Intramolecular interactions of the regulatory domains of the Bcr–Abl kinase reveal a novel control mechanism

AbstractBackground The Abl nonreceptor tyrosine kinase is implicated in a range of cellular processes and its transforming variants are involved in human leukemias. The N-terminal regulatory region of the Abl protein contains Src homology domains SH2 and SH3 which have been shown to be important for the regulation of its activity in vivo. These domains are often found together in the same protein and biochemical data suggest that the functions of one domain can be influenced by the other.Results We have determined the crystal structure of the Abl regulatory region containing the SH3 and SH2 domains. In general, the individual domains are very similar to those of previously solved structures, although the Abl SH2 domain contains a loop which is extended so that one side of the resulting phosphotyrosine-binding pocket is open. In our structure the protein exists as a monomer with no intermolecular contacts to which a biological function may be attributed. However, there is a significant intramolecular contact between a loop of the SH3 domain and the extended loop of the SH2 domain. This contact surface includes the SH2 loop segment that is responsible for binding the phosphate moiety of phosphotyrosine-containing proteins and is therefore critical for orienting peptide interactions.Conclusions The crystal structure of the composite Abl SH3–SH2 domain provides the first indication of how SH2 and SH3 domains communicate with each other within the same molecule and why the presence of one directly influences the activity of the other. This is the first clear evidence that these two domains are in contact with each other. The results suggest that this direct interaction between the two domains may affect the ligand binding properties of the SH2 domain, thus providing an explanation for biochemical and functional data concerning the Bcr–Abl kinase

Inter-Observer Variation in the Pathologic Identification of Extranodal Extension in Nodal Metastasis from Papillary Thyroid Carcinoma

Background: Extranodal extension (ENE) in lymph node metastases has been shown to worsen the prognosis of papillary thyroid cancer (PTC). Despite the clinical significance of ENE, there are no stringent criteria for its microscopic diagnosis, and its identification is subject to inter-observer variability. The objective of this study was to determine the level of agreement among expert pathologists in the identification of ENE in PTC cases. Methods: Eleven expert pathologists from the United States, Italy, and Canada were asked to review 61 scanned slides of representative permanent sections of PTC specimens from Mount Sinai Beth Israel Medical Center in New York. Each slide was evaluated for the presence of ENE. The pathologists were also asked to report the criteria they use to identify ENE. Results: The overall strength of agreement in identifying ENE was only fair (??=?0.35), and the proportion of observed agreement was 0.68. The proportions of observed agreement for the identification of perinodal structures (fat, nerve, skeletal, and thick-walled vessel involvement) ranged from 0.61 to 0.997. Conclusions: Overall agreement for the identification of ENE is poor. The lack of agreement results from both variation in pathologists' identification of features and disagreement on the histologic criteria for ENE. This lack of concordance may help explain some of the discordant information regarding prognosis in clinical studies when this feature is identified.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140272/1/thy.2015.0551.pd

Inter-Observer Variation in the Pathologic Identification of Minimal Extrathyroidal Extension in Papillary Thyroid Carcinoma

Background: Extrathyroidal extension (ETE) is a significant prognostic factor in papillary thyroid carcinoma (PTC). Minimal extrathyroidal extension (mETE) is characterized by involvement of the sternothyroid muscle or perithyroid soft tissue, and is generally identified by light microscope examination. Patients with mETE, identified pathologically, are automatically upstaged to pT3. However, the prognostic implications of mETE have been a source of controversy in the literature. Moreover, there is also controversy surrounding the identification of mETE on pathological specimens. The objective of this study was to determine the level of agreement among expert pathologists in the identification of mETE in PTC cases. Methods: Eleven expert pathologists from the United States, Italy, and Canada were asked to perform a review of 69 scanned slides of representative permanent sections of PTC specimens. Each slide was evaluated for the presence of mETE. The pathologists were also asked to list the criteria they use to identify mETE. Results: The overall strength of agreement for identifying mETE was slight (??=?0.14). Inter-pathologist agreement was best for perithyroidal skeletal muscle involvement (??=?0.46, moderate agreement) and worst for invasion around thick-walled vascular structures (??=?0.02, slight agreement). In addition, there was disagreement over the constellation of histologic features that are diagnostic for mETE, which affected overall agreement for diagnosing mETE. Conclusions: Overall agreement for the identification of mETE is poor. Disagreement is a result of both variation in individual pathologists' interpretations of specimens and disagreement on the histologic criteria for mETE. Thus, the utility of mETE in staging and treatment of PTC is brought into question. The lack of concordance may explain the apparent lack of agreement regarding the prognostic significance of this pathologic feature.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/140271/1/thy.2015.0508.pd

The perihelion activity of comet 67P/Churyumov-Gerasimenko as seen by robotic telescopes

Around the time of its perihelion passage the observability of 67P/Churyumov-Gerasimenko from Earth was limited to very short windows each morning from any given site, due to the low solar elongation of the comet. The peak in the comet's activity was therefore difficult to observe with conventionally scheduled telescopes, but was possible where service/queue scheduled mode was possible, and with robotic telescopes. We describe the robotic observations that allowed us to measure the total activity of the comet around perihelion, via photometry (dust) and spectroscopy (gas), and compare these results with the measurements at this time by Rosetta's instruments. The peak of activity occurred approximately two weeks after perihelion. The total brightness (dust) largely followed the predictions from Snodgrass et al. (2013), with no significant change in total activity levels from previous apparitions. The CN gas production rate matched previous orbits near perihelion, but appeared to be relatively low later in the year

The Main Belt Comets and ice in the Solar System

We review the evidence for buried ice in the asteroid belt; specifically the questions around the so-called Main Belt Comets (MBCs). We summarise the evidence for water throughout the Solar System, and describe the various methods for detecting it, including remote sensing from ultraviolet to radio wavelengths. We review progress in the first decade of study of MBCs, including observations, modelling of ice survival, and discussion on their origins. We then look at which methods will likely be most effective for further progress, including the key challenge of direct detection of (escaping) water in these bodies

Light dynamically regulates growth rate and cellular organisation of the Arabidopsis root meristem

Large-scale methods and robust algorithms are needed for a quantitative analysis of cells status/geometry in situ. It allows the understanding the cellular mechanisms that direct organ growth in response to internal and environmental cues. Using advanced whole-stack imaging in combination with pattern analysis, we have developed a new approach to investigate root zonation under different dark/light conditions. This method is based on the determination of 3 different parameters: cell length, cell volume and cell proliferation on the cell-layer level. This method allowed to build a precise quantitative 3D cell atlas of the Arabidopsis root tip. Using this approach we showed that the meristematic (proliferation) zone length differs between cell layers. Considering only the rapid increase of cortex cell length to determine the meristematic zone overestimates of the proliferation zone for epidermis/cortex and underestimates it for pericycle. The use of cell volume instead of cell length to define the meristematic zone correlates better with cell proliferation zone

A 3D digital atlas of the root tip and its use to investigate changes in the root apical meristem induced by the oncogene

International audienc

Analysis of dynamic gene expression responses to altered gravity in the wildtype and auxin efflux carrier mutants of the model plant Arabidopsis thaliana

Plant roots are among most intensively studied biological systems in gravity research. Altered gravity induces asymmetric cell growth leading to root bending. Differential distribution of the phytohormone auxin underlies root's responses to gravity being coordinated by auxin efflux transporters from the PIN family. The objective of this study was to compare early transcriptomic changes in roots of Arabidopsis thaliana using experiments on board of parabolic flights, suborbital and orbital flights, and ground-based facilities for simulated microgravity conditions to correlate these changes to auxin distribution. By comparing immediate and initial responses of the gene expression to the different gravitational forces identified primary gravity regulated genes and resolved time-effects in gene expression leading to an understanding of the underlying physiological responses and adaptive processes. High-resolution imaging in combination with computational approaches further resolved phenotypic changes initiated by altered gravity at the cellular level. Our study provides important insights towards understanding signal transduction processes in altered gravity conditions by combining experimental platforms with the analysis of different genetic mutants in the model Arabidopsis

2-D Clinostat for Simulated Microgravity Experiments with Arabidopsis Seedlings

Ground-based simulators of microgravity such as fast rotating 2-D clinostats are valuable tools to study gravity related processes. We describe here a versatile g-value-adjustable 2-D clinostat that is suitable for plant analysis. To avoid seedling adaptation to 1 g after clinorotation, we designed chambers that allow rapid fixation. A detailed protocol for fixation, RNA isolation and the analysis of selected genes is described. Using this clinostat we show that mRNA levels of LONG HYPOCOTYL 5 (HY5), MIZU-KUSSEI 1 (MIZ1) and microRNA MIR163 are down- regulated in 5-day-old Arabidopsis thaliana roots after 3 min and 6 min of clinorotation using a maximal reduced g-force of 0.02 g, hence demonstrating that this 2-D clinostat enables the characterization of early transcriptomic events during root response to microgravity. We further show that this 2-D clinostat is able to compensate the action of gravitational force as both gravitropic-dependent statolith sedimentation and subsequent auxin redistribution (monitoring DR5rev :: GFP reporter) are abolished when plants are clinorotated. Our results demonstrate that 2-D clinostats equipped with interchangeable growth chambers and tunable rotation velocity are suitable for studying how plants perceive and respond to simulated microgravity