry (AMS) radiocarbon dating. Of these, four were halved and sent to two different laboratories to minimize laboratory bias. The dating of these samples is ~1000 BC. Khirbet Qeiyafa is currently the earliest known example of a fortified city in the Kingdom of Judah and contributes direct evidence to the heated debate on the biblical narrative relating to King David. Was he the real historical ruler of an urbanized state-level society in the early 10th century BC or was this level of social development reached only at the end of the 8th century BC? We can conclude that there were indeed fortified centers in the Davidic kingdom from the studies presented. In addition, the dating of Khirbet Qeiyafa has far-reaching implications for the entire Levant. The discovery of Cypriot pottery at the site connects the 14C datings to Cyprus and the renewal of maritime trade between the island and the mainland in the Iron Age. A stone temple model from Khirbet Qeiyafa, decorated with triglyphs and a recessed doorframe, points to an early date for the development of this typical royal architecture of the Iron Age Levant.

The Ultraviolet-Bright, Slowly Declining Transient PS1-11af as a Partial Tidal Disruption Event

We present the Pan-STARRS1 discovery of the long-lived and blue transient PS1-11af, which was also detected by Galaxy Evolution Explorer with coordinated observations in the near-ultraviolet (NUV) band. PS1-11af is associated with the nucleus of an early type galaxy at redshift z = 0.4046 that exhibits no evidence for star formation or active galactic nucleus activity. Four epochs of spectroscopy reveal a pair of transient broad absorption features in the UV on otherwise featureless spectra. Despite the superficial similarity of these features to P-Cygni absorptions of supernovae (SNe), we conclude that PS1-11af is not consistent with the properties of known types of SNe. Blackbody fits to the spectral energy distribution are inconsistent with the cooling, expanding ejecta of a SN, and the velocities of the absorption features are too high to represent material in homologous expansion near a SN photosphere. However, the constant blue colors and slow evolution of the luminosity are similar to previous optically selected tidal disruption events (TDEs). The shape of the optical light curve is consistent with models for TDEs, but the minimum accreted mass necessary to power the observed luminosity is only 0.002 M, which points to a partial disruption model. A full disruption model predicts higher bolometric luminosities, which would require most of the radiation to be emitted in a separate component at high energies where we lack observations. In addition, the observed temperature is lower than that predicted by pure accretion disk models for TDEs and requires reprocessing to a constant, lower temperature. Three deep non-detections in the radio with the Very Large Array over the first two years after the event set strict limits on the production of any relativistic outflow comparable to Swift J1644+57, even if off-axis.

The emerging roles of DNA methylation in the clinical management of prostate cancer

Aberrant DNA methylation is one of the hallmarks of carcinogenesis and has been recognized in cancer cells for more than 20 years. The role of DNA methylation in malignant transformation of the prostate has been intensely studied, from its contribution to the early stages of tumour development to the advanced stages of androgen independence. The most significant advances have involved the discovery of numerous targets such as GSTP1, Ras-association domain family 1A (RASSF1A) and retinoic acid receptor beta2 (RARbeta2) that become inactivated through promoter hypermethylation during the course of disease initiation and progression. This has provided the basis for translational research into methylation biomarkers for early detection and prognosis of prostate cancer. Investigations into the causes of these methylation events have yielded little definitive data. Aberrant hypomethylation and how it impacts upon prostate cancer has been less well studied. Herein we discuss the major developments in the fields of prostate cancer and DNA methylation, and how this epigenetic modification can be harnessed to address some of the key issues impeding the successful clinical management of prostate cancer.