Discovery of an Allosteric Ligand Binding Site in SMYD3 Lysine Methyltransferase

SMYD3 is a multifunctional epigenetic enzyme with lysine methyltransferase activity and various interaction partners. It is implicated in the pathophysiology of cancers but with an unclear mechanism. To discover tool compounds for clarifying its biochemistry and potential as a therapeutic target, a set of drug-like compounds was screened in a biosensor-based competition assay. Diperodon was identified as an allosteric ligand; its R and S enantiomers were isolated, and their affinities to SMYD3 were determined (K_D=42 and 84 μM, respectively). Co-crystallization revealed that both enantiomers bind to a previously unidentified allosteric site in the C-terminal protein binding domain, consistent with its weak inhibitory effect. No competition between diperodon and HSP90 (a known SMYD3 interaction partner) was observed although SMYD3–HSP90 binding was confirmed (K_D=13 μM). Diperodon clearly represents a novel starting point for the design of tool compounds interacting with a druggable allosteric site, suitable for the exploration of noncatalytic SMYD3 functions and therapeutics with new mechanisms of action.     

Sugar-Pucker Force-Induced Transition in Single-Stranded DNA

The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples range from DNA hybridization, DNA ligand binding, DNA unwinding by helicases, etc. To date, ssDNA elasticity has been studied with different methods in molecules of varying sequence and contour length. A dispersion of results has been reported and the value of the persistence length has been found to be larger for shorter ssDNA molecules. We carried out pulling experiments with optical tweezers to characterize the elastic response of ssDNA over three orders of magnitude in length (60–14 k bases). By fitting the force-extension curves (FECs) to the Worm-Like Chain model we confirmed the above trend:the persistence length nearly doubles for the shortest molecule (60 b) with respect to the longest one (14 kb). We demonstrate that the observed trend is due to the different force regimes fitted for long and short molecules, which translates into two distinct elastic regimes at low and high forces. We interpret this behavior in terms of a force-induced sugar pucker conformational transition (C3′-endo to C2′-endo) upon pulling ssDNA.     

Melatonin for Neonatal Encephalopathy: From Bench to Bedside

Neonatal encephalopathy is a leading cause of morbidity and mortality worldwide. Although therapeutic hypothermia (HT) is now standard practice in most neonatal intensive care units in high resource settings, some infants still develop long-term adverse neurological sequelae. In low resource settings, HT may not be safe or efficacious. Therefore, additional neuroprotective interventions are urgently needed. Melatonin’s diverse neuroprotective properties include antioxidant, anti-inflammatory, and anti-apoptotic effects. Its strong safety profile and compelling preclinical data suggests that melatonin is a promising agent to improve the outcomes of infants with NE. Over the past decade, the safety and efficacy of melatonin to augment HT has been studied in the neonatal piglet model of perinatal asphyxia. From this model, we have observed that the neuroprotective effects of melatonin are time-critical and dose dependent. Therapeutic melatonin levels are likely to be 15–30 mg/L and for optimal effect, these need to be achieved within the first 2–3 h after birth. This review summarises the neuroprotective properties of melatonin, the key findings from the piglet and other animal studies to date, and the challenges we face to translate melatonin from bench to bedside.     

Novel TTLL5 Variants Associated with Cone-Rod Dystrophy and Early-Onset Severe Retinal Dystrophy

Variants of the TTLL5 gene, which encodes tubulin tyrosine ligase-like family member five, are a rare cause of cone dystrophy (COD) or cone-rod dystrophy (CORD). To date, only a few TTLL5 patients have been clinically and genetically described. In this study, we report five patients harbouring biallelic variants of TTLL5. Four adult patients presented either COD or CORD with onset in the late teenage years. The youngest patient had a phenotype of early onset severe retinal dystrophy (EOSRD). Genetic analysis was performed by targeted next generation sequencing of gene panels and assessment of copy number variants (CNV). We identified eight variants, of which six were novel, including two large multiexon deletions in patients with COD or CORD, while the EOSRD patient harboured the novel homozygous p.(Trp640*) variant and three distinct USH2A variants, which might explain the observed rod involvement. Our study highlights the role of TTLL5 in COD/CORD and the importance of large deletions. These findings suggest that COD or CORD patients lacking variants in known genes may harbour CNVs to be discovered in TTLL5, previously undetected by classical sequencing methods. In addition, variable phenotypes in TTLL5-associated patients might be due to the presence of additional gene defects.     

Superior corrosion protection performance of polypdopamine-intercalated CeO2/polyurethane nanocomposite coatings on steel in 3.5% NaCl solution

Journal of Applied Electrochemistry - Newly synthesized polyurethane (PU)–polydopamine (Pda)/CeO2 (cerium oxide) nanocomposite-coated mild steel was investigated for its corrosion protection...     

Antimicrobial effects of chitosans and chitooligosaccharides, upon Staphylococcus aureus and Escherichia coli, in food model systems

The objective of this study was to elucidate the controversial relationship between the molecular weight (MW) of chitosans and their antibacterial activity (upon different inoculum levels, at several concentrations). The influence of food components on the activity was also ascertained, as well as acceptance by a sensory panel. All the compounds tested exhibited antibacterial activity against Staphylococcus aureus and Escherichia coli. This activity was shown to be closely dependent on the inoculum level, MW and concentration used. Within 4h at 10(3) cells/mL, all five compounds, at every concentration (0.5%, 0.25% and 0.1%, w/v), proved to be bactericidal; for higher inocula, 0.1% (w/v) was only bacteriostatic; at 10(7) or 10(5) cells/mL, and independently of the inoculum level, 0.25% (w/v) of any chitooligosaccharide (COS) mixture was sufficient to reduce the E. coli initial population by at least 3 log cycles; COS never exhibited bactericidal action over S. aureus, unlike high and medium MW chitosans-which, at 0.5% (w/v), presented a bactericidal effect even against 10(7) cells/mL. When incorporated in liquid food matrices, medium and high MW chitosans maintained their activity, for both matrices and bacteria, although a slower activity was noticeable in milk; however, COS lost their activity upon both bacteria in milk after 4-8h. Furthermore, addition of chitosans to apple juice led to several unpleasant off-flavors, such as astringency and after taste--which increased in magnitude with MW.     

Protection of deoxyribose and DNA from degradation by using aqueous extracts of several wild plants

BACKGROUND: Aqueous extracts of 48 herbal plants were obtained via alternative extraction protocols, and were assayed for their capacity to protect deoxyribose and DNA itself from degradation (or, conversely, for their capacity to promote DNA degradation), using electrophoresis as analytical tool. RESULTS: For a given (constant) volume of extract, deoxyribose protection ranged from 14.13 ± 1.35% (mean ± SD) inhibition by dwarf mallow powder infusion, up to 106.51 ± 15.93% inhibition by avocado powder infusion. DNA protection was tested at two extract concentrations, and was slightly greater at the higher concentration. Pro‐oxidant effects were essentially absent. CONCLUSION: The anti‐oxidative roles of plants upon deoxyribose and DNA displayed by our experimental results were rather promising with regards to practical applications of those plants, viz. as ingredients in the formulation of nutraceutical beverages and/or foods. Copyright © 2007 Society of Chemical Industry     

Rehabilitating rivers and enhancing ecosystem services in a water-scarcity context: the Yarqon River

After the creation of the state of Israel in 1948, the increase in urban and agricultural water demand and the increased flow of poorly treated sewage had a severe impact in one of the most ecologically important rivers in Israel, the Yarqon. The attempt to reverse this situation began with the creation of the Yarqon River Authority in 1988. In the last 20 years, the authority has implemented or collaborated in several projects that have significantly contributed to enhancing the provision of ecological services. This article aims to analyze the case of the pollution and subsequent rehabilitation of aquatic ecosystem services in the Israeli water-scarcity context.     

Eutrophication, phytoplankton dynamics and nutrient removal in two man-made urban lakes (Palácio de Cristal and Serralves), Porto, Portugal

Urban lakes are prone to eutrophication because of a number of factors, including a high water residence time (slow flushing rate), and high nutrient loads from artificial feeding of waterfowl and fish by visitors and from waterfowl faeces, falling leaves and nutrient run‐off from adjacent areas. This study focuses on the ecology of two similar‐sized urban lakes in Porto, Portugal, that exhibit some differing characteristics conducive to different trophic states and nutrient removal efficiencies. Although similar in many aspects, the two reservoirs developed quite diverse phytoplankton communities. The higher nitrogen load to Palácio de Cristal Lake could be the result of the higher concentration in its underground influent stream, while a less‐oxidized nitrogen form (ammonia) is higher in Serralves Lake. Nitrate concentrations are higher in Palácio de Cristal Lake than in Serralves as a result mainly of high nitrate loads (maximum values above 80 mg L⁻¹) in its influent stream. Interestingly, however, its nitrate removal efficiency is greater than for Serralves Lake. Cyanobacteria are the dominal phytoplankton In both lakes throughout the year. However, only one genus of this group (Pseudoanabaena mucicola) was the dominant phytoplankton in Palácio de Cristal Lake, while five Cyanobacteria species co‐dominated in Serralves lake. Regular monitoring of Cyanobacteria and their toxins in urban recreation lakes is advised.