Design of an Acidic pH-Activated NIR Fluorescent Convertible Rhodamine-Hemicyanine Probe-Peptide Conjugate for Living Cancer Cell Active Targeted Selective Tracking of Lysosomes.

We have synthesized an acidic pH-activatable dual targeting ratiometric fluorescent probe-peptide conjugate using the SPPS protocol on Rink amide AM resin. Living carcinoma cell specific active targeting, successive cell penetration, and selective staining of lysosomes are accomplished. Real-time monitoring of lysosomes, 3D, and multicolor cancer cell imaging are also attained. The de novo design consists of the integration of multifunctionality into a single molecular scaffold, e. g., RGDS peptide residue to target cancer cell surface overexpressed receptor αVß3 integrin, live-cell penetrating organic unsymmetrical rhodamine-hemicyanine chromophore comprising a lysosome targeting morpholine group, and an acidic pH openable spiro-lactam ring for a visible-to-NIR switchable ratiometric response. Water-soluble fluorescent probe-peptide conjugate exhibits intramolecular spirolactamization at basic pH through Arg amide N. The visible spirolactam state predominantly exists at physiological and basic pH and can be switched to the highly conjugated NIR open amide state (λem=735 nm) through spiro-lactam ring opening triggered by acidic pH with a huge bathochromic shift (Δλabs=336 nm, ΔλFL=265 nm). Moreover, pH-sensitive ratiometric optical switching is achieved. This in situ acidic cancer cell lysosome activatable multifunctional fluorophore-peptide conjugate shows augmented molar absorptivity, enhanced quantum yield, and improved fluorescence lifetime at acidic lysosomal pH; negligible cytotoxicity; and dual targeted ratiometric imaging capability of living cancer cell selective lysosomes with a pKa value of 5.1.

Acidic pH or salt treatment can convert soluble antibody aggregates in culture harvest into monomers and improve Protein A chromatography step yield.

While purifying a regular monospecific antibody, we found that the Protein A step yield was much lower than expected. Further studies revealed that the antibody formed large-size aggregates that did not bind to the Protein A resin, hence leading to dropped recovery. In an attempt to solve this low yield issue, we found that mildly acidic pH or ammonium sulfate treatment can partially convert the aggregates into monomers. In addition, when acidic pH treated culture harvest was processed by Protein A chromatography, the yield was restored to the normal range, suggesting that the monomers recovered from aggregates regained Protein A binding capability. Thus, low pH treatment of culture harvest can be potentially used as a general approach for improving Protein A step yield in cases where non-binding antibody aggregates are formed through noncovalent interactions.

Application of dairy wastewater as substrate for bioremediation of coal mine drainage in planted horizontal flow constructed wetland.

Coal mine drainage (CMD) is an environmental threat due to its high volume, low pH, presence of toxic metals, and absence of biodegradable organics. The present study aims to treat CMD in a horizontal sub-surface flow constructed wetland (CW) using dairy wastewater as an organic source. CW was planted with Typha angustifolia. Characteristics of synthetic CMD were (except pH, all unit mg/L) pH 1.9; Fe: 100, SO42-: 1,000, Mn: 6, Zn: 5, Co: 1, Ni: 1, and Cr: 1. CMD was mixed with synthetic dairy wastewater (pH: 5.05, COD: 2,700 mg/L, BOD: 1,600 mg/L) in the ratio of 3:1. Alkalinity of 120-190 mg/L CaCO3 was generated and effluent pH improved from 2.2 to 6.6. Metals precipitated as metal sulfide or hydroxide. Sulfate removal was hindered due to the synergistic toxicity of several metals. Except for Mn, all other effluent parameters were within the discharge limit for disposal in inland surface water.

There is limited information available on the advantages of using organic rich wastewater as a substrate for treatment of low carbon coal mine drainage (CMD). Coal mine drainage was mixed with dairy wastewater and treated in horizontal flow constructed wetland. Organic removal, metal removal, sulfate removal, and pH improvement of mixed wastewater are investigated in the present study.

Impact of multilamellar formulations on stratum corneum lipid organization and epidermal lipid barrier enhancement (Part II).

INTRODUCTION: The integrity of the stratum corneum (SC) is crucial for the skin's barrier function, protecting against environmental stressors and minimizing transepidermal water loss. Advances in skincare formulations have introduced multilamellar systems designed to emulate the SC's lipid composition and organization. This study hypothesizes that the application of a multilamellar cream will significantly impact the SC's lipid content and lamellar structure, thereby enhancing the epidermal barrier. METHODS: A saturated phosphatidylcholine-based multilamellar cream was applied to a cohort of adult subjects with very dry skin. Electron microscopy was utilized to analyse the micro-morphology of the cream and its integration into the lipid-depleted SC. Lipid analysis was conducted to quantify changes in the intercellular lipid matrix. RESULTS: Transmission-electron microscopy (TEM) imaging demonstrated that the multilamellar cream possesses a structured arrangement comparable to the natural SC architecture. Short-term application revealed a time-dependent restoration of lipid bilayers, while a 14-day regimen showed a marked increase in lipid lamellae density and length within the SC. Lipid analysis indicated a significant increase in total lipid content, with notable enhancements in ceramide and free fatty acid levels, without altering cholesterol levels. Lipid ratio analysis further confirmed the rebalancing of the SC's lipid composition. DISCUSSION: The multilamellar cream selectively increased specific lipids critical for barrier function, suggesting an action mechanism that aligns with the skin's natural regulatory processes. This selective augmentation indicates the potential of the formulation to not only restore but also enhance the epidermal barrier, with the maintenance of physiological lipid ratios suggesting compatibility with intrinsic repair mechanisms. CONCLUSION: The study confirms that a multilamellar cream can significantly improve the SC's lipid composition and structural integrity, indicating enhanced barrier function. They are pivotal for skincare professionals, dermatologists, and product developers, enriching the understanding of multilamellar creams' benefits and applications in improving epidermal barrier function.

INTRODUCTION: l'intégrité de la couche cornée (SC, stratum corneum) est essentielle pour la fonction de barrière cutanée, protégeant contre les facteurs de stress environnementaux et réduisant au minimum la perte d'eau transépidermique. Les progrès en matière de formulations pour soins de la peau ont introduit des systèmes multilamellaires conçus pour simuler la composition et l'organisation lipidique du SC. Cette étude émet l'hypothèse que l'application d'une crème multilamellaire aura un impact significatif sur la teneur en lipides et la structure lamellaire du SC, améliorant ainsi la barrière épidermique. MÉTHODES: Une crème multilamellaire à base de phosphatidylcholine saturée a été appliquée à une cohorte de sujets adultes présentant une peau très sèche. La microscopie électronique a été utilisée pour analyser la micromorphologie de la crème et son intégration dans le SC délipidé. Une analyse lipidique a été réalisée pour quantifier les changements dans la matrice lipidique intercellulaire. RÉSULTATS: l'imagerie par TEM a démontré que la crème multilamellaire possède un agencement structuré comparable à l'architecture naturelle du SC. L'application à court terme a révélé une restauration dépendante du temps des bicouches lipidiques, tandis qu'un schéma posologique de 14 jours a montré une augmentation marquée de la densité et de la longueur des lamelles lipidiques au sein du SC. L'analyse lipidique a indiqué une augmentation significative de la teneur lipidique totale, avec des améliorations notables des taux de céramide et d'acides gras libres, sans altérer les taux de cholestérol. L'analyse du rapport lipidique a confirmé le rééquilibrage de la composition lipidique du SC. DISCUSSION: la crème multilamellaire a augmenté de manière sélective les lipides spécifiques essentiels à la fonction de barrière, suggérant un mécanisme d'action qui s'aligne sur les processus de régulation naturels de la peau. Cette augmentation sélective indique le potentiel de la formulation non seulement à restaurer, mais également à améliorer la barrière épidermique, avec le maintien des rapports lipidiques physiologiques suggérant une compatibilité avec les mécanismes de réparation intrinsèques. CONCLUSION: l'étude confirme qu'une crème multilamellaire peut améliorer de manière significative la composition lipidique et l'intégrité structurelle du SC, ce qui indique une meilleure fonction de barrière. Ils sont essentiels pour les professionnels de la peau, les dermatologues et les développeurs de produits, et enrichissent la compréhension des bénéfices et des applications des crèmes multilamellaires dans l'amélioration de la fonction de la barrière épidermique.

Clinical efficacy of a multilamellar cream on skin physiology and microbiome in an epidermal stress model: A controlled double-blinded study.

INTRODUCTION: Stratum corneum (SC) is essential for skin barrier function, mitigating water loss and shielding against potentially harmful substances and allergens. The SC's lipid matrix, arranged in a lamellar structure, is integral to its protective role. Our study explores the restoration effects of a multilamellar cream with an acidic pH compared to a basic placebo cream on skin physiology and its interaction with the skin microbiome after stress induction via tape stripping (TS). MATERIALS AND METHODS: In this double-blind study, 14 healthy participants aged 21-58 years were assessed pre- and post-tape stripping, followed by a 14 days application of a multilamellar test cream and a placebo cream with evaluations on days 7, 14 and 17 for sustained effects. Skin physiology was analysed in terms of epidermal barrier function, SC hydration and surface pH. The microbiome was analysed by 16S rRNA amplicon sequencing the 16S rRNA gene using Illumina MiSeq, with subsequent species identification. RESULTS: Our study showed significant improvements in skin barrier repair and SC hydration with verum, particularly after 14 days of application, while both creams initially enhanced stratum corneum hydration. No significant changes in surface-pH were detected. The skin microbiome analysis revealed that TS slightly decreased alpha diversity, a trend that verum significantly reversed, enhancing diversity beyond baseline levels after 14 days. Overall, while both creams contributed to a broader microbial phyla diversity over time, no significant changes in the abundance of specific genera or species were noted between treatments. DISCUSSION AND CONCLUSION: Our study delineates the efficacy of a pH-optimized multilamellar cream in enhancing epidermal barrier recovery and SC hydration post-sequential TS, in contrast to an unstructured basic placebo. Verum cream significantly improved skin barrier function and SC hydration at day 14, with sustained effects evident beyond the treatment period. Furthermore, the multilamellar formulation facilitated the restitution of cutaneous microbiome diversity, a key indicator of healthy skin ecology, underscoring the symbiotic relationship between barrier integrity and microbial composition. These findings underscore the importance of multilamellar emollient structures in dermatological therapeutics, with potential implications for the design of advanced skincare interventions that holistically support cutaneous resilience and homeostasis.

INTRODUCTION: La couche cornée (stratum corneum, SC) est essentielle pour la fonction de barrière cutanée, atténuant la perte d'eau et protégeant contre les substances et allergènes potentiellement nocifs. Disposée selon une structure lamellaire, la matrice lipidique de la SC est constitutive de son rôle protecteur. Notre étude explore les effets de restauration d'une crème multilamellaire à pH acide par rapport à une crème placebo de base sur la physiologie de la peau et son interaction avec le microbiome de la peau après induction de stress via un test tape stripping (TS). MATÉRIELS ET MÉTHODES: Dans cette étude en double aveugle, 14 participants en bonne santé âgés de 21 à 58 ans ont été évalués avant et après tape stipping, puis ont procédé à l'application pendant 14 jours d'une crème test multilamellaire et d'une crème placebo avec des évaluations aux jours 7, 14 et 17 pour les effets durables. La physiologie de la peau a été analysée en termes de fonction de la barrière épidermique, d'hydratation SC et de pH de surface. Le microbiome a été analysé par séquençage de l'amplicon de l'ARNr 16S sur le gène de l'ARNr 16S à l'aide d'Illumina MiSeq, avec identification ultérieure des espèces. RÉSULTATS: Notre étude a montré des améliorations significatives de la réparation de la barrière cutanée et de l'hydratation SC avec le traitement actif, en particulier après 14 jours d'application, tandis que les deux crèmes avaient initialement amélioré l'hydratation de la couche cornée. Aucun changement significatif du pH de surface n'a été détecté. L'analyse du microbiome cutané a révélé que le TS diminuait légèrement la diversité alpha, une tendance qui s'est significativement inversée avec le traitement actif : une amélioration de la diversité au­delà des taux initiaux était observée après 14 jours. Dans l'ensemble, bien que les deux crèmes aient contribué à une plus grande diversité des phyla microbiennes au fil du temps, aucune variation significative dans l'abondance de genres ou d'espèces spécifiques n'a été observée entre les traitements. DISCUSSION ET CONCLUSION: Notre étude délimite l'efficacité d'une crème multilamellaire à pH optimisé pour améliorer la réparation de la barrière épidermique et l'hydratation SC après un TS séquentiel, contrairement à un placebo basique non structuré. La crème contenant le traitement actif a significativement amélioré la fonction de barrière cutanée et l'hydratation SC au jour 14, avec des effets durables évidents au­delà de la période de traitement. En outre, la formulation multilamellaire a facilité la restitution de la diversité du microbiome cutané, un indicateur clé d'une écologie de peau en bonne santé, soulignant la relation symbiotique entre l'intégrité de la barrière et la composition microbienne. Ces résultats soulignent l'importance des structures émollientes multilamellaires dans les traitements dermatologiques, avec des implications potentielles pour la conception d'interventions cutanées avancées qui soutiennent de manière holistique la résilience cutanée et l'homéostasie.

Structural insights at acidic pH of dye-decolorizing peroxidase from Bacillus subtilis.

Dye-decolorizing peroxidases (DyPs), a type of heme-containing oxidoreductase enzymes, catalyze the peroxide-dependent oxidation of various industrial dyes as well as lignin and lignin model compounds. In our previous work, we have recently reported the crystal structures of class A-type DyP from Bacillus subtilis at pH 7.0 (BsDyP7), exposing the location of three binding sites for small substrates and high redox-potential substrates. The biochemical studies revealed the optimum acidic pH for enzyme activity. In the present study, the crystal structure of BsDyP at acidic pH (BsDyP4) reveals two-monomer units stabilized by intermolecular salt bridges and a hydrogen bond network in a homo-dimeric unit. Based on the monomeric structural comparison of BsDyP4 and BsDyP7, minor differences were observed in the loop regions, that is, LI (Ala64-Gln71), LII (Glu96-Lys108), LIII (Pro117-Leu124), and LIV (Leu295-Asp303). Despite these differences, BsDyP4 adopts similar heme architecture as well as three substrate-binding sites to BsDyP7. In BsDyP4, a shift in Asp187, heme pocket residue discloses the plausible reason for optimal acidic pH for BsDyP activity. This study provides insight into the structural changes in BsDyP at acidic pH, where BsDyP is biologically active.

Metabolic adaptations of cancer in extreme tumor microenvironments.

Cancer cells are highly heterogeneous to adapt to extreme tumor microenvironments (TMEs). TMEs challenge cancer cells via hypoxia, nutrition starvation, and acidic pH, promoting invasion and metastasis concomitant with genetic, epigenetic, and metabolic alterations. Metabolic adaptation to an extreme TME could allow cancer cells to evade cell death and immune responses, as well as resulting in drug resistance, recurrence, and poor patient prognosis. Therefore, elucidation of the metabolic adaptation of malignant cancer cells within TMEs is necessary, however, most are still elusive. Recently, adaptation of cancer cells within the TME can be analyzed via cell-cell interactions at the single-cell level. In addition, information into organelle-organelle interactions has recently been obtained. These cell-cell, and organelle-organelle interactions demonstrate the potential as new cancer therapy targets, as they play essential roles in the metabolic adaptation of cancer cells to the TME. In this manuscript, we review (1) metabolic adaptations within tumor microenvironments through (2) cell-to-cell, and (3) organelle-organelle metabolic interactions.

Seneca Valley virus enters cells through multiple pathways and traffics intracellularly via the endolysosomal pathway.

Seneca Valley virus (SVV, also known as Senecavirus A), an oncolytic virus, is a nonenveloped, positive-strand RNA virus and the sole member of the genus Senecavirus within the family Picornaviridae. The mechanisms of SVV entry into cells are currently almost unknown. In the present study, we found that SVV entry into HEK293T cells is acidic pH-dependent by using ammonium chloride (NH4Cl) and chloroquine, both of which could inhibit SVV infection. We confirmed that dynamin II is required for SVV entry by using dynasore, silencing the dynamin II protein, or expressing the dominant-negative (DN) K44A mutant of dynamin II. Then, we discovered that chlorpromazine (CPZ) treatment or knockdown of the clathrin heavy chain (CLTC) protein significantly inhibited SVV infection. In addition, overexpression of CLTC promoted SVV infection. Caveolin-1 and membrane cholesterol were also required for SVV endocytosis. Notably, utilizing genistein, EIPA or nocodazole, we observed that macropinocytosis and microtubules are not involved in SVV entry. Furthermore, overexpression of the Rab7 and Rab9 proteins but not the Rab5 or Rab11 proteins promoted SVV infection. The findings were further validated by the knockdown of four Rabs and Lamp1 proteins, indicating that after internalization, SVV is transported from late endosomes to the trans-Golgi network (TGN) or lysosomes, respectively, eventually releasing its RNA into the cytosol from the lysosomes. Our findings concretely revealed SVV endocytosis mechanisms in HEK293T cells and provided an insightful theoretical foundation for further research into SVV oncolytic mechanisms.

Stress-induced non-replicating Mycobacterium smegmatis incorporates exogenous fatty acids into glycopeptidolipids.

Nontuberculous mycobacteria (NTM) such as Mycobacterium smegmatis accumulate high levels of glycopeptidolipids (GPLs) on their outer surface. The biosynthesis of GPLs is critically linked to biofilm formation by NTM which also includes opportunistic pathogens such as Mycobacterium abscessus. Although GPLs have been investigated in many earlier studies, the biosynthesis of GPLs using exogenous fatty acids in M. smegmatis subjected to stresses encountered by mycobacteria during infection of the human body has not been studied. Therefore, we subjected M. smegmatis to different combinations of the three stresses of hypoxia, acidic pH and nutrient starvation and report here that the metabolic incorporation of radiolabeled long-chain fatty acids into alkali-stable GPLs was significantly increased under these stress conditions. Endogenously synthesized fatty acids were not preferred for GPL biosynthesis by M. smegmatis subjected to the triple stress combination. Our observations indicate that GPLs may play important roles in cell surface modifications associated with the non-replicating state of M. smegmatis. Our experimental model reported here would be useful in the further study of GPL biosynthesis from exogenous fatty acid sources in M. smegmatis subjected to hypoxia, nutrient starvation and acidic stress conditions and help in the screening of candidate drugs that target this biochemical pathway in pathogenic NTM.

High-efficiency production of the antimicrobial peptide pediocin PA-1 in metabolically engineered Corynebacterium glutamicum using a microaerobic process at acidic pH and elevated levels of bivalent calcium ions.

BACKGROUND: Pediocin PA-1 is a bacteriocin of recognized value with applications in food bio-preservation and the medical sector for the prevention of infection. To date, industrial manufacturing of pediocin PA-1 is limited by high cost and low-performance. The recent establishment of the biotechnological workhorse Corynebacterium glutamicum as recombinant host for pediocin PA-1 synthesis displays a promising starting point towards more efficient production. RESULTS: Here, we optimized the fermentative production process. Following successful simplification of the production medium, we carefully investigated the impact of dissolved oxygen, pH value, and the presence of bivalent calcium ions on pediocin production. It turned out that the formation of the peptide was strongly supported by an acidic pH of 5.7 and microaerobic conditions at a dissolved oxygen level of 2.5%. Furthermore, elevated levels of CaCl2 boosted production. The IPTG-inducible producer C. glutamicum CR099 pXMJ19 Ptac pedACDCg provided 66 mg L-1 of pediocin PA-1 in a two-phase batch process using the optimized set-up. In addition, the novel constitutive strain Ptuf pedACDCg allowed successful production without the need for IPTG. CONCLUSIONS: The achieved pediocin titer surpasses previous efforts in various microbes up to almost seven-fold, providing a valuable step to further explore and develop this important bacteriocin. In addition to its high biosynthetic performance C. glutamicum proved to be highly robust under the demanding producing conditions, suggesting its further use as host for bacteriocin production.

Rhodamine-Based Cyclic Hydroxamate as Fluorescent pH Probe for Imaging of Lysosomes.

Monitoring the microenvironment within specific cellular regions is crucial for a comprehensive understanding of life events. Fluorescent probes working in different ranges of pH regions have been developed for the local imaging of different pH environments. Especially, rhodamine-based fluorescent pH probes have been of great interest due to their ON/OFF fluorescence depending on the spirolactam ring's opening/closure. By introducing the N-alkyl-hydroxamic acid instead of the alkyl amines in the spirolactam of rhodamine, we were able to tune the pH range where the ring opening and closing of the spirolactam occurs. This six-membered cyclic hydroxamate spirolactam ring of rhodamine B proved to be highly fluorescent in acidic pH environments. In addition, we could monitor pH changes of lysosomes in live cells and zebrafish.

Iron (Fe) toxicity, uptake, translocation, and physio-morphological responses in Catharanthus roseus.

Iron (Fe) toxicity in plant species depends on the availability of Fe in the soil, uptake ability by the root system, and translocation rate to other parts of the plant. The aim of this study was to assess Fe uptake by root tissues of Catharanthus roseus, translocation rate to leaf tissues, and the impairment of plant physio-morphological characteristics. Fe uptake by the roots (~ 700 µg g-1 DW) of C. roseus was observed during the early exposure period (1 week), and translocation factor from root to shoot was fluctuated as an independent strategy. A high level of Fe content in the root tissues significantly inhibited root length and root dry weight. Under acidic pH condition, an enrichment of Fe in the shoots (~ 400 µg g-1 DW) led to increase in leaf temperature (> 2.5 °C compared to control) and crop stress index (> 0.6), resulting in stomatal closure, subsequently decreasing CO2 assimilation rate and H2O transpiration rate. An increment of CSI in Fe-stressed plants was negatively related to stomatal conductance, indicating stomatal closure with an increase in Fe in the leaf tissues. High Fe levels in the leaf tissues directly induced toxic symptoms including leaf bronzing, leaf spotting, leaf necrosis, leaf chlorosis, and leaf senescence in C. roseus plants. In summary, C. roseus was identified as a good candidate plant for Fe phytoextraction, depending on Fe bioaccumulation, therefore 50 mM Fe treatment was designated as an excess Fe to cause the growth inhibition, especially in the prolonged Fe incubation periods. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-023-01379-5.

LysX2 is a Mycobacterium tuberculosis membrane protein with an extracytoplasmic MprF-like domain.

BACKGROUND: Aminoacyl-phosphatidylglycerol (aaPG) synthases are bacterial enzymes that usually catalyze transfer of aminoacyl residues to the plasma membrane phospholipid phosphatidylglycerol (PG). The result is introduction of positive charges onto the cytoplasmic membrane, yielding reduced affinity towards cationic antimicrobial peptides, and increased resistance to acidic environments. Therefore, these enzymes represent an important defense mechanism for many pathogens, including Staphylococcus aureus and Mycobacterium tuberculosis (Mtb), which are known to encode for lysyl-(Lys)-PG synthase MprF and LysX, respectively. Here, we used a combination of bioinformatic, genetic and bacteriological methods to characterize a protein encoded by the Mtb genome, Rv1619, carrying a domain with high similarity to MprF-like domains, suggesting that this protein could be a new aaPG synthase family member. However, unlike homologous domains of MprF and LysX that are positioned in the cytoplasm, we predicted that the MprF-like domain in LysX2 is in the extracytoplasmic region. RESULTS: Using genetic fusions to the Escherichia coli proteins PhoA and LacZ of LysX2, we confirmed this unique membrane topology, as well as LysX and MprF as benchmarks. Expression of lysX2 in Mycobacterium smegmatis increased cell resistance to human ß-defensin 2 and sodium nitrite, enhanced cell viability and delayed biofilm formation in acidic pH environment. Remarkably, MtLysX2 significantly reduced the negative charge on the bacterial surface upon exposure to an acidic environment. Additionally, we found LysX2 orthologues in major human pathogens and in rapid-growing mycobacteria frequently associated with human infections, but not in environmental and non-pathogenic mycobacteria. CONCLUSIONS: Overall, our data suggest that LysX2 is a prototype of a new class within the MprF-like protein family that likely enhances survival of the pathogenic species through its catalytic domain which is exposed to the extracytoplasmic side of the cell membrane and is required to decrease the negative charge on the bacterial surface through a yet uncharacterized mechanism.

Influence of acidic pH on antimicrobial activity of different calcium silicate based-endodontic sealers.

OBJECTIVE: To investigate the antibacterial activity of calcium silicate-based sealers (CSBSs) against Enterococcus faecalis biofilm in a neutral or acidic condition. MATERIALS AND METHODS: Dentin cylinders (4 mm length) were prepared and infected with 3-week-old E. faecalis. The samples were filled with BioRoot RCS (BR), EndoSequence BC (ES), and NeoMTA Plus (NMTA) and incubated in either neutral or acidic conditions for 7 days (n=10/group). Sterile or infected samples alone were used as the positive and negative control. The root canal sealers were removed after 7 days, and the remaining bacteria on dentinal walls were determined by colony-forming units (CFUs/ml), and three samples from each group were visualized under a confocal laser scanning microscope (CLSM). The pH was also measured (n=3/group) after 4 h and 7 days of incubation at 37°C in both conditions. RESULTS: In the neutral condition, all sealers significantly decreased the log-CFU values (p<0.05), while in the acidic condition, the log-CFU reduction was less for ES and NMTA, but a higher reduction was observed in BR (p<0.05). The antibacterial activity of CSBSs was similar in neutral conditions (p>0.05), and BR showed a greater antibacterial effect than ES and NMTA in the acidic condition (p<0.05). The pH of BR, ES, and NMTA ranged from 8.2 to 8.8 in the neutral condition in the presence of dentin after 7 days. However, acidic conditions reduced the pH values to 7.8 for BR, 6.0 for ES, and 5.8 for NMTA. CONCLUSIONS: All CSBSs showed similar antibacterial activity in neutral conditions, while acidic pH had a reducing antibacterial effect on CSBSs. CLINICAL RELEVANCE: Inflammatory pH decreased the antibacterial properties of CSBSs depending on the sealer type.

Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla

The hydrangea (Hydrangea macrophylla (Thunb). Ser.), an ornamental plant, has good marketing potential and is known for its capacity to change the colour of its inflorescence depending on the pH of the cultivation media. The molecular mechanisms causing these changes are still uncertain. In the present study, transcriptome and targeted metabolic profiling were used to identify molecular changes in the RNAome of hydrangea plants cultured at two different pH levels. De novo assembly yielded 186,477 unigenes. Transcriptomic datasets provided a comprehensive and systemic overview of the dynamic networks of the gene expression underlying flower colour formation in hydrangeas. Weighted analyses of gene co-expression network identified candidate genes and hub genes from the modules linked closely to the hyper accumulation of Al3+ during different stages of flower development. F3'5'H, ANS, FLS, CHS, UA3GT, CHI, DFR, and F3H were enhanced significantly in the modules. In addition, MYB, bHLH, PAL6, PAL9, and WD40 were identified as hub genes. Thus, a hypothesis elucidating the colour change in the flowers of Al3+-treated plants was established. This study identified many potential key regulators of flower pigmentation, providing novel insights into the molecular networks in hydrangea flowers.

Structural Insights into the Ligand-Binding and -Releasing Mechanism of Helicoverpa armigera Pheromone-Binding Protein PBP1.

Cotton bollworm (Helicoverpa armigera) is a worldwide agricultural pest in which the transport of pheromones is indispensable and perceived by pheromone-binding proteins (PBPs). However, three-dimensional structure, pheromone binding, and releasing mechanisms of PBPs are not completely illustrated. Here, we solved three structures of the cotton bollworm HarmPBP1 at different pH values and its complex with ligand, Z-9-hexadecenal. Although apo-HarmPBP1 adopts a common PBP scaffold of six α-helices surrounding a predominantly hydrophobic central pocket, the conformation is greatly distinct from other apo-PBPs. The Z-9-hexadecenal is bound mainly by hydrophobic interaction. The pheromone can enter this cavity through an opening between the helices α5 and α6, as well as the loop between α3 and α4. Structural analysis suggests that ligand entry into the pocket is followed by a shift of Lys94 and Lys138, which may act as a lid at the opening of the pocket. Acidic pH will cause a subtle structural change of the lid, which in turn affects its ligand-binding ability, differently from other family proteins. Taken together, this study provides structural bases for the interactions between pheromones and PBPs, the pH-induced conformational switch, and the design of small inhibitors to control cotton bollworms by disrupting male-female chemosensory communication.

Design and Engineering of Hypoxia and Acidic pH Dual-Stimuli-Responsive Intelligent Fluorescent Nanoprobe for Precise Tumor Imaging.

Stimulus-responsive fluorescence imaging modality shows great promise for detection of tumor due to the advantages of high sensitivity, simplicity and noninvasiveness. However, some non-cancer regions including nodules and inflammation may also exhibit a stimulus-related characteristic, which cause the problem of nonspecific responsiveness and then cause "false positive" results for tumor recognition. Herein, hypoxia and acidic pH, two typical features strongly associated with tumor invasion, progression and metastasis in tumor microenvironment (TME), are chosen as dual stimuli to fabricate "dual lock-and-key" fluorescent nanoprobe for highly specific and precise imaging of tumor cells. Mesoporous silica coated gold nanorods (AuNR@mSiO2 ) are employed as nanocarrier and nanoquencher to load the pH-sensitive fluorescent reporter (Rho-TP). Azobenzene (azo) which can be reduced to amines by the highly expressed azoreductase under hypoxic conditions, is elected as the effective gatekeeper for AuNR@mSiO2 by forming complex with ß-cyclodextrin polymer via host-guest interaction (azo/ß-CDP). By elaborately combining the hypoxia-responsive gatekeeper and pH-responsive fluorescent signal reporter into one nanoprobe, sensitive and specific imaging of tumor cells can be realized. The fabricated dual lock-and-key fluorescent nanoprobe successfully further apply in tumor-bearing mice model, which indicate potential of early diagnosis and assessment of cancer treatment.

Acidic pH-Induced Conformational Changes in Chikungunya Virus Fusion Protein E1: a Spring-Twisted Region in the Domain I-III Linker Acts as a Hinge Point for Swiveling Motion of Domains.

Chikungunya virus (CHIKV), a mosquito-transmitted alphavirus, enters a cell through endocytosis, followed by viral and cell membrane fusion. The fusion protein, E1, undergoes an acid pH-induced pre- to postfusion conformation change during membrane fusion. As part of the conformation change, E1 dissociates from the receptor-binding protein, E2, and swivels its domains I and II over domain III to form an extended intermediate and then eventually to form a postfusion hairpin homotrimer. In this study, we tested if the domain I-III linker acts as a "hinge" for the swiveling motion of E1 domains. We found a conserved spring-twisted structure in the linker, stabilized by a salt bridge between a conserved arginine-aspartic acid pair, as a "hinge point" for domain swiveling. Molecular dynamics (MD) simulation of the CHIKV E1 or E2-E1 structure predicted that the spring-twisted region untwists at pH 5.5. Corroborating the prediction, introduction of a "cystine staple" at the hinge point, replacing the conserved arginine-aspartic acid pair with cysteine residues, resulted in loss of fusion activity of E1. MD simulation also predicted domain I-III swiveling at acidic pH. We tested if breaking the His 331-Lys 16 H bond between domains I and III, seen only in the prefusion conformation, is important for domain swiveling. When domains I and III are "stapled" by introducing a disulfide bond in between, E1 showed loss of fusion activity, implying that domain I and III dissociation is a critical acid pH-induced step in membrane fusion. However, replacement of His 331 with an acidic residue did not affect the pH threshold for fusion, suggesting His 331 is not an acid-sensing residue.IMPORTANCEAedes mosquito-transmitted viruses such as the Zika, dengue, and chikungunya viruses have spread globally. CHIKV, similar to many other enveloped viruses, enters cells in sequential steps: step 1 involves receptor binding followed by endocytosis, and step 2 involves viral-cell membrane fusion in the endocytic vesicle. The viral envelope surface protein, E1, performs membrane fusion. E1 is triggered to undergo conformational changes by acidic pH of the maturing endosome. Different domains of E1 rearrange during the pre- to postfusion conformation change. Using in silico analysis of the E1 structure and different biochemical experiments, we explained a structural mechanism of key conformational changes in E1 triggered by acidic pH. We noted two important structural changes in E1 at acidic pH. In the first, a spring-twisted region in a loop connecting two domains (I and III) untwists, bringing a swiveling motion of domains on each other. In the second, breaking of interactions between domains I and III and domain separation are required for membrane fusion. This knowledge will help devise new therapeutic strategies to block conformation changes in E1 and thus viral entry.

Xanthene-based Fluorescence Turn-on Probe for Highly Acidic pH Range in Aqueous Solution.

A xanthene-based probe, Xanth-NPr, is developed as a molecular system that exhibits sensitivity for the highly acidic environments with fluorescence turn-on behavior. Xanth-NPr is designed on the principle of photoinduced electron transfer (PET), which controls the fluorescence profile of the probe. The structure of Xanth-NPr contains the dipropylaniline group as a PET promoting unit. Xanth-NPr exhibited quenched fluorescence as long as it is present in neutral or moderately acidic conditions. However, in the highly acidic pH range, it displayed a strong red-colored fluorescence at 592 nm as the protonation of dipropylaniline moiety inhibits the PET process. A model probe Xanth-M without any PET promoting unit was also synthesized. The model probe along with theoretical calculations was employed to explain the role of the PET process in regulating the fluorescence behavior of Xanth-NPr. Xanth-NPr showed linear fluorescence response as a function of pH in the range of 1 to 4.1 with the pKa value of 2.72. Likewise, its fluorescence profile is not altered by the presence of biologically relevant cations.

Acetotrophic sulfate-reducing consortia develop active biofilms on zeolite and glass beads in batch cultures at initial pH 3.

Sulfate-reducing microbial communities remain a suitable option for the remediation of acid mine drainage using several types of carrier materials and appropriate reactor configurations. However, acetate prevails as a product derived from the incomplete oxidation of most organic substrates by sulfate reducers, limiting the efficiency of the whole process. An established sulfate-reducing consortium, able to degrade acetate at initial acidic pH (3.0), was used to develop biofilms over granular activated carbon (GAC), glass beads, and zeolite as carrier materials. In batch assays using glycerol, biofilms successfully formed on zeolite, glass beads, and GAC with sulfide production rates of 0.32, 0.26, and 0.14 mmol H2S/L·d, respectively, but only with glass beads and zeolite, acetate was degraded completely. The planktonic and biofilm communities were determined by the 16S rRNA gene analysis to evaluate the microbial selectivity of the carrier materials. In total, 46 OTUs (family level) composed the microbial communities. Ruminococcaceae and Clostridiaceae families were present in zeolite and glass beads, whereas Peptococcaceae was mostly enriched on zeolite and Desulfovibrionaceae on glass beads. The most abundant sulfate reducer in the biofilm of zeolite was Desulfotomaculum sp., while Desulfatirhabdium sp. abounded in the planktonic community. With glass beads, Desulfovibrio sp. dominated the biofilm and the planktonic communities. Our results indicate that both materials (glass beads and zeolite) selected different key sulfate-reducing microorganisms able to oxidize glycerol completely at initial acidic pH, which is relevant for a future application of the consortium in continuous bioreactors to treat acidic streams. KEY POINTS: • Complete consumption of glycerol and acetate at acidic pH by sulfate reduction. • Glass beads and zeolite are suitable materials to form sulfate-reducing biofilms. • Acetotrophic sulfate-reducing bacteria attached to zeolite preferably.