Native Mass Spectrometry for the Study of PROTAC GNE-987-Containing Ternary Complexes

PRO teolysis TA rgeting C himeras (PROTACs) promote the degradation, rather than inhibition, of a drug target as a mechanism for therapeutic treatment. Bifunctional PROTAC molecules allow simultaneous binding of both the target protein and an E3-Ubiquitin ligase, bringing the two proteins into close spatial proximity to allow ubiquitinylation and degradation of the target protein via the cell's endogenous protein degradation pathway. We utilized native mass spectrometry (MS) to study the ternary complexes promoted by the previously reported PROTAC GNE-987 between Brd4 bromodomains 1 and 2, and Von Hippel Lindeau E3-Ubiquitin Ligase. Native MS at high resolution allowed us to measure ternary complex formation as a function of PROTAC concentration to provide a measure of complex affinity and stability, whilst simultaneously measuring other intermediate protein species. Native MS provides a high-throughput, low sample consumption, direct screening method to measure ternary complexes for PROTAC development.     

Continuation methods for approximate large scale object sequencing

Machine Learning - We propose a set of highly scalable algorithms for the combinatorial data analysis problem of seriating similarity matrices. Seriation consists of finding a permutation of data...     

Parametric study for tensile properties of molded high-density polyethylene for applications in additive manufacturing and sustainable designs

Test specimens following ASTM D638 standards are frequently used to measure the tensile properties of reinforced and unreinforced polymers machined with traditional machining and emerging manufacturing methods (additive manufacturing/3D printing). However, designs of large engineering structures may rely on mechanical properties based on ASTM D3039 for fiber-reinforced polymer composites. This parametric study examines the scaling effects present in uniaxial tensile test specimens of molded high-density polyethylene (HDPE), with geometries ranging from Types I to IV of ASTM D638 to ASTM D3039. HDPE is a thermoplastic polymer that is recyclable, can be 3D-printed, and has a wide range of engineering applications, from bottles to pipes to radiation protection shielding. The mechanical properties test results for the molded HDPE samples are validated using a Monte Carlo simulation to estimate uncertainties for the probability distribution of maximum stress at the yield point. A Finite Element study based on the empirical model shows how the proposed approach can be adopted for design purposes. The results of this work are a useful tool to enhance confidence in the tensile mechanical properties of ASTM D638 Types II and IV geometries as statistically similar to those of ASTM D3039 samples, impacting engineering designs with traditional and emerging manufacturing methods.     

7,8-Dihydro-8-oxoguanosine Lesions Inhibit the Theophylline Aptamer or Change Its Selectivity

Aptamers are attractive constructs due to their high affinity/selectivity towards a target. Here 7,8-dihydro-8-oxoguanosine (8-oxoG) has been used, due in part to its unique H-bonding capabilities (Watson–Crick or Hoogsteen), to expand the “RNA alphabet”. Its impact on the theophylline RNA aptamer was explored by modifying its binding pocket at positions G11, G25, or G26. Structural probing, with RNases A and T₁, showed that modification at G11 leads to a drastic structural change, whereas the G25-/G26-modified analogues exhibited cleavage patterns similar to that of the canonical construct. The recognition properties towards three xanthine derivatives were then explored through thermophoresis. Modifying the aptamer at position G11 led to binding inhibition. Modification at G25, however, changed the selectivity towards theobromine (K_d≈160 μm ), with a poor affinity for theophylline (K_d>1.5 mm ) being observed. Overall, 8-oxoG can have an impact on the structures of aptamers in a position-dependent manner, leading to altered target selectivity.     

A cathode support structure for use in a magnetron oscillator experiment

A low temperature co-fired ceramic (LTCC) material system has been used to develop a protype field emission cathode structure for use in an experimental magnetron oscillator. The structure is designed for used with 30 gated field emission array (GFEA) die electrically connected through silver metal traces and electrical vias. To approximate a cylinder, the cathode structure (48 mm long and 13.7 mm in diameter) is comprised of 10 faceted plates which cover the GFEA dies. Slits in the facet plates allow electron injection. The GFEA die (3 mm × 8 mm) are placed in axial columns of 3 and spaced azimuthally around a cylindrical support structure in a staggered configuration resulting in 10 azimuthal locations. LTCC manufacturing techniques were developed in order to fabricate the newly designed cathode with seven layers wrapped to form the cylinder with electrical traces and vias. Two different cathode wrapping techniques and two different via filling techniques were studied and compared. Two different facet plate manufacturing techniques were studied. Finally, four different support stand configurations for firing the cylindrical structure were also compared with a square post stand having the best circularity and linearity measurements of the fired structure.     

Aptamer-Functionalized Nanoparticles in Targeted Delivery and Cancer Therapy

Using nanoparticles to carry and delivery anticancer drugs holds much promise in cancer therapy, but nanoparticles per se are lacking specificity. Active targeting, that is, using specific ligands to functionalize nanoparticles, is attracting much attention in recent years. Aptamers, with their several favorable features like high specificity and affinity, small size, very low immunogenicity, relatively low cost for production, and easiness to store, are one of the best candidates for the specific ligands of nanoparticle functionalization. This review discusses the benefits and challenges of using aptamers to functionalize nanoparticles for active targeting and especially presents nearly all of the published works that address the topic of using aptamers to functionalize nanoparticles for targeted drug delivery and cancer therapy.     

Novel insights on the impact of top water on Steam‐Assisted Gravity Drainage in a point bar reservoir

As efforts are made to efficiently exploit and recover bitumen resources in Canada, increasingly more complex reservoirs in the Athabasca area continue to challenge the application of Steam‐Assisted Gravity Drainage (SAGD) technology. Several studies have been done to investigate the impact of heterogeneities/complexities such as shale barriers, lean zones, and top and bottom water on the performance of the SAGD process. However, the literature is deficient for point bar deposits with top water zones, a common occurrence in oil sands systems. This study, by using thermal reservoir simulation, examines SAGD performance in a point bar deposit reservoir where an overlying top water and an inclined heterolithic strata (IHS) is present. The results show that where the top water is unconfined and steam injection pressure is higher than that of the top water zone, there is a loss of thermal energy, but the top water does not impact steam chamber development. At steam injection pressure lower than that of the top water zone, top water continuously drains into the reservoir and constrains the size of the chamber. However, the IHS zone helps to delay drainage of the top water into the chamber when steam is injected at underbalanced conditions. Finally, under proper steam injection pressure conditions, top water production can be considerably delayed.