Chronic pain exacerbates memory impairment and pathology of Aß and tau by upregulating IL-1ß and p-65 signaling in a mouse model of Alzheimer's disease.

BACKGROUND: Chronic pain is linked to cognitive impairment; however, the underlying mechanisms remain unclear. In the present study, we examined these mechanisms in a well-established mouse model of Alzheimer's disease (AD). METHODS: Neuropathic pain was modeled in 5-month-old transgenic APPswe/PS1dE9 (APP/PS1) mice by partial ligation of the sciatic nerve on the left side, and chronic inflammatory pain was modeled in another group of APP/PS1 mice by injecting them with complete Freund's adjuvant on the plantar surface of the left hind paw. Six weeks after molding, the animals were tested to assess pain threshold (von Frey filament), learning, memory (novel object recognition, Morris water maze, Y-maze, and passive avoidance), and depression-like symptoms (sucrose preference, tail suspension, and forced swimming). After behavioral testing, mice were sacrificed and the levels of p65, amyloid-ß (residues 1-42) and phospho-tau in the hippocampus and cerebral cortex were assayed using western blotting, while interleukin (IL)-1ß levels were measured by enzyme-linked immunosorbent assay. RESULTS: Animals subjected to either type of chronic pain showed lower pain thresholds, more severe deficits in learning and memory, and stronger depression-like symptoms than the corresponding control animals. Either type of chronic pain was associated with upregulation of p65, amyloid-ß (1-42), and IL-1ß in the hippocampus and cerebral cortex, as well as higher levels of phosphorylated tau. CONCLUSIONS: Chronic pain may exacerbate cognitive deficits and depression-like symptoms in APP/PS1 mice by worsening pathology related to amyloid-ß and tau and by upregulating signaling involving IL-1ß and p65.

Preparation of a phenylboronic acid and aldehyde bi-functional group modified silica absorbent and applications in removing Cr(vi) and reducing to Cr(iii).

Cr(vi) is a great threat to the ecological environment and human health, so it is urgent to remove Cr(vi) from the environment. In this study, a novel silica gel adsorbent SiO2-CHO-APBA containing phenylboronic acids and aldehyde groups was prepared, evaluated and applied for removing Cr(vi) from water and soil samples. The adsorption conditions including pH, adsorbent dosage, initial concentration of Cr(vi), temperature and time were optimized. Its ability in removing Cr(vi) was investigated and compared with three other common adsorbents, SiO2-NH2, SiO2-SH and SiO2-EDTA. Data showed SiO2-CHO-APBA had the highest adsorption capacity of 58.14 mg g-1 at pH 2 and could reach adsorption equilibrium in about 3 h. When 50 mg SiO2-CHO-APBA was added in 20 mL of 50 mg L-1 Cr(vi) solution, more than 97% of Cr(vi) was removed. A mechanism study revealed that a cooperative interaction of both the aldehyde and boronic acid groups is attributed to Cr(vi) removal. The reducing function was gradually weakened with the consumption of the aldehyde group, which was oxidized to a carboxyl group by Cr(vi). This SiO2-CHO-APBA adsorbent was successfully used for the removal of Cr(vi) from soil samples with satisfactory results which indicates a good potential in agriculture and other fields.

Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study.

Training deep graph neural networks (GNNs) is notoriously hard. Besides the standard plights in training deep architectures such as vanishing gradients and overfitting, it also uniquely suffers from over-smoothing, information squashing, and so on, which limits their potential power for encoding the high-order neighbor structure in large-scale graphs. Although numerous efforts are proposed to address these limitations, such as various forms of skip connections, graph normalization, and random dropping, it is difficult to disentangle the advantages brought by a deep GNN architecture from those "tricks" necessary to train such an architecture. Moreover, the lack of a standardized benchmark with fair and consistent experimental settings poses an almost insurmountable obstacle to gauge the effectiveness of new mechanisms. In view of those, we present the first fair and reproducible benchmark dedicated to assessing the "tricks" of training deep GNNs. We categorize existing approaches, investigate their hyperparameter sensitivity, and unify the basic configuration. Comprehensive evaluations are then conducted on tens of representative graph datasets including the recent large-scale Open Graph Benchmark, with diverse deep GNN backbones. We demonstrate that an organic combo of initial connection, identity mapping, group and batch normalization attains the new state-of-the-art results for deep GNNs on large datasets. Codes are available: https://github.com/VITA-Group/Deep_GCN_Benchmarking.

Preparation of boronic acid and carboxyl-modified molecularly imprinted polymer and application in a novel chromatography mediated hollow fiber membrane to selectively extract glucose from cellulose hydrolysis.

A novel boronic acid and carboxyl-modified glucose molecularly imprinted polymer were prepared through suspension polymerization, which is based on 1.0 mmol glucose as a template, 1.2 mmol methacrylamidophenylboronic acid, and 6.8 mmol methacrylic acids as monomers, 19 mmol ethyleneglycol dimethacrylate, and 1 mmol methylene-bis-acrylamide as crosslinkers. The prepared glucose-molecularly imprinted polymer had a particle size of 25-70 µm, and was thermally stable below 215°C, with a specific surface area of 174.82 m2/ g and average pore size of 9.48 nm. The best selectivity between glucose and fructose was 2.71 and the maximum adsorption capacity of glucose- molecularly imprinted polymer was up to 236.32 mg/ g which was consistent with the Langmuir adsorption model. The similar adsorption abilities in six successive runs and the good desorption rate (99.4%) verified glucose-molecularly imprinted polymer could be reused. It was successfully used for extracting glucose from cellulose hydrolysis. The adsorption amount of glucose was 2.61 mg/mL and selectivity between glucose and xylose reached 4.12. A newly established chromatography (glucose-molecularly imprinted polymer) mediated hollow fiber membrane method in time separated pure glucose from cellulose hydrolysates on a large scale, and purified glucose solution with a concentration of 3.84 mg/mL was obtained, which offered a feasible way for the industrial production of glucose from cellulose hydrolysates.

The DUB family in Populus: identification, characterization, evolution and expression patterns.

BACKGROUND: The deubiquitinase (DUB) family constitutes a group of proteases that regulate the stability or reverse the ubiquitination of many proteins in the cell. These enzymes participate in cell-cycle regulation, cell division and differentiation, diverse physiological activities such as DNA damage repair, growth and development, and response to stress. However, limited information is available on this family of genes in woody plants. RESULTS: In the present study, 88 DUB family genes were identified in the woody model plant Populus trichocarpa, comprising 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM genes with similar domains. According to phylogenetic analysis, the PtrUBP genes were classified into 16 groups, the PtrUCH genes into two, the PtrOTU genes into eight, the PtrMJD genes into two, and the PtrJAMM genes into seven. Members of same subfamily had similar gene structure and motif distribution characteristics. Synteny analysis of the DUB family genes from P. thrchocarpa and four other plant species provided insight into the evolutionary traits of DUB genes. Expression profiles derived from previously published transcriptome data revealed distinct expression patterns of DUB genes in various tissues. On the basis of the results of analysis of promoter cis-regulatory elements, we selected 16 representative PtrUBP genes to treatment with abscisic acid, methyl jasmonate, or salicylic acid applied as a foliar spray. The majority of PtrUBP genes were upregulated in response to the phytohormone treatments, which implied that the genes play potential roles in abiotic stress response in Populus. CONCLUSIONS: The results of this study broaden our understanding of the DUB family in plants. Analysis of the gene structure, conserved elements, and expression patterns of the DUB family provides a solid foundation for exploration of their specific functions in Populus and to elucidate the potential role of PtrUBP gene in abiotic stress response.

Exploring the molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43 using molecular dynamics simulation and free energy calculation.

Transactivation response element RNA/DNA-binding protein 43 (TDP-43) is involved in the regulation of alternative splicing of human neurodegenerative disease-related genes through binding to long UG-rich RNA sequences. Mutations in TDP-43, most in the homeodomain, cause neurological disorders such as amyotrophic lateral sclerosis and fronto temporal lobar degeneration. Several mutants destabilize the structure and disrupt RNA-binding activity. The biological functions of these mutants have been characterized, but the structural basis behind the loss of RNA-binding activity is unclear. Focused on the specific TDP-43-ssRNA complex (PDB code 4BS2), we applied molecular dynamics simulations and the molecular mechanics Poisson-Boltzmann surface area free energy calculation to characterize and explore the structural and dynamic effects between ssRNA and TDP-43. The energetic analysis indicated that the intermolecular van der Waals interaction and nonpolar solvation energy play an important role in the binding process of TDP-43 and ssRNA. Compared with the wild-type TDP-43, the reduction of the polar or non-polar interaction between all the mutants F149A, D105A/S254A, R171A/D174A, F147L/F149L/F229L/F231L and ssRNA is the main reason for the reduction of its binding free energy. Decomposing energies suggested that the extensive interactions between TDP-43 and the nitrogenous bases of ssRNA are responsible for the specific ssRNA recognition by TDP-43. These results elucidated the TDP-43-ssRNA interaction comprehensively and further extended our understanding of the previous experimental data. The uncovering of TDP-43-ssRNA recognition mechanism will provide us useful insights and new chances for the development of anti-neurodegenerative drugs.

Preparation of a magnetic and recyclable superparamagnetic silica support with a boronic acid group for immobilizing Pd catalysts and its applications in Suzuki reactions.

Palladium is one of the best metal catalysts for Suzuki cross-coupling reaction to synthesize unsymmetrical biaryl compounds. However, homogeneous palladium (Pd) is limited in an industrial scale due to the high cost, separation, removal, and recovery issues. In this paper, a novel, high activity magnetic nanoparticles (Fe3O4@SiO2-APBA-Pd) catalyst was prepared by a simple, cost-effective procedure. The as-prepared functional nanoparticles (Fe3O4@SiO2-APBA) with boric acid group immobilized Pd through adding Pd(OAc)2 to Fe3O4@SiO2-APBA in absolute ethanol and maintaining for a certain time under a nitrogen atmosphere. The as-prepared catalyst was characterized by FT-IR, SEM, EDX, TEM, ICP-MS, XPS, and XRD. The results showed that the Pd (0.2-0.6 nm) was successfully anchored on the magnetic silica material with boric acid group. The amount of Pd was 0.800 mmol g-1. This magnetic nanostructure (8-15 nm) is especially beneficial as a nanocatalyst because each nanoparticle can catalyze a reaction in a certain time without steric restriction, which could effectively improve the reaction efficiency. The current nanoparticles with the Pd catalyst could be used as a novel, green, and efficient heterogeneous catalyst for Suzuki reactions. This catalyst showed promising catalytic activity and excellent yields toward 14 kinds of Suzuki coupling reactions under mild reaction conditions, which was similar to homogeneous Pd and many reported heterogeneous Pd catalysts. In addition, the turnover number (TON) and turnover frequency (TOF) for the Suzuki reaction were high. TOF and TON were 9048 h-1 and 20 250 for the Suzuki reaction of bromobenzene and phenylboronic acid. Furthermore, the nanoparticles could be easily separated by a magnet, and could be used repeatedly seven times without any significant loss in activity.

The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements.

BACKGROUND: Tetracentron sinense is an endemic and endangered deciduous tree. It belongs to the Trochodendrales, one of four early diverging lineages of eudicots known for having vesselless secondary wood. Sequencing and resequencing of the T. sinense genome will help us understand eudicot evolution, the genetic basis of tracheary element development, and the genetic diversity of this relict species. RESULTS: Here, we report a chromosome-scale assembly of the T. sinense genome. We assemble the 1.07 Gb genome sequence into 24 chromosomes and annotate 32,690 protein-coding genes. Phylogenomic analyses verify that the Trochodendrales and core eudicots are sister lineages and showed that two whole-genome duplications occurred in the Trochodendrales approximately 82 and 59 million years ago. Synteny analyses suggest that the γ event, resulting in paleohexaploidy, may have only happened in core eudicots. Interestingly, we find that vessel elements are present in T. sinense, which has two orthologs of AtVND7, the master regulator of vessel formation. T. sinense also has several key genes regulated by or regulating TsVND7.2 and their regulatory relationship resembles that in Arabidopsis thaliana. Resequencing and population genomics reveals high levels of genetic diversity of T. sinense and identifies four refugia in China. CONCLUSIONS: The T. sinense genome provides a unique reference for inferring the early evolution of eudicots and the mechanisms underlying vessel element formation. Population genomics analysis of T. sinense reveals its genetic diversity and geographic structure with implications for conservation.

Haematobium irritans and Haematobium titillans as potential vectors of Parabronema skrjabini in camels (Camelus bactrianus) in Inner Mongolia, China.

Parabronema skrjabini is one of the most harmful nematodes to camels and is responsible for economic losses in animal husbandry industry. There is an urgent need for in-depth studies of potential vectors of the nematode due to its scant regarding information. As previous studies indicated that flies may be the vectors of P. skrjabini, we captured flies in the main camel-producing areas of Inner Mongolia. After autopsy of the specimens of two species of horn flies, we observed the morphology of the suspected nematode larvae found in them. Internal transcribed spacer ribosomal-DNA gene sequences were considered the best candidate to confirm the species of the larvae found. Our results showed that the homology compared with P. skrjabini was 99.5% in GenBank. Subsequently, we preliminarily identified two species of horn flies through morphological observation and then sequenced the mitochondrial-DNA-gene cytochrome oxidase subunit I obtained from two species of horn flies, with 100 and 99.2% similarity to sequences deposited in GenBank, respectively. Thus, we identified Haematobia titillans and Haematobia irritans and provided evidence for their potential role as vectors of parabronemosis. Our study provides reference for future research on the life history of the nematode and the vectors of parabronemosis.

Genome-Wide Identification and Characterization of Hexokinase Genes in Moso Bamboo (Phyllostachys edulis).

Plant hexokinases (HXKs) are a class of multifunctional proteins that not only act as the enzymes required for hexose phosphorylation but also serve as sugar sensors that repress the expression of some photosynthetic genes when internal glucose level increases and regulators of cell metabolism and some sugar-related signaling pathways independent on their catalytic actives. The HXKs have been studied in many plants; however, limited information is available on HXKs of moso bamboo (Phyllostachys edulis). In this study, we identified and characterized 12 hexokinase genes in moso bamboo. Phylogenetic analysis revealed that the moso bamboo hexokinases (PeHXKs) were classifiable into five subfamilies which represented the three types of hexokinases in plants. Gene structure and conserved motif analysis showed that the PeHXK genes contained diverse numbers of introns and exons and that the encoded proteins showed similar motif organization within each subfamily. Multiple sequence alignment revealed that the PeHXK proteins contained conserved domains, such as phosphate 1 (P1), phosphate 2 (P2), adenosine, and a sugar-binding domain. Evolutionary divergence analysis indicated that the PeHXK, OsHXK, and BdHXK families underwent negative selection and experienced a large-scale duplication event approximately 19-319 million years ago. Expression analysis of the PeHXK genes in the leaf, stem, root, and rhizome of moso bamboo seedlings indicated that the PeHXKs perform pivotal functions in the development of moso bamboo. A protein subcellular localization assay showed that PeHXK5a, PeHXK8, and PeHXK3b were predominantly localized in mitochondria, and PeHXK8 protein was also detected in the nucleus. The HXK activity of the PeHXK5a, PeHXK8, and PeHXK3b was verified by a functional complementation assay using the HXK-deficient triple-mutant yeast strain YSH7.4-3C (hxk1, hxk2, and glk1), and the results showed that the three PeHXKs had the plant HXK-specific enzyme traits. The present findings would provide a foundation for further functional analysis of the PeHXK gene family.

Protein partners of plant ubiquitin-specific proteases (UBPs).

As one type of deubiquitinases (DUBs), ubiquitin-specific proteases (UBPs) play an extensive and significant role in plant life involving the regulation of plant development and stress responses. However, comprehensive studies are still needed to determine the functional mechanisms, which are largely unclear. Here, we summarized recent progress of plant UBPs' functional partners, particularly the molecular mechanisms by which UBPs work with their partners. We believe that functional analyses of UBPs and their partners will provide new insights into protein deubiquitination and lead to a better understanding of the physiological roles of UBPs in plants.

The cystathionine γ-lyase/hydrogen sulfide pathway mediates the trimetazidine-induced protection of H9c2 cells against hypoxia/reoxygenation-induced apoptosis and oxidative stress.

OBJECTIVE: Trimetazidine is a piperazine-derived metabolic agent. It exerts cardioprotective effects against myocardial ischemia/reperfusion (I/R) injury. In addition, studies confirm that the cystathionine γ-lyase (CSE)/hydrogen sulfide (H2S) pathway serves a beneficent role in attenuating myocardial I/R injury. However, the underlying role of the CSE/H2S pathway in the trimetazidine-induced protection against myocardial I/R injury remains elusive. Therefore, this study investigated whether trimetazidine ameliorates hypoxia/reoxygenation (H/R)-induced H9c2 cardiomyocyte injuries in an in vitro cell model of myocardial I/R injury, by enhancing the CSE/H2S pathway. METHODS: The H9c2 cell viability was determined with a cell counting Kit-8. RESULTS: Trimetazidine significantly increased the cell viability and decreased lactate dehydrogenase (LDH) release in H/R-treated H9c2 cells. Additionally, trimetazidine increased the H2S levels and the CSE mRNA and protein levels, promoting the CSE/H2S pathway under H/R conditions. The inhibition of the CSE/H2S pathway, induced by transfection with specific siRNA against human CSE (si-CSE), eliminated the trimetazidine-induced upregulation of cell viability, downregulation of LDH release, increase of caspase-3 activity and apoptosis regulator BAX expression, and the decrease of apoptosis regulator Bcl-2 expression, which suggests involvement of the CSE/H2S pathway in trimetazidine-induced cardioprotection. Furthermore, trimetazidine mitigated the H/R-induced increase in reactive oxygen species production and NADPH oxidase 2 expression, and decrease in superoxide dismutase activity and glutathione level, in H9c2 cells. These effects were also reversed by si-CSE. CONCLUSION: This study revealed that the CSE/H2S pathway mediates the trimetazidine-induced protection of H9c2 cardiomyocytes against H/R-induced damage by inhibiting apoptosis and oxidative stress.

Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis).

The largest group of deubiquitinases-ubiquitin-specific proteases (UBPs)-perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.