Effect of bet missense mutations on bromodomain function, inhibitor binding and stability

Lysine acetylation is an important epigenetic mark regulating gene transcription and chromatin structure. Acetylated lysine residues are specifically recognized by bromodomains, small protein interaction modules that read these modification in a sequence and acetylation dependent way regulating the recruitment of transcriptional regulators and chromatin remodelling enzymes to acetylated sites in chromatin. Recent studies revealed that bromodomains are highly druggable protein interaction domains resulting in the development of a large number of bromodomain inhibitors. BET bromodomain inhibitors received a lot of attention in the oncology field resulting in the rapid translation of early BET bromodomain inhibitors into clinical studies. Here we investigated the effects of mutations present as polymorphism or found in cancer on BET bromodomain function and stability and the influence of these mutants on inhibitor binding. We found that most BET missense mutations localize to peripheral residues in the two terminal helices. Crystal structures showed that the three dimensional structure is not compromised by these mutations but mutations located in close proximity to the acetyl-lysine binding site modulate acetyl-lysine and inhibitor binding. Most mutations affect significantly protein stability and tertiary structure in solution, suggesting new interactions and an alternative network of protein-protein interconnection as a consequence of single amino acid substitution. To our knowledge this is the first report studying the effect of mutations on bromodomain function and inhibitor binding

Improving Class Pace for Deaf and Hard-of-Hearing Students

Following multimedia lectures in mainstream classrooms in university education is challenging for deaf and hard-of-hearing (DHH) students even when they are provided accommodations to best address their individual needs. Due to multiple visual sources of information (teacher, slides, interpreter, blackboard), these students struggle to divide their attention among several simultaneous sources of input, which may result in their missing important parts of the lecture content; as a result, DHH students’ access to information can be limited in comparison to that of their hearing peers, and so their academic achievements may be impacted. This paper introduces SlidePacer, a tool aimed at improving coordination between the instructor’s speech, the sign language interpretation of the lecture and the slide projection change. The goal of this software is to prevent DHH students’ loss of information by promoting an adequate pace of the lecture, which can contribute to their learning and academic achievements. We conclude with discussion of future work

Detergency and its implications for oil emulsion sieving and separation

Separating petroleum hydrocarbons from water is an important problem to address in order to mitigate the disastrous effects of hydrocarbons on aquatic ecosystems. A rational approach to address the problem of marine oil water separation is to disperse the oil with the aid of surfactants in order to minimize the formation of large slicks at the water surface and to maximize the oil-water interfacial area. Here we investigate the fundamental wetting and transport behavior of such surfactant-stabilized droplets and the flow conditions necessary to perform sieving and separation of these stabilized emulsions. We show that, for water soluble surfactants, such droplets are completely repelled by a range of materials (intrinsically underwater superoleophobic) due to the detergency effect; therefore, there is no need for surface micro/nanotexturing or chemical treatment to repel the oil and prevent fouling of the filter. We then simulate and experimentally investigate the effect of emulsion flow rate on the transport and impact behavior of such droplets on rigid meshes to identify the minimum pore opening (w) necessary to filter a droplet with a given diameter (d) in order to minimize the pressure drop across the mesh and therefore maximize the filtering efficiency, which is strongly dependent on w. We define a range of flow conditions and droplet sizes where minimum droplet deformation is to be expected and therefore find that the condition of is sufficient for efficient separation. With this new understanding, we demonstrate the use of a commercially available filter--without any additional surface engineering or functionalization--to separate oil droplets from a surfactant stabilized emulsion with a flux of 11,000 L m$^{-2}$ hr$^{-1}$ bar$^{-1}$. We believe these findings can inform the design of future oil separation materials

Continuous enzyme-coupled assay of phosphate- or pyrophosphate-releasing enzymes

A coupled enzyme assay able to monitor the kinetics of reactions catalyzed by phosphate- or pyrophosphate-releasing enzymes is presented here. The assay is based on the concerted action of inorganic pyrophosphatase (PPase), purine nucleoside phosphorylase (PNPase), and xanthine oxidase (XOD). In the presence of phosphate, PNPase catalyzes the phosphorolysis of inosine, generating hypoxanthine, which is oxidized to uric acid by XOD. The uric acid accordingly formed can be spectrophotometrically monitored at 293 nm, taking advantage of a molar extinction coefficient which is independent of pH between 6 and 9. The coupled assay was tested using DNA polymerases as a model system. The activity of Klenow enzyme was quantitatively determined, and it was found in agreement with the corresponding activity determined by traditional methods. Moreover, the continuous coupled assay was used to determine K-m and V-max of Klenow enzyme, yielding values in good agreement with previous observations. Finally, the coupled assay was also used to determine the activity of partially purified DNA polymerases, revealing its potential use to monitor purification of phosphate- or pyrophosphate-releasing enzymes

Strengths of the resonances at 436, 479, 639, 661, and 1279 keV in the 22^{22}Ne(p,γ\gamma)23^{23}Na reaction

The $^{22}$Ne(p,$\gamma$)$^{23}$Na reaction is included in the neon-sodium cycle of hydrogen burning. A number of narrow resonances in the Gamow window dominates the thermonuclear reaction rate. Several resonance strengths are only poorly known. As a result, the $^{22}$Ne(p,$\gamma$)$^{23}$Na thermonuclear reaction rate is the most uncertain rate of the cycle. Here, a new experimental study of the strengths of the resonances at 436, 479, 639, 661, and 1279 keV proton beam energy is reported. The data have been obtained using a tantalum target implanted with $^{22}$Ne. The strengths $\omega\gamma$ of the resonances at 436, 639, and 661 keV have been determined with a relative approach, using the 479 and 1279 keV resonances for normalization. Subsequently, the ratio of resonance strengths of the 479 and 1279 keV resonances was determined, improving the precision of these two standards. The new data are consistent with, but more precise than, the literature with the exception of the resonance at 661 keV, which is found to be less intense by one order of magnitude. In addition, improved branching ratios have been determined for the gamma decay of the resonances at 436, 479, and 639 keV.Comment: Final version, now using the Kelly et al. (2015) data [15] for normalization; 10 pages, 7 figures, 3 table

Vegetated ditches for the mitigation of pesticides runoff in the po valley

In intensive agricultural systems runoff is one of the major potential diffuse pollution path- ways for pesticides and poses a risk to surface water. Ditches are common in the Po Valley and can potentially provide runoff mitigation for the protection of watercourses. The effec- tiveness depends on ditch characteristics, so there is an urgent need for site-specific field trials. The use of a fugacity model (multimedia model) can allows recognition of the mitiga- tion main processes. A field experiment was conducted in order to evaluate the mitigation capacity of a typical vegetated ditch, and results were compared with predictions by a fugacity model. To evaluate herbicide mitigation after an extreme runoff, the ditch was flooded with water containing mesotrione, S-metolachlor and terbuthylazine. Two other sub- sequent floods with uncontaminated water were applied 27 and 82 days later to evaluate herbicides release. Results show that the ditch can immediately reduce runoff concentration of herbicides by at least 50% even in extreme flooding conditions. The half-distances were about 250 m. As a general rule, a runoff of 1 mm from 5 ha is mitigated by 99% in 100 m of vegetated ditch. Herbicides retention in the vegetated ditch was reversible, and the second flood mobilized 0.03-0.2% of the previous one, with a concentration below the drinking water limit of 0.1 \u3bcg L-1. No herbicide was detected in the third flood, because the residual amount in the ditch was too low. Fugacity model results show that specific physical-chemi- cal parameters may be used and a specific soil-sediment-plant compartment included for modelling herbicides behaviour in a vegetated ditch, and confirm that accumulation is low or negligible for herbicides with a half-life of 40 days or less. Shallow vegetated ditches can thus be included in a general agri-environment scheme for the mitigation of pesticides runoff together with wetlands and linear buffer strips. These structures are present in the land- scape, and their environmental role can be exploited by proper management