Multiplexed, multimodal profiling of the intracellular activity, interactions, and druggability of protein variants using LABEL-seq

Multiplexed assays of variant effect are powerful tools for assessing the impact of protein sequence variation, but are limited to measuring a single protein property and often rely on indirect readouts of intracellular protein function. Here, we developed LAbeling with Barcodes and Enrichment for biochemicaL analysis by sequencing (LABEL-seq), a platform for the multimodal profiling of thousands of protein variants in cultured human cells. Multimodal measurement of ~20,000 variant effects for ~1,600 BRaf variants using LABEL-seq revealed that variation at positions that are frequently mutated in cancer had minimal effects on folding and intracellular abundance but could dramatically alter activity, protein-protein interactions, and druggability. Integrative analysis of our multimodal measurements identified networks of positions with similar roles in regulating BRaf's signaling properties and enabled predictive modeling of variant effects on complex processes such as cell proliferation and small molecule-promoted degradation. LABEL-seq provides a scalable approach for the direct measurement of multiple biochemical effects of protein variants in their native cellular context, yielding insight into protein function, disease mechanisms, and druggability.

Profiling of drug resistance in Src kinase at scale uncovers a regulatory network coupling autoinhibition and catalytic domain dynamics

Kinase inhibitors are effective cancer therapies, but resistance often limits clinical efficacy. Despite the cataloging of numerous resistance mutations, our understanding of kinase inhibitor resistance is still incomplete. Here, we comprehensively profiled the resistance of ∼3,500 Src tyrosine kinase mutants to four different ATP-competitive inhibitors. We found that ATP-competitive inhibitor resistance mutations are distributed throughout Src's catalytic domain. In addition to inhibitor contact residues, residues that participate in regulating Src's phosphotransferase activity were prone to the development of resistance. Unexpectedly, we found that a resistance-prone cluster of residues located on the top face of the N-terminal lobe of Src's catalytic domain contributes to autoinhibition by reducing catalytic domain dynamics, and mutations in this cluster led to resistance by lowering inhibitor affinity and promoting kinase hyperactivation. Together, our studies demonstrate how drug resistance profiling can be used to define potential resistance pathways and uncover new mechanisms of kinase regulation.

Spherically shaped micro-structured antireflective surfaces

An antireflecting micro-structured interface, working in the resonance domain, and made from a bi-periodic array of semi-spherical hollowing-out in a silicon substrate is presented. Its parameters such as sphere radius and position of sphere centers from the surface are optimized numerically. A simple and robust process is described allowing such kind of antireflective surfaces to be fabricated for the infrared range. Spectral and angular reflectance measurement demonstrates the efficiency of the antireflective micro-structured interface which can easily be adapted for the visible range and for photovoltaic applications by a simple homothetic modification of the micro-structure typical dimensions.

Enhanced antireflecting properties of micro-structured top-flat pyramids

This paper aims at modeling bi-periodic micro-structured silicon surfaces exhibiting broadband antireflection properties in the infrared range using Rigorous Coupled-Wave Analysis (RCWA). These structures of pyramidal shape, which typical dimensions are smaller than the wavelength, are not in the Effective Medium Theory (EMT) validity domain. The influence of various opto-geometrical parameters such as period, depth, shape of the pattern is examined. The antireflective properties of such bi-periodic patterned surfaces are then discussed using the photonic crystal theory and photonic band diagrams description. Correlations between the density of Bloch modes, their localizations with respect to the incident medium light line and the surface reflectance are presented.

Effect of feeding glyphosate-tolerant (roundup-ready events GA21 or nk603) corn compared with reference hybrids on feedlot steer performance and carcass characteristics

Three experiments were conducted to compare the feeding value of genetically enhanced corn (Roundup Ready corn events GA21 and nk603) with nontransgenic hybrids. The four treatments included two separate reference hybrids (REF), the near-isogenic control hybrid (CON), and the genetically enhanced corn (RR), resulting in two preplanned comparisons of CON vs. RR and RR vs. the average of REF. In Exp. 1 (RR event GA21), 175 steers (BW = 427 kg) were fed in 25 pens with seven pens per corn hybrid, except CON, which contained four pens due to limited quantities of that hybrid. In Exp. 2 (RR event nk603), 196 steers (BW = 420 kg) were fed in 28 pens with seven pens per corn. In Exp. 3 (RR event nk603), 200 steers were fed in 20 pens, with a similar treatment design to Exp. 2 and five pens per corn. All experiments were conducted as completely randomized designs and utilized corn produced at University of Illinois (Exp. 1 and 2) and University of Nebraska (Exp. 3) research farms under identity-preserved protocols. In all experiments, DMI, ADG, and feed efficiency were similar (P > 0.30) between RR and REF. In Exp. 1 and Exp. 2, RR was not different (P > 0.25) than CON for growth performance. In Exp. 3, RR was not different from CON for ADG and DMI (P > 0.15) or for feed efficiency (P = 0.08). No differences were observed between RR and CON or RR and REF for carcass weight, longissimus dorsi area, and marbling scores in any of the experiments. Subtle differences were observed between RR and either CON or REF for fat depth in each experiment; however, cattle fed RR were not consistently greater and varied from either the CON or the REF (but not both contrasts) within an experiment. Based on these results, insertion of glyphosate-tolerant genes had no significant effect on nutritive quality of corn. Performance and carcass characteristics were not influenced, which suggests that Roundup Ready corn is similar to conventional, nontransgenic corn when fed to finishing feedlot cattle.

Postnatal development and the differential expression of presynaptic terminal-associated proteins in the developing retina of the Brazilian opossum, Monodelphis domestica

In the present study we have characterized the postnatal (PN) development of the retina in the Brazilian opossum, Monodelphis domestica. Monodelphis, a small, pouchless marsupial, undergoes a protracted period of postnatal development. Using bromodeoxyuridine immunohistochemistry, we have investigated postnatal neurogenesis of the retina. In addition, we have examined the differentiation of the retina by using antibodies directed against the presynaptic terminal-associated proteins synaptotagmin, Rab3A, synaptophysin and synaptosomal-associated protein-25 (SNAP-25), and have characterized their spatial and temporal distribution during postnatal development. This study is the first systematic comparison of the developmental expression of multiple presynaptic terminal-associated proteins in relation to retinal neurogenesis and differentiation. At birth (1PN), the Monodelphis retina was relatively undifferentiated morphologically and birthdating analysis revealed mitotically active cells throughout the retina. The 8PN retina was organized into two cellular layers: an outer region of mitotically active neuroepithelial cells and an inner region of postmitotic cells. The inner plexiform layer formed between 5PN and 10PN, and exhibited unique patterns of immunoreactivity with the antibodies used in this analysis. By 25PN the retina was well laminated, and synaptotagmin-, Rab3A-, synaptophysin- and SNAP-25-like immunoreactivities exhibited distinct and specific patterns within the plexiform layers, although they had not yet achieved their mature, adult patterns. These results indicate that each of these proteins exhibits developmentally regulated changes in its cellular localization, and therefore may play important roles during morphogenesis and synaptogenesis of the vertebrate retina.

[Cervical limits and contour forms as a function of material technology]

The objectives of tooth preparation for porcelain crowns are emphasized in this article. The forms of contour described by Gonon, LE Huche, Poggioli and Leibowitch are reviewed in the first part. In the second part, the profile of the cervical limits and their evolution are described, according to the materials used. The importance of the marginal fit, in relation to microleakage and esthetics, is related in the third part.

[The trapped popliteal artery syndrome. About one bilateral case (author's transl)]

The authors report on a new case of trapped popliteal artery syndrome. It was bilateral and revealed on one side by acute thrombotic ischemia, leading on this occasion to discovery of the opposite trap. They insist on the extremely easy diagnosis based on a dynamic examination of the limb. The distal pulses must be felt in intermediary position, then after tensing of the gastrocnemia by dorsiflexion of the foot and hyper extension of the knee. Blood velocity measurement by Doppler probes and bifemoralangiography, both dynamic, must precede imperative surgery.