Joint effects about antibiotics combined using with antibiotics or phytochemicals on Aeromonas hydrophila.

Aeromonas hydrophila is highly prevalent in aquaculture animals and aquaculture environment. Due to the abuse of antibiotics, A. hydrophila can change the antibiotic resistance spectrum directly and affect human health indirectly. The use of combined drugs replacement therapy and the long-term coexistence with drug-resistant bacteria are the reality that human beings have to face in dealing with the problem of antibiotic resistance in the future. This study showed the characteristics and trends through abundant results of combined effects related with the combinations of antibiotic and the combinations of antibiotic and phytochemical on A. hydrophila, and revealed the antagonism probability of combinations of antibiotic and phytochemical is significantly higher than that of the combinations of antibiotic. Meanwhile, the combinations of antibiotic and phytochemical could protect the host cells which also achieved the same effectiveness as combination of antibiotics, and the enrichment pathway was proved to be relatively discrete. In addition, the possible mechanism about the reverse "U" shape of the combined effect curve on wild/antibiotic-resistant bacteria was clarified, and it was confirmed that the antagonism for the combinations of antibiotic and phytochemical might has the significance in inhibiting the evolution of bacterial resistance mutations. This study was aims to provide theoretical basis and some clues for the antibiotic resistance control associated with A. hydrophila.

ZEPPI: Proteome-scale sequence-based evaluation of protein-protein interaction models.

We introduce ZEPPI (Z-score Evaluation of Protein-Protein Interfaces), a framework to evaluate structural models of a complex based on sequence coevolution and conservation involving residues in protein-protein interfaces. The ZEPPI score is calculated by comparing metrics for an interface to those obtained from randomly chosen residues. Since contacting residues are defined by the structural model, this obviates the need to account for indirect interactions. Further, although ZEPPI relies on species-paired multiple sequence alignments, its focus on interfacial residues allows it to leverage quite shallow alignments. ZEPPI can be implemented on a proteome-wide scale and is applied here to millions of structural models of dimeric complexes in the Escherichia coli and human interactomes found in the PrePPI database. PrePPI's scoring function is based primarily on the evaluation of protein-protein interfaces, and ZEPPI adds a new feature to this analysis through the incorporation of evolutionary information. ZEPPI performance is evaluated through applications to experimentally determined complexes and to decoys from the CASP-CAPRI experiment. As we discuss, the standard CAPRI scores used to evaluate docking models are based on model quality and not on the ability to give yes/no answers as to whether two proteins interact. ZEPPI is able to detect weak signals from PPI models that the CAPRI scores define as incorrect and, similarly, to identify potential PPIs defined as low confidence by the current PrePPI scoring function. A number of examples that illustrate how the combination of PrePPI and ZEPPI can yield functional hypotheses are provided.

Phosphodiesterase 5A regulates the vomeronasal pump in mice.

The vomeronasal organ (VNO) is a specialized chemoreceptive structure in many vertebrates that detects chemical stimuli, mostly pheromones, which often elicit innate behaviors such as mating and aggression. Previous studies in rodents have demonstrated that chemical stimuli are actively transported to the VNO via a blood vessel-based pumping mechanism, and this pumping mechanism is necessary for vomeronasal stimulation in behaving animals. However, the molecular mechanisms that regulate the vomeronasal pump remain mostly unknown. In this study, we observed a high level of expression of phosphodiesterase 5A (PDE5A) in the vomeronasal blood vessel of mice. We provided evidence to support the potential role of PDE5A in vomeronasal pump regulation. Local application of PDE5A inhibitors-sildenafil or tadalafil-to the vomeronasal organ (VNO) reduced stimulus delivery into the VNO, decreased the pheromone-induced activity of vomeronasal sensory neurons, and attenuated male-male aggressive behaviors. PDE5A is well known to play a role in regulating blood vessel tone in several organs. Our study advances our understanding of the molecular regulation of the vomeronasal pump.

Light affects the prefrontal cortex via intrinsically photosensitive retinal ganglion cells.

The ventromedial prefrontal cortex (vmPFC) is a part of the limbic system engaged in the regulation of social, emotional, and cognitive states, which are characteristically impaired in disorders of the brain such as schizophrenia and depression. Here, we show that intrinsically photosensitive retinal ganglion cells (ipRGCs) modulate, through light, the integrity, activity, and function of the vmPFC. This regulatory role, which is independent of circadian and mood alterations, is mediated by an ipRGC-thalamic-corticolimbic pathway. Lack of ipRGC signaling in mice causes dendritic degeneration, dysregulation of genes involved in synaptic plasticity, and depressed neuronal activity in the vmPFC. These alterations primarily undermine the ability of the vmPFC to regulate emotions. Our discovery provides a potential light-dependent mechanism for certain PFC-centric disorders in humans.

Designing highly efficient oxygen evolution reaction electrocatalyst of high-entropy oxides FeCoNiZrOx: Theory and experiment.

The correlations between the experimental methods and catalytic activities are urgent to be defined for the design of highly efficient catalysts. In this work, a new oxygen evolution reaction electrocatalyst of high-entropy oxide (HEO) FeCoNiZrOx was designed and analyzed by experimental and theoretical methods. On account of the shortened coordinate bond along with the increased annealing temperature, the atomic/electronic structures of active site were adjusted quantitatively with the aid of the pre-designed correlator of d electron density, which contributed to adjust the catalytic activity of HEO specimens. The prepared HEO specimen exhibited the low overpotentials of 245 mV at 10 mA cm-2 and 288 mV at 100 mA cm-2 with small Tafel slope of 35.66 mV dec-1, fast charge transfer rate, and stable electrocatalytic activity. This strategy would be adopted to improve the catalytic activity of HEO by adjusting the d electron density of transition metal ions with suitable preparation method.

The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.

Histones compact and store DNA in both Eukarya and Archaea, forming heterodimers in Eukarya and homodimers in Archaea. Despite this, the folding mechanism of histones across species remains unclear. Our study addresses this gap by investigating 11 types of histone and histone-like proteins across humans, Drosophila, and Archaea through multiscale molecular dynamics (MD) simulations, complemented by NMR and circular dichroism experiments. We confirm and elaborate on the widely applied "folding upon binding" mechanism of histone dimeric proteins and report a new alternative conformation, namely, the inverted non-native dimer, which may be a thermodynamically metastable configuration. Protein sequence analysis indicated that the inverted conformation arises from the hidden ancestral head-tail sequence symmetry underlying all histone proteins, which is congruent with the previously proposed histone evolution hypotheses. Finally, to explore the potential formations of homodimers in Eukarya, we utilized MD-based AWSEM and AI-based AlphaFold-Multimer models to predict their structures and conducted extensive all-atom MD simulations to examine their respective structural stabilities. Our results suggest that eukaryotic histones may also form stable homodimers, whereas their disordered tails bring significant structural asymmetry and tip the balance towards the formation of commonly observed heterotypic dimers.

Phytochemical study on ethyl acetate fraction of Lepidium obtusum Basin.

Three undescribed compounds (1-3), including two butenolides and one indol alkaloids. Together with twenty-one known compounds (4-24) were isolated and identified from Lepidium obtusum Basin. Their structures were elucidated by spectroscopic analysis and ECD calculations. The isolated compounds were tested for their antimicrobial, antioxidant, and anti-inflammatory activities. Among them, compounds 11, 12, 14, 21 and 23 showed moderated antimicrobial activities against (Candida albicans, E. coli, Staphylococcus aureus). Compounds 11, 12, 14, 15, 17 and 18 exhibited potent antioxidant activities against ABTS and DPPH. Compound 1 exhibited moderated anti-inflammatory activities. Compounds 4-24 were isolated from this plant for the first time.

ZEPPI: proteome-scale sequence-based evaluation of protein-protein interaction models.

We introduce ZEPPI (Z-score Evaluation of Protein-Protein Interfaces), a framework to evaluate structural models of a complex based on sequence co-evolution and conservation involving residues in protein-protein interfaces. The ZEPPI score is calculated by comparing metrics for an interface to those obtained from randomly chosen residues. Since contacting residues are defined by the structural model, this obviates the need to account for indirect interactions. Further, although ZEPPI relies on species-paired multiple sequence alignments, its focus on interfacial residues allows it to leverage quite shallow alignments. ZEPPI performance is evaluated through applications to experimentally determined complexes and to decoys from the CASP-CAPRI experiment. ZEPPI can be implemented on a proteome-wide scale as evidenced by calculations on millions of structural models of dimeric complexes in the E. coli and human interactomes found in the PrePPI database. A number of examples that illustrate how these tools can yield novel functional hypotheses are provided.

WITHDRAWN: Light affects the prefrontal cortex via intrinsically photosensitive retinal ganglion cells.

This manuscript has been withdrawn by bioRxiv following a formal request by the NIH Intramural Research Integrity Office owing to lack of author consent.

PrePPI: A structure informed proteome-wide database of protein-protein interactions.

We present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural clues within a Bayesian framework to compute a likelihood ratio (LR) for essentially every possible pair of proteins in a proteome; the current database is for the human interactome. The structural modeling (SM) clue is derived from templatebased modeling and its application on a proteome-wide scale is enabled by a unique scoring function used to evaluate a putative complex. The updated version of PrePPI leverages AlphaFold structures that are parsed into individual domains. As has been demonstrated in earlier applications, PrePPI performs extremely well as measured by receiver operating characteristic curves derived from testing on E. coli and human protein-protein interaction (PPI) databases. A PrePPI database of ~1.3 million human PPIs can be queried with a webserver application that comprises multiple functionalities for examining query proteins, template complexes, 3D models for predicted complexes, and related features ( https://honiglab.c2b2.columbia.edu/PrePPI ). PrePPI is a state-of- the-art resource that offers an unprecedented structure-informed view of the human interactome.

Specific regulation of BACH1 by the hotspot mutant p53R175H reveals a distinct gain-of-function mechanism.

Although the gain of function (GOF) of p53 mutants is well recognized, it remains unclear whether different p53 mutants share the same cofactors to induce GOFs. In a proteomic screen, we identified BACH1 as a cellular factor that recognizes the p53 DNA-binding domain depending on its mutation status. BACH1 strongly interacts with p53R175H but fails to effectively bind wild-type p53 or other hotspot mutants in vivo for functional regulation. Notably, p53R175H acts as a repressor for ferroptosis by abrogating BACH1-mediated downregulation of SLC7A11 to enhance tumor growth; conversely, p53R175H promotes BACH1-dependent tumor metastasis by upregulating expression of pro-metastatic targets. Mechanistically, p53R175H-mediated bidirectional regulation of BACH1 function is dependent on its ability to recruit the histone demethylase LSD2 to target promoters and differentially modulate transcription. These data demonstrate that BACH1 acts as a unique partner for p53R175H in executing its specific GOFs and suggest that different p53 mutants induce their GOFs through distinct mechanisms.

PrePPI: A Structure Informed Proteome-wide Database of Protein-Protein Interactions.

We present an updated version of the Predicting Protein-Protein Interactions (PrePPI) webserver which predicts PPIs on a proteome-wide scale. PrePPI combines structural and non-structural evidence within a Bayesian framework to compute a likelihood ratio (LR) for essentially every possible pair of proteins in a proteome; the current database is for the human interactome. The structural modeling (SM) component is derived from template-based modeling and its application on a proteome-wide scale is enabled by a unique scoring function used to evaluate a putative complex. The updated version of PrePPI leverages AlphaFold structures that are parsed into individual domains. As has been demonstrated in earlier applications, PrePPI performs extremely well as measured by receiver operating characteristic curves derived from testing on E. coli and human protein-protein interaction (PPI) databases. A PrePPI database of ∼1.3 million human PPIs can be queried with a webserver application that comprises multiple functionalities for examining query proteins, template complexes, 3D models for predicted complexes, and related features (https://honiglab.c2b2.columbia.edu/PrePPI). PrePPI is a state-of-the-art resource that offers an unprecedented structure-informed view of the human interactome.

Synthesis and Activity of Aurone and Indanone Derivatives.

INTRODUCTION: Based on bioactive group splicing, classical bioisosterism, and the rule of alkene insertion, forty-eight aurone, and indanone derivatives were designed and synthesized. They were evaluated for inhibitory activity against C. albicans, E. coli, and S. aureus. Among them, thirty compounds exhibited moderate to excellent antibacterial activity. METHODS: The maximum circle of inhibition was 18 mm (compounds B15, B16, and E7), and the minimum values of MIC and MBC were respectively 15.625 µM (compounds A5 and D2) and 62.5 µM (compounds A6, A8, and E7). RESULTS: The SAR showed that aurone and indanone derivatives could strongly inhibit the growth of Gram-positive bacteria. The introduction of electron-withdrawing groups or hydroxyl is beneficial to the activity. It was exciting that the 3-phenylallylbenzofuranone and 3-allylindanone skeletons with antimicrobial activity were first reported in this study. Compounds A5 and E7 were selected for molecular docking studies with targets MetRS (PBD: 7WPI) and PBP (PDB: 6C3K) to determine the binding interactions at the active site. CONCLUSION: On this basis, the physicochemical and pharmacological properties of the compounds were predicted and analyzed. The influence of these properties on antimicrobial activity and their implications for subsequent work were discussed. The ADMET (Absorption, Distribution, Metabolism, Excretion, Toxicity) predictions showed that most of the compounds had good pharmacokinetic profiles and high safety profiles.

Multifaceted roles of WRKY transcription factors in abiotic stress and flavonoid biosynthesis.

Increasing biotic and abiotic stresses are seriously impeding the growth and yield of staple crops and threatening global food security. As one of the largest classes of regulators in vascular plants, WRKY transcription factors play critical roles governing flavonoid biosynthesis during stress responses. By binding major W-box cis-elements (TGACCA/T) in target promoters, WRKYs modulate diverse signaling pathways. In this review, we optimized existing WRKY phylogenetic trees by incorporating additional plant species with WRKY proteins implicated in stress tolerance and flavonoid regulation. Based on the improved frameworks and documented results, we aim to deduce unifying themes of distinct WRKY subfamilies governing specific stress responses and flavonoid metabolism. These analyses will generate experimentally testable hypotheses regarding the putative functions of uncharacterized WRKY homologs in tuning flavonoid accumulation to enhance stress resilience.

ERF subfamily transcription factors and their function in plant responses to abiotic stresses.

Ethylene Responsive Factor (ERF) subfamily comprise the largest number of proteins in the plant AP2/ERF superfamily, and have been most extensively studied on the biological functions. Members of this subfamily have been proven to regulate plant resistances to various abiotic stresses, such as drought, salinity, chilling and some other adversities. Under these stresses, ERFs are usually activated by mitogen-activated protein kinase induced phosphorylation or escape from ubiquitin-ligase enzymes, and then form complex with nucleic proteins before binding to cis-element in promoter regions of stress responsive genes. In this review, we will discuss the phylogenetic relationships among the ERF subfamily proteins, summarize molecular mechanism how the transcriptional activity of ERFs been regulated and how ERFs of different subgroup regulate the transcription of stress responsive genes, such as high-affinity K+ transporter gene PalHKT1;2, reactive oxygen species related genes LcLTP, LcPrx, and LcRP, flavonoids synthesis related genes FtF3H and LhMYBSPLATTER, etc. Though increasing researches demonstrate that ERFs are involved in various abiotic stresses, very few interact proteins and target genes of them have been comprehensively annotated. Hence, future research prospects are described on the mechanisms of how stress signals been transited to ERFs and how ERFs regulate the transcriptional expression of stress responsive genes.

Distribution and regional variation of wall shear stress in the curved middle cerebral artery using four-dimensional flow magnetic resonance imaging.

Background: To investigate the distribution and regional variation of wall shear stress (WSS) in the curved middle cerebral artery (MCA) in healthy individuals using four-dimensional (4D) flow magnetic resonance imaging (MRI). Methods: A total of 44 healthy participants (18 males; mean ages: 27.16±5.69 years) were included in this cross-sectional study. The WSS parameters of mean, minimum, and maximum values, the coefficient of variation of time-averaged WSS (TAWSSCV), and the maximum values of the oscillatory shear index (OSI) were calculated and compared in the curved proximal (M1) segments. Three cross-sectional planes were selected: the location perpendicular to the beginning of the long axis of the curved M1 segment of the MCA (proximal section), the most curved M1 location (curved M1 section), and the location before the insular (M2) segment bifurcation (distal section). The WSS and OSI parameters of the proximal, curved, and distal sections of the curved M1 segment were compared, including the inner and outer curvatures of the curved M1 section. Results: Of the curved M1 segments, the curved M1 section had significantly lower minimum TAWSS values than the proximal (P=0.031) and distal sections (P=0.002), and the curved M1 section had significantly higher maximum OSI values than the distal section (P=0.001). The TAWSSCV values at the curved M1 section were significantly higher than the proximal (P=0.001) and distal sections (P<0.001). At the curved M1 section, the inner curvature showed a significantly lower minimum TAWSS (P=0.013) and higher maximum OSI values (P=0.002) than the outer curvature. Conclusions: There are distribution variation of WSS and OSI parameters at the curved M1 section of the curved MCA, and the inner curvature of the curved M1 section has the lowest WSS and highest OSI distribution. The local hemodynamic features of the curved MCA may be related to the predilection for atherosclerotic plaque development.

The value of immunotherapy in children with initial short-term frequent seizures.

This study aimed to discuss clinical characteristics, therapy, and antibody prevalence in epilepsy (APE) score for short-term, frequent epileptic seizures in children who are autoimmune-antibody negative and respond well to immunotherapy. The clinical characteristics, imaging manifestations, electrophysiology, and effective treatment plan of 9 children who met the above criteria were retrospectively analyzed in the Pediatric Neurology Department of Qilu Hospital at Shandong University from June 2019 to December 2021. All 9 patients (6 boys, 3 girls; aged 13 months-11 years and 5 months, median 3.5 years) had acute-onset seizures within 3 months. All had previous normal growth/development with no family history of disease. Seizure types were focal motor seizures (6), generalized tonic-clonic seizures (2), and generalized secondary-to-focal (1); occurred >10 times/day; and lasted <1 min/episode. Formal treatment with ≥2 types of antiseizure medicine (ASM) achieved an unsatisfactory effect. Cranial magnetic resonance imaging showed an abnormal result in 1 case. The APE score was ≥4 in 3 cases and <4 in 6 cases. All patients experienced symptomatic relief with immunotherapy; subsequently, 8 patients were free of recurrence and 1 had significantly reduced seizure frequency. Autoimmune antibody screening is recommended for children who were previously well and have acute-onset epilepsy; high frequency, short-duration seizures; no good response to 2 types of ASM; and other etiologic factors excluded, even with APE score <4. Even with negative autoimmune antibody results, the possibility of autoimmune epilepsy should be considered for urgent initiation of immunotherapy, which can achieve good results.

Satellite glia modulate sympathetic neuron survival, activity, and autonomic function.

Satellite glia are the major glial cells in sympathetic ganglia, enveloping neuronal cell bodies. Despite this intimate association, the extent to which sympathetic functions are influenced by satellite glia in vivo remains unclear. Here, we show that satellite glia are critical for metabolism, survival, and activity of sympathetic neurons and modulate autonomic behaviors in mice. Adult ablation of satellite glia results in impaired mTOR signaling, soma atrophy, reduced noradrenergic enzymes, and loss of sympathetic neurons. However, persisting neurons have elevated activity, and satellite glia-ablated mice show increased pupil dilation and heart rate, indicative of enhanced sympathetic tone. Satellite glia-specific deletion of Kir4.1, an inward-rectifying potassium channel, largely recapitulates the cellular defects observed in glia-ablated mice, suggesting that satellite glia act in part via K+-dependent mechanisms. These findings highlight neuron-satellite glia as functional units in regulating sympathetic output, with implications for disorders linked to sympathetic hyper-activity such as cardiovascular disease and hypertension.

Chemical Profiling of Kaliziri Injection and Quantification of Six Caffeoyl Quinic Acids in Beagle Plasma by LC-MS/MS.

Vitiligo is a stubborn multifactorial skin disease with a prevalence of approximately 1% in the global population. Kaliziri, the seeds of Vernonia anthelmintica (L.) Willd., is a well-known traditional Uyghur medicine for the treatment of vitiligo. Kaliziri injections is a Chinese-marketed treatment approved by the China Food and Drug Administration for the treatment of vitiligo. The significant effects of Kaliziri injection have been thoroughly studied. However, chemical components studies and plasma quantification studies are lacking for Kaliziri injection. Ultra-high-performance liquid chromatography coupled with hybrid quadrupole orbitrap mass spectrometry was employed to comprehensively characterize the caffeoyl quinic acid derivatives present in Kaliziri injection. Based on accurate mass measurements, key fragmental ions and comparisons with reference standards, 60 caffeoyl quinic acid derivatives were identified in Kaliziri injections, including caffeoyl quinic acids, coumaroyl caffeoyl quinic acids, dicaffeoyl quinic acids, feruloyl caffeoyl quinic acids, and dicaffeoyl quinic acid hexosides. Moreover, an HPLC-MS/MS method was developed and validated for the quantitative analysis of 5-caffeoyl quinic acid, 4-caffeoyl quinic acid, 1,3-dicaffeoyl quinic acid, 3,4-dicaffeoyl quinic acid, 3,5-dicaffeoyl quinic acid and 4,5-dicaffeoyl quinic acid in beagle plasma. The quantitative HPLC-MS/MS method was applied to quantify these six major caffeoyl quinic acids in beagle plasma after the subcutaneous administration of Kaliziri injection. All of the six analytes reached their peak plasma of concentrations within 30 min.

Diversity of satellite glia in sympathetic and sensory ganglia.

Satellite glia are the major glial type found in sympathetic and sensory ganglia in the peripheral nervous system, and specifically, contact neuronal cell bodies. Sympathetic and sensory neurons differ in morphological, molecular, and electrophysiological properties. However, the molecular diversity of the associated satellite glial cells remains unclear. Here, using single-cell RNA sequencing analysis, we identify five different populations of satellite glia from sympathetic and sensory ganglia. We define three shared populations of satellite glia enriched in immune-response genes, immediate-early genes, and ion channels/ECM-interactors, respectively. Sensory- and sympathetic-specific satellite glia are differentially enriched for modulators of lipid synthesis and metabolism. Sensory glia are also specifically enriched for genes involved in glutamate turnover. Furthermore, satellite glia and Schwann cells can be distinguished by unique transcriptional signatures. This study reveals the remarkable heterogeneity of satellite glia in the peripheral nervous system.