Troubleshooting methods for the generation of novel pseudotyped viruses

A pseudotyped virus (PV) is a virus particle with an envelope protein originating from a different virus. The ability to dictate which envelope proteins are expressed on the surface has made pseudotyping an important tool for basic virological studies such as determining the cellular targets of the envelope protein of the virus as well as identification of potential antiviral compounds and measuring specific antibody responses. In this review, we describe the common methodologies employed to generate PVs, with a focus on approaches to improve the efficacy of PV generation

The impact of deep-sea fisheries and implementation of the UNGA Resolutions 61/105 and 64/72. Report of an international scientific workshop

The scientific workshop to review fisheries management, held in Lisbon in May 2011, brought together 22 scientists and fisheries experts from around the world to consider the United Nations General Assembly (UNGA) resolutions on high seas bottom fisheries: what progress has been made and what the outstanding issues are. This report summarises the workshop conclusions, identifying examples of good practice and making recommendations in areas where it was agreed that the current management measures fall short of their target

Troubleshooting methods for the generation of novel pseudotyped viruses

A pseudotyped virus (PV) is a virus particle with an envelope protein originating from a different virus. The ability to dictate which envelope proteins are expressed on the surface has made pseudotyping an important tool for basic virological studies such as determining the cellular targets of the envelope protein of the virus as well as identification of potential antiviral compounds and measuring specific antibody responses. In this review, we describe the common methodologies employed to generate PVs, with a focus on approaches to improve the efficacy of PV generation

The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study

<p>Introduction: Children presenting for the first time with inflammatory bowel disease (IBD) offer a unique opportunity to study aetiological agents before the confounders of treatment. Microaerophilic bacteria can exploit the ecological niche of the intestinal epithelium; Helicobacter and Campylobacter are previously implicated in IBD pathogenesis. We set out to study these and other microaerophilic bacteria in de-novo paediatric IBD.</p> <p>Patients and Methods: 100 children undergoing colonoscopy were recruited including 44 treatment naïve de-novo IBD patients and 42 with normal colons. Colonic biopsies were subjected to microaerophilic culture with Gram-negative isolates then identified by sequencing. Biopsies were also PCR screened for the specific microaerophilic bacterial groups: Helicobacteraceae, Campylobacteraceae and Sutterella wadsworthensis.</p> <p>Results: 129 Gram-negative microaerophilic bacterial isolates were identified from 10 genera. The most frequently cultured was S. wadsworthensis (32 distinct isolates). Unusual Campylobacter were isolated from 8 subjects (including 3 C. concisus, 1 C. curvus, 1 C. lari, 1 C. rectus, 3 C. showae). No Helicobacter were cultured. When comparing IBD vs. normal colon control by PCR the prevalence figures were not significantly different (Helicobacter 11% vs. 12%, p = 1.00; Campylobacter 75% vs. 76%, p = 1.00; S. wadsworthensis 82% vs. 71%, p = 0.312).</p> <p>Conclusions: This study offers a comprehensive overview of the microaerophilic microbiota of the paediatric colon including at IBD onset. Campylobacter appear to be surprisingly common, are not more strongly associated with IBD and can be isolated from around 8% of paediatric colonic biopsies. S. wadsworthensis appears to be a common commensal. Helicobacter species are relatively rare in the paediatric colon.</p&gt

The Irish Coral Task Force and Atlantic Coral Ecosystem Study: Report on Two Deep-Water Coral Conservation Stakeholder Workshops Held in Galway in 2000 and 2002

Increasing public and media awareness of the unique nature of European deep-water corals has put the focus firmly on the need for sustainable management of European offshore living resources. The well documented destruction of deep-water corals off Norway and potentially along the entire European margin combined with extremely slow coral habitat recovery rates, has created a sense of urgency to move towards implementation of the appropriate management measures to ensure the long-term survival of this spectacular and important habitat. In the process, deep-water coral conservation has become in many ways a paradigm for a shift away from traditional sectoral driven resource management approaches, towards an inclusive integrated ecosystem approach to the management of European offshore resources. The EU Fifth Framework Programme, in an effort to increase the socio-economic impact of its R&D projects strongly encouraged the formation of scientist-stakeholder partnerships and development of a suitable research-product delivery mechanism. The major (€2.1 million) European Union funded research project: the Atlantic Coral Ecosystem Study successfully responded to these new challenges in a number of innovative ways. In particular, the establishment of an ACES project-stakeholder partnership through consultative workshops, provided a means for stakeholders to prioritise the scientific research and created a forum for rapid dissemination of scientific results. Complementary initiatives arising from these meetings, such as the formation of the ad hoc Irish Coral Task Force, provided a mechanism whereby scientific findings could be translated into policy advice for the appropriate national authorities. This report serves as a record of the consultative process undertaken during two stakeholder workshops held in Galway on 23rd June 2000 and 24th June 2002. Section A contains conclusions and summary records of the two meetings. Section B contains a series of papers presented at the workshops to provide detailed information on: cold-water coral research and conservation initiatives; fishing related issues; oil and gas related issues and conservation legislation and legal issues. The 2000 meeting was sponsored by the Atlantic Coral Ecosystem Study, while the 2002 meeting was sponsored by the Marine Institute (Ireland), as part of its support for the Irish Coral Task Force and ACES. Between the first and the second meeting, the need for scientific advice to support the designation of Special Areas of Conservation to protect corals under the EU Habitats Directive became a clear priority. Finally, it is obvious that much work remains to be done to achieve effective protection of deep-water corals and similarly threatened 'hot spots' of marine biodiversity along the European shelf and slope. It is also clear, however, that successful implementation of conservation measures will require on-going dialogue with stakeholders, and their participation in the decision making process.Funder: Marine Institut

Absence of mucosa-associated colonic Helicobacters in an Australian urban population

Application of nested PCR for Helicobacter species to 416 samples obtained at colonoscopy from 15 patients with Crohn's disease, 12 with ulcerative colitis, and 43 controls revealed H. pylori DNA in only 6 individuals with no disease association. No other Helicobacter species were detected in ileal or colonic samples.J Clin Microbio

Mutational signatures in esophageal adenocarcinoma define etiologically distinct subgroups with therapeutic relevance

Esophageal adenocarcinoma (EAC) has a poor outcome, and targeted therapy trials have thus far been disappointing owing to a lack of robust stratification methods. Whole-genome sequencing (WGS) analysis of 129 cases demonstrated that this is a heterogeneous cancer dominated by copy number alterations with frequent large-scale rearrangements. Co-amplification of receptor tyrosine kinases (RTKs) and/or downstream mitogenic activation is almost ubiquitous; thus tailored combination RTK inhibitor (RTKi) therapy might be required, as we demonstrate in vitro. However, mutational signatures showed three distinct molecular subtypes with potential therapeutic relevance, which we verified in an independent cohort (n = 87): (i) enrichment for BRCA signature with prevalent defects in the homologous recombination pathway; (ii) dominant T>G mutational pattern associated with a high mutational load and neoantigen burden; and (iii) C>A/T mutational pattern with evidence of an aging imprint. These subtypes could be ascertained using a clinically applicable sequencing strategy (low coverage) as a basis for therapy selection

Dual wavelength digital holography for 3D particle image velocimetry

A multi-exposure digital in-line hologram of a moving particle field is recorded by two different wavelengths and at different times. As a result, during the reconstruction step, each hologram can be independently and accurately reconstructed for each wavelength. This procedure enables avoiding the superimposition of particles images that may be close to each other in multi-exposure holography. The feasibility is demonstrated by using a standard particle sizing reticle and shows the potential of this method for particle velocity measurement