Transcriptome analysis of a parasitic clade V nematode:comparative analysis of potential molecular anthelmintic targets in Cylicostephanus goldi

Clade V nematodes comprise several parasitic species that include the cyathostomins, primary helminth pathogens of horses. Next generation transcriptome datasets are available for eight parasitic clade V nematodes, although no equine parasites are included in this group. Here, we report next generation transcriptome sequencing analysis for the common cyathostomin species, Cylicostephanus goldi. A cDNA library was generated from RNA extracted from 17 C. goldi male and female adult parasites. Following sequencing using a 454 GS FLX pyrosequencer, a total of 475,215 sequencing reads were generated, which were assembled into 26,910 contigs. Using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, 27% of the transcriptome was annotated. Further in-depth analysis was carried out by comparing the C. goldi dataset with the next generation transcriptomes and genomes of other clade V nematodes, with the Oesophagostomum dentatum transcriptome and the Haemonchus contortus genome showing the highest levels of sequence identity with the cyathostomin dataset (45%). The C. goldi transcriptome was mined for genes associated with anthelmintic mode of action and/or resistance. Sequences encoding proteins previously associated with the three major anthelmintic classes used in horses were identified, with the exception of the P-glycoprotein group. Targeted resequencing of the glutamate gated chloride channel α4 subunit (glc-3), one of the primary targets of the macrocyclic lactone anthelmintics, was performed for several cyathostomin species. We believe this study reports the first transcriptome dataset for an equine helminth parasite, providing the opportunity for in-depth analysis of these important parasites at the molecular level. Sequences encoding enzymes involved in key processes and genes associated with levamisole/pyrantel and macrocyclic lactone resistance, in particular the glutamate gated chloride channels, were identified. This novel data will inform cyathostomin biology and anthelmintic resistance studies in future.

Glycemic targets in the second and third trimester of pregnancy for women with type 1 diabetes

OBJECTIVE: To assess the relationship between second and third trimester glycemic control and adverse outcomes in pregnant women with type 1 diabetes, as uncertainty exists about optimum glycemic targets.

RESEARCH DESIGN AND METHODS: Pregnancy outcomes were assessed prospectively in 725 women with type 1 diabetes from the Diabetes and Pre-eclampsia Intervention Trial. HbA1c (A1C) values at 26 and 34 weeks' gestation were categorized into five groups, the lowest, <6.0% (42 mmol/mol), being the reference. Average pre- and postprandial results from an eight-point capillary glucose profile the previous day were categorized into five groups, the lowest (preprandial <5.0 mmol/L and postprandial <6.0 mmol/L) being the reference.

RESULTS: An A1C of 6.0-6.4% (42-47 mmol/mol) at 26 weeks' gestation was associated with a significantly increased risk of large for gestational age (LGA) (odds ratio 1.7 [95% CI 1.0-3.0]) and an A1C of 6.5-6.9% (48-52 mmol/mol) with a significantly increased risk of preterm delivery (odds ratio 2.5 [95% CI 1.3-4.8]), pre-eclampsia (4.3 [1.7-10.8]), need for a neonatal glucose infusion (2.9 [1.5-5.6]), and a composite adverse outcome (3.2 [1.3-8.0]). These risks increased progressively with increasing A1C. Results were similar at 34 weeks' gestation. Glucose data showed less consistent trends, although the risk of a composite adverse outcome increased with preprandial glucose levels between 6.0 and 6.9 mmol/L at 34 weeks (3.3 [1.3-8.0]).

CONCLUSIONS: LGA increased significantly with an A1C ≥6.0 (42 mmol/mol) at 26 and 34 weeks' gestation and with other adverse outcomes with an A1C ≥6.5% (48 mmol/mol). The data suggest that there is clinical utility in regular measurement of A1C during pregnancy.

Particle-in-cell simulation study of the interaction between a relativistically moving leptonic micro-cloud and ambient electrons

Context. The jets of compact accreting objects are composed of electrons and a mixture of positrons and ions. These outflows impinge on the interstellar or intergalactic medium and both plasmas interact via collisionless processes. Filamentation (beam-Weibel) instabilities give rise to the growth of strong electromagnetic fields. These fields thermalize the interpenetrating plasmas. 

Aims. Hitherto, the effects imposed by a spatial non-uniformity on filamentation instabilities have remained unexplored. We examine the interaction between spatially uniform background electrons and a minuscule cloud of electrons and positrons. The cloud size is comparable to that created in recent laboratory experiments and such clouds may exist close to internal and external shocks of leptonic jets. The purpose of our study is to determine the prevalent instabilities, their ability to generate electromagnetic fields and the mechanism, by which the lepton micro-cloud transfers energy to the background plasma. 

Methods. A square micro-cloud of equally dense electrons and positrons impinges in our particle-in-cell (PIC) simulation on a spatially uniform plasma at rest. The latter consists of electrons with a temperature of 1 keV and immobile ions. The initially charge- and current neutral micro-cloud has a temperature of 100 keV and a side length of 2.5 plasma skin depths of the micro-cloud. The side length is given in the reference frame of the background plasma. The mean speed of the micro-cloud corresponds to a relativistic factor of 15, which is relevant for laboratory experiments and for relativistic astrophysical outflows. The spatial distributions of the leptons and of the electromagnetic fields are examined at several times. 

Results. A filamentation instability develops between the magnetic field carried by the micro-cloud and the background electrons. The electromagnetic fields, which grow from noise levels, redistribute the electrons and positrons within the cloud, which boosts the peak magnetic field amplitude. The current density and the moduli of the electromagnetic fields grow aperiodically in time and steadily along the direction that is anti-parallel to the cloud's velocity vector. The micro-cloud remains conjoined during the simulation. The instability induces an electrostatic wakefield in the background plasma. 

Conclusions. Relativistic clouds of leptons can generate and amplify magnetic fields even if they have a microscopic size, which implies that the underlying processes can be studied in the laboratory. The interaction of the localized magnetic field and high-energy leptons will give rise to synchrotron jitter radiation. The wakefield in the background plasma dissipates the kinetic energy of the lepton cloud. Even the fastest lepton micro-clouds can be slowed down by this collisionless mechanism. Moderately fast charge- and current neutralized lepton micro-clouds will deposit their energy close to relativistic shocks and hence they do not constitute an energy loss mechanism for the shock.

Microneedle characterisation: the need for universal acceptance criteria and GMP specifications when moving towards commercialisation

With interest in microneedles as a novel drug transdermal delivery system increasing rapidly since the late 1990s (Margetts and Sawyer Contin Educ Anaesthesia Crit Care Pain. 7(5):171-76, 2007), a diverse range of microneedle systems have been fabricated with varying designs and dimensions. However, there are still very few commercially available microneedle products. One major issue regarding microneedle manufacture on an industrial scale is the lack of specific quality standards for this novel dosage form in the context of Good Manufacturing Practice (GMP). A range of mechanical characterisation tests and microneedle insertion analysis techniques are used by researchers working on microneedle systems to assess the safety and performance profiles of their various designs. The lack of standardised tests and equipment used to demonstrate microneedle mechanical properties and insertion capability makes it difficult to directly compare the in use performance of candidate systems. This review highlights the mechanical tests and insertion analytical techniques used by various groups to characterise microneedles. This in turn exposes the urgent need for consistency across the range of microneedle systems in order to promote innovation and the successful commercialisation of microneedle products.

Functional genomics to identify therapeutic prophylactic targets

Infectious diseases are a leading cause of global human mortality. The use of antimicrobials remains the most common strategy for treatment. However, the isolation of pathogens resistant to virtually all antimicrobials makes it urgent to develop effective therapeutics based on new targets. Here we review a new drug discovery paradigm focusing on identifying and targeting host factors important for infection as well as pathogen determinants involved in disease progression. We summarize innovative strategies which by combining bioinformatics with transcriptomics and chemical genetics have already identified host factors essential for pathogen entry, survival and replication. We describe how the discovery of RNA interference which allows loss-of-function studies has facilitated functional genomic studies in human cells. It is expected that these studies will identify targets to be used as host-directed drug therapy which, together with antimicrobials targeting microbial virulence factors, will efficiently eliminate the invading pathogen.

Abstract 1905: Defining a therapeutic classification of breast cancer by actionable targets

Breast cancer remains a frequent cause of female cancer death despite the great strides in elucidation of biological subtypes and their reported clinical and prognostic significance. We have defined a general cohort of breast cancers in terms of putative actionable targets, involving growth and proliferative factors, the cell cycle, and apoptotic pathways, both as single biomarkers across a general cohort and within intrinsic molecular subtypes.

We identified 293 patients treated with adjuvant chemotherapy. Additional hormonal therapy and trastuzumab was administered depending on hormonal and HER2 status respectively. We performed immunohistochemistry for ER, PR, HER2, MM1, CK5/6, p53, TOP2A, EGFR, IGF1R, PTEN, p-mTOR and e-cadherin. The cohort was classified into luminal (62%) and non-luminal (38%) tumors as well as luminal A (27%), luminal B HER2 negative (22%) and positive (12%), HER2 enriched (14%) and triple negative (25%). Patients with luminal tumors and co-overexpression of TOP2A or IGF1R loss displayed worse overall survival (p=0.0251 and p=0.0008 respectively). Non-luminal tumors had much greater heterogeneous expression profiles with no individual markers of prognostic significance. Non-luminal tumors were characterised by EGFR and TOP2A overexpression, IGF1R, PTEN and p-mTOR negativity and extreme p53 expression.

Our results indicate that only a minority of intrinsic subtype tumors purely express single novel actionable targets. This lack of pure biomarker expression is particular prevalent in the triple negative subgroup and may allude to the mechanism of targeted therapy inaction and myriad disappointing trial results. Utilising a combinatorial biomarker approach may enhance studies of targeted therapies providing additional information during design and patient selection while also helping decipher negative trial results.

Moving on, not out: when young people remain homeless

This article explores the contours of continued housing instability among a group of young people who are participants in a qualitative longitudinal study of youth homelessness in Dublin, Ireland, and considers the limitations of the ‘acculturation’ thesis in explaining long-term homelessness amongst the young. Baseline interviews were conducted with 40 young people, aged 14–23 years, in 2004, and follow-up interviews were conducted with 30 research participants successfully ‘tracked’ in 2005–06. By the time of follow-up, 17 of those interviewed had exited homelessness and 13 remained homeless. The article focuses on the latter group with the aim of exploring the processes and experiences associated with their continued homelessness. The findings presented demonstrate the adverse impact of their ongoing movement through emergency services targeting the under-18s, including their greater immersion in drug and criminal lifestyles. A majority had experienced one or more period of incarceration by the time of follow-up, and many were users of adult homeless services. Whilst some dimensions of young people's accounts are suggestive of a process of acculturation to street and hostel life, we argue that their continued homelessness is better explained as a consequence of their ongoing and unresolved transience and, in particular, their continued dependence on emergency hostel accommodation. The implications of the findings for policy and service provision for homeless young people are discussed.

Moving from Batch to Continuous Operation for the Liquid Phase Dehydrogenation of Tetrahydrocarbazole

Despite the numerous advantages of continuous processing, high-value chemical production is still dominated by batch techniques. In this paper, we investigate options for the continuous dehydrogenation of 1,2,3,4- tetrahydrocarbazole using a trickle bed reactor operating under realistic liquid velocities with and without the addition of a hydrogen acceptor. Here, a commercial 5 wt % Pd/Al₂O₃ catalyst was observed to slowly deactivate, hence proving unsuitable for continuous use. This deactivation was attributed to the strong adsorption of a byproduct on the surface of the support. Application of a base washing technique resolved this issue and a stable continuous reaction has been demonstrated. As was previously shown for the batch reaction, the addition of a hydrogen acceptor gas (propene) can increase the overall catalytic activity of the system. 

In silico analysis and DHPLC screening strategy identifies novel apoptotic gene targets of aberrant promoter hypermethylation in prostate cancer

BACKGROUND: Aberrant DNA methylation has been implicated as a key survival mechanism in cancer, whereby promoter hypermethylation silences genes essential for many cellular processes including apoptosis. Limited data is available on the methylation profile of apoptotic genes in prostate cancer (CaP). The aim of this study was to profile methylation of apoptotic-related genes in CaP using denaturing high performance liquid chromatography (DHPLC).

METHODS: Based on an in silico selection process, 13 genes were screened for methylation in CaP cell lines using DHPLC. Quantitative methylation specific PCR was employed to determine methylation levels in prostate tissue specimens (n = 135), representing tumor, histologically benign prostate, high-grade prostatic intraepithelial neoplasia and benign prostatic hyperplasia. Gene expression was measured by QRT-PCR in cell lines and tissue specimens.

RESULTS: The promoters of BIK, BNIP3, cFLIP, TMS1, DCR1, DCR2, and CDKN2A appeared fully or partially methylated in a number of malignant cell lines. This is the first report of aberrant methylation of BIK, BNIP3, and cFLIP in CaP. Quantitative methylation analysis in prostate tissues identified 5 genes (BNIP3, CDKN2A, DCR1, DCR2 and TMS1) which were frequently methylated in tumors but were unmethylated in 100% of benign tissues. Furthermore, 69% of tumors were methylated in at least one of the five-gene panel. In the case of all genes, except BNIP3, promoter hypermethylation was associated with concurrent downregulation of gene expression.

CONCLUSION: Future examination of this "CaP apoptotic methylation signature" in a larger cohort of patients is justified to further evaluate its value as a diagnostic and prognostic marker.