Low cost, high performance GPU computing solution for atomic resolution cryoEM single-particle reconstruction

General Purpose Graphic Processing Unit(GPGPU) is used widely for achieving\nhigh performance or high throughput in parallel programming. This capability of\nGPGPUs is very famous in the new era and mostly used for scientific computing\nwhich requires more processing power than normal personal computers. Therefore,\nmost of the programmers, researchers and industry use this new concept for\ntheir work. However, achieving high-performance or high-throughput using GPGPUs\nare not an easy task compared with conventional programming concepts in the CPU\nside. In this research, the CPU's cache memory optimization techniques have\nbeen adopted to the GPGPU's cache memory to identify rare performance\nimprovement techniques compared to GPGPU's best practices. The cache\noptimization techniques of blocking, loop fusion, array merging and array\ntranspose were tested on GPGPUs for finding suitability of these techniques.\nFinally, we identified that some of the CPU cache optimization techniques go\nwell with the cache memory system of the GPGPU and shows performance\nimprovements while some others show the opposite effect on the GPGPUs compared\nwith the CPUs.\n

Computer models of water distribution networks are commonly used to simulate large systems under complex dynamic scenarios. These models normally use so-called demand-driven solvers, which determine the nodal pressures and pipe flow rates that correspond to specified nodal demands. This paper investigates the use of data parallel high performance computing (HPC) techniques to accelerate demand-driven hydraulic solvers. The sequential code of the solver implemented in the CWSNet library is analysed to understand which computational blocks contribute the most to the total computation time of a hydraulic simulation. The results obtained show that, contrary to popular belief, the linear solver is not the code block with the highest impact on the simulation time, but the pipe head loss computation. Two data parallel HPC techniques, single instruction multiple data (SIMD) operations and general purpose computation on graphics processing units (GPGPU), are used to accelerate the pipe head loss computation and linear algebra operations in new implementations of the hydraulic solver of CWSNet library. The results obtained on different network models show that the use of this techniques can improve significantly the performance of a demand-driven hydraulic solver.

Real-time and decision taking selection of single-particles during automated cryo-EM sessions based on neuro-fuzzy method

The Chikungunya virus is carried by mosquitos and can cause a number of diseases in humans including encephalitis, which can be fatal in some cases, and severe arthritis. A recent mutation in the E1 protein of the virus has allowed it to efficiently reproduce in a different species of mosquitos, leading to a Chikungunya epidemic in Réunion Island in 2005 and the subsequent infection of millions of individuals in Africa and Asia. The virus also has the potential to spread to many areas of Europe and the Americas. Chikungunya virus has a single-stranded RNA genome that codes for four non-structural proteins and five structural proteins. Based on this knowledge it has been possible to develop virus-like particles that can be used to immunise non-human primates against Chikungunya infection by inducing antibody production. However, the development of vaccines for Chikungunya in humans will require a deeper understanding of how these antibodies produced by the vaccine interact with the virus and more detailed information about the structures of the virus and antibodies. Sun et al. have used two techniques – X-ray crystallography and electron cryo-microscopy – to determine the structure of Chikungunya virus-like particles, and to obtain new insights into the interactions of these particles with four related antibodies. Electron cryo-microscopy was used to figure out the structure of the particles at near atomic resolution, and X-ray crystallography was used to determine the atomic resolution structures of two of the four Fab antibodies that neutralize the Chikungunya virus. Electron cryo-microscopy was also used to probe the complex formed by the interactions between the virus-like particles and the antibodies. Sun et al. were able to identify the likely viral receptor site that is blocked by three of the antibodies when they neutralize the virus; the fourth antibody is thought to act by immobilizing one of the domains of protein E2, thereby hiding the “fusion loop” that allows the virus to enter and infect human tissue. It is hoped that these findings will contribute to efforts to combat the spread of the Chikungunya virus worldwide.

Electron cryomicroscopy (cryo-EM) is a powerful tool in structural biology for determining 3D structures of macromolecular complexes. In the previous decade, many technological advancements have been introduced to improve the methodology of single particle cryo-EM, and hence the resolution of its protein reconstructions. These advancements include developments in both software algorithms and microscope hardware. Despite all these developments, the resolution of single particle cryo-EM cannot surpass 1.5 Å, a barrier blocking direct visualization of atomic details of the protein structure. Here, we show that by improving the optical performance of the electron microscope with new hardware, such resolution barrier can be removed, and atomic resolution of 1.25 Å can be reached with an engineered protein apoferritin. The atomic resolution protein structure helped set benchmarks for validating data quality in high resolution cryo-EM. We found that the new microscope also benefited to other proteins with lower contrast and higher flexibility, such as proteasome, chaperonin and fatty acid synthetase. For these proteins, sample properties and behavior were the major limitations. We anticipate that this would be alleviated by introducing other new microscope hardware, so that in the future, time and effort of structural biologists can concentrate on biochemical preparation of the sample, and single particle cryo-EM can routinely yield high quality protein structures at atomic resolution.

In modern structural biology, there are three major methods for structural biologists to obtain structural information of macromolecules: cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR), and X-ray crystallography. Cryo-EM, in comparison with the other two methods, allows structural biologists to obtain the structures of various macromolecules in a more native and less perturbed system. Over the past decade, cryo-EM has enabled scientists to determine the structures of protein complexes at atomic resolution and made a profound impact in molecular bioscience and pharmaceutical sectors. Along with cryo-EM, another emerging technique called cryo-electron tomography (cryo-ET) has gained increasing importance in structural biology. It has the potential to visualize macromolecular complexes and assemblies in their native environments at high resolution, but there are still some challenges for small, sparse subjects and in approaching atomic resolution in situ. This chapter summarizes the major steps involved in structure determination using cryo-EM and cryo-ET and highlights the major challenges for in situ cryo-ET. We also present a few examples of near-atomic resolution structure determination of macromolecular assemblies both in purified systems in vitro and in native contexts in situ. Future perspectives are discussed as well.

Effects of cryo-EM cooling on structural ensembles of biomolecules and their solvation shell.

IntroductionPulmonary segmentectomy, when combined with hilar and mediastinal lymphadenectomy, is currently considered the gold standard treatment for early-stage lung tumors (NSCLC) smaller than 2 cm in diameter. The preoperative planning for segmentectomies usually includes a contrast-enhanced CT with 2D reconstructions (axial, coronary, and sagittal). Recent technological advances allow 3D (volume rendering) reconstructions of preoperative CT scans, intended to improve the surgeon’s understanding of the segmental anatomy.The study aims to investigate the added value of 3D reconstruction in enhancing the surgeon’s understanding of anatomical structures, thus facilitating surgical planning and improving oncological outcomes.Methods and analysisThis is a prospective, randomized, controlled study.Patients will be randomized into two groups:1. Group 2D: the preoperative workup for these patients will consist of a contrast-enhanced chest CT with two-dimensional (2D) reconstructions (axial, coronary, and sagittal);2. Group 3D: the preoperative workup for these patients will consist of a contrast-enhanced chest CT with two-dimensional (2D) reconstructions (axial, coronary, and sagittal) and a 3D reconstruction (volume rendering) of the same chest CT employing dedicated software.The primary endpoints will be negative margin (R0) resection rate, resection margin (staple line-to-tumor distance), and thoracotomy conversions.We will use Fisher’s exact test for binary outcomes and Mann–Whitney U test for continuous outcomes. For subgroup analyses, we will use regression. Multivariable analyses will be based on logistic regression for binary outcomes and linear regression for continuous outcomes.Ethics and disseminationThe protocol and the model informed consent forms have been reviewed and approved by the ethics committee (N.: 1–2023) concerning scientific content and compliance with applicable research and human subject regulations.A Subcommittee on Publications was established to review all publications and report its recommendations to the steering committee. The anonymized participant-level dataset and statistical code for generating the results will not be publicly available.Trial registrationThe protocol was registered at ClinicalTrials.gov (ID: NCT05716815; Prospective rAndomized sTudy efficaCy tHree-dimensional rEconstructions Segmentectomy - Full-Text View - ClinicalTrials.gov). Jan 19, 2023.

Chemical modifications of ribosomal RNAs (rRNAs) and proteins expand their topological repertoire, and together with the plethora of bound ligands, fine-tune ribosomal function. Detailed knowledge of this natural composition provides important insights into ribosome genesis and function and clarifies some aspects of ribosomopathies. The discovery of new structural properties and functional aspects of ribosomes has gone hand in hand with cryo-electron microscopy (cryo-EM) and its technological development. In line with the ability to visualize atomic details – a prerequisite for identifying chemical modifications and ligands in cryo-EM maps – in this work we present the structure of the 60S ribosomal subunit from HeLa cells at the very high global resolution of 1.78 Å. We identified 113 rRNA modifications and four protein modifications including uL2-Hisβ-ox216, which stabilizes the local structure near the peptidyl transferase centre via an extended hydrogen-bonding network. We can differentiate metal ions Mg2+ and K+, polyamines spermine, spermidine and putrescine and identify thousands of water molecules binding to the 60S subunit. Approaching atomic resolution cryo-EM has become a powerful tool to examine fine details of macromolecular structures that will expand our knowledge about translation and other biological processes in the future and assess the variability of the chemical space due to differences between species/tissues or varying physicochemical environment.

Solving the structures of macromolecular complexes.

3D medical volume reconstruction using web services

To build three-dimensional (3-D) visible model for surgical treatment of infection of fascial spaces of hand. Serial thin cross-sections (0.2 mm) of hand were made by cryomicrotome, and the thin cross-sections of metacarpal parts were observed. A personal computer was employed to reconstruct 3-D model of metacarpal fascial space. The shapes, locations and adjacent relations of the mid-palmar space, thenar space and metacarpal bones were displayed clearly from computerized 3-D model, which could be the cross-reference of the cross-sections expediently. The computerized 3-D reconstruction of metacarpal fascial spaces can provide some guidance for surgical treatment of infection and other diseases of metacarpal fascial spaces.

While advances in single-particle cryo-EM have enabled the structural determination of macromolecular complexes at atomic resolution, particle orientation bias (the 'preferred' orientation problem) remains a complication for most specimens. Existing solutions have relied on biochemical and physical strategies applied to the specimen and are often complex and challenging. Here, we develop spIsoNet, an end-to-end self-supervised deep learning-based software to address map anisotropy and particle misalignment caused by the preferred-orientation problem. Using preferred-orientation views to recover molecular information in under-sampled views, spIsoNet improves both angular isotropy and particle alignment accuracy during 3D reconstruction. We demonstrate spIsoNet's ability to generate near-isotropic reconstructions from representative biological systems with limited views, including ribosomes, β-galactosidases and a previously intractable hemagglutinin trimer dataset. spIsoNet can also be generalized to improve map isotropy and particle alignment of preferentially oriented molecules in subtomogram averaging. Therefore, without additional specimen-preparation procedures, spIsoNet provides a general computational solution to the preferred-orientation problem.

We discuss recent advancements in structural biology methods for investigating sites of protein-protein interactions. We will inform readers outside the field of structural biology about techniques beyond crystallography, and how these different technologies can be utilized for drug development. Advancements in cryo-electron microscopy (cryoEM) and micro-electron diffraction (microED) may change how we view atomic resolution structural biology, such that well-ordered macrocrystals of protein complexes are not required for interface identification. However, some drug discovery applications, such as lead peptide compound generation, may not require atomic resolution; mass spectrometry techniques can provide an expedited path to generation of lead compounds. New crosslinking compounds, more user-friendly data analysis, and novel protocols such as protein painting can advance drug discovery programs, even in the absence of atomic resolution structural data. Finally, artificial intelligence and machine learning methods, while never truly replacing experimental methods, may provide rational ways to stratify potential druggable regions identified with mass spectrometry into higher and lower priority candidates. Electron diffraction of nanocrystals combines the benefits of both x-ray diffraction and cryoEM, and may prove to be the next generation of atomic resolution protein-protein interface identification. However, in situations such as peptide drug discovery, mass spectrometry techniques supported by advancements in computational methods will likely prove sufficient to support drug discovery efforts. In addition, these methods can be significantly faster than any crystallographic or cryoEM methods for identification of interacting regions.

Introduction: CT scanning generate tridimensional reconstructions to permit the observation of paranasal sinuses and nasal cavity, and other anatomic structures of our body. The use and application of the 3D reconstructions generated from files of CT examination. The evaluation before sinus surgery through 3D reconstructions from the CT files may help the surgeon for diagnosis, preoperative planning and to acquire more information than with the traditional two-dimensional images obtained with the three different plans: axial, coronal and sagittal. Objective: To investigate and demonstrate the reliability and the feasibility of the evaluation before sinus surgery through 3D reconstructions from CT examinations of patients with a free software. Method: The reconstructions were carried out before the surgeries in order to assess the paranasal sinuses and nasal cavity for 45 patients. After this study, the surgery was digitally stored. Conclusion: With simple tools and personal computer, we evaluated the possibility to generate 3D reconstructions, the preoperative knowledge of the paranasal sinuses and nasal cavity may generate benefits during the performance of surgeries.