The lysine 2-hydroxyisobutyrylome of Helicobacter pylori: Indicating potential roles of lysine 2-hydroxyisobutyrylation in the bacterial metabolism.

Helicobacter pylori (H. pylori) is a pathogen which colonizes the stomach, causing ulcers, chronic gastritis and other related diseases. Protein post-translational modifications (PTMs) in bacteria mainly include glycosylation, ubiquitination, nitrosylation, methylation, phosphorylation and acetylation, all of which have divergent functions in the physiology and pathology of the bacterium. Lysine 2-hydroxyisobutyrylation (Khib) is a newly discovered type of PTM in recent years in some kinds of organisms, and this PTM is involved in the regulation of a variety of metabolic process, such as bacterial glucose metabolism, lipid metabolism and protein synthesis. This study performed the first qualitative lysine 2-hydroxyisobutyrylome in H. pylori, and a total of 4419 Khib sites in 812 proteins were identified. The results show that Khib sites are mainly located in the key functional regions or active domains of proteins involved in nickel-trafficking, energy production, virulence factors, anti-oxidation, metal resistance, and ribosome biosynthesis in H. pylori. The study presented here provides new hints in the metabolism and pathology of H. pylori and the proteins with Khib modification may be potentially promising targets for the further development of antibiotics, especially considering the high occurrence of treatment failure of H. pylori failure due to development of antibiotics-resistance.

Intramolecular Charge Transfer of Gold Nanoclusters for pH Indicating.

The investigation of the intramolecular charge transfer (ICT) process of gold nanoclusters (AuNCs) is critical to understand the unique features of the nanomaterials, which also benefits their further applications. Herein, 6-methyl-2-thiouracil (CH3-2-TU) and polyvinylpyrrolidone (PVP)-stabilized AuNCs are prepared, and the ICT behaviors are carefully studied. Protonation or deprotonation of the ligands around AuNCs could be used to regulate the ICT state, influencing the electron distribution and band gap. Shifted fluorescence emission phenomena are thus observed, which respond to external pH stimuli. In addition, the AuNCs are developed as color-switchable indicators for the highly sensitive detection of biogenic amines. As a proof of concept, the performance of this strategy in the evaluation of food spoilage by probing pH conditions is validated with satisfactory results. The discoveries in this work offer a convenient route to regulate the optical properties of AuNCs and the design of pH-based sensing applications.

Nano-Impact Electrochemical Biosensing Based on a CRISPR-Responsive DNA Hydrogel.

Nano-impact electrochemistry (NIE) enables simple, rapid, and high-throughput biocoupling and biomolecular recognition. However, the low effective collision frequency limits the sensitivity. In this study, we propose a novel NIE sensing strategy amplified by the CRISPR-responsive DNA hydrogel and cascade DNA assembly. By controlling the phase transition of DNA hydrogel and the self-electrolysis of silver nanoparticles, we can obtain significant electrochemical responses. The whole process includes target miRNA-induced strand displacement amplification, catalytic hairpin assembly, and CRISPR/Cas trans-cutting. Thus, ultrahigh sensitivity is promised. This NIE biosensing strategy achieves a limit of detection as low as 4.21 aM for miR-141 and demonstrates a high specificity for practical applications. It may have wide applicability in nucleic acid sensing and shows great potential in disease diagnosis.

Wash-Free and High-Contrast Imaging of Single-Nucleotide Variation in Single Cells Using Transcription-Amplified Light-Up RNA Aptamer.

Single-nucleotide variation (SNV) imaging can indicate cellular heterogeneity and spatial pattern, but it remains challenging to produce high-gain signal while also yielding single-nucleotide resolution. Herein, we developed a light-up strategy for visualizing SNVs based on transcription amplification, enabling wash-free and high-contrast imaging of SNVs inside cells. The discrimination of SNVs is achieved by ligase-assisted transcription reaction. Employing a light-up RNA aptamer as a reporter eliminates nonspecific probe binding and the washing process and contributes to a 2-fold improvement of signal gain compared to that using the fluorescence in situ hybridization (FISH) method. The method allowed us to precisely quantify drug-resistant strains in the bacteria mixture and identify drug-resistant Salmonella enterica (S. enterica) isolated from poultry farm. Using this approach, we explored the colonization features of drug-resistant and drug-sensitive S. enterica in the mice intestinal tract and screened the prebiotics for Salmonella colonization inhibition. The SNV imaging method promises for the interrogation of genotypes in physiological and pathological states at the single-cell level.

The mechanisms of metronidazole resistance of Helicobacter pylori: A transcriptomic and biochemical study.

Helicobacter pylori (H. pylori) is a bacterial pathogen in the stomach, causing gastritis, gastric ulcer, duodenal ulcer and even gastric cancer. The triple therapy containing one bismuth-containing compound or a proton-pump inhibitor with two antibiotics was the cornerstone of the treatment of H. pylori infections. However the drug resistance of Helicobacter pylori is more and more common, which leads to the continued decline in the radical cure rate. The purpose of this study was to investigate the mechanism of metronidazole resistance of H. pylori through transcriptomics and biochemical characterizations. In this study, a 128-time-higher metronidazole-resistant H. pylori strain compared to the sensitive strain was domesticated, and 374 significantly differential genes were identified by transcriptomic sequencing as compared to the metronidazole-sensitive strain. Through GO and KEGG enrichment analysis, antibiotic-resistance pathways were found to be mainly involved in redox, biofilm formation and ABC transportation, and the results were verified by qRT-PCR. The subsequent biochemical analysis found that the urease activity of the drug-resistant strain decreased, and whereas the capabilities of bacterial energy production, membrane production and diffusion ability increased. The work here will drop hints for the mechanisms of antibiotic-resistance of H. pylori and provide promising biomarkers for the further development of new-kind drugs to treat metronidazole-resistant H. pylori.

Associated Risk Factors and Diagnostic Value of Fiberoptic Bronchoscopy for Protracted Bacterial Bronchitis in Children.

Objective: Untreated protracted bacterial bronchitis (PBB), a chronic wet cough prevalent in children, may lead to chronic suppurative lung disease. However, clinical diagnostic criteria are currently nonspecific; thus, PBB may be misdiagnosed. Thus, we assessed the diagnostic value of fiberoptic bronchoscopy (FOB) and the risk factors associated with PBB. Methods: Children with chronic cough at The First Affiliated Hospital of Anhui Medical University from January 2015 to May 2020 were enrolled and allocated to a suspected PBB (n = 141) or a non-PBB (n = 206) group. All children underwent extensive laboratory, chest imaging, and allergen tests. Children with suspected PBB underwent FOB with bronchoalveolar lavage; lavage and sputum samples were cultured. Results: All 347 children had a chronic wet cough for approximately 2 months. Of 141 children with suspected PBB, 140 received FOB with bronchoalveolar lavage. Visible tracheal changes included pale mucosa, mucosal congestion, edema, swelling, and increased secretions attached to the wall. Sputum was visible primarily in the left main bronchus (78.7%), left lower lobe (59.6%), right upper lobe (62.4%), and right lower lobe (64.5%). Sputum properties and amounts significantly differed between children with vs. without PBB (P < 0.05). Dermatophagoides (odds ratio (OR), 2.642; 95% CI, 1.283-5.369), milk protein (OR, 2.452; 95% CI, 1.243-4.836) allergies, and eczema (OR, 1.763; 95% CI, 1.011-3.075) were risk factors significantly associated with PBB. Conclusion: Dermatophagoides, milk protein, and eczema were associated with an increased risk of PBB. Sputum distribution and tracheal wall changes observed through FOB may distinguish PBB and assist in its diagnosis.

Chlorination-Mediated π-π Stacking Enhances the Photodynamic Properties of a NIR-II Emitting Photosensitizer with Extended Conjugation.

NIR-II-emitting photosensitizers (PSs) have attracted great research interest due to their promising clinical applications in imaging-guided photodynamic therapy (PDT). However, it is still challenging to realize highly efficient PDT on NIR-II PSs. In this work, we develop a chlorination-mediated π-π organizing strategy to improve the PDT of a PS with conjugation-extended A-D-A architecture. The significant dipole moment of the carbon-chlorine bond and the strong intermolecular interactions of chlorine atoms bring on compact π-π stacking in the chlorine-substituted PS, which facilitates energy/charge transfer and promotes the photochemical reactions of PDT. Consequently, the resultant NIR-II emitting PS exhibits a leading PDT performance with a yield of reactive oxygen species higher than that of previously reported long-wavelength PSs. These findings will enlighten the future design of NIR-II emitting PSs with enhanced PDT efficiency.

Fold-LTR-TCP: protein fold recognition based on triadic closure principle.

As an important task in protein structure and function studies, protein fold recognition has attracted more and more attention. The existing computational predictors in this field treat this task as a multi-classification problem, ignoring the relationship among proteins in the dataset. However, previous studies showed that their relationship is critical for protein homology analysis. In this study, the protein fold recognition is treated as an information retrieval task. The Learning to Rank model (LTR) was employed to retrieve the query protein against the template proteins to find the template proteins in the same fold with the query protein in a supervised manner. The triadic closure principle (TCP) was performed on the ranking list generated by the LTR to improve its accuracy by considering the relationship among the query protein and the template proteins in the ranking list. Finally, a predictor called Fold-LTR-TCP was proposed. The rigorous test on the LE benchmark dataset showed that the Fold-LTR-TCP predictor achieved an accuracy of 73.2%, outperforming all the other competing methods.

Seroprevalence of Kaposi's sarcoma-associated herpesvirus and risk factors in Jiuquan area, China.

The seroprevalence of Kaposi's sarcoma-associated herpesvirus (KSHV) is high in Xinjiang, China. But the seroprevalence of KSHV and risk factors are still unknown in Gansu which is adjacent to Xinjiang. Six hundred and seventy-eight serum samples of the general population and 87 serum samples of syphilis patients from Jiuquan, Gansu were tested for antibodies against KSHV, including one latent protein (ORF73) and two lytic proteins (ORF65 and K8.1) using the ELISA. The total KSHV-seropositive rate was 15.9% in 678 serum samples in the Jiuquan area, and the KSHV-seropositive rate of males was higher than females (18.0% vs. 14.6%, p > 0.05). The Uygur, Kazakh, Hui, Manchu, and Mongolian populations had a higher seroprevalence of KSHV than the Han population (43.8%, 40.0%, 34.5%, 30.3%, 35.0% vs. 11.0%, respectively) among the ethnic groups in Jiuquan. Compared to the Han, Uygur, Kazak, Hui, Manchu, and Mongolian people had an increase in the risk of KSHV of 528.9%, 439.1%, 325.6%, 251.6%, and 335.4% (p < 0.001, p < 0.001, p < 0.001, p = 0.002, p = 0.003, respectively). The serum prevalence of KSHV in subjects aged < 20 years, 20-50 years, and >50 years was 13.8%, 14.7%, and 20.1%, respectively. Compared to the subjects aged < 20 years, 20-50 years and >50 years had an increase in the risk of KSHV of 7.4% and 56.9% (p = 0.829 and p = 0.204, respectively). Compared to the positive rate of KSHV in the general population of Anhui, the positive rate of KSHV was significantly higher in the general population of the Jiuquan area (15.9% vs. 9%, p < 0.01). There was no significant difference in the positive rate of KSHV between the Han population of Jiuquan and the Han population of Anhui (p > 0.05). In the population of syphilis patients in the Jiuquan area, the positive rate of KSHV was 30.7%, which was higher than that of the general population in the Gansu area (p < 0.05). This study indicates that Gansu has a high seroprevalence of KSHV. Ethnicity and syphilis are risk factors for KSHV infection.

Effect of different surgical approaches on the prognosis of patients with postoperative radiotherapy for stage IIB-IVA esophageal squamous cancer.

OBJECTIVE: To investigate the effect and clinical significance of different thoracic surgical approaches for patients with stage IIB-IVA esophageal squamous cell carcinoma on the survival and prognosis of postoperative radiotherapy patients. METHODS: One hundred thirty-two patients with stage IIB-IVA esophageal squamous cancer who received radiotherapy after surgery were screened for baseline characteristics and survival analysis. The Kaplan-Meier method was used to draw the survival curve for the follow-up data, and the log-rank test was used to compare the difference in survival rate between the two groups. The Cox regression model was used for multivariate survival analysis. RESULT: For stage IIB-IVA esophageal squamous cell carcinoma, the results of multivariate analysis showed that different surgical methods and clinical staging were independent factors affecting the survival and prognosis of patients after radiotherapy. The 1-, 3-, and 5-year survival rates of patients with advanced esophageal cancer through the left chest approach were 84.2%, 61.4%, and 36.8% respectively. The 1-, 3-, and 5-year survival rates of patients with advanced esophageal cancer through the right chest approach were 73.3%, 40.0%, and 21.3% respectively. There was no significant difference in the 1-year survival rate (P = 0.135) between the two surgical procedures. The 3-year survival rate (P < 0.05) and the 5-year survival rate (P < 0.05) were significantly different. CONCLUSION: For patients with stage IIB-IVA esophageal squamous cell carcinoma undergoing radiotherapy after surgery, the long-term survival prognosis of patients after the left thoracic approach is significantly higher than that of the right thoracic approach.

Interaction of remimazolam benzenesulfonate and human serum albumin: a simulated physiological study.

Here, to elucidate the interaction mechanism and physicochemical properties of remimazolam and human serum albumin interactions, techniques such as fluorescence, circular dichroism (CD) spectroscopy, and isothermal titration calorimetry have been applied for study. The thermodynamic parameters at body temperature (ΔS = -207 J·mol-1 ·K-1 , ΔS = -9.76 × 104 J·mol-1 and ΔG = -3.34 × 104 J·mol-1 ; 310 K) manifests one strong binding site on the protein, which was modulated by van der Waals forces and hydrogen bonds. What is more, the results of CD, synchronous and three-dimensional fluorescence showed that remimazolam altered the microenvironment of the protein amino acid residues. A distance of 2.1 nm between the remimazolam and Trp shows the potential for resonance energy transfer. Furthermore, these results potentially provide information for illustrating the pharmacodynamics and toxicodynamics of remimazolam when it is applied clinically.

Oligomeric Acceptor: A "Two-in-One" Strategy to Bridge Small Molecules and Polymers for Stable Solar Devices.

Oligomeric acceptors are expected to combine the advantages of both highly developed small molecular and polymeric acceptors. However, organic solar cells (OSCs) based on oligomers lag far behind due to their slow development and low diversity. Here, three oligomeric acceptors were produced through oligomerization of small molecules. The dimer dBTICγ-EH achieved the best power conversion efficiencies (PCEs) of 14.48 % in bulk heterojunction devices and possessed a T80 (80 % of the initial PCE) lifetime of 1020 h under illumination, which were far better than that of small molecular and polymeric acceptors. More excitingly, it showed PCEs of 16.06 % in quasi-planar heterojunction (Q-PHJ) devices which is the highest value OSCs using oligomeric acceptors to date. These results suggest that oligomerization of small molecules is a promising strategy to achieve OSCs with optimized performance between the high efficiency and durable stability, and offer oligomeric materials a bright future in commercial applications.

Light-Harvesting Fluorescent Spherical Nucleic Acids Self-Assembled from a DNA-Grafted Conjugated Polymer for Amplified Detection of Nucleic Acids.

The ultralow concentration of nucleic acids in complex biological samples requires fluorescence probes with high specificity and sensitivity. Herein, a new kind of spherical nucleic acids (SNAs) is developed by using fluorescent π-conjugated polymers (FCPs) as a light-harvesting antenna to enhance the signal transduction of nucleic acid detection. Specifically, amphiphilic DNA-grafted FCPs are synthesized and self-assemble into FCP-SNA structures. Tuning the hydrophobicity of the graft copolymer can adjust the size and light-harvesting capability of the FCP-SNAs. We observe that more efficient signal amplification occurs in larger FCP-SNAs, as more chromophores are involved, and the energy transfer can go beyond the Förster radius. Accordingly, the optimized FCP-SNA shows an antenna effect of up to 37-fold signal amplification and the limit of detection down to 1.7 pM in microRNA detection. Consequently, the FCP-SNA is applied to amplified in situ nucleic acid detecting and imaging at the single-cell level.

Side-Chain-Tuned Molecular Packing Allows Concurrently Boosted Photoacoustic Imaging and NIR-II Fluorescence.

It is generally considered that photoacoustic imaging (PAI) and fluorescence imaging (FLI) cannot be enhanced concurrently, as they are dependent on competitive photophysical processes at the single-molecule level. Herein, we reveal that BDTR9-OC8 and BDTR9-C8, which have identical π-conjugated backbones but are substituted by side chains of different rigidity, show distinct phototheranostic properties in the aggregated state. The NIR-II FLI and PAI brightness of BDTR9-C8 nanoparticles are enhanced by 4.6 and 1.4 times compared with BDTR9-OC8 nanoparticles. Theoretical calculations and GIWAXS analysis revealed that BDTR9-C8 with rigid side chains shows a relative amorphous condensed state, which will benefit the efficient transportation of photo-generated excitons and phonons, subsequently enhancing the FLI and PAI signals. Besides, both nanoparticles exhibit excellent photothermal conversion efficiency due to their strong light-harvesting capability and are considered effective photothermal therapy materials. This work provides an illuminating strategy for material design in the future.

Evaluation of serum IgM and IgG antibodies in COVID-19 patients by enzyme linked immunosorbent assay.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is sweeping the world since the end of 2019. The titer change of antibodies against SARS-CoV-2 needs to be further clarified, the clinical and preventive value of antibodies still needs to be further investigated. An enzyme-linked immunosorbent assay (ELISA) was established by coating with SARS-CoV-2 recombinant spike protein and used to detect serum immunoglobulin M (IgM) and immunoglobulin G (IgG) antibodies against SARS-CoV-2 in coronavirus disease 2019 patients to evaluate the pattern of changes of antibodies. The specificity of the ELISA for detection SARS-CoV-2 IgM and IgG were 96% (144/150) and 100% (150/150), respectively. The sensitivity of ELISA was 100% (150/150) for IgM, and 99.3% (149/150) for IgG. SARS-CoV-2-SP-IgM and SP-IgG antibodies could be detected on Day 1 of hospitalization in 12.5% patients, and SP-IgM began to decrease after reaching its peak at around 22-28 days, and become negative at Month 3 in 30% patients and negative at Month 7 in 79% of these patients after onset; IgG reached its peak around Day 22-28 and kept at a high level within the longest observation period for 4 months, it dropped very sharply at 7 months. The positive rates of SP-IgM and SP-IgG were higher than those of reverse transcription-polymerase chain reaction on Day 7 and 4. The established indirect ELISA has good specificity and sensitivity. IgM and IgG against SARS-CoV-2 appeared almost simultaneously in the early stage, and the level of IgG antibodies could not maintain a high plateau in the observation period of 7 months. Our data will help develop the diagnosis and vaccine of SARS-CoV-2.

NaOTs-promoted transition metal-free C-N bond cleavage to form C-X (X = N, O, S) bonds.

Multifunctional transformation of amide C-N bond cleavage is reported. The protocol applies to benzamide, thioamide, alcohols, and mercaptan under similar reaction conditions catalyzed by NaOTs. It is noteworthy that NaOTs can not only be recycled and reused for up to three cycles without significant loss in catalytic activity, but also catalyze gram-grade reactions. This study provides a novel solution with mild conditions and a simple procedure for transformation of multiple amides.

Universal and differential transcriptional regulatory pathways involved in the preparation of summer and winter diapauses in Pieris melete.

Much progress has been made in understanding the environmental and hormonal systems regulating winter diapause. However, transcriptional regulation of summer diapause is still largely unknown, making it difficult to understand an all-around regulation profile of seasonal adaptation. To bridge this gap, comparison RNA-seq to profile the transcriptome and to examine differential gene expression profiles between non-diapause, summer diapause, and winter diapause groups were performed. A total number of 113 million reads were generated and assembled into 79,117 unigenes, with 37,492 unigenes categorized into 58 functional gene ontology groups, 25 clusters of orthologous group categories, and 256 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. KEGG analysis mapped 2108 differentially expressed genes to 48 and 67 pathways for summer and winter diapauses, respectively. Enrichment statistics showed that 11 identical pathways similarly overlapped in the top 20 enriched functional groups both related to summer and winter diapauses. We also identified 35 key candidate genes for universal and differential functions related to summer and winter diapause preparation. Furthermore, we identified some genes involved in the signaling and metabolic pathways that may be the key drivers to integrate environmental signals into the summer and winter diapause preparation. The current study provided valuable insights into global molecular mechanisms underpinning diapause preparation.

The calcium-dependent protein kinase ZmCDPK7 functions in heat-stress tolerance in maize.

Global warming poses a serious threat to crops. Calcium-dependent protein kinases (CDPKs)/CPKs play vital roles in plant stress responses, but their exact roles in plant thermotolerance remains elusive. Here, we explored the roles of heat-induced ZmCDPK7 in thermotolerance in maize. ZmCDPK7-overexpressing maize plants displayed higher thermotolerance, photosynthetic rates, and antioxidant enzyme activity but lower H2 O2 and malondialdehyde (MDA) contents than wild-type plants under heat stress. ZmCDPK7-knockdown plants displayed the opposite patterns. ZmCDPK7 is attached to the plasma membrane but can translocate to the cytosol under heat stress. ZmCDPK7 interacts with the small heat shock protein sHSP17.4, phosphorylates sHSP17.4 at Ser-44 and the respiratory burst oxidase homolog RBOHB at Ser-99, and upregulates their expression. Site-directed mutagenesis of sHSP17.4 to generate a Ser-44-Ala substitution reduced ZmCDPK7's enhancement of catalase activity but enhanced ZmCDPK7's suppression of MDA accumulation in heat-stressed maize protoplasts. sHSP17.4, ZmCDPK7, and RBOHB were less strongly upregulated in response to heat stress in the abscisic acid-deficient mutant vp5 versus the wild type. Pretreatment with an RBOH inhibitor suppressed sHSP17.4 and ZmCDPK7 expression. Therefore, abscisic acid-induced ZmCDPK7 functions both upstream and downstream of RBOH and participates in thermotolerance in maize by mediating the phosphorylation of sHSP17.4, which might be essential for its chaperone function.

Assessment on the Coupling Effects of Drip Irrigation and Se-Enriched Organic Fertilization in Tomato Based on Improved Entropy Weight Coefficient Model.

Selenium (Se) is an essential micronutrient for human beings and plants are the current main sources of Se element in Asian diet. Therefore a feasible way to increase people's Se intake is to increase Se content in plants. In this paper, we focus on how the tomato (Solanum Lycopersicum) yield and quality are influenced by the effect of irrigation amount, Se-enriched and high-calcium organic fertilizer and compound fertilizer amount respectively. The results from a two-year experiment show that the combination of Se-enriched organic fertilizer and compound fertilizer can significantly increase the tomato yield comparing with the use of NPK organic or compound fertilizer. It is also shown that by applying more Se-enriched and high-calcium organic fertilizer the contents of Se, Lycopene, Vitamin C (Vc) and soluble sugar in tomato fruit can be increased considerably. It was found that the highest Se content was achieved using 100% Se-enriched organic fertilizer combined with irrigation at 100% in 2016 and 100% Se-enriched organic fertilizer with irrigation at 80% in 2017. Deficit irrigation (80%) can help to increase Water Use Efficiency (WUE) and the Se and VC contents in tomato yield. Therefore in order to improve the Se-enriched tomato yield and quality, it is suggested to apply 100% Se-enriched organic fertilizer and adopt the deficit irrigation at 80%.

Advances in Research on the Toxicological Effects of Selenium.

Selenium is a trace element necessary for the growth of organisms. Moreover, selenium supplementation can improve the immunity and fertility of the body, as well as its ability to resist oxidation, tumors, heavy metals, and pathogenic microorganisms. However, owing to the duality of selenium, excessive selenium supplementation can cause certain toxic effects on the growth and development of the body and may even result in death in severe cases. At present, increasing attention is being paid to the development and utilization of selenium as a micronutrient, but its potential toxicity tends to be neglected. This study systematically reviews recent research on the toxicological effects of selenium, aiming to provide theoretical references for selenium toxicology-related research and theoretical support for the development of selenium-containing drugs, selenium-enriched dietary supplements, and selenium-enriched foods.