Deep learning applications in protein crystallography.

Deep learning techniques can recognize complex patterns in noisy, multidimensional data. In recent years, researchers have started to explore the potential of deep learning in the field of structural biology, including protein crystallography. This field has some significant challenges, in particular producing high-quality and well ordered protein crystals. Additionally, collecting diffraction data with high completeness and quality, and determining and refining protein structures can be problematic. Protein crystallographic data are often high-dimensional, noisy and incomplete. Deep learning algorithms can extract relevant features from these data and learn to recognize patterns, which can improve the success rate of crystallization and the quality of crystal structures. This paper reviews progress in this field.

TERSE/PROLIX (TRPX) - a new algorithm for fast and lossless compression and decompression of diffraction and cryo-EM data.

High-throughput data collection in crystallography poses significant challenges in handling massive amounts of data. Here, TERSE/PROLIX (or TRPX for short) is presented, a novel lossless compression algorithm specifically designed for diffraction data. The algorithm is compared with established lossless compression algorithms implemented in gzip, bzip2, CBF (crystallographic binary file), Zstandard(zstd), LZ4 and HDF5 with gzip, LZF and bitshuffle+LZ4 filters, in terms of compression efficiency and speed, using continuous-rotation electron diffraction data of an inorganic compound and raw cryo-EM data. The results show that TRPX significantly outperforms all these algorithms in terms of speed and compression rate. It was 60 times faster than bzip2 (which achieved a similar compression rate), and more than 3 times faster than LZ4, which was the runner-up in terms of speed, but had a much worse compression rate. TRPX files are byte-order independent and upon compilation the algorithm occupies very little memory. It can therefore be readily implemented in hardware. By providing a tailored solution for diffraction and raw cryo-EM data, TRPX facilitates more efficient data analysis and interpretation while mitigating storage and transmission concerns. The C++20 compression/decompression code, custom TIFF library and an ImageJ/Fiji Java plugin for reading TRPX files are open-sourced on GitHub under the permissive MIT license.

Machine learning for classifying narrow-beam electron diffraction data.

As an alternative approach to X-ray crystallography and single-particle cryo-electron microscopy, single-molecule electron diffraction has a better signal-to-noise ratio and the potential to increase the resolution of protein models. This technology requires collection of numerous diffraction patterns, which can lead to congestion of data collection pipelines. However, only a minority of the diffraction data are useful for structure determination because the chances of hitting a protein of interest with a narrow electron beam may be small. This necessitates novel concepts for quick and accurate data selection. For this purpose, a set of machine learning algorithms for diffraction data classification has been implemented and tested. The proposed pre-processing and analysis workflow efficiently distinguished between amorphous ice and carbon support, providing proof of the principle of machine learning based identification of positions of interest. While limited in its current context, this approach exploits inherent characteristics of narrow electron beam diffraction patterns and can be extended for protein data classification and feature extraction.

Effects of ß-amyloid (1-42) Administration on the Main Neurogenic Niches of the Adult Brain: Amyloid-Induced Neurodegeneration Influences Neurogenesis.

Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder and warrants further study as well as timely treatment. Additionally, the mechanisms of the brain's intrinsic defense against chronic injury are not yet fully understood. Herein, we examined the response of the main neurogenic niches to amyloid exposure and the associated changes in structure and synaptic activity. Flow cytometry of Nestin-, Vimentin-, Nestin/Vimentin-, NeuN-, GFAP-, NeuN/GFAP-, NSE-, BrdU-, Wnt-, BrdU/Wnt-, VEGF-, Sox14-, VEGF/Sox14-, Sox10-, Sox2-, Sox10/Sox2-, Bax-, and Bcl-xL-positive cells was performed in the subventricular zone (SVZ), hippocampus, and cerebral cortex of rat brains on 90th day after intracerebroventricular (i.c.v.) single injection of a fraction of ß-amyloid (Aß) (1-42). The relative structural changes in these areas and disruptions to synaptic activity in the entorhinal cortex-hippocampus circuit were also evaluated. Our flow analyses revealed a reduction in the numbers of Nestin-, Vimentin-, and Nestin/Vimentin-positive cells in neurogenic niches and the olfactory bulb. These changes were accompanied by an increased number of BrdU-positive cells in the hippocampus and SVZ. The latter changes were strongly correlated with changes in the numbers of VEGF- and VEGF/Sox14-positive cells. The morphological changes were characterized by significant neural loss, a characteristic shift in entorhinal cortex-hippocampus circuit activity, and decreased spontaneous alternation in a behavioral test. We conclude that although an injection of Aß (1-42) induced stem cell proliferation and triggered neurogenesis at a certain stage, this process was incomplete and led to neural stem cell immaturity. We propose the idea of enhancing adult neurogenesis as a promising strategy for preventing dementia at healthy elderly people andpeople at high risk for developing AD, or treating patients diagnosed with AD.

The Involvement of Insulin-Like Growth Factor 1 and Nerve Growth Factor in Alzheimer's Disease-Like Pathology and Survival Role of the Mix of Embryonic Proteoglycans: Electrophysiological Fingerprint, Structural Changes and Regulatory Effects on Neurotrophins.

Alzheimer's disease (AD)-associated neurodegeneration is triggered by different fragments of amyloid beta (Aß). Among them, Aß (25-35) fragment plays a critical role in the development of neurodegeneration-it reduces synaptic integrity by disruption of excitatory/inhibitory ratio across networks and alters the growth factors synthesis. Thus, in this study, we aimed to identify the involvement of neurotrophic factors-the insulin-like growth factor 1 (IGF-1) and nerve growth factor (NGF)-of AD-like neurodegeneration induced by Aß (25-35). Taking into account our previous findings on the neuroprotective effects of the mix of proteoglycans of embryonic genesis (PEG), it was suggested to test its regulatory effect on IGF-1 and NGF levels. To evaluate the progress of neurodegeneration, in vivo electrophysiological investigation of synaptic activity disruption of the entorhinal cortex-hippocampus circuit at AD was performed and the potential recovery effects of PEG with relative structural changes were provided. To reveal the direct effects of PEG on brain functional activity, the electrophysiological pattern of the single cells from nucleus supraopticus, sensomotor cortex and hippocampus after acute injection of PEG was examined. Our results demonstrated that after i.c.v. injection of Aß (25-35), the level of NGF decreased in cerebral cortex and hypothalamus, and, in contrast, increased in hippocampus, prompting its multidirectional role in case of brain damage. The concentration of IGF-1 significantly increased in all investigated brain structures. The administration of PEG balanced the growth factor levels accompanied by substantial restoration of neural tissue architecture and synaptic activity. Acute injection of PEG activated the hypothalamic nucleus supraopticus and hippocampal neurons. IGF-1 and NGF levels were found to be elevated in animals receiving PEG in an absence of amyloid exposure. We suggest that IGF-1 and NGF play a critical role in the development of AD. At the same time, it becomes clear that the neuroprotective effects of PEG are likely mediated via the regulation of neurotrophins.

Embryonic proteoglycans regulate monoamines in the rat frontal cortex and hippocampus in Alzheimer's disease-like pathology.

Using the rat Alzheimer's disease (AD)-like model we have analyzed the hippocampal short-term potentiation, levels of monoamines, and morphological changes in the hippocampal and cortical neurons after the administration of proteoglycans of embryonic origin (PEG). Results showed that the levels of monoamines and especially norepinephrine in the target AD brain structures were found elevated, except serotonin, which was unaffected in the hippocampus, but decreased in the frontal cortex. These changes were accompanied by the substantial structural damage of cortical and hippocampal neurons. PEG was able to reverse most of these changes. In addition, PEG administration had regime-dependent effects on a short-term potentiation pattern of hippocampal neurons. The elevated levels of key elements of brain monoaminergic system in the model of AD support the hypothesis of the important role of monoamines in the excessive synaptic excitation resulting in cognitive dysfunction in AD brain. The neuroprotective effect of PEG, as manifested by the recovery of the monoaminergic system, suggests this bioactive substance as a perspective therapeutic agent for the treatment of AD.

Alzheimer's disease-like pathology-triggered oxidative stress, alterations in monoamines levels, and structural damage of locus coeruleus neurons are partially recovered by a mix of proteoglycans of embryonic genesis.

Alzheimer's disease (AD) pathogenesis includes oxidative damage and perturbations of monoamines. However, as many details of these alterations are not known, we have investigated the changes in monoamine levels as well as the free radical oxidation processes (FRO) in the brainstem of rats that were administered i.c.v. Aß (25-35) (rat model of AD-like pathology). The level of oxidative stress was found elevated in the brainstem along with the increased concentrations of monoamines, especially norepinephrine in the locus coeruleus (LC) area of the brainstem. This was accompanied by the substantial structural damage of monoaminergic neurons of LC. In addition, we have tested the ability of proteoglycans of embryonic genesis (PEG) that were shown previously to act as neuroprotectors, to restore the AD-triggered alterations in monoaminergic system and FRO. Indeed, PEG reduced the increased FRO and upregulated monoamines in the brainstem of Aß (25-35) treated animals. Administration of PEG to control animals led to the increase of the antioxidant capacity as well as the intensity of free radical oxidation processes. Our study confirms the important role of the brainstem FRO and monoamine shifts in AD development along with the known aggregation of Ab peptide and Tau hyperphosphorylation. We suggest that at the early stages of AD development, with still functional neurons, regulation of monoamine levels via stabilizing FRO processes can be beneficial. Our data demonstrate the regulatory action of PEG on the monoamine disturbances and the level of oxidative stress in the AD damaged structures, suggesting its possible therapeutic application in AD.

The role of monoamines in the development of Alzheimer's disease and neuroprotective effect of a proline rich polypeptide.

INTRODUCTION: We have analyzed the alterations in the brain monoaminergic system using the rat model of AD-like pathology. In addition, we have investigated potential neuroprotective effects of the hypothalamic proline-rich polypeptide (PRP-1). METHODS: Histochemical staining, HPLC, chemiluminescent and bioluminescence assays. RESULTS: The levels of monoamines in the target AD brain structures were found elevated, except serotonin, which was unaffected in both hippocampus and brainstem and decreased in frontal cortex. This was accompanied by the substantial structural damage of cortical, hippocampal, as well as the monoaminergic neurons of locus coeruleus and oxidative stress. PRP-1 was able to reverse most of these changes. DISCUSSION: The increased levels of major brain monoamines in the model of AD supports the hypothesis of the important role of monoamines in the excessive synaptic excitation resulting in cognitive dysfunction in AD brain. The neuroprotective effect of PRP-1 as manifested by the recovery of monoaminergic system suggests this bioactive compound as a perspective therapeutic agent for the treatment of AD.