Interactive Local Super-Resolution Reconstruction of Whole-Body MRI Mouse Data: A Pilot Study with Applications to Bone and Kidney Metastases

In small animal imaging studies, when the locations of the micro-structures of interest are unknown a priori, there is a simultaneous need for full-body coverage and high resolution. In MRI, additional requirements to image contrast and acquisition time will often make it impossible to acquire such images directly. Recently, a resolution enhancing post-processing technique called super-resolution reconstruction (SRR) has been demonstrated to improve visualization and localization of micro-structures in small animal MRI by combining multiple low-resolution acquisitions. However, when the field-of-view is large relative to the desired voxel size, solving the SRR problem becomes very expensive, in terms of both memory requirements and computation time. In this paper we introduce a novel local approach to SRR that aims to overcome the computational problems and allow researchers to efficiently explore both global and local characteristics in whole-body small animal MRI. The method integrates state-of-the-art image processing techniques from the areas of articulated atlas-based segmentation, planar reformation, and SRR. A proof-of-concept is provided with two case studies involving CT, BLI, and MRI data of bone and kidney tumors in a mouse model. We show that local SRR-MRI is a computationally efficient complementary imaging modality for the precise characterization of tumor metastases, and that the method provides a feasible high-resolution alternative to conventional MRI.     

CellDynaMo–stochastic reaction-diffusion-dynamics model: Application to search-and-capture process of mitotic spindle assembly

We introduce a Stochastic Reaction-Diffusion-Dynamics Model (SRDDM) for simulations of cellular mechanochemical processes with high spatial and temporal resolution. The SRDDM is mapped into the CellDynaMo package, which couples the spatially inhomogeneous reaction-diffusion master equation to account for biochemical reactions and molecular transport within the Langevin Dynamics (LD) framework to describe dynamic mechanical processes. This computational infrastructure allows the simulation of hours of molecular machine dynamics in reasonable wall-clock time. We apply SRDDM to test performance of the Search-and-Capture of mitotic spindle assembly by simulating, in three spatial dimensions, dynamic instability of elastic microtubules anchored in two centrosomes, movement and deformations of geometrically realistic centromeres with flexible kinetochores and chromosome arms. Furthermore, the SRDDM describes the mechanics and kinetics of Ndc80 linkers mediating transient attachments of microtubules to the chromosomal kinetochores. The rates of these attachments and detachments depend upon phosphorylation states of the Ndc80 linkers, which are regulated in the model by explicitly accounting for the reactions of Aurora A and B kinase enzymes undergoing restricted diffusion. We find that there is an optimal rate of microtubule-kinetochore detachments which maximizes the accuracy of the chromosome connections, that adding chromosome arms to kinetochores improve the accuracy by slowing down chromosome movements, that Aurora A and kinetochore deformations have a small positive effect on the attachment accuracy, and that thermal fluctuations of the microtubules increase the rates of kinetochore capture and also improve the accuracy of spindle assembly.     

Does plasma membrane H+-ATPase activation by fusicoccin involve protein kinase?

Sugar beet ( Beta vulgaris L.) root suspension-cultured cells were converted to protoplasts which responded to fusicoccin (FC) by a rise in cytoplasmic pH (pH_cyt) averaging 0.25 units in the fluorimetric assay. This effect was blocked by erythrosin B, a specific inhibitor of the plasma membrane H₊-ATPase. A protein kinase inhibitor, staurosporine also caused cytosolic alkalinization that was sensitive to H⁺-ATPase inhibitors. Most strikingly, the effect of staurosporine was suppressed by fusicoccin and vice versa. Addition of okadaic acid, entailing overall protein phosphorylation, also led to H⁺-ATPase activation, whereupon fusicoccin lost its effect on proton transport. In parallel, kinetic and inhibitor analyses demonstrated that FC binding to the protoplast plasma membrane involved two sites with dissociation constants of 1 n M and 0.2 μ M and was indifferent to phosphorylation and dephosphorylation inhibitors. Thus, it could be concluded that (1) the effect of FC on cytoplasmic pH probably depends on the phosphorylation state of plasma membrane proteins and may have either sign; (2) the activation of H⁺-ATPase by FC most likely proceeds directly through conformational receptor-enzyme interaction.     

A Subthreshold High-Pressure Discharge Excited by a Microwave Beam: Physical Basics and Applications

A new form of discharge excited by a microwave beam in a high-pressure (up to atmospheric and higher) gas in free space and in a closed chamber is discussed. For the first time, the discharge was implemented by means of a gyrotron with a pulse power of 200 ≤ P ≤ 600 kW, a pulse duration of 0.5 ≤ τ ≤ 20 ms, and a wavelength of λ = 0.4 cm. Under deeply subthreshold conditions in atmospheric-pressure air, a plasma column with a length of L = 50 cm was generated by a microwave beam formed with the help of a quasi-optical transmission line. With the use of the MIG-3 gyrotron complex with the above parameters, generation of a plasma column with a length of several meters is possible in principle. The parameters and structure of the formation of the plasma investigated make it possible to class it as a self-non-self-sustained (SNSS) discharge, discovered and described for the first time at the Prokhorov General Physics Institute, Russian Academy of Sciences. One of the important applications of this type of discharge is plasmachemical cleaning of the urban air environment of hazardous contaminants.     

Ant–aphid relations in the south of Western Siberia (Hymenoptera: Formicidae; Hemiptera: Aphididae)

Aphids, the main suppliers of energy-rich honeydew, play an important role in the life of ants. However, the data on the trophobiotic ant–aphid associations in the majority of regions are still limited. We present the first data on the ant–aphid relations in the south of Western Siberia. Investigations were carried out in the most typical biotopes of forest-steppe and steppe zones in the territory of Novosibirsk and Kurgan regions (Russia) during 1993–2014. There were revealed 35 species of ants and 198 species of aphids. Detected 456 ant–aphid associations involved 28 ant species and 134 myrmecophilous aphids. Seven ant species were found to consume honeydew of 9 non-myrmecophilous aphids, scraping it from the plant. This behaviour is typical of subdominant and subordinate ants which do not protect their foraging areas. Ants associate with various numbers of aphid species. About 36% of ants attended aphid colonies of less than 5 species. The largest number of myrmecophilous aphids is associated with L. niger (Linnaeus, 1758) (103 species), Formica pratensis Retzius, 1783 (50), Formica rufa group (25–33), F. (Serviformica) fusca Linnaeus, 1758 (26) and F. (S.) cunicularia Latreille, 1798 (27). Different ants play unequal roles in the formation of trophobiotic interactions with aphids. Due to complex territorial and foraging behaviour, including high functional specialization among honeydew collectors, dominant ants of Formica s. str. are one of the leaders in this process. The role of L. niger and Formica ants of the subgenus Serviformica requires further detailed investigation.     

Small molecule compounds that induce cellular senescence

To date, dozens of stress‐induced cellular senescence phenotypes have been reported. These cellular senescence states may differ substantially from each other, as well as from replicative senescence through the presence of specific senescence features. Here, we attempted to catalog virtually all of the cellular senescence‐like states that can be induced by low molecular weight compounds. We summarized biological markers, molecular pathways involved in senescence establishment, and specific traits of cellular senescence states induced by more than fifty small molecule compounds.     

Ste20-like protein kinase SLK (LOSK) regulates microtubule organization by targeting dynactin to the centrosome

The microtubule- and centrosome-associated Ste20-like kinase (SLK; long Ste20-like kinase [LOSK]) regulates cytoskeleton organization and cell polarization and spreading. Its inhibition causes microtubule disorganization and release of centrosomal dynactin. The major function of dynactin is minus end–directed transport along microtubules in a complex with dynein motor. In addition, dynactin is required for maintenance of the microtubule radial array in interphase cells, and depletion of its centrosomal pool entails microtubule disorganization. Here we demonstrate that SLK (LOSK) phosphorylates the p150^Glued subunit of dynactin and thus targets it to the centrosome, where it maintains microtubule radial organization. We show that phosphorylation is required only for centrosomal localization of p150^Glued and does not affect its microtubule-organizing properties: artificial targeting of nonphosphorylatable p150^Glued to the centrosome restores microtubule radial array in cells with inhibited SLK (LOSK). The phosphorylation site is located in a microtubule-binding region that is variable for two isoforms (1A and 1B) of p150^Glued expressed in cultured fibroblast-like cells (isoform 1B lacks 20 amino acids in the basic microtubule-binding domain). The fact that SLK (LOSK) phosphorylates only a minor isoform 1A of p150^Glued suggests that transport and microtubule-organizing functions of dynactin are distinctly divided between the two isoforms. We also show that dynactin phosphorylation is involved in Golgi reorientation in polarized cells.     

Disturbance-free rapid solution exchange for magnetic tweezers single-molecule studies

Single-molecule manipulation technologies have been extensively applied to studies of the structures and interactions of DNA and proteins. An important aspect of such studies is to obtain the dynamics of interactions; however the initial binding is often difficult to obtain due to large mechanical perturbation during solution introduction. Here, we report a simple disturbance-free rapid solution exchange method for magnetic tweezers single-molecule manipulation experiments, which is achieved by tethering the molecules inside microwells (typical dimensions–diameter (D): 40–50 μm, height (H): 100 μm; H:D∼2:1). Our simulations and experiments show that the flow speed can be reduced by several orders of magnitude near the bottom of the microwells from that in the flow chamber, effectively eliminating the flow disturbance to molecules tethered in the microwells. We demonstrate a wide scope of applications of this method by measuring the force dependent DNA structural transitions in response to solution condition change, and polymerization dynamics of RecA on ssDNA/SSB-coated ssDNA/dsDNA of various tether lengths under constant forces, as well as the dynamics of vinculin binding to α-catenin at a constant force (< 5 pN) applied to the α-catenin protein.     

Analysis of Content of 2-Oxoacids in Rat Brain Extracts Using High-Performance Liquid Chromatography

Biochemistry (Moscow) - 2-Oxoacids are involved in a number of important metabolic processes and can be used as biomarkers in some human diseases. A new optimized method for quantification of...