Reaction profiling of a set of acrylamide-based human tissue transglutaminase inhibitors

The major function of the enzyme human tissue transglutaminase (TG2) is the crosslinking of proteins via a transamidation between the γ-carboxamide of a glutamine and the ε-amino group of a lysine. Overexpression of TG2 can lead to undesirable outcomes and has been linked to conditions such as fibrosis, celiac disease and neurodegenerative diseases. Accordingly, TG2 is a tempting drug target. The most effective TG2 inhibitors to date are small-molecule peptidomimetics featuring electrophilic warheads that irreversibly modify the active site catalytic cysteine (CYS277). In an effort to facilitate the design of such TG2 inhibitors, we undertook a quantum mechanical reaction profiling of the Michael reaction between a set of six acrylamide-based known TG2 inhibitors and the TG2 CYS277. The inhibitors were docked into the active site and the coordinates were refined by MD simulations prior to modelling the covalent modification of the CYS277 thiolate. The results of QM/MM MD umbrella sampling applied to reaction coordinates driving the Michael reaction are presented for two approximations of the Michael reaction: a concerted reaction (simultaneous thiolate attack onto the acrylamide warhead and pronation from the adjacent HIS335) and a two-stage reaction (consecutive thiolate attack and protonation). The two-stage approximation of the Michael reaction gave the better results for the evaluation of acrylamide-based potential TG2 inhibitors in silico. Good correlations were observed between the experimental TG2 IC50 data and the calculated activation energies over the range 0.0061 – 6.3 µM (three orders of magnitude) and we propose that this approach may be used to evaluate acrylamide-based potential TG2 inhibitors

A Catalytic Mechanism for Cysteine N-Terminal Nucleophile Hydrolases, as Revealed by Free Energy Simulations

The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors

PRNP Haplotype Associated with Classical BSE Incidence in European Holstein Cattle

Background: Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease of cattle. The bovine prion gene (PRNP) contains regions of both high and low linkage disequilibrium (LD) that appear to be conserved across Bos taurus populations. The region of high LD, which spans the promoter and part of intron 2, contains polymorphic loci that have been associated with classical BSE status. However, the complex genetic architecture of PRNP has not been systematically tested for an association with classical BSE. Methodology/Principal Findings: In this study, haplotype tagging single nucleotide polymorphisms (htSNPs) within PRNP were used to test for association between PRNP haplotypes and BSE disease. A combination of Illumina goldengate assay, sequencing and PCR amplification was used to genotype 18 htSNPs and 2 indels in 95 BSE case and 134 control animals. A haplotype within the region of high LD was found to be associated with BSE unaffected animals (p-value = 0.000114). Conclusion/Significance: A PRNP haplotype association with classical BSE incidence has been identified. This result suggests that a genetic determinant in or near PRNP may influence classical BSE incidence in cattle

Compilation of a panel of informative single nucleotide polymorphisms for bovine identification in the Northern Irish cattle population

<p>Abstract</p> <p>Background</p> <p>Animal identification is pivotal in governmental agricultural policy, enabling the management of subsidy payments, movement of livestock, test scheduling and control of disease. Advances in bovine genomics have made it possible to utilise inherent genetic variability to uniquely identify individual animals by DNA profiling, much as has been achieved with humans over the past 20 years. A DNA profiling test based on bi-allelic single nucleotide polymorphism (SNP) markers would offer considerable advantages over current short tandem repeat (STR) based industry standard tests, in that it would be easier to analyse and interpret. In this study, a panel of 51 genome-wide SNPs were genotyped across panels of semen DNA from 6 common breeds for the purposes of ascertaining allelic frequency. For SNPs on the same chromosome, the extent of linkage disequilbrium was determined from genotype data by Expectation Maximization (EM) algorithm. Minimum probabilities of unique identification were determined for each breed panel. The usefulness of this SNP panel was ascertained by comparison to the current bovine STR Stockmarks II assay. A statistically representative random sampling of bovine animals from across Northern Ireland was assembled for the purposes of determining the population allele frequency for these STR loci and subsequently, the minimal probability of unique identification they conferred in sampled bovine animals from Northern Ireland.</p> <p>Results</p> <p>6 SNPs exhibiting a minor allele frequency of less than 0.2 in more than 3 of the breed panels were excluded. 2 Further SNPs were found to reside in coding areas of the cattle genome and were excluded from the final panel. The remaining 43 SNPs exhibited genotype frequencies which were in Hardy Weinberg Equilibrium. SNPs on the same chromosome were observed to have no significant linkage disequilibrium/allelic association. Minimal probabilities of uniquely identifying individual animals from each of the breeds were obtained and were observed to be superior to those conferred by the industry standard STR assay.</p> <p>Conclusions</p> <p>The 43 SNPs characterised herein may constitute a starting point for the development of a SNP based DNA identification test for European cattle.</p

A five-year retrospective study of the epidemiological characteristics and visual outcomes of patients hospitalized for ocular trauma in a Mediterranean area

<p>Abstract</p> <p>Background</p> <p>To determine the epidemiological characteristics and visual outcome of ocular trauma in southern Italy.</p> <p>Methods</p> <p>All cases of ocular trauma admitted to Department of Ophthalmology of Palermo University, Italy, from January 2001–December 2005 were retrospectively reviewed for open- or closed-globe injury (OGI or CGI). Data extracted included age, sex, residence, initial and final visual acuity (VA), cause and treatment of injury, hospitalization. The injuries were classified by Ocular Trauma Classification System (OTCS) and Birmingham Eye Trauma Terminology (BETT). We also referred to the Ocular Trauma Score (OTS) in evaluating the final visual outcome.</p> <p>Results</p> <p>Of the 298 eyes, there were 146 OGI and 152 CGI. Fifty eyes (16.8%) had an intraocular foreign body (IOFB). The annual incidence of eye injuries was 4.9 per 100,000. Most injuries occurred in men (84.6%, p < 0.0005), with an average age of 33.0 vs. 49.9 for women (p = 0.005). Cause of injury differed significantly by gender (p = 0.001) and urban vs. rural location (p = 0.009). The most frequent causes in men were outdoor activities related injuries (30.9%), work-related (25.4%), and sport-related (17.5%), and in women were home-related (52.2%) and outdoor activities related injuries (30.4%). In urban areas, road accidents were more frequent; in rural areas, work-related injuries were more frequent with a greater rate of IOFBs than in urban areas (p = 0.002).</p> <p>The incidence of OGI and CGI differed in work-related injuries (p < 0.0005), sport-related injuries (p < 0.0005), and assaults (p = 0.033). The final visual acuity was 20/40 (6/12) or better in 144 eyes (48.3%), 20/40–20/200 (6/12–6/60) in 90 eyes (30.2%), and <20/200 (6/60) or less in 46 eyes (15.5%). Eighteen eyes (6%) had a final acuity of no light perception. Of those eyes that presented with hand motion vision or better, 220 (86.6%) had a final vision of better than 20/200 (6/60). Initial visual acuity was found to be correlated with final visual acuity (Spearman's correlation coefficient = 0.658; p < 0.001). The likelihood of the final visual acuities in the OTS categories was correlated to that of the OTS study group in 12 of 14 cases (85.7%).</p> <p>Conclusion</p> <p>This analysis provides insight into the epidemiology of patients hospitalized for ocular trauma. The findings indicate that ocular trauma is a significant cause of visual loss in this population.</p

Hybris – An Innovative Concept for Future General Aviation

The market analysis and fundamental conceptual design considerations related to Hybris, a new general aviation aircraft concept, are illustrated. Hybris aims at demonstrating innovative technologies for drastic chemical and noise pollution reduction, while maintaining competitiveness in terms of operating costs and flight performance. The key element of innovation in the design is the use of structural batteries, i.e. multifunctional composites that can store energy and sustain mechanical loads, which represent a cutting-edge technology likely to unfold its potential in the field of aeronautics

Promoting biological phosphorus removal in a full scale pre-denitrification wastewater treatment plant

A survey conducted in Italy revealed that less than 0.5% out of a sample of over 2,000 municipal wastewater treatment plants is equipped with an enhanced biological phosphorus removal process. Conditions promoting biological phosphorus removal have been investigated by monitoring three real plants equipped with, respectively: (A) simultaneous chemical precipitation; (B) enhanced biological removal powered by chemical precipitation; (C) tertiary chemical precipitation with evidence of phosphate accumulating bacteria. An anaerobic compartment revealed essential for the growth of these microorganisms, the readily degradable organic concentration in the influent playing a minor role. Mapping dissolved oxygen and oxidation-reduction potential in different compartments of plant (C) was carried out to understand the reasons why phosphate accumulating bacteria were found even in the absence of anaerobic reactor. Finally, the possibility to exploit the biological phosphorus removal in plant (C), by adjusting the aeration conditions, was explored and an economic analysis showed this to be a preferable approach with respect to the chemical removal of phosphorus