A molten globule ensemble primes Arf1-GDP for the nucleotide switch.

The adenosine di-phosphate (ADP) ribosylation factor (Arf) small guanosine tri-phosphate (GTP)ases function as molecular switches to activate signaling cascades that control membrane organization in eukaryotic cells. In Arf1, the GDP/GTP switch does not occur spontaneously but requires guanine nucleotide exchange factors (GEFs) and membranes. Exchange involves massive conformational changes, including disruption of the core ß-sheet. The mechanisms by which this energetically costly switch occurs remain to be elucidated. To probe the switch mechanism, we coupled pressure perturbation with nuclear magnetic resonance (NMR), Fourier Transform infra-red spectroscopy (FTIR), small-angle X-ray scattering (SAXS), fluorescence, and computation. Pressure induced the formation of a classical molten globule (MG) ensemble. Pressure also favored the GDP to GTP transition, providing strong support for the notion that the MG ensemble plays a functional role in the nucleotide switch. We propose that the MG ensemble allows for switching without the requirement for complete unfolding and may be recognized by GEFs. An MG-based switching mechanism could constitute a pervasive feature in Arfs and Arf-like GTPases, and more generally, the evolutionarily related (Ras-like small GTPases) Rags and Gα GTPases.

Pressure pushes tRNALys3 into excited conformational states.

Conformational dynamics play essential roles in RNA function. However, detailed structural characterization of excited states of RNA remains challenging. Here, we apply high hydrostatic pressure (HP) to populate excited conformational states of tRNALys3, and structurally characterize them using a combination of HP 2D-NMR, HP-SAXS (HP-small-angle X-ray scattering), and computational modeling. HP-NMR revealed that pressure disrupts the interactions of the imino protons of the uridine and guanosine U-A and G-C base pairs of tRNALys3. HP-SAXS profiles showed a change in shape, but no change in overall extension of the transfer RNA (tRNA) at HP. Configurations extracted from computational ensemble modeling of HP-SAXS profiles were consistent with the NMR results, exhibiting significant disruptions to the acceptor stem, the anticodon stem, and the D-stem regions at HP. We propose that initiation of reverse transcription of HIV RNA could make use of one or more of these excited states.

Quantitative Lipidome Analysis of Boiled Chicken Egg Yolk under Different Heating Intensities.

The effects of the four heating intensities (hot-spring egg yolk, HEY; soft-boiled egg yolk, SEY; normal-boiled egg yolk, NEY; and over-boiled egg yolk, OEY) on lipidomes of boiled egg yolks were investigated. The results indicated that four heating intensities had no significant effect on the total abundance of lipids and lipid categories except for bile acids, lysophosphatidylinositol, and lysophosphatidylcholine. However, of all the 767 lipids quantified, the differential abundance of 190 lipids was screened among the egg yolk samples at four heating intensities. Soft-boiling and over-boiling altered the assembly structure of the lipoproteins through thermal denaturation and affected the binding of lipids and apoproteins, resulting in an increase in low-to-medium-abundance triglycerides. The decreased phospholipid and increased lysophospholipid and free fatty acid in HEY and SEY suggests potential hydrolysis of phospholipids under relatively low-intensity heating. Results provide new insights into the effect of heating on the lipid profiles of egg yolk and would support the public's choice of cooking method for egg yolks.

Divergence of Liver Lipidomes in Tibetan and Yorkshire Pigs Living at Different Altitudes.

The Tibetan pig is a characteristic breed of the Qinghai-Tibet Plateau with distinct physiological and meat quality attributes. The liver lipid profile can offer an important perspective to explore the uniqueness of Tibetan pigs. A quantitative comparison of liver lipidomes revealed significant differences in the lipid profiles between Tibetan and Yorkshire pigs raised at different altitudes. The abundance of lipids in the livers of pigs raised at a high altitude was higher than that of pigs raised at a lower altitude, whereas the abundance of lipids in the livers of Yorkshire pigs was higher than that of Tibetan pigs raised at the same altitude. Of the 1101 lipids identified, 323 and 193 differentially abundant lipids (DALs) were identified in the pairwise comparisons of Tibetan and Yorkshire pigs raised at different altitudes, respectively. The DALs of Tibetan pigs consisted mainly of 161 triglycerides, along with several acylcarnitines, represented by carnitine C2:0, and significant changes in the abundance of some phospholipids. The DALs of Yorkshire pigs were more complex, with significant increases in the abundance of triglycerides, cholesteryl esters, and free fatty acids, and decreases in the abundance of some phospholipids. This research provides strong theoretical and data support for the high-quality development of the highland livestock industry.

Quantitative lipidomic analysis of chicken egg yolk during its formation.

BACKGROUND: The accumulation of lipids in egg yolk during its formation represents a knowledge gap between food science and animal science research to which researchers in either field have not paid sufficient attention. Therefore, the egg yolk samples during different periods of formation (yellow follicle, YF; small hierarchical follicles, SF; and the largest hierarchical follicle, LF) were prepared, and their fatty acid compositions and lipidomes were quantitatively compared. RESULTS: The fatty acid profiles and lipidomes of egg yolks at the three stages of formation were significantly different. The relative content of oleic acid and palmitic acid were increased, but that of the main polyunsaturated fatty acids (linoleic acid, linolenic acid and docosahexaenoic acid) was decreased in the SF period to the LF period. Among the 786 lipid molecular species identified, 150 and 46 differentially abundant lipids (DALs) were identified in the pairwise comparison of YF/SF (early stage of egg yolk formation) and SF/LF (late stage of egg yolk formation), respectively. Triglycerides and diglycerides, represented by TG(14:0/18:1/20:1) and DG(18:1/18:1/0:0), were decreased, whereas free fatty acids (especially free unsaturated fatty acids) were greatly increased during yolk formation. The changes in phospholipids were complex; the relative abundance of phosphatidylcholine [represented by PC(18:0/22:5)] decreased, whereas phosphatidylethanolamine [represented by PE(18:0/18:0)] increased. In addition, the relative abundance of lysophosphatidylcholine [represented by LPC(18:1/0:0)] was increased during egg yolk formation. CONCLUSION: The transport and accumulation of lipids into the egg yolk is dynamically adjusted during its formation, and the transport and timing of different lipid molecular species are different. © 2022 Society of Chemical Industry.

Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation.

Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.

CsMYB96 confers resistance to water loss in citrus fruit by simultaneous regulation of water transport and wax biosynthesis.

A Citrus sinensis R2R3 MYB transcription factor (CsMYB96) has previously been shown to be strongly associated with the expression of many genes related to wax biosynthesis in the fruit. In this study, CsMYB96 was found to alleviate water loss by simultaneously regulating the expression of genes encoding plasma membrane intrinsic proteins (CsPIPs) and wax-related genes. Expression profiling indicated that CsPIP1;1 and CsPIP2;4 had high expression that was representative of other aquaporins, and they were down-regulated in the peel of post-harvest citrus fruit. CsPIP2;4 was further characterized as the predominant CsPIP, with high expression and high-water channel activity. Transient overexpression of CsPIP2;4 accelerated water loss in citrus fruit. In silico analysis further indicated that the expression of CsMYB96 had a significant negative correlation with that of CsPIPs. In vivo and in vitro experiments confirmed that CsMYB96 was able to directly repress the expression of CsPIPs. In addition, CsMYB96 was able to activate wax-related genes and promote wax biosynthesis for defense against water loss. Transient and stable overexpression of CsMYB96 reduced water loss from both citrus fruit and Arabidopsis.

Prognostic Value of PTENP1 Expression in Patients with Cancer: a Systematic Review and Meta-Analysis.

BACKGROUND: Downregulation of PTENP1 was reported in different malignant tumors. However, the function and significance of PTENP1 in the clinical pathology and prognosis of tumors are not very clear. Therefore, we performed this research to analyze and elucidate the correlations between the PTENP1 expression and clinical pathological parameters and outcome of patients in different types of cancer. METHODS: Literature on PTENP1 was retrieved from PubMed, EMBASE, Web of Science, Cochrane Library, CNKI, Wan Fang, Springer, Ovid, and Medline databases. Pooled ORs (odds ratios) or HRs (hazard ratios) with 95% CIs were utilized to examine the relationship between the PTENP1 and clinical pathological traits and outcome of patients with different tumor types. RESULTS: Eight studies comprising 1,047 patients were enrolled and analyzed in this research. Down-regulation of PTENP1 was correlated with differentiation (OR: 2.57; 95% CI: 1.14 - 5.80), TNM stage (OR: 0.24; 95% CI: 0.13 - 0.43), and LNM (OR: 0.27; 95% CI: 0.14 - 0.52). Moreover, PTENP1 expression level was correlated with OS in the eight types of tumors (pooled HR: 0.49; 95% CI: 0.39, 0.61). CONCLUSIONS: Low expression of PTENP1 might predict poor prognosis in patients with various carcinomas. PTENP1 may play an important role as a new prognostic indicator in patients with different malignant tumors.

Construction of bionanoparticles based on Angelica polysaccharides for the treatment of stroke.

Ischemic stroke is an acute and severe neurological disease, resulting in disability and death. The poor drug delivery to cerebral ischemic regions is a key challenge of ischemic stroke treatment. Inspired by the ability of Macrophage membranes to cross the blood-brain barrier, We prepared amphiphilic nanoparticles (AOE@TMP) by linking Angelica polysaccharide (APS) and Ethyl ferulate (EF) using oxalate bond (OL) as the linker arm, with an inner core encapsulated with Tetramethylpyrazine (TMP), and finally using macrophage membrane camouflage (MAOE@TMP). The experimental results show that MAOE@TMP can successfully deliver drugs to the site of brain injury and specifically release it in the microenvironment of the brain injury site, and the three active ingredients in the herb pair could potentiate and significantly reduce the cerebral infarction size.

Protein unfolded states populated at high and ambient pressure are similarly compact.

The relationship between the dimensions of pressure-unfolded states of proteins compared with those at ambient pressure is controversial; resolving this issue is related directly to the mechanisms of pressure denaturation. Moreover, a significant pressure dependence of the compactness of unfolded states would complicate the interpretation of folding parameters from pressure perturbation and make comparison to those obtained using alternative perturbation approaches difficult. Here, we determined the compactness of the pressure-unfolded state of a small, cooperatively folding model protein, CTL9-I98A, as a function of temperature. This protein undergoes both thermal unfolding and cold denaturation, and the temperature dependence of the compactness at atmospheric pressure is known. High-pressure small angle x-ray scattering studies, yielding the radius of gyration and high-pressure diffusion ordered spectroscopy NMR experiments, yielding the hydrodynamic radius were carried out as a function of temperature at 250 MPa, a pressure at which the protein is unfolded. The radius of gyration values obtained at any given temperature at 250 MPa were similar to those reported previously at ambient pressure, and the trends with temperature are similar as well, although the pressure-unfolded state appears to undergo more pronounced expansion at high temperature than the unfolded state at atmospheric pressure. At 250 MPa, the compaction of the unfolded chain was maximal between 25 and 30°C, and the chain expanded upon both cooling and heating. These results reveal that the pressure-unfolded state of this protein is very similar to that observed at ambient pressure, demonstrating that pressure perturbation represents a powerful approach for observing the unfolded states of proteins under otherwise near-native conditions.

Acute toxic encephalopathy following bromadiolone intoxication: a case report.

BACKGROUND: Clinically, bromadiolone poisoning is characterized by severe bleeding complications in various organs and tissues. Bromadiolone-induced toxic encephalopathy is extremely rare. Here, we report a special case of bromadiolone-induced reversible toxic encephalopathy in a patient who had symmetrical lesions in the deep white matter. CASE PRESENTATION: A 23-year-old woman mainly presented with dizziness, fatigue, alalia and unsteady gait after the ingestion of bromadiolone. The laboratory examinations showed normal coagulation levels. Brain magnetic resonance imaging (MRI) showed apparent diffusion restriction in the bilateral deep white matter. The clinical manifestations and MRI alterations were reversible within one month of treatment with vitamin K. The neuropsychological assessment showed no neurodegenerative changes at the 2-year follow-up. CONCLUSION: With the increased use of bromadiolone as a rodenticide, more cases of ingestion have been reported annually over the past several years. Bromadiolone-induced toxic encephalopathy has no special clinical manifestations and is potentially reversible with timely treatment. Because of the reversible restricted diffusion on diffusion-weighted images (DWI) and low apparent diffusion coefficient (ADC) values, transient intramyelinic cytotoxic oedema is thought to be the cause rather than persistent ischaemia. The underlying pathophysiological mechanism is still unknown and may be coagulant-independent. This clinical case extends the current knowledge about neurotoxicity in cases of bromadiolone poisoning and indicates that MRI is useful for the early detection of bromadiolone-induced toxic encephalopathy.

The biological function of m6A demethylase ALKBH5 and its role in human disease.

Human AlkB homolog H5 (ALKBH5) is a primary m6A demethylase, which is dysregulated and acts as a biological and pharmacological role in human cancers or non-cancers. ALKBH5 plays a dual role in various cancers through regulating kinds of biological processes, such as proliferation, migration, invasion, metastasis and tumor growth. In addition, it takes a great part in human non-cancer, including reproductive system diseases. The underlying regulatory mechanisms of ALKBH5 that relys on m6A-dependent modification are implicated with long non-coding RNA, cancer stem cell, autophagy and hypoxia. ALKBH5 is also an independent prognostic indicator in various cancers. In this review, we summarized the current evidence on ALKBH5 in diverse human cancers or non-cancers and its potential as a prognostic target.

Application of ARIMA model in monitoring the use rate of antibiotics in outpatients in 2010 - 2018
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OBJECTIVES: In order to continuously promote the rational clinical application of antibacterial drugs and provide data support for hospital scientific management decision-making, we evaluated the use rate of antibiotics in outpatients in 2010 - 2018. MATERIALS AND METHODS: A retrospective analysis of the use rate of antibiotics in outpatients from January 2010 to October 2018 was performed in our hospital. We analyzed the antibacterial use rate in each month in outpatients and evaluated the changes in the antibacterial use rate in outpatients over the past 9 years. Autoregressive integrated moving average (ARIMA) model was established and verified, and we predicted the trends of antibacterial use rate in outpatients from November 2018 to March 2019. RESULTS: The level of clinical rational drug use management in our hospital is continually improving. The average monthly use rate of antibiotic drugs in outpatients in 2010 - 2013 decreased from 13.04 to 12.28% in 2014 - 2018 (p = 0.002). The goodness-of-fit of the ARIMA model is high. The verification results show that the model can accurately predict the changing trend. The average absolute error of the actual value and the fitted value of the antibiotic drug use rate was 0.76% from January to October 2018. The established ARIMA model can better simulate the trend of antibacterial use rate in outpatients. CONCLUSION: The model can be applied to the short-term prediction and dynamic analysis of antibacterial use rate in outpatients, helping hospitals to reasonably evaluate and monitor the use of clinical antibiotics and provide decision-making services for hospital management.

Small non-coding RNA STnc640 regulates expression of fimA fimbrial gene and virulence of Salmonella enterica serovar Enteritidis.

BACKGROUND: Small non-coding RNAs (sRNAs) regulate bacterial gene expression at the post-transcriptional level. STnc640 is a type of sRNA that was identified in Salmonella Typhimurium. RESULTS: In this study, STnc640 in Salmonella Enteritidis was confirmed to be an Hfq-dependent sRNA. TargetRNA software analysis showed that fimbrial genes fimA and bcfA were likely to be the target genes of STnc640. To investigate the target mRNAs and function of STnc640 in pathogenicity, we constructed the deletion mutant strain 50336△stnc640 and the complemented strain 50336△stnc640/pstnc640 in Salmonella Enteritidis 50336. The RT-qPCR results showed that the mRNA level of fimA was decreased, while bcfA was unchanged in 50336△stnc640 compared with that in the wild type (WT) strain. The adhesion ability of 50336△stnc640 to Caco-2 cells was increased compared to the 50336 WT strain. The virulence of 50336△stnc640 was enhanced in a one-day-old chicken model of S. Enteritidis disease as determined by quantifying the 50% lethal dose (LD50) of the bacterial strains. CONCLUSIONS: The results demonstrate that STnc640 contributes to the virulence of Salmonella Enteritidis.

Comparation of vancomycin penetration into cerebrospinal fluid in postoperative intracranial infection and community-acquired meningitis patients.

WHAT IS KNOWN AND OBJECTIVE: To compare the penetration of vancomycin into cerebrospinal fluid (CSF) in patients with postoperative intracranial infection and community-acquired meningitis, and to identify related factors influencing the penetration in these two diseases. METHODS: The concentrations of vancomycin in serum and CSF were determined by enzyme amplified immunoassay, and the CSF-to-serum ratios were calculated. The correlation between CSF-to-serum ratios of vancomycin and CSF elements was analyzed. RESULTS AND DISCUSSION: In postoperative intracranial infection patients and community-acquired meningitis patients, the vancomycin concentration in CSF was 1.90 ± 1.29 mg/L and 2.47 ± 1.15 mg/L, while the CSF-to-serum ratio was 0.19 ± 0.12 and 0.26 ± 0.12, respectively. There was a significant correlation between vancomycin serum concentration and bodyweight (P < 0.05). The CSF-to-serum ratio in postoperative intracranial infection patients was correlated to white blood cell count in CSF. However, in community-acquired meningitis patients, no relationship was seen with regards to CSF white blood cell count, protein or glucose. WHAT IS NEW AND CONCLUSION: Cerebrospinal fluid vancomycin penetration was similar in postoperative intracranial infection and community-acquired meningitis patients. The CSF-to-serum ratio was only correlated to CSF white blood cell count in postoperative intracranial infection patients.

Pathogenic Providencia alcalifaciens strain that causes fatal hemorrhagic pneumonia in piglets.

Investigation of a serious pig disease with high mortality and typical lung lesions yielded a bacterial isolate identified as Providencia alcalifaciens based on the 16S ribosomal DNA sequence analysis. The pathogenicity of this bacterial isolate was confirmed in piglets and mice. The bacterial strain caused the typical illness in piglets, which suffered serious dyspnea and hemorrhagic pneumonia. The drug resistance spectrum of the bacterium was also determined. The results indicated that the isolate is resistant to 12 antibiotics and intermediately resistant to 10 antibiotics out of the 34 antibiotics tested. The current study is the first to report a serious lung disease in piglets caused by a multidrug resistant P. alcalifaciens isolate, which should be given more attention during surveillance and diagnostics.

Health Hazards Associated with Dietary Exposure of Female Rat to Cadmium-Contaminated Cooked Rice: Biochemical, Hormonal, and Histopathological Analysis.

The actual exposure, bioavailability, and body burden of dietary cadmium (Cd) vary with the food matrix. Here, we evaluated the health hazards of 45-day long-term exposure of growing Sprague-Dawley (SD) female rats to a natural and endogenous Cd-contaminated brown and white cooked rice dietary model. Cd was found mainly in the duodenum, kidney, and liver; the cecum and colon also contained substantial amounts of Cd in rats fed Cd-contaminated cooked white rice (cWR-test) but not Cd-contaminated cooked brown rice (cBR-test). Damage due to Cd exposure was reflected in liver dysfunction, altered estradiol levels, and distinctive pathologies in organ systems, although urinary Cd (U-Cd) excretion and blood Cd (B-Cd) were not detectable, suggesting that these are not the most accurate or appropriate biomarkers for evaluating dietary Cd exposure. Brown rice, despite being higher in Cd, can reduce Cd absorption and distribution in organs and increase the volume of Cd-containing feces, even achieving slightly higher excretion and lower apparent absorption rates of Cd than white rice, thereby reducing Cd damage to the body. The beneficial components of brown rice such as more dietary fiber, rice bran oil and polyphenol were speculated therefore to confer a degree of protection or repair. Nevertheless, the high apparent absorption levels observed here (> 5%) and signs of significant physical damage indicate that more stringent Cd intake guidelines and measures are needed to minimize Cd levels in rice.

Four new erythroneurine leafhopper species from karst areas in Southwestern China (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini).

Four new erythroneurine leafhopper species, Empoascanaraaparaoides Wang & Song, sp. nov., Motagamengyangensis Wang & Song, sp. nov., Motagaacicularis Wang & Song, sp. nov., and Tautoneuraqingxiuensis Wang & Song, sp. nov. from karst areas in Southwestern China, are described and illustrated.

Research Note: Comprehensive proteomic, phosphoproteomic, and N-glycoproteomic analysis of chicken egg yolk plasma.

Chicken egg yolk plasma (EYP), the supernatant fraction of egg yolk obtained by water dilution and centrifugation, is a rich source of various bioactive substances and a significant bearer of yolk-emulsifying properties. This study utilized proteomics to conduct a comprehensive and in-depth analysis of both common and modified EYP proteins (phosphorylated proteins and N-glycosylated proteins). Total of 208 proteins were identified in EYP, including 42 phosphorylated proteins with 137 phosphorylation sites and 150 N-glycoproteins with 332 N-glycosylation sites. Among the phosphorylation sites, tyrosine accounted for 80.6%, while the N-glycosylation sites predominantly featured "N-X-T" motifs, accounting for 58.7%. Functional enrichment analysis revealed that most proteins were involved in regulating enzyme activity and inhibition with a particular focus on modulating peptidase activity. Notably, vitellogenins-2 (30 phosphorylation sites, 9 N-glycosylation sites) and apolipoprotein B (10 phosphorylation sites, 56 N-glycosylation sites) were the 2 proteins with the most modification sites. Additionally, EYP was found to contain the highly N-glycosylated complement proteins C3 and C4. These findings provide new insights into the protein composition of EYP and its roles in chicken embryo development and immune defense, offering a theoretical foundation for the application of EYP in various fields.