Combatting persister cells: The daunting task in post-antibiotics era.

Over the years, much attention has been drawn to antibiotic resistance bacteria, but drug inefficacy caused by a subgroup of special phenotypic variants - persisters - has been largely neglected in both scientific and clinical field. Interestingly, this subgroup of phenotypic variants displayed their power of withstanding sufficient antibiotics exposure in a mechanism different from antibiotic resistance. In this review, we summarized the clinical importance of bacterial persisters, the evolutionary link between resistance, tolerance, and persistence, redundant mechanisms of persister formation as well as methods of studying persister cells. In the light of our recent findings of membrane-less organelle aggresome and its important roles in regulating bacterial dormancy depth, we propose an alternative approach for anti-persister therapy. That is, to force a persister into a deeper dormancy state to become a VBNC (viable but non-culturable) cell that is incapable of regrowth. We hope to provide the latest insights on persister studies and call upon more research interest into this field.

Nanoparticles Promote Bacterial Antibiotic Tolerance via Inducing Hyperosmotic Stress Response.

With the rapid development of nanotechnology, nanoparticles (NPs) are widely used in all fields of life. Nowadays, NPs have shown extraordinary antimicrobial activities and become one of the most popular strategies to combat antibiotic resistance. Whether they are equally effective in combating bacterial persistence, another important reason leading to antibiotic treatment failure, remains unknown. Persister cells are a small subgroup of phenotypic drug-tolerant cells in an isogenic bacterial population. Here, various types of NPs are used in combination with different antibiotics to destroy persisters. Strikingly, rather than eradicating persister cells, a wide range of NPs promote the formation of bacterial persistence. It is uncovered by PCR, thermogravimetric analysis, intracellular potassium ion staining, and molecular dynamics simulation that the persister promotion effect is achieved through exerting a hyperosmotic pressure around the cells. Moreover, protein mass spectrometry, fluorescence microscope images, and SDS-PAGE indicate NPs can further hijack cell osmotic regulatory circuits by inducing aggregation of outer membrane protein OmpA and OmpC. These findings question the efficacy of using NPs as antimicrobial agents and raise the possibility that widely used NPs may facilitate the global emergence of bacterial antibiotic tolerance.

Photothermal therapy may be a double-edged sword by inducing the formation of bacterial antibiotic tolerance.

Photothermal nanoparticles are thought to be the most suitable candidates against infectious disease by disrupting the cell membrane or inhibiting cellular metabolism. However, cells with low-metabolic activity states may be endowed with greater ability against harsh environments including antibiotic treatment. For now, it remains unexplored whether and how photothermal therapy (PTT) gives rise to bacterial antibiotic tolerance. In this study, we showed that although it exhibits excellent bactericidal ability, PTT with typical photothermal nanoparticle gold nanocages (AuNCs) can give rise to a subpopulation of cells with great ability of antibiotic tolerance. The subpopulation exhibits delayed growth and decreased cellular ATP levels, indicating a low metabolic state. Specifically, after AuNCs attach to the surface of a bacterial cell, photothermal manipulation can induce cell membrane shrinkage and block the bacterial respiratory chain. Besides, heat shock induces protein aggregation and leads to the dysfunction of a number of important proteins. The heat shock protein DnaK is closely associated with protein aggregation and plays a vital role in modulating antibiotic tolerance, providing a potential therapeutic target.

Genomic and transcriptomic profiling of hepatoid adenocarcinoma of the stomach.

Hepatoid adenocarcinoma of the stomach (HAS), a rare subtype of gastric cancer (GC), has a low incidence but a high mortality rate. Little is known about the molecular features of HAS. Here we applied whole-exome sequencing (WES) on 58 tumours and the matched normal controls from 54 HAS patients, transcriptome sequencing on 30 HAS tumours, and single-cell RNA sequencing (scRNA-seq) on one HAS tumour. Our results reveal that the adenocarcinomatous component and hepatocellular-like component of the same HAS tumour originate monoclonally, and HAS is likely to initiate from pluripotent precursor cells. HAS has high stemness and high methionine cycle activity compared to classical GC. Two genes in the methionine cycle, MAT2A, and AHCY are potential targets for HAS treatments. We provide the first integrative genomic profiles of HAS, which may facilitate its diagnosis, prognosis, and treatment.

Humic Acid Extracts Leading to the Photochemical Bromination of Phenol in Aqueous Bromide Solutions: Influences of Aromatic Components, Polarity and Photochemical Activity.

Dissolved organic matter (DOM) is considered to play an important role in the abiotic transformation of organobromine compounds in marine environment, for it produces reactive intermediates photochemically and is recognized as a significant source of reactive halogen species in seawater. However, due to the complex composition of DOM, the relationship between the natural properties of DOM and its ability to produce organobromine compounds is less understood. Here, humic acid (HA) was extracted and fractionated based on the polarity and hydrophobicity using silica gel, and the influences of different fractions (FA, FB and FC) on the photochemical bromination of phenol was investigated. The structural properties of HA fractions were characterized by UV-vis absorption, Fourier transform infrared spectroscopy and fluorescence spectroscopy, and the photochemical reactivity of HA fractions was assessed by probing triplet dissolved organic matter (3DOM*), singlet oxygen (1O2) and hydroxyl radical (•OH). The influences of HA fractions on the photo-bromination of phenol were investigated in aqueous bromide solutions under simulated solar light irradiation. FA and FB with more aromatic and polar contents enhanced the photo-bromination of phenol more than the weaker polar and aromatic FC. This could be attributed to the different composition and chemical properties of the three HAs' fractions and their production ability of •OH and 3DOM*. Separating and investigating the components with different chemical properties in DOM is of great significance for the assessment of their environmental impacts on the geochemical cycle of organic halogen.

Berberine reverses multidrug resistance in Candida albicans by hijacking the drug efflux pump Mdr1p.

Clinical use of antimicrobials faces great challenges from the emergence of multidrug-resistant pathogens. The overexpression of drug efflux pumps is one of the major contributors to multidrug resistance (MDR). Reversing the function of drug efflux pumps is a promising approach to overcome MDR. In the life-threatening fungal pathogen Candida albicans, the major facilitator superfamily (MFS) transporter Mdr1p can excrete many structurally unrelated antifungals, leading to MDR. Here we report a counterintuitive case of reversing MDR in C. albicans by using a natural product berberine to hijack the overexpressed Mdr1p for its own importation. Moreover, we illustrate that the imported berberine accumulates in mitochondria and compromises the mitochondrial function by impairing mitochondrial membrane potential and mitochondrial Complex I. This results in the selective elimination of Mdr1p overexpressed C. albicans cells. Furthermore, we show that berberine treatment can prolong the mean survival time of mice with blood-borne dissemination of Mdr1p overexpressed multidrug-resistant candidiasis. This study provides a potential direction of novel anti-MDR drug discovery by screening for multidrug efflux pump converters.

Severe hyponatremia in preeclampsia: a case report and review of the literature.

PURPOSE: To summarize the clinical characteristics and treatments of preeclampsia complicated with hyponatremia. METHODS: We reported a new case of preeclampsia complicated with severe hyponatremia; searched for relevant articles from the PubMed, Scopus and Cochrane databases; and reviewed all reported cases. RESULTS: Twenty-one reported cases were found. Our case is 22nd, and the serum sodium level in this case was the lowest reported. After treatment comprising fluid restriction, hypertonic saline and caesarean section, a relatively good outcome was achieved. In all reported cases, SIADH, preeclampsia or the combined effect of preeclampsia and induced nephrotic syndrome were the speculated pathogeny. Termination was performed due to adverse manifestations; six cases underwent transvaginal deliveries, and sixteen cases underwent caesarean section. Fifteen patients recovered from hyponatremia within 72 h after delivery. CONCLUSION: The pathogenesis of hyponatremia occurring in patients with preeclampsia is still unclear. Termination of the pregnancy led to a stabilization of the sodium level, ICU monitoring was necessary, and fluid restriction and hypertonic saline intake were applied; however, there was no evidence of the effectiveness of the treatments.

Insight Into the Formation Paths of Methyl Bromide From Syringic Acid in Aqueous Bromide Solutions Under Simulated Sunlight Irradiation.

Methyl bromide (CH3Br) is one of the largest natural sources of bromine in the stratosphere, where it leads to ozone depletion. This paper reported the photochemical production of CH3Br from syringic acid (SA) that has been used as an environmentally relevant model compound for terrestrially-derived dissolved organic matter. The formation of CH3Br increased with the increase of bromide ion concentration ranging from 0.8 to 80 mmol L-1. Ferric ions (Fe(III)) enhanced CH3Br production, while chloride inhibited it, with or without Fe(III). Meanwhile, methyl chloride (CH3Cl) was generated in the presence of chloride and was inhibited by Fe(III). The different effects of Fe(III) on the formation of CH3Cl and CH3Br indicate their diverse formation paths. Based on the intermediates identified by liquid chromatography-mass spectrometry and the confirmation of the formation of Fe(III)-SA complexes, it was proposed that there were two formation paths of CH3Br from SA in the bromide-enriched water under simulated sunlight irradiation. One path was via nucleophilic attack of Br- on the excited state protonation of SA; the other was via the combination of methyl radical and bromine radical when Fe(III) was present. This work suggests that the photochemical formation of CH3Br may act as a potential natural source of CH3Br in the bromide-enriched environmental matrix, and helps in better understanding the formation mechanism of CH3Br.

Methyl bromide production from dissolved organic matter under simulated sunlight irradiation and the important effect of ferric ions.

The oceans play an important role in the biogeochemical cycle of methyl bromide (CH3Br), as not only the sinks but also the sources. However, many uncertainties exist regarding the way of CH3Br generation in the marine environment. To illustrate the possibility of photochemical formation of CH3Br in saline water, its generation in bromide aqueous solution containing humic acid (HA) and ferric ions (Fe(iii)) was investigated. CH3Br was obviously generated after irradiation, and its amounts increased with increasing HA concentration from 0.82 to 12.2 mgC L-1. Fe(iii) significantly promoted CH3Br production, and the described production process in the presence of Fe(iii) was pH-dependent, decreasing with the increase of pH. Finally, the concentrations of CH3Br in natural coastal seawater and seawater with HA were measured, and the results showed that CH3Br was significantly generated under irradiation. Our results suggest that the photochemical process of dissolved organic matter may be one source of CH3Br in the marine environment.

Photochemical Generation of Methyl Chloride from Humic Aicd: Impacts of Precursor Concentration, Solution pH, Solution Salinity and Ferric Ion.

Methyl chloride (CH3Cl) is presently understood to arise from biotic and abiotic processes in marine systems. However, the production of CH3Cl via photochemical processes has not been well studied. Here, we reported the production of CH3Cl from humic acid (HA) in sunlit saline water and the effects of the concentration of HA, chloride ions, ferric ions and pH were investigated. HA in aqueous chloride solutions or natural seawater were irradiated under an artificial light, and the amounts of CH3Cl were determined using a purge-and-trap and gas chromatography-mass spectrometry. CH3Cl was generated upon irradiation and its amount increased with increasing irradiation time and the light intensity. The formation of CH3Cl increased with an increase of HA concentration ranging from 2 mg L-1 to 20 mg L-1 and chloride ion concentration ranging from 0.02 mol L-1 to 0.5 mol L-1. The photochemical production of CH3Cl was pH-dependent, with the highest amount of CH3Cl generating near neutral conditions. Additionally, the generation of CH3Cl was inhibited by ferric ions. Finally, natural coastal seawater was irradiated under artificial light and the concentration of CH3Cl rose significantly. Our results suggest that the photochemical process of HA may be a source of CH3Cl in the marine environment.

A General Workflow for Characterization of Nernstian Dyes and Their Effects on Bacterial Physiology.

The electrical membrane potential (Vm) is one of the components of the electrochemical potential of protons across the biological membrane (proton motive force), which powers many vital cellular processes. Because Vm also plays a role in signal transduction, measuring it is of great interest. Over the years, a variety of techniques have been developed for the purpose. In bacteria, given their small size, Nernstian membrane voltage probes are arguably the favorite strategy, and their cytoplasmic accumulation depends on Vm according to the Nernst equation. However, a careful calibration of Nernstian probes that takes into account the tradeoffs between the ease with which the signal from the dye is observed and the dyes' interactions with cellular physiology is rarely performed. Here, we use a mathematical model to understand such tradeoffs and apply the results to assess the applicability of the Thioflavin T dye as a Vm sensor in Escherichia coli. We identify the conditions in which the dye turns from a Vm probe into an actuator and, based on the model and experimental results, propose a general workflow for the characterization of Nernstian dye candidates.

ATP-Dependent Dynamic Protein Aggregation Regulates Bacterial Dormancy Depth Critical for Antibiotic Tolerance.

Cell dormancy is a widespread mechanism used by bacteria to evade environmental threats, including antibiotics. Here we monitored bacterial antibiotic tolerance and regrowth at the single-cell level and found that each individual survival cell shows different "dormancy depth," which in return regulates the lag time for cell resuscitation after removal of antibiotic. We further established that protein aggresome-a collection of endogenous protein aggregates-is an important indicator of bacterial dormancy depth, whose formation is promoted by decreased cellular ATP level. For cells to leave the dormant state and resuscitate, clearance of protein aggresome and recovery of proteostasis are required. We revealed that the ability to recruit functional DnaK-ClpB machineries, which facilitate protein disaggregation in an ATP-dependent manner, determines the lag time for bacterial regrowth. Better understanding of the key factors regulating bacterial regrowth after surviving antibiotic attack could lead to new therapeutic strategies for combating bacterial antibiotic tolerance.

Active efflux in dormant bacterial cells - New insights into antibiotic persistence.

Bacterial persisters are phenotypic variants of an isogenic cell population that can survive antibiotic treatment and resume growth after the antibiotics have been removed. Cell dormancy has long been considered the principle mechanism underlying persister formation. However, dormancy alone is insufficient to explain the full range of bacterial persistence. Our recent work revealed that in addition to 'passive defense' via dormancy, persister cells employ 'active defense' via enhanced efflux activity to expel drugs. This finding suggests that persisters combine two seemingly contradictory mechanisms to tolerate antibiotic attack. Here, we review the passive and active aspects of persister formation, discuss new insights into the process, and propose new techniques that can facilitate the study of bacterial persistence.

Rice Dwarf Virus P2 Protein Hijacks Auxin Signaling by Directly Targeting the Rice OsIAA10 Protein, Enhancing Viral Infection and Disease Development.

The phytohormone auxin plays critical roles in regulating myriads of plant growth and developmental processes. Microbe infection can disturb auxin signaling resulting in defects in these processes, but the underlying mechanisms are poorly understood. Auxin signaling begins with perception of auxin by a transient co-receptor complex consisting of an F-box transport inhibitor response 1/auxin signaling F-box (TIR1/AFB) protein and an auxin/indole-3-acetic acid (Aux/IAA) protein. Auxin binding to the co-receptor triggers ubiquitination and 26S proteasome degradation of the Aux/IAA proteins, leading to subsequent events, including expression of auxin-responsive genes. Here we report that Rice dwarf virus (RDV), a devastating pathogen of rice, causes disease symptoms including dwarfing, increased tiller number and short crown roots in infected rice as a result of reduced sensitivity to auxin signaling. The RDV capsid protein P2 binds OsIAA10, blocking the interaction between OsIAA10 and OsTIR1 and inhibiting 26S proteasome-mediated OsIAA10 degradation. Transgenic rice plants overexpressing wild-type or a dominant-negative (degradation-resistant) mutant of OsIAA10 phenocopy RDV symptoms are more susceptible to RDV infection; however, knockdown of OsIAA10 enhances the resistance of rice to RDV infection. Our findings reveal a previously unknown mechanism of viral protein reprogramming of a key step in auxin signaling initiation that enhances viral infection and pathogenesis.

Enhanced Efflux Activity Facilitates Drug Tolerance in Dormant Bacterial Cells.

Natural variations in gene expression provide a mechanism for multiple phenotypes to arise in an isogenic bacterial population. In particular, a sub-group termed persisters show high tolerance to antibiotics. Previously, their formation has been attributed to cell dormancy. Here we demonstrate that bacterial persisters, under ß-lactam antibiotic treatment, show less cytoplasmic drug accumulation as a result of enhanced efflux activity. Consistently, a number of multi-drug efflux genes, particularly the central component TolC, show higher expression in persisters. Time-lapse imaging and mutagenesis studies further establish a positive correlation between tolC expression and bacterial persistence. The key role of efflux systems, among multiple biological pathways involved in persister formation, indicates that persisters implement a positive defense against antibiotics prior to a passive defense via dormancy. Finally, efflux inhibitors and antibiotics together effectively attenuate persister formation, suggesting a combination strategy to target drug tolerance.

Real-Time Visualization of Perylene Nanoclusters in Water and Their Partitioning to Graphene Surface and Macrophage Cells.

Hydrophobic organic chemicals (HOCs) are of special ecotoxicological concern because they can be directly incorporated and bioconcentrated in living organisms. However, the effects of self-clustering of HOCs on their environmental behavior and toxicology have not yet received enough attention. With the use of a recently developed technique, single-molecule fluorescence microscopy, the motion and distribution of perylene nanoclusters (PNCs) formed in water at very low concentration (1 µM) were visualized with high temporal and spatial resolution. The liquid-solid interface process of PNCs adsorbing onto graphene was also recorded. Instead of the traditional view of HOC adsorption as a single molecule, our study revealed the characteristic of irreversible adsorption of perylene onto the carbonaceous surface in the form of nanoclusters, exhibiting random sequential "car-parking" events. More interestingly, the transport of PNCs across the cell membrane was also captured in real time, demonstrating that they entered macrophage cells by endocytosis. Supplementing the well-recognized routine of passive diffusion through a membrane lipid bilayer, the uptake of HOCs in the form of nanoclusters by endocytosis is proposed to be an additional but important mechanism for their uptake into living cells. The distribution of HOCs in environmental systems in the form of nanoclusters, exemplified by PNCs in this study, may have significant implications for understanding their environmental fate and potential toxicological effects.

Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus.

The P9-1 protein of Rice black streaked dwarf virus accumulates in viroplasm inclusions, which are structures that appear to play an important role in viral morphogenesis and are commonly found in viruses in the family Reoviridae. Crystallographic analysis of P9-1 revealed structural features that allow the protein to form dimers via hydrophobic interactions. Each dimer has carboxy-terminal regions, resembling arms, that extend to neighboring dimers, thereby uniting sets of four dimers via lateral hydrophobic interactions, to yield cylindrical octamers. The importance of these regions for the formation of viroplasm-like inclusions was confirmed by the absence of such inclusions when P9-1 was expressed without its carboxy-terminal arm. The octamers are vertically elongated cylinders resembling the structures formed by NSP2 of rotavirus, even though there are no significant similarities between the respective primary and secondary structures of the two proteins. Our results suggest that an octameric structure with an internal pore might be important for the functioning of the respective proteins in the events that occur in the viroplasm, which might include viral morphogenesis.

Rice dwarf viruses with dysfunctional genomes generated in plants are filtered out in vector insects: implications for the origin of the virus.

Rice dwarf virus (RDV), with 12 double-stranded RNA (dsRNA) genome segments (S1 to S12), replicates in and is transmitted by vector insects. The RDV-plant host-vector insect system allows us to examine the evolution, adaptation, and population genetics of a plant virus. We compared the effects of long-term maintenance of RDV on population structures in its two hosts. The maintenance of RDV in rice plants for several years resulted in gradual accumulation of nonsense mutations in S2 and S10, absence of expression of the encoded proteins, and complete loss of transmissibility. RDV maintained in cultured insect cells for 6 years retained an intact protein-encoding genome. Thus, the structural P2 protein encoded by S2 and the nonstructural Pns10 protein encoded by S10 of RDV are subject to different selective pressures in the two hosts, and mutations accumulating in the host plant are detrimental in vector insects. However, one round of propagation in insect cells or individuals purged the populations of RDV that had accumulated deleterious mutations in host plants, with exclusive survival of fully competent RDV. Our results suggest that during the course of evolution, an ancestral form of RDV, of insect virus origin, might have acquired the ability to replicate in a host plant, given its reproducible mutations in the host plant that abolish vector transmissibility and viability in nature.

The P2 capsid protein of the nonenveloped rice dwarf phytoreovirus induces membrane fusion in insect host cells.

Insect transmission is an essential process of infection for numerous plant and animal viruses. How an insect-transmissible plant virus enters an insect cell to initiate the infection cycle is poorly understood, especially for nonenveloped plant and animal viruses. The capsid protein P2 of rice dwarf virus (RDV), which is nonenveloped, is necessary for insect transmission. Here, we present evidence that P2 shares structural features with membrane-fusogenic proteins encoded by enveloped animal viruses. When RDV P2 was ectopically expressed and displayed on the surface of insect Spodoptera frugiperda cells, it induced membrane fusion characterized by syncytium formation at low pH. Mutational analyses identified the N-terminal and a heptad repeat as being critical for the membrane fusion-inducing activity. These results are corroborated with results from RDV-infected cells of the insect vector leafhopper. We propose that the RDV P2-induced membrane fusion plays a critical role in viral entry into insect cells. Our report that a plant viral protein can induce membrane fusion has broad significance in studying the mechanisms of virus entry into insect cells and insect transmission of nonenveloped plant and animal viruses.

Interaction of rice dwarf virus outer capsid P8 protein with rice glycolate oxidase mediates relocalization of P8.

Yeast two-hybrid and coimmunoprecipitation assays indicated that P8, an outer capsid protein of Rice dwarf phytoreovirus (RDV), interacts with rice glycolate oxidase (GOX), a typical enzyme of peroxisomes. Confocal immunofluorescence microscopy revealed that P8 was colocalized with GOX in peroxisomes. Time course analysis demonstrated that the localization of P8 in Spodoptera frugiperda cells changed from diffuse to discrete, punctuate inclusions during expression from 24 to 48 h post inoculation. Coexpression of GOX with P8 may target P8 into peroxisomes, which serve as replication sites for a number of viruses. Therefore, we conclude that the interaction of P8 with the GOX of host cells leads to translocation of P8 into peroxisomes and we further propose that the interaction between P8 and GOX may play important roles in RDV targeting into the replication site of host cells. Our findings have broad significance in studying the mechanisms whereby viruses target appropriate replication sites and begin their replication.