scholarly journals Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM

2021 ◽  
Author(s):  
Bronwyn A. Lucas ◽  
Benjamin A. Himes ◽  
Liang Xue ◽  
Timothy Grant ◽  
Julia Mahamid ◽  
...  
Keyword(s):  
Template Matching ◽  
Molecular Mechanisms ◽  
Computational Cost ◽  
Complementary Information ◽  
Macromolecular Assemblies ◽  
Versatile Tool ◽  
A Cell ◽  
High Computational Cost ◽  
A Current

AbstractOver the last decade, single-particle electron cryo-microscopy has become one of the main techniques contributing to the growing library of high-resolution structures of macromolecules and their assemblies. For a full understanding of molecular mechanisms, however, it is important to place them into the broader context of a cell. Traditionally, this context can be visualized in 3D by electron cryo-tomography, and more recently, has also been studied by template matching of 2D images of cells and viruses. A current limitation of the latter approach is the high computational cost that limits the throughput and widespread adoption of this method. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells and demonstrate that it can function as a versatile tool for in situ visual proteomics and in situ structure determination. We compare the results with 3D template matching of tomograms acquired on identical sample locations. We identify strengths and weaknesses of both techniques which offer complementary information about target localization and identity.

scholarly journals Locating Macromolecular Assemblies in Cells by 2D Template Matching with cisTEM

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Bronwyn A Lucas ◽  
Benjamin A Himes ◽  
Liang Xue ◽  
Tim Grant ◽  
Julia Mahamid ◽  
...  
Keyword(s):  
High Resolution ◽  
Template Matching ◽  
Molecular Mechanisms ◽  
Computational Cost ◽  
Molecular Complexes ◽  
Three Dimensions ◽  
Macromolecular Assemblies ◽  
False Positive Detection ◽  
Versatile Tool

For a more complete understanding of molecular mechanisms, it is important to study macromolecules and their assemblies in the broader context of the cell. This context can be visualized at nanometer resolution in three dimensions (3D) using electron cryo-tomography, which requires tilt series to be recorded and computationally aligned, currently limiting throughput. Additionally, the high-resolution signal preserved in the raw tomograms is currently limited by a number of technical difficulties, leading to an increased false-positive detection rate when using 3D template matching to find molecular complexes in tomograms. We have recently described a 2D template matching approach that addresses these issues by including high-resolution signal preserved in single-tilt images. A current limitation of this approach is the high computational cost that limits throughput. We describe here a GPU-accelerated implementation of 2D template matching in the image processing software cisTEM that allows for easy scaling and improves the accessibility of this approach. We apply 2D template matching to identify ribosomes in images of frozen-hydrated Mycoplasma pneumoniae cells with high precision and sensitivity, demonstrating that this is a versatile tool for in situ visual proteomics and in situ structure determination. We benchmark the results with 3D template matching of tomograms acquired on identical sample locations and identify strengths and weaknesses of both techniques, which offer complementary information about target localization and identity.

scholarly journals Role of the Crosstalk between Autophagy and Apoptosis in Cancer

2013 ◽  
Vol 2013 ◽  
pp. 1-14 ◽  
Author(s):  
Minfei Su ◽  
Yang Mei ◽  
Sangita Sinha
Keyword(s):  
Cell Death ◽  
Molecular Mechanisms ◽  
Cancer Therapeutics ◽  
Coordinate Regulation ◽  
Macromolecular Assemblies ◽  
Cell Death Pathway ◽  
Survival Pathway ◽  
A Cell ◽  
Type Ii Cell

Autophagy and apoptosis are catabolic pathways essential for organismal homeostasis. Autophagy is normally a cell-survival pathway involving the degradation and recycling of obsolete, damaged, or harmful macromolecular assemblies; however, excess autophagy has been implicated in type II cell death. Apoptosis is the canonical programmed cell death pathway. Autophagy and apoptosis have now been shown to be interconnected by several molecular nodes of crosstalk, enabling the coordinate regulation of degradation by these pathways. Normally, autophagy and apoptosis are both tumor suppressor pathways. Autophagy fulfils this role as it facilitates the degradation of oncogenic molecules, preventing development of cancers, while apoptosis prevents the survival of cancer cells. Consequently, defective or inadequate levels of either autophagy or apoptosis can lead to cancer. However, autophagy appears to have a dual role in cancer, as it has now been shown that autophagy also facilitates the survival of tumor cells in stress conditions such as hypoxic or low-nutrition environments. Here we review the multiple molecular mechanisms of coordination of autophagy and apoptosis and the role of the proteins involved in this crosstalk in cancer. A comprehensive understanding of the interconnectivity of autophagy and apoptosis is essential for the development of effective cancer therapeutics.

Structure of Palladium Single-Crystal Films Prepared by Flash Evaporation onto (001) NaCl Substrates

1970 ◽  
Vol 28 ◽  
pp. 456-457
Author(s):  
L. E. Murr ◽  
G. Wong
Keyword(s):  
Single Crystal ◽  
High Vacuum ◽  
Ultra High Vacuum ◽  
High Rate ◽  
Flash Evaporation ◽  
Optimum Load ◽  
Single Crystal Films ◽  
Crystal Films ◽  
A Current

Palladium single-crystal films have been prepared by Matthews in ultra-high vacuum by evaporation onto (001) NaCl substrates cleaved in-situ, and maintained at ∼ 350° C. Murr has also produced large-grained and single-crystal Pd films by high-rate evaporation onto (001) NaCl air-cleaved substrates at 350°C. In the present work, very large (∼ 3cm2), continuous single-crystal films of Pd have been prepared by flash evaporation onto air-cleaved (001) NaCl substrates at temperatures at or below 250°C. Evaporation rates estimated to be ≧ 2000 Å/sec, were obtained by effectively short-circuiting 1 mil tungsten evaporation boats in a self-regulating system which maintained an optimum load current of approximately 90 amperes; corresponding to a current density through the boat of ∼ 4 × 104 amperes/cm2.

An Alternate Algorithm for (3x3) Median Filtering of Digital Images

2012 ◽  
Vol 2 (1) ◽  
pp. 7-9 ◽  
Author(s):  
Satinderjit Singh
Keyword(s):  
Median Filter ◽  
Computational Cost ◽  
Spatial Coherence ◽  
General Purpose ◽  
Median Filtering ◽  
Basic Algorithm ◽  
Temporal Complexity ◽  
Filter Kernel ◽  
One Step ◽  
High Computational Cost

Median filtering is a commonly used technique in image processing. The main problem of the median filter is its high computational cost (for sorting N pixels, the temporal complexity is O(N·log N), even with the most efficient sorting algorithms). When the median filter must be carried out in real time, the software implementation in general-purpose processorsdoes not usually give good results. This Paper presents an efficient algorithm for median filtering with a 3x3 filter kernel with only about 9 comparisons per pixel using spatial coherence between neighboring filter computations. The basic algorithm calculates two medians in one step and reuses sorted slices of three vertical neighboring pixels. An extension of this algorithm for 2D spatial coherence is also examined, which calculates four medians per step.

Methods for studying dissolved oxygen levels in coastal and estuarine waters receiving combined sewer overflows

1995 ◽  
Vol 32 (2) ◽  
pp. 95-103
Author(s):  
José A. Revilla ◽  
Kalin N. Koev ◽  
Rafael Díaz ◽  
César Álvarez ◽  
Antonio Roldán
Keyword(s):  
Dissolved Oxygen ◽  
Coastal Waters ◽  
Computational Cost ◽  
Oxygen Deficit ◽  
Alternative Methods ◽  
Coastal Zones ◽  
Combined Sewer Overflows ◽  
Sewer Systems ◽  
Combined Sewer ◽  
High Computational Cost

One factor in determining the transport capacity of coastal interceptors in Combined Sewer Systems (CSS) is the reduction of Dissolved Oxygen (DO) in coastal waters originating from the overflows. The study of the evolution of DO in coastal zones is complex. The high computational cost of using mathematical models discriminates against the required probabilistic analysis being undertaken. Alternative methods, based on such mathematical modelling, employed in a limited number of cases, are therefore needed. In this paper two alternative methods are presented for the study of oxygen deficit resulting from overflows of CSS. In the first, statistical analyses focus on the causes of the deficit (the volume discharged). The second concentrates on the effects (the concentrations of oxygen in the sea). Both methods have been applied in a study of the coastal interceptor at Pasajes Estuary (Guipúzcoa, Spain) with similar results.

scholarly journals HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Nature ◽  
2021 ◽  
Author(s):  
Fides Zenk ◽  
Yinxiu Zhan ◽  
Pavel Kos ◽  
Eva Löser ◽  
Nazerke Atinbayeva ◽  
...  
Keyword(s):  
Genome Organization ◽  
Molecular Mechanisms ◽  
High Throughput Sequencing ◽  
De Novo ◽  
Early Embryo ◽  
Heterochromatin Protein ◽  
Chromosome Conformation ◽  
3D Genome ◽  
Genome Reorganization

AbstractFundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown1,2. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo.

scholarly journals Visualizing Profiles of Large Datasets of Weighted and Mixed Data

Mathematics ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 891
Author(s):  
Aurea Grané ◽  
Alpha A. Sow-Barry
Keyword(s):  
Multidimensional Scaling ◽  
Random Sample ◽  
Simulation Study ◽  
Clustering Algorithm ◽  
Computational Cost ◽  
Interpolation Formula ◽  
Large Datasets ◽  
Mixed Data ◽  
Multivariate Techniques ◽  
High Computational Cost

This work provides a procedure with which to construct and visualize profiles, i.e., groups of individuals with similar characteristics, for weighted and mixed data by combining two classical multivariate techniques, multidimensional scaling (MDS) and the k-prototypes clustering algorithm. The well-known drawback of classical MDS in large datasets is circumvented by selecting a small random sample of the dataset, whose individuals are clustered by means of an adapted version of the k-prototypes algorithm and mapped via classical MDS. Gower’s interpolation formula is used to project remaining individuals onto the previous configuration. In all the process, Gower’s distance is used to measure the proximity between individuals. The methodology is illustrated on a real dataset, obtained from the Survey of Health, Ageing and Retirement in Europe (SHARE), which was carried out in 19 countries and represents over 124 million aged individuals in Europe. The performance of the method was evaluated through a simulation study, whose results point out that the new proposal solves the high computational cost of the classical MDS with low error.

Herpesvirus-Associated Proliferative Skin Disease in Frogs and Toads: Proposed Pathogenesis

2021 ◽  
pp. 030098582110063
Author(s):  
Francesco C. Origgi ◽  
Patricia Otten ◽  
Petra Lohmann ◽  
Ursula Sattler ◽  
Thomas Wahli ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rana Temporaria ◽  
Skin Lesions ◽  
Bufo Bufo ◽  
Careful Examination ◽  
Altered Expression ◽  
Expression Of Genes ◽  
Cell Remodeling ◽  
Tissue Changes

A comparative study was carried out on common and agile frogs ( Rana temporaria and R. dalmatina) naturally infected with ranid herpesvirus 3 (RaHV3) and common toads ( Bufo bufo) naturally infected with bufonid herpesvirus 1 (BfHV1) to investigate common pathogenetic pathways and molecular mechanisms based on macroscopic, microscopic, and ultrastructural pathology as well as evaluation of gene expression. Careful examination of the tissue changes, supported by in situ hybridization, at different stages of development in 6 frogs and 14 toads revealed that the skin lesions are likely transient, and part of a tissue cycle necessary for viral replication in the infected hosts. Transcriptomic analysis, carried out on 2 naturally infected and 2 naïve common frogs ( Rana temporaria) and 2 naturally infected and 2 naïve common toads ( Bufo bufo), revealed altered expression of genes involved in signaling and cell remodeling in diseased animals. Finally, virus transcriptomics revealed that both RaHV3 and BfHV1 had relatively high expression of a putative immunomodulating gene predicted to encode a decoy receptor for tumor necrosis factor in the skin of the infected hosts. Thus, the comparable lesions in infected frogs and toads appear to reflect a concerted epidermal and viral cycle, with presumptive involvement of signaling and gene remodeling host and immunomodulatory viral genes.

Reliability and reliability-based sensitivity analysis of self-centering buckling restrained braces using meta-models

2021 ◽  
pp. 1045389X2110263
Author(s):  
Seyede Vahide Hashemi ◽  
Mahmoud Miri ◽  
Mohsen Rashki ◽  
Sadegh Etedali
Keyword(s):  
Failure Probability ◽  
Limit State ◽  
Computational Cost ◽  
Sensitivity Analyses ◽  
State Function ◽  
Reliability Indices ◽  
Buckling Restrained Brace ◽  
Polynomial Response Surface ◽  
Nonlinear Dynamic Analyses ◽  
High Computational Cost

This paper aims to carry out sensitivity analyses to study how the effect of each design variable on the performance of self-centering buckling restrained brace (SC-BRB) and the corresponding buckling restrained brace (BRB) without shape memory alloy (SMA) rods. Furthermore, the reliability analyses of BRB and SC-BRB are performed in this study. Considering the high computational cost of the simulation methods, three Meta-models including the Kriging, radial basis function (RBF), and polynomial response surface (PRSM) are utilized to construct the surrogate models. For this aim, the nonlinear dynamic analyses are conducted on both BRB and SC-BRB by using OpenSees software. The results showed that the SMA area, SMA length ratio, and BRB core area have the most effect on the failure probability of SC-BRB. It is concluded that Kriging-based Monte Carlo Simulation (MCS) gives the best performance to estimate the limit state function (LSF) of BRB and SC-BRB in the reliability analysis procedures. Considering the effects of changing the maximum cyclic loading on the failure probability computation and comparison of the failure probability for different LSFs, it is also found that the reliability indices of SC-BRB were always higher than the corresponding reliability indices determined for BRB which confirms the performance superiority of SC-BRB than BRB.

Sign in / Sign up

Export Citation Format

Share Document