Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

Enhanced medial-axis-based block-structured meshing in 2-D

New techniques are presented for using the medial axis to generate decompositions on which high quality block-structured meshes with well-placed mesh singularities can be generated. Established medial-axis-based meshing algorithms are effective for some geometries, but in general, they do not produce the most favourable decompositions, particularly when there are geometric concavities. This new approach uses both the topological and geometric information in the medial axis to establish a valid and effective arrangement of mesh singularities for any 2-D surface. It deals with concavities effectively and finds solutions that are most appropriate to the geometric shapes. Resulting meshes are shown for a number of example models.

Developing employability within a university engineering curriculum

This article provides case studies for incorporating employability in a higher education setting. A professional studies module for a small class (30 students) of third-year aerospace engineers gave insight into industrial challenges while promoting career development. It was delivered mainly by industrial speakers and involved practical tasks and workshops. A more sustainable employability curriculum now supports students in all four years of the School’s three degree programmes, offering a structured development of skills and sector understanding. A notable increase in students obtaining sandwich year placements has been observed.

RNA interference in adult Ascaris suum - an opportunity for the development of a functional genomics platform that supports organism-, tissue- and cell-based biology in a nematode parasite

The sustainable control of animal parasitic nematodes requires the development of efficient functional genomics platforms to facilitate target validation and enhance anthelmintic discovery. Unfortunately, the utility of RNA interference (RNAi) for the validation of novel drug targets in nematode parasites remains problematic. Ascaris suum is an important veterinary parasite and a zoonotic pathogen. Here we show that adult A. suum is RNAi competent, and highlight the induction, spread and consistency of RNAi across multiple tissue types. This platform provides a new opportunity to undertake whole organism-, tissue- and cell-level gene function studies to enhance target validation processes for nematode parasites of veterinary/medical significance.

A study protocol for a pilot randomised trial of a structured education programme for the self-management of type 2 diabetes for adults with intellectual disabilities

BACKGROUND: The need for structured education programmes for type 2 diabetes is a high priority for many governments around the world. One such national education programme in the United Kingdom is the DESMOND Programme, which has been shown to be robust and effective for patients in general. However, these programmes are not generally targeted to people with intellectual disabilities (ID), and robust evidence on their effects for this population is lacking. We have adapted the DESMOND Programme for people with ID and type 2 diabetes to produce an amended programme known as DESMOND-ID. This protocol is for a pilot trial to determine whether a large-scale randomised trial is feasible, to test if DESMOND-ID is more effective than usual care in adults with ID for self-management of their type 2 diabetes, in particular as a means to reduce glycated haemoglobin (Hb1Ac), improve psychological wellbeing and quality of life and promote a healthier lifestyle. This protocol describes the rationale, methods, proposed analysis plan and organisational and administrative details.

METHODS/DESIGN: This trial is a two arm, individually randomised, pilot trial for adults with ID and type 2 diabetes, and their family and/or paid carers. It compares the DESMOND-ID programme with usual care. Approximately 36 adults with mild to moderate ID will be recruited from three countries in the United Kingdom. Family and/or paid carers may also participate in the study. Participants will be randomly assigned to one of two conditions using a secure computerised system with robust allocation concealment. A range of data will be collected from the adults with ID (biomedical, psychosocial and self-management strategies) and from their carers. Focus groups with all the participants will assess the acceptability of the intervention and the trial.

DISCUSSION: The lack of appropriate structured education programmes and educational materials for this population leads to secondary health conditions and may lead to premature deaths. There are significant benefits to be gained globally, if structured education programmes are adapted and shown to be successful for people with ID and other cognitive impairments.

TRIAL REGISTRATION: Registered with International Standard Randomised Controlled Trial (identifier: ISRCTN93185560 ) on 10 November 2014.

Sustainable binders for concrete: a structured approach from waste screening to binder composition development

Worldwide, the building sector requires the production of 4 billion tonnes of cement annually, consuming more than 40% of global energy. Alkali activated “cementless” binders have recently emerged as a novel eco-friendly construction material with a promising potential to replace ordinary Portland cement. These binders consist of a class of inorganic polymer formed mainly by the reaction between an alkaline solution and an aluminosilicate source. Precursor materials for this reaction can be found in secondary material streams from different industrial sectors, from energy to agro-alimentary. However, the suitability of these materials in developing the polymerisation reaction must be assessed through a detailed chemical and physical characterisation, ensuring the availability of required chemical species in the appropriate quantity and physical state. Furthermore, the binder composition needs to be defined in terms of proper alkali activation dosages, water content in the mix, and curing conditions. The mix design must satisfy mechanical requirements and compliance to desired engineering properties (workability, setting time) for ensuring the suitability of the binder in replacing Portland cement in concrete applications. This paper offers a structured approach for the development of secondary material-based binders, from their identification to mix design and production procedure development. Essential features of precursor material can be determined through chemical and physical characterisation methods and advanced microscope techniques. Important mixing parameters and binder properties requirements are examined and some examples of developed binders are reported.

Dual interfacial modifications of hierarchically structured iodine-doped ZnO photoanodes for high-efficiency dye-sensitized solar cells

A nanocomposite porous electrode structure consisting of hierarchical iodine-doped zinc oxide (I-ZnO) aggregates combined with the two simple solution-processed interfacial modifications i.e. a ZnO compact layer (CL) and a TiO2 protective layer (PL) has been developed in order to understand electron transport and recombination in the photoanode matrix, together with boosting the conversion efficiency of I-ZnO based dye-sensitized solar cells (DSCs). Electrochemical impedance spectra demonstrate that ZnO CL pre-treatment and TiO2 PL post-treatment synergistically reduce charge-transfer resistance and suppress electron recombination. Furthermore, the electron lifetime in two combined modifications of IZnO + CL + PL photoelectrode is the longest in comparison with the other three photoelectrodes. As a consequence, the overall conversion efficiency of I-ZnO + CL + PL DSC is significantly enhanced to 6.79%, with a 36% enhancement compared with unmodified I-ZnO DSC. Moreover, the stability of I-ZnO + CL + PL cell is improved as compared to I-ZnO one. The mechanism of electron transfer and recombination upon the introduction of ZnO CL and TiO2 PL is also proposed in this work.

N-linked glycosylation supports cross-talk between receptor tyrosine kinases and androgen receptor

Prostate cancer is the second most common cause of cancer-associated deaths in men and signalling via a transcription factor called androgen receptor (AR) is an important driver of the disease. Androgen treatment is known to affect the expression and activity of other oncogenes including receptor tyrosine kinases (RTKs). In this study we report that AR-positive prostate cancer cell-lines express 50% higher levels of enzymes in the hexosamine biosynthesis pathway (HBP) than AR-negative prostate cell-lines. HBP produces hexosamines that are used by endoplasmic reticulum and golgi enzymes to glycosylate proteins targeted to plasma-membrane and secretion. Inhibition of O-linked glycosylation by ST045849 or N-linked glycosylation with tunicamycin decreased cell viability by 20%. In addition, tunicamycin inhibited the androgen-induced expression of AR target genes KLK3 and CaMKK2 by 50%. RTKs have been shown to enhance AR activity and we used an antibody array to identify changes in the phosphorylation status of RTKs in response to androgen stimulation. Hormone treatment increased the activity of Insulin like Growth Factor 1-Receptor (IGF-1R) ten-fold and this was associated with a concomitant increase in the N-linked glycosylation of the receptor, analyzed by lectin enrichment experiments. Glycosylation is known to be important for the processing and stability of RTKs. Inhibition of N-linked glycosylation resulted in accumulation of IGF-1R pro-receptor with altered mobility as shown by immunoprecipitation. Confocal imaging revealed that androgen induced plasma-membrane localization of IGF-1R was blocked by tunicamycin. In conclusion we have established that the glycosylation of IGF-1R is necessary for the full activation of the receptor in response to androgen treatment and that perturbing this process can break the feedback loop between AR and IGF-1R activation in prostate cells. Achieving similar results selectively in a clinical setting will be an important challenge in the future.

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins

BACKGROUND: Prostate cancer (PCa) is a clinically and pathologically heterogeneous disease. The rapid development of sequencing technology has the potential to deliver new biomarkers with emphasis on aggressive disease and to revolutionise personalised cancer treatment. However, a prostate harbouring cancer commonly contains multiple separate tumour foci, with the potential to aggravate tumour sampling. The level of intraprostatic tumour heterogeneity remains to be determined.

OBJECTIVE: To determine the level of intraprostatic tumour heterogeneity through genome-wide, high-resolution profiling of multiple tumour samples from the same individual.

DESIGN, SETTINGS, AND PARTICIPANTS: Multiple tumour samples were obtained from four individuals following radical prostatectomy. One individual (SWE-1) contained >70% cancer cells in all tumour samples, whereas the other three (SWE-2 to SWE-4) required the use of laser capture microdissection for tumour cell enrichment. Subsequently, DNA was extracted from all tissue samples, and exome sequencing was performed. All tumour foci of SWE-1 were also profiled using a high-resolution array for the identification of copy number alterations (CNA).

OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: Shared somatic high-frequency single nucleotide variants (SNV) and CNAs were used to infer the level of intraprostatic tumour heterogeneity.

RESULTS AND LIMITATIONS: No high-frequency mutations, common for the three tumour samples of SWE-1, were identified. Ten randomly chosen positions were validated with Sanger sequencing in all foci, which verified the exome data. The high level of intraprostatic heterogeneity was consistent in all individuals. In total, three out of four individuals harboured tumours without an apparent common somatic denominator. Although we cannot exclude the presence of common structural rearrangements, a high-density array was used for the detection of deletions and amplifications in SWE-1, which agreed with the exome data.

CONCLUSIONS: We present evidence for the presence of somatically independent tumours within the same prostate. This finding will have implications for personalised cancer treatment and biomarker discovery.

Common Themes in Multi-block Structured Quad/Hex Mesh Generation

The automatic generation of structured multi-block quadrilateral (quad) and hexahedral (hex) meshes has been researched for many years without definitive success. The core problem in quad / hex mesh generation is the placement of mesh singularities to give the desired mesh orientation and distribution [1]. It is argued herein that existing approaches (medial axis, paving / plastering, cross / frame fields) are actually alternative views of the same concept. Using the information provided by the different approaches provides additional insight into the problem.

Gene-associated markers can assign origin in a weakly structured fish, Atlantic herring

Regulations on the exploitation of populations of commercially important fish species and the ensuing consumer interest in sustainable products have increased the need to accurately identify the population of origin of fish and fish products. Although genomics-based tools have proven highly useful, there are relatively few examples in marine fish displaying accurate origin assignment. We synthesize data for 156 single-nucleotide polymorphisms typed in 1039 herring, Clupea harengus L., spanning the Northeast Atlantic to develop a tool that allows assignment of individual herring to their regional origin. We show the method's suitability to address specific biological questions, as well as management applications. We analyse temporally replicated collections from two areas, the Skagerrak (n = 81, 84, 66) and the western Baltic (n = 52, 52). Both areas harbour heavily fished mixed-origin stocks, complicating management issues. We report novel genetic evidence that herring from the Baltic Sea contribute to catches in the North Sea, and find support that western Baltic feeding aggregations mainly constitute herring from the western Baltic with contributions from the Eastern Baltic. Our study describes a general approach and outlines a database allowing individual assignment and traceability of herring across a large part of its East Atlantic distribution.

Neurology assessment by objective structured video examination (OSVE)

Summary
Background
The ability to carry out a neurological examination and make an appropriate differential diagnosis is one of the mainstays of our final Bachelor of Medicine (MB) exam; however, with the introduction of objective structured clinical examinations (OSCEs) it has become impossible to arrange for adequate numbers of suitable real patients to participate in the exam.

Context
It is vital that newly qualified doctors can perform a basic neurological examination, interpret the physical signs and formulate a differential diagnosis.

It is vital that newly qualified doctors can perform a basic neurological examination

Innovation
Since 2010 we have introduced an objective structured video examination (OSVE) of a neurological examination of a real patient as part of our final MB OSCE exam. The students view clips of parts of the examination process. They answer questions on the signs that are demonstrated and formulate a differential diagnosis.

Implications
This type of station is logistically a lot easier to organise than a large number of real patients at different examination sites. The featured patients have clearly demonstrated signs and, as every student sees the same patient, are perfectly standardised. It is highly acceptable to examiners and performed well as an assessment tool. There are, however, certain drawbacks in that we are not examining the student's examination technique or their interaction with the patient. Also, certain signs, in particular the assessment of muscle tone and power, are more difficult for a student to estimate in this situation

Home and Workplace Built Environment Supports for Physical Activity

BACKGROUND: Physical inactivity has been associated with obesity and related chronic diseases. Understanding built environment (BE) influences on specific domains of physical activity (PA) around homes and workplaces is important for public health interventions to increase population PA.

PURPOSE: To examine the association of home and workplace BE features with PA occurring across specific life domains (work, leisure, and travel).

METHODS: Between 2012 and 2013, telephone interviews were conducted with participants in four Missouri metropolitan areas. Questions included sociodemographic characteristics, home and workplace supports for PA, and dietary behaviors. Data analysis was conducted in 2013; logistic regression was used to examine associations between BE features and domain-specific PA.

RESULTS: In home neighborhoods, seven of 12 BE features (availability of fruits and vegetables, presence of shops and stores, bike facilities, recreation facilities, crime rate, seeing others active, and interesting things) were associated with leisure PA. The global average score of home neighborhood BE features was associated with greater odds of travel PA (AOR=1.99, 95% CI=1.46, 2.72); leisure PA (AOR=1.84, 95% CI=1.44, 2.34); and total PA (AOR=1.41, 95% CI=1.04, 1.92). Associations between workplace neighborhoods' BE features and workplace PA were small but in the expected direction.

CONCLUSIONS: This study offers empirical evidence on BE supports for domain-specific PA. Findings suggest that diverse, attractive, and walkable neighborhoods around workplaces support walking, bicycling, and use of public transit. Public health practitioners, researchers, and worksite leaders could benefit by utilizing worksite domains and measures from this study for future BE assessments.

Choice of commuting mode among employees: Do home neighborhood environment, worksite neighborhood environment, and worksite policy and supports matter?

BACKGROUND: Promoting the use of public transit and active transport (walking and cycling) instead of car driving is an appealing strategy to increase overall physical activity.

PURPOSE: To quantify the combined associations between self-reported home and worksite neighborhood environments, worksite support and policies, and employees' commuting modes.

METHOD: Between 2012 and 2013, participants residing in four Missouri metropolitan areas were interviewed via telephone (n = 1,338) and provided information on socio-demographic characteristics, home and worksite neighborhoods, and worksite support and policies. Commuting mode was self-reported and categorized into car driving, public transit, and active commuting. Commuting distance was calculated using geographic information systems. Commuters providing completed data were included in the analysis. Multivariate logistic regression models were used to examine the correlates of using public transit and active commuting.

RESULT: The majority of participants reported commuting by driving (88.9%); only 4.9% used public transit and 6.2% used active modes. After multivariate adjustment, having transit stops within 10-15 minutes walking distance from home (p=0.05) and using worksite incentive for public transit (p<0.001) were associated with commuting by public transit. Commuting distance (p<0.001) was negatively associated with active commuting. Having free or low cost recreation facilities around the worksite (p=0.04) and using bike facilities to lock bikes at the worksite (p<0.001) were associated with active commuting.

CONCLUSION: Both environment features and worksite supports and policies are associated with the choice of commuting mode. Future studies should use longitudinal designs to investigate the potential of promoting alternative commuting modes through worksite efforts that support sustainable commuting behaviors as well as the potential of built environment improvements.