Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ

The RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same function, but surprisingly, instead of dsRNA binding domains, it harbors two Z-DNA/Z-RNA-binding domains belonging to the Zalpha domain family. Zalpha domains have also been found in other proteins, which have key roles in the regulation of interferon responses such as ADAR1 and DNA-dependent activator of IFN-regulatory factors (DAI) and in viral proteins involved in immune response evasion such as the poxviral E3L and the Cyprinid Herpesvirus 3 ORF112. The underlying mechanism of nucleic acids binding and stabilization by Zalpha domains is still unclear. Here, we present two crystal structures of the zebrafish PKZ Zalpha domain (DrZalpha(PKZ)) in alternatively organized complexes with a (CG)6 DNA oligonucleotide at 2 and 1.8 Å resolution. These structures reveal novel aspects of the Zalpha interaction with DNA, and they give insights on the arrangement of multiple Zalpha domains on DNA helices longer than the minimal binding site.FCT fellowship: (SFRH/BPD/71629/2010), ESRF BAG program, Instituto Gulbenkian de Ciência

Book Review

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149225/1/jpy12840_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149225/2/jpy12840.pd

Herpes Zoster Ophthalmicus: A Devastating Disease Coming Back with Vengeance or Finding Its Nemesis?

Herpes zoster ophthalmicus is a frequent, painful, and debilitating condition caused by the reactivation of the varicella-zoster virus alongside the ophthalmic branch of the trigeminal nerve. Twenty-five percent of adults will develop the disease during their lifetime with the risk increasing to one in two over the age of 50. Herpes zoster ophthalmicus presents with a plethora of ocular manifestations ranging from the characteristic rash in the distribution of the ophthalmic branch of the fifth cranial nerve to more severe keratouveitis, disciform keratitis, and even retinal necrosis. Up to 20% of affected patients develop post-herpetic neuralgia which can persist for years after the acute episode, resulting in potentially devastating consequences for the patient’s social, financial, and professional circumstances, as well as their quality of life and daily activities. Shingles prevention studies indicated that the herpes zoster vaccine markedly reduces the burden of the disease, as well as the incidence of both infection and post-herpetic neuralgia. Here we review the vaccinations available for herpes zoster, the reasons behind their limited adoption so far, as well as the future perspectives and challenges associated with this debilitating disease in the era of herpes zoster vaccination and coronavirus disease pandemic

Conjugatable water-soluble Pt(ii) and Pd(ii) porphyrin complexes: Novel nano- and molecular probes for optical oxygen tension measurement in tissue engineering

Measurement of oxygen tension in compressed collagen sheets was performed using matrix-embedded optical oxygen sensors based on platinum(II) and palladium(II) porphyrins supported on polyacrylamide nanoparticles. Bespoke, fully water-soluble, mono-functionalised Pt(II) and Pd(II) porphyrin complexes designed for conjugation under mild conditions were obtained using microwave-assisted metallation. The new sensors display a linear response (1/τ vs. O₂) to varying oxygen tension over a biologically relevant range (7.0 × 10⁻⁴ to 2.7 × 10⁻¹ mM) in aqueous solutions; a behaviour that is maintained following conjugation to polyacrylamide nanoparticles, and following embedding of the nanosensors in compressed collagen sheets, paving the way to innovative approaches for real-time resolution of oxygen gradients throughout 3D matrices useful for tissue regeneration

The conceptual design of SeamFrame

This project deliverable provides the underlying architecture of a concept for linking models and databases and it provides the design of SeamFrame, delivering its architecture to provide an integration framework for models and simulation algorithms, supported by procedures for data handling and spatial representation, quality control, output visualization and documentatio