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Spermidine is an essential biomarker related to antiaging. Although the detection of spermidine levels is in high demand in life science fields, easy-to-use analytical tools without sample purification have not yet been fully established. Herein, we propose an organic field-effect transistor-based chemical sensor for quantifying the spermidine concentration in commercial cosmetics. An extended-gate structure was employed for organic field-effect transistor (OFET)-based chemical sensing in aqueous media. A coordination-bond-based sensing system was introduced into the OFET device to visualize the spermidine detection information through changes in the transistor characteristics. The extended-gate-type OFET has shown quantitative responses to spermidine, which indicates sufficient detectability (i. e., the limit of detection for spermidine: 2.3 μM) considering actual concentrations in cosmetics. The applicability of the OFET-based chemical sensor for cosmetic analysis was validated by instrumental analysis using high-performance liquid chromatography. The estimated recovery rates for spermidine in cosmetic ingredient products (108-111 %) suggest the feasibility of cosmetic analysis based on the OFET-based chemical sensor., (© 2024 The Authors. ChemistryOpen published by Wiley-VCH GmbH.)

In this paper the effects on the interaction of highly positively charged substitution-inert platinum polynuclear complexes (SI-PPCs) with negatively charged DNA and heparin are examined and compared by theoretical chemistry methods. Electrostatic and hydrogen bonding interactions contribute to the overall effects on the biomolecule. Root Mean Square (RMS) deviation, Solvent Accessible Surface, RMS fluctuation, and interaction analysis all confirm similar effects on both biomolecules, dictated predominantly by the total positive charge and total number of hydrogen bonds formed. Especially, changes in structural parameters suggesting condensation and reduction of available surface area will reduce or prevent normal protein recognition and may thus potentially inhibit biological mechanisms related to apoptosis (DNA) or reduced vascularization viability (HEP). Thermodynamic analyses supported these findings with favourable interaction energies. The comparison of DNA and heparin confirms the general intersectionality between the two biomolecules and confirms the intrinsic dual-nature function of this chemotype. The distinction between the two-limiting mode of actions (HS or DNA-centred) could reflect an intriguing balance between extracellular (GAG) and intracellular (DNA) binding and affinities. The results underline the need to fully understand GAG-small molecule interactions and their contribution to drug pharmacology and related therapeutic modalities. This report contributes to that understanding., Competing Interests: Declaration of competing interest The authors of the manuscript entitled “Spermine and Spermidine SI-PPCs: Molecular Dynamics Reveals Enhanced Biomolecular Interactions” have no conflict of interests related to this manuscript., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Polyamines, characterized by their polycationic nature, are ubiquitously present in all organisms and play numerous cellular functions. Among polyamines, spermidine stands out as the predominant type in both prokaryotic and eukaryotic cells. The PotD-PotABC protein complex in Escherichia coli , belonging to the adenosine triphosphate-binding cassette transporter family, is a spermidine-preferential uptake system. Here, we report structural details of the polyamine uptake system PotD-PotABC in various states. Our analyses reveal distinct "inward-facing" and "outward-facing" conformations of the PotD-PotABC transporter, as well as conformational changes in the "gating" residues (F222, Y223, D226, and K241 in PotB; Y219 and K223 in PotC) controlling spermidine uptake. Therefore, our structural analysis provides insights into how the PotD-PotABC importer recognizes the substrate-binding protein PotD and elucidates molecular insights into the spermidine uptake mechanism of bacteria.

Over the years, osteosarcoma therapy has had a significative improvement with the use of a multidrug regime strategy, increasing the survival rates from less than 20 % to circa 70 %. Different types of development of new antineoplastic agents are critical to achieve irreversible damage to cancer cells, while preserving the integrity of their healthy counterparts. In the present study, complexes with two and three Pd(II) centres linked by the biogenic polyamines: spermine (Pd 2 SpmCl 4 ) and spermidine (Pd 3 Spd 2 Cl 6 ) were tested against non-malignant (osteoblasts, HOb) and cancer (osteosarcoma, MG-63) human cell lines. Either alone or in combination according to the EURAMOS-1 protocol, they were used versus cisplatin as a drug reference. By evaluating the cytotoxic effects of both therapeutic approaches (single and drug combination) in HOb and MG-63 cell lines, the selective anti-tumoral potential is assessed. To understand the different treatments at a molecular level, Synchrotron Radiation Fourier Transform Infrared and Raman microspectroscopies were applied. Principal component analysis and hierarchical cluster analysis are applied to the vibrational data, revealing the major metabolic changes caused by each drug, which were found to rely on DNA, lipids, and proteins, acting as biomarkers of drug-to-cell impact. The main changes were observed for the B-DNA native conformation to either Z-DNA (higher in the presence of polynuclear complexes) or A-DNA (preferably after cisplatin exposure). Additionally, a higher effect upon variation in proteins content was detected in drug combination when compared to single drug administration proving the efficacy of the EURAMOS-1 protocol with the new drugs tested., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)

Polyamines are essential analytes due to their critical role in various biological processes and human health in general. Due to their role as regulators for cell growth and proliferation (putrescine and spermine), as neuroprotectors, gero-, and cardiovascular protectors (spermidine), and as bacterial growth indicators (cadaverine), rapid, simple, and cost-effective methods for polyamine detection in biofluids are in demand. The present study focuses on the development and investigation of self-assembled and fluorescent host⋅dye chemo-sensors based on sulfonated pillar[5]arene for the specific detection of polyamines. Binding studies, as well as stability and functionality assessments of the turn-on chemosensors for selective polyamine detection in saline and biologically relevant media, are shown. Furthermore, the practical applicability of the developed chemo-sensors is demonstrated in biofluids such as human urine and saliva., (© 2024 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Acute pancreatitis (AP) is an acute inflammatory gastrointestinal disease, the mortality and morbility of which has been on the increase in the past years. Spermidine, a natural polyamine, has a wide range of pharmacological effects including anti-inflammation, antioxidation, anti-aging, and anti-tumorigenic. This study aimed to investigate the reliable targets and molecular mechanisms of spermidine in treating AP. By employing computational biology methods including network pharmacology, molecular docking, and molecular dynamics (MD) simulations, we explored the potential targets of spermidine in improving AP with dietary supplementation. The computational biology results revealed that spermidine had high degrees (degree: 18, betweenness: 38.91; degree: 18, betweenness: 206.41) and stable binding free energy (ΔG bind : - 12.81 ± 0.55 kcal/mol, - 15.00 ± 1.00 kcal/mol) with acetylcholinesterase (AchE) and serotonin transporter (5-HTT). Experimental validation demonstrates that spermidine treatment could reduce the necrosis and AchE activity in pancreatic acinar cells. Cellular thermal shift assay (CETSA) results revealed that spermidine could bind to and stabilize the 5-HTT protein in acinar cells. Moreover, spermidine treatment impeded the rise of the expression of 5-HTT in pancreatic tissues of caerulein induced acute pancreatitis mice. In conclusion, serotonin transporter might be a reliable target of spermidine in treating AP. This study provides new idea for the exploration of potential targets of natural compounds., (© 2023. The Author(s), under exclusive licence to Springer Nature Switzerland AG.)

As one of the most widespread musculoskeletal diseases worldwide, intervertebral disc degeneration (IVDD) remains an intractable clinical problem. Currently, oxidative stress has been widely considered as a significant risk factor in the IVDD pathological changes, and targeting oxidative stress injury to improve the harsh microenvironment may provide a novel and promising strategy for disc repair. It is evident that spermidine (SPD) has the ability to attenuate oxidative stress across several disease models. However, limited research exists regarding its impact on oxidative stress within the intervertebral disc. Moreover, enhancing the local utilization rate of SPD holds great significance in IVDD management. This study aimed to develop an intelligent biodegradable mesoporous polydopamine (PDA) nanoplatform for sustained release of SPD. The obtained PDA nanoparticles with spherical morphology and mesoporous structure released loaded-therapeutic molecules under low pH and H 2 O 2 . Combined treatment with SPD loaded into PDA nanoparticles (SPD/PDA) resulted in better therapeutic potential than those with SPD alone on oxidative stress injury. Furthermore, both SPD and SPD/PDA could induce anti-inflammatory M2 macrophage polarization. Upon injection into degenerative IVDs, the SPD/PDA group achieved a good repair efficacy with a long-term therapeutic effect. These findings indicated that the synergized use of SPD with responsive drug delivery nanocarriers may steadily scavenge reactive oxygen species and provide an effective approach toward the treatment of IVDD., Competing Interests: Declaration of competing interest The authors declare that they have no competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Polyamines (PAs) including putrescine (PUT), spermidine (SPD) and spermine (SPM) are small, versatile molecules with two or more positively charged amino groups. Despite their importance for almost all forms of life, their specific roles in molecular and cellular biology remain partly unknown. The molecular structures of PAs suggest two presumable biological functions: (i) as potential buffer systems and (ii) as interactants with poly-negatively charged molecules like nucleic acids. The present report focuses on the question, whether the molecular structures of PAs are essential for such functions, or whether other simple molecules like small peptides with closely spaced positively charged side chains might be suitable as well. Consequently, we created titration curves for PUT, SPD, and SPM, as well as for oligolysines like tri-, tetra-, and penta-lysine. None of the molecules provided substantial buffering capacity at physiological intracellular pH values. Apparently, the most important mechanism for intracellular pH homeostasis in neurons is not a buffer system but is provided by the actions of the sodium-hydrogen and the bicarbonate-chloride antiporters. In a similar approach we investigated the interaction with DNA by following the extinction at 260 nm when titrating DNA with the above molecules. Again, PUT and tri-lysine were not able to interact with herring sperm DNA, while SPD and SPM were. Obviously, the presence of several positively charged groups on its own is not sufficient for the interaction with nucleic acids. Instead, the precise spacing of these groups is necessary for biological activity., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Rieck et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Oral cancer accounts for 50%-70% of all cancer-related deaths in India and ranks sixth among the most frequent cancers globally. Roughly 90% of oral malignancies are histologically arise from squamous cells and are therefore called oral squamous cell carcinoma. Organic polycations known as biogenic polyamines, for example, putrescine (Put), spermidine (Spd), and spermine (Spm), are vital for cell proliferation, including gene expression control, regulation of endonuclease-mediated fragmentation of DNA, and DNA damage inhibition. Higher Spm and Spd levels have been identified as cancer biomarkers for detecting tumour development in various cancers. The current study utilises tannic acid, a polyphenolic compound, as a reducing and capping agent to fabricate AuNPs via a one-step microwave-assisted synthesis. The fabricated TA@AuNPs were utilised as a nanoprobe for colourimetric sensing of polyamines in PBS. When TA@AuNPs are added to the polyamine, the amine groups in polyamines interact with the phenolic groups of TA@AuNPs via hydrogen bonding or electrostatic interactions. These interactions cause the aggregation of TA@AuNPs, resulting in a red shift of the Surface Plasmon Resonance band of TA@AuNPs from 530 nm to 560 nm. The nanoprobe was found to be highly specific for Spm at low concentrations. TA@AuNPs were able to detect Spm successfully in artificial saliva samples. On recording the RGB values of the sensing process using a smartphone app, it was found that as the nanoparticles aggregated due to the presence of Spm, the intensity of the R -value decreased, indicating the aggregation of TA@AuNPs due to interaction with the polyamine., (© 2024 IOP Publishing Ltd.)

Titanium (Ti) and its alloys have been widely employed in the treatment of orthopedics and other hard tissue diseases. However, Ti-based implants are bioinert and suffer from bacterial infections and poor osseointegration in clinical applications. Herein, we successfully modified Ti with a porous N -halaminated spermidine-containing polymeric coating (Ti-SPD-Cl) through alkali-heat treatment, surface grafting and chlorination, and it has both excellent antibacterial and osteogenic abilities to significantly enhance osseointegration. The as-obtained Ti-SPD-Cl contains abundant N-Cl groups and demonstrates effective antibacterial ability against S. aureus and E. coli . Meanwhile, due to the presence of the spermidine component and construction of a porous hydrophilic surface, Ti-SPD-Cl is also beneficial for maintaining cell membrane homeostasis and promoting cell adhesion, exhibiting good biocompatibility and osteogenic ability. The rat osteomyelitis model demonstrates that Ti-SPD-Cl can effectively suppress bacterial infection and enhance bone-implant integration. Thus, Ti-SPD-Cl shows promising clinical applicability in the prevention of orthopedic implant infections and poor osseointegration.

Exploring biopolymer-based antibacterial packaging materials is promising to tackle the issues caused by petroleum plastic pollution and microbial contamination. Herein, a novel packaging material with two antibacterial modes, continuous and efficient, is constructed by dispersing positively charged spermidine carbon dots (Spd-CDs) in a carrageenan/polyvinyl alcohol (CP) composite biopolymer. The obtained nanocomposite film (CP/CDs film) not only gradually releases the ultra-small Spd-CDs but also rapidly generates reactive oxygen species to inhibit the reproduction of E. coli and S. aureus. Benefiting from the complementary advantages of carrageenan and polyvinyl alcohol, as well as the addition of Spd-CDs, the CP/CDs films exhibit high transparency, good mechanical performance, water vapor barrier ability, low migration, etc. The CP/CDs film as a packaging material is validated to be effective in preventing microbial contamination of pork samples. Our prepared nanocomposite film with sustainability and efficient antibacterial properties is expected as food active packaging., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

An ideal hydrogel for stem cell therapy would be injectable and efficiently promote stem cell proliferation and differentiation in body. Herein, an injectable, single-component hydrogel with hyaluronic acid (HA) modified with phenylboronic acid (PBA) and spermidine (SM) is introduced. The resulting HAps (HA-PBA-SM) hydrogel is based on the reversible crosslinking between the diol and the ionized PBA, which is stabilized by the SM. It has a shear-thinning property, enabling its injection through a syringe to form a stable hydrogel inside the body. In addition, HAps hydrogel undergoes a post-injection "self-curing," which stiffens the hydrogel over time. This property allows the HAps hydrogel to meet the physical requirements for stem cell therapy in rigid tissues, such as bone, while maintaining injectability. The hydrogel enabled favorable proliferation of human mesenchymal stem cells (hMSCs) and promoted their differentiation and mineralization. After the injection of hMSCs-containing HAps into a rat femoral defect model, efficient osteogenic differentiation of hMSCs and bone regeneration is observed. The study demonstrates that simple cationic modification of PBA-based hydrogel enabled efficient gelation with shear-thinning and self-curing properties, and it would be highly useful for stem cell therapy and in vivo bone regeneration., (© 2024 The Authors. Advanced Science published by Wiley‐VCH GmbH.)

Large DNA molecules (>20 kb) are difficult analytes prone to breakage during serial manipulations and cannot be 'rescued' as full-length amplicons. Accordingly, to present, modify and analyze arrays of large, single DNA molecules, we created an easily realizable approach offering gentle confinement conditions or immobilization via spermidine condensation for controlled delivery of reagents that support live imaging by epifluorescence microscopy termed 'Gel-Stacks.' Molecules are locally confined between two hydrogel surfaces without covalent tethering to support time-lapse imaging and multistep workflows that accommodate large DNA molecules. With a thin polyacrylamide gel layer covalently bound to a glass surface as the base and swappable, reagent-infused, agarose slabs on top, DNA molecules are stably presented for imaging during reagent delivery by passive diffusion.

Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families, the odorant receptors and the trace amine-associated receptors 1,2 (TAARs). TAARs emerged following the divergence of jawed and jawless fish, and comprise a large monophyletic family of receptors that recognize volatile amine odorants to elicit both intraspecific and interspecific innate behaviours such as attraction and aversion 3-5 . Here we report cryo-electron microscopy structures of mouse TAAR9 (mTAAR9) and mTAAR9-G s or mTAAR9-G olf trimers in complex with β-phenylethylamine, N,N-dimethylcyclohexylamine or spermidine. The mTAAR9 structures contain a deep and tight ligand-binding pocket decorated with a conserved D 3.32 W 6.48 Y 7.43 motif, which is essential for amine odorant recognition. In the mTAAR9 structure, a unique disulfide bond connecting the N terminus to ECL2 is required for agonist-induced receptor activation. We identify key structural motifs of TAAR family members for detecting monoamines and polyamines and the shared sequence of different TAAR members that are responsible for recognition of the same odour chemical. We elucidate the molecular basis of mTAAR9 coupling to G s and G olf by structural characterization and mutational analysis. Collectively, our results provide a structural basis for odorant detection, receptor activation and G olf coupling of an amine olfactory receptor., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Four novel bacterial strains, designated as RG327 T , SE158 T , RB56-2 T and SE220 T , were isolated from wet soil in the Republic of Korea. To determine their taxonomic positions, the strains were fully characterized. On the basis of genomic information (16S rRNA gene and draft genome sequences), all four isolates represent members of the genus Sphingomonas . The draft genomes of RG327 T , SE158 T , RB56-2 T and SE220 T consisted of circular chromosomes of 2 226 119, 2 507 338, 2 593 639 and 2 548 888 base pairs with DNA G+C contents of 64.6, 63.6, 63.0 and 63.1 %, respectively. All the isolates contained ubiquinone Q-10 as the predominant quinone compound and a fatty acid profile with C 16 : 0 , C 17 : 1 ω6 c , C 18 : 1 2-OH , summed feature 3 (C 16 : 1 ω7 c /C 16 : 1 ω6c) and summed feature 8 (C 18 : 1 ω 7c /C 18 : 1 ω6 c ) as the major fatty acids, supporting the affiliation of strains RG327 T , SE158 T , RB56-2 T and SE220 T to the genus Sphingomonas . The major identified polar lipids in all four novel isolates were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid and phosphatidylcholine. Moreover, the physiological, biochemical results and low level of DNA-DNA relatedness and average nucleotide identity values allowed the phenotypic and genotypic differentiation of RG327 T , SE158 T , RB56-2 T and SE220 T from other species of the genus Sphingomonas with validly published names and indicated that they represented novel species of the genus Sphingomonas , for which the names Sphingomonas anseongensis sp. nov. (RG327 T = KACC 22409 T = LMG 32497 T ), Sphingomonas alba sp. nov. (SE158 T = KACC 224408 T = LMG 324498 T ), Sphingomonas brevis (RB56-2 T = KACC 22410 T = LMG 32496 T ) and Sphingomonas hankyongi sp. nov., (SE220 T = KACC 22406 T = LMG 32499 T ) are proposed.

Spermidine is an aliphatic polyamine that directs a set of biological processes. This work aimed to use UV-Vis spectroscopy, fluorescence spectroscopy, thermal stability, kinetic methods, docking, and molecular dynamic simulations to examine the influence of spermidine trihydrochloride (SP) on the structure and function of pepsin. The results of the fluorescence emission spectra indicated that spermidine could quench pepsin's intrinsic emission in a static quenching process, resulting in the formation of the pepsin-spermidine complex. The results discovered that spermidine had a strong affinity to the pepsin structure because of its high binding constant. The obtained results from spectroscopy and molecular dynamic approaches showed the binding interaction between spermidine and pepsin, induced micro-environmental modifications around tryptophan residues that caused a change in the tertiary and secondary structure of the enzyme. FTIR analysis showed hypochromic effects in the spectra of amide I and II and redistribution of the helical structure. Moreover, the molecular dynamic (MD) and docking studies confirmed the experimental data. Both experimental and molecular dynamics simulation results clarified that electrostatic bond interactions were dominant forces., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Spermidine is a polyamine molecule that performs various cellular functions, such as DNA and RNA stabilization, autophagy modulation, and eIF5A formation, and is generated from putrescine by aminopropyltransferase spermidine synthase (SpdS). During synthesis, the aminopropyl moiety is donated from decarboxylated S-adenosylmethionine to form putrescine, with 5'-deoxy-5'-methylthioadenosine being produced as a byproduct. Although the molecular mechanism of SpdS function has been well-established, its structure-based evolutionary relationships remain to be fully understood. Moreover, only a few structural studies have been conducted on SpdS from fungal species. Here, we determined the crystal structure of an apo-form of SpdS from Kluyveromyces lactis ( Kl SpdS) at 1.9 Å resolution. Structural comparison with its homologs revealed a conformational change in the α6 helix linked to the gate-keeping loop, with approximately 40° outward rotation. This change caused the catalytic residue Asp170 to move outward, possibly due to the absence of a ligand in the active site. These findings improve our understanding of the structural diversity of SpdS and provide a missing link that expands our knowledge of the structural features of SpdS in fungal species.

A novel Gram-stain-negative, aerobic, rod-shaped, non-motile, cream-coloured strain (G124 T ) was isolated from ginseng soil collected in Yeongju, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain G124 T belongs to a distinct lineage within the genus Sphingomonas (family Sphingomonadaceae , order Sphingomonadales and class Alphaproteobacteria ). Strain G124 T was closely related to Sphingomonas rhizophila THG-T61 T (98.5 % 16S rRNA gene sequence similarity), Sphingomonas mesophila SYSUP0001 T (98.3 %), Sphingomonas edaphi DAC4 T (97.6 %) and Sphingomonas jaspsi TDMA-16 T (97.6 %). The strain contained ubiquinone 10 as the major respiratory quinone. The major polar lipid profile of strain G124 T comprised phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipids. The predominant cellular fatty acids of strain G124 T were summed feature 8 (C 18 : 1  ω 7 c /C 18 : 1  ω 6 c ; 33.4 %), summed feature 3 (C 16 : 1  ω 6 c /C 16 : 1  ω 7 c ; 27.2 %) and C 16 : 0 (18.3 %). The genome size of strain G124 T was 2 549 305 bp. The genomic DNA G+C content is 62.0 mol%. The average nucleotide identity and digital DNA-DNA hybridization values between strain G124 T and other Sphingomonas species were in the range of 71.2-75.9 % and 18.7-19.9 %, respectively. Based on the polyphasic analysis such as biochemical, phylogenetic and chemotaxonomic characteristics, strain G124 T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas cremea sp. nov. is proposed. The type strain is G124 T (=KACC 21691 T =LMG 31729 T ).

Caffeic acid (CA) is a naturally occurring plant-derived polyphenol possessing diverse biological properties. However, the poor water-solubility of CA restricts its widespread applications. On the other hand, biogenic amines such as spermine and spermidine are natural constituents in eukaryotes. In this work, we present water-soluble complexes of CA with spermine and spermidine by exploiting the acid-base interaction. Four different compositions have been prepared by varying the CA to amine ratios, whose chemical structures have been probed in detail using Fourier-transform infrared spectroscopy (FT-IR) and nuclear magnetic resonance (NMR) studies that have revealed the acid-base interaction between the constituent precursors. The obtained acid-base complexes at their native pH values have shown enhanced antibacterial and antioxidant activities than pristine CA. Further, the CA-polyamine complexes have shown high anticancer performances in the concentration range that is compatible with the normal cell lines.

Self-assembled DNA nanostructures hold great potentials in biomedical applications. Nevertheless, the negatively charged DNA backbone and susceptivity to enzyme degradation pose challenges to this regard. Engineering the surface properties of DNA nanostructures by assembling DNA with guest molecules in magnesium-free system is promising to solve these issues. In this study, the polyamines-mediated DNA self-assembly with an emphasis on the valency of polyamines is investigated. Both spermine, spermidine, and putrescine can assemble DNA tetrahedron under appropriate concentrations. The cytotoxicity and cellular uptake efficiencies vary with the polyamine valency. Compared with magnesium-assembled DNA tetrahedron, polyamine-assembled DNA tetrahedron exhibits higher cellular uptake efficiency and serum stability. Circular dichroism spectrum results indicate that polyamines induce DNA conformation slightly shifting from B form to A form. The improved performances of polyamine-assembled DNA tetrahedrons under physiological settings are attributed to the surface properties that altered by guest molecules polyamine. The current study suggests that engineering the surface properties of DNA nanostructures by assembling them with guest cationic species is promising to further their biomedical applications., (© 2022 Wiley-VCH GmbH.)

Spermidine alkaloids are a kind of natural products possessing an aliphatic triamine structure with three or four methylene groups between two N-atoms. Spermidine alkaloids exist in plants, microorganisms, and marine organisms, which usually form amide structures with cinnamic acid or fatty acid derivatives. Their unique structures showed a wide range of biological activities such as neuroprotective, anti-aging, anti-cancer, antioxidant, anti-inflammatory, and antimicrobial. In order to better understand the research status of spermidine alkaloids and promote their applications in human health, this paper systematically reviewed the biological sources, structures, pharmacological actions, and synthetic processes of spermidine alkaloids over the past two decades. This will help to open up new pharmacological investigation fields and better drug design based on these spermidine alkaloids., (Copyright © 2022 Elsevier Masson SAS. All rights reserved.)

A Gram-negative, aerobic, rod-shaped bacterium, designated DM2-R-LB4 T was isolated from Cannabis sativa L. 'Cheungsam' in Andong, Republic of Korea. The strain DM2-R-LB4 T grew at temperatures of 15-45 °C (optimum, 30-37 °C), pH of 5.5-9 (optimum, 8.0), and 0-2 % (w/v) NaCl concentration (optimum, 0%). Phylogenetic analyses based on the 16S rRNA gene sequences revealed that strain DM2-R-LB4 T is related to species of the genus Sphingomonas , and shared 97.8 and 97.5% similarity to Sphingomonas kyenggiensis KCTC 42244 T and Sphingomonas leidyi DSM 4733 T , respectively. The DNA G+C content was 67.9 mol% and genome analysis of the strain DM2-R-LB4 T revealed that the genome size was 4 386 171 bp and contained 4 009 predicted protein-coding genes. The average nucleotide identity (ANI) values between strain DM2-R-LB4 T and S. kyenggiensis KCTC 42244 T , and S. leidyi DSM 4733 T was 76.8 and 76.7 %, respectively, while the values of digital DNA-DNA hybridization (dDDH) were 20.7 and 20.6 %, respectively. C 14 : 0 2-OH, C 16 : 0 , and summed feature 8 (C 18 : 1  ω6c and/or C 18 : 1  ω7c) were the major fatty acids (>10 %) in the strain DM2-R-LB4 T . The polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), sphingoglycolipid (SGL), glycolipid (GL), phospholipid (PL), and two unidentified polar lipids (L1 and L2). Ubiquinone-10 (Q-10) was the only respiratory quinone. The polyamine pattern was found to contain homospermidine, putrescine, and spermidine. The results of phylogenetic anlayses, polyphasic studies, revealed that strain DM2-R-LB4 T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas cannabina sp. nov., is proposed. The type strain is DM2-R-LB4 T (=KCTC 92075 T = GDMCC 1.3018 T ).

Histone deacetylases (HDACs) are important epigenetic regulators involved in many diseases, especially cancer. Five HDAC inhibitors have been approved for anticancer therapy and many are in clinical trials. Among the 11 zinc-dependent HDACs, HDAC10 has received relatively little attention by drug discovery campaigns, despite its involvement, e. g., in the pathogenesis of neuroblastoma. This is due in part to a lack of robust enzymatic conversion assays. In contrast to the protein lysine deacetylase and deacylase activity of most other HDAC subtypes, it has recently been shown that HDAC10 has strong preferences for deacetylation of oligoamine substrates like acetyl-putrescine or -spermidine. Hence, it is also termed a polyamine deacetylase (PDAC). Here, we present the first fluorescent enzymatic conversion assay for HDAC10 using an aminocoumarin-labelled acetyl-spermidine derivative to measure its PDAC activity, which is suitable for high-throughput screening. Using this assay, we identified potent inhibitors of HDAC10-mediated spermidine deacetylation in vitro. Based on the oligoamine preference of HDAC10, we also designed inhibitors with a basic moiety in appropriate distance to the zinc binding hydroxamate that showed potent inhibition of HDAC10 with high selectivity, and we solved a HDAC10-inhibitor structure using X-ray crystallography. We could demonstrate selective cellular target engagement for HDAC10 but a lysosomal phenotype in neuroblastoma cells that was previously associated with HDAC10 inhibition was not observed. Thus, we have developed new chemical probes for HDAC10 that allow further clarification of the biological role of this enzyme., (© 2022 The Authors. ChemBioChem published by Wiley-VCH GmbH.)

The roles and molecular interactions of polyamines (PAs) in the nucleus are not fully understood. Here their effect on nucleosome stability, a key regulatory factor in eukaryotic gene control, is reported, as measured in agarose embedded nuclei of H2B-GFP expressor HeLa cells. Nucleosome stability was assessed by quantitative microscopy [1,2] in situ, in close to native state of chromatin, preserving the nucleosome constrained topology of the genomic DNA. A robust destabilizing effect was observed in the millimolar concentration range in the case of spermine, spermidine as well as putrescine, which was strongly pH and salt concentration-dependent, and remained significant also at neutral pH. The integrity of genomic DNA was not affected by PA treatment, excluding DNA break-elicited topological relaxation as a factor in destabilization. The binding of PAs to DNA was demonstrated by the displacement of ethidium bromide, both from deproteinized nuclear halos and from plasmid DNA. The possibility that DNA methylation patterns may be influenced by PA levels is contemplated in the context of gene expression and DNA methylation correlations identified in the NCI-60 panel-based CellMiner database: methylated loci in subsets of high-ODC1 cell lines and the dependence of PER3 DNA methylation on PA metabolism., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

A novel rod-shaped, Gram-stain-negative, aerobic bacterial strain, designated Cra20 T , was isolated from the root surface of Leontopodium leontopodioides collected in the Tianshan Mountains, Xinjiang, PR China. Phylogenetic analysis based on 16S rRNA gene sequences, indicated that strain Cra20 T was affiliated with the genus Sphingomonas , and was most closely related to Sphingomonas gei ZFGT-11 T (99.0 %), Sphingomonas naasensis KIS18-15 T (97.8%) and Sphingomonas kyeonggiensis THG-DT81 T (97.2 %). The average nucleotide identity values between strain Cra20 T , S. gei ZFGT-11 T , S. naasensis KIS18-15 T and S. kyeonggiensis THG-DT81 T were 86.2, 84.2 and 78.2 %, respectively. The genomic DNA G+C content of strain Cra20 T was 65.6 mol% (whole genome sequence), and Q-10 was the predominant ubiquinone. The major cellular fatty acids of strain Cra20 T were summed feature 8 (comprising C 18 : 1  ω 6 c and/or C 18 : 1  ω 7 c , 67.3 %) and C 14 : 0 2-OH (6.4 %). On the basis of genotypic, phenotypic and biochemical data, strain Cra20 T is considered to represent a novel species of the genus Sphingomonas , for which the name Sphingomonas psychrotolerans sp. nov. is proposed. The type strain is Cra20 T (=CGMCC 1.15510 T =NBRC 112697 T ).

The polyamines, spermine (Spm) and spermidine (Spd), are important for cell growth and function. Their homeostasis is strictly controlled, and a key downregulator of the polyamine pool is the polyamine-inducible protein, antizyme 1 (OAZ1). OAZ1 inhibits polyamine uptake and targets ornithine decarboxylase (ODC), the rate-limiting enzyme of polyamine biosynthesis, for proteasomal degradation. Here we report, for the first time, that polyamines induce dimerization of mouse recombinant full-length OAZ1, forming an (OAZ1) 2 -Polyamine complex. Dimerization could be modulated by functionally active C -methylated spermidine mimetics (MeSpds) by changing the position of the methyl group along the Spd backbone-2-MeSpd was a poor inducer as opposed to 1-MeSpd, 3-MeSpd, and Spd, which were good inducers. Importantly, the ability of compounds to inhibit polyamine uptake correlated with the efficiency of the (OAZ1) 2 -Polyamine complex formation. Thus, the (OAZ1) 2 -Polyamine complex may be needed to inhibit polyamine uptake. The efficiency of polyamine-induced ribosomal +1 frameshifting of OAZ1 mRNA could also be differentially modulated by MeSpds-2-MeSpd was a poor inducer of OAZ1 biosynthesis and hence a poor downregulator of ODC activity unlike the other MeSpds. These findings offer new insight into the OAZ1-mediated regulation of polyamine homeostasis and provide the chemical tools to study it.

Despite the fact that a range of vaccines against COVID-19 have already been created and are used for mass vaccination, the development of effective, safe, technological, and affordable vaccines continues. We have designed a vaccine that combines the recombinant protein and DNA vaccine approaches in a self-assembled particle. The receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 was conjugated to polyglucin:spermidine and mixed with DNA vaccine (pVAXrbd), which led to the formation of particles of combined coronavirus vaccine (CCV-RBD) that contain the DNA vaccine inside and RBD protein on the surface. CCV-RBD particles were characterized with gel filtration, electron microscopy, and biolayer interferometry. To investigate the immunogenicity of the combined vaccine and its components, mice were immunized with the DNA vaccine pVAXrbd or RBD protein as well as CCV-RBD particles. The highest antigen-specific IgG and neutralizing activity were induced by CCV-RBD, and the level of antibodies induced by DNA or RBD alone was significantly lower. The cellular immune response was detected only in the case of DNA or CCV-RBD vaccination. These results demonstrate that a combination of DNA vaccine and RBD protein in one construct synergistically increases the humoral response to RBD protein in mice.

Tetragonisca angustula honey was fractioned in a SiO 2 column to furnish three fractions (A-C) in which four hydroxycinnamic acid-Spermidine amides (HCAAs), known as N', N″, N‴-tris-p-coumaroyl spermidine, N', N″-dicaffeoyl, N‴-coumaroyl spermidine, N', N″, N‴-tris-caffeoyl spermidine and N', N″-dicaffeoyl and N‴-feruloyl spermidine were identified in the fractions B and C by electrospray ionization tandem mass spectrometry. A primary culture model previously infected with Neospora caninum (72 h) was used to evaluate the honey fractions (A-C) for two-time intervals: 24 and 72 h. Parasitic reduction ranged from 38% on fraction C (12.5 µg/ml), after 24 h, to 54% and 41% with fractions B and C (25 µg/ml) after 72 h of treatment, respectively. Additionally, HCAAs did not show any cell toxicity for 24 and 72 h. For infected cultures (72 h), the active fractions B (12.5 µg/ml) and C (25 µg/ml) decreased their NO content. In silico studies suggest that HCAAs may affect the parasite's redox pathway and improve the oxidative effect of NO released from infected cells. Here, we presented for the first time, that HCAAs from T. angustula honey have the potential to inhibit the growth of N. caninum protozoa., (© 2021 John Wiley & Sons Ltd.)

A profound understanding of the molecular interactions between receptors and ligands is important throughout diverse research, such as protein design, drug discovery, or neuroscience. What determines specificity and how do proteins discriminate against similar ligands? In this study, we analyzed factors that determine binding in two homologs belonging to the well-known superfamily of periplasmic binding proteins, PotF and PotD. Building on a previously designed construct, modes of polyamine binding were swapped. This change of specificity was approached by analyzing local differences in the binding pocket as well as overall conformational changes in the protein. Throughout the study, protein variants were generated and characterized structurally and thermodynamically, leading to a specificity swap and improvement in affinity. This dataset not only enriches our knowledge applicable to rational protein design but also our results can further lay groundwork for engineering of specific biosensors as well as help to explain the adaptability of pathogenic bacteria., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-CFT640 T , isolated from vineyard soil sampled in Taiwan. Cells of strain CC-CFT640 T were aerobic, non-motile, nitrate-reducing rods. Test results were positive for catalase, oxidase and proteinase activities. Optimal growth occurred at 30 °С and pH 7. Strain CC-CFT640 T showed highest 16S rRNA gene sequence similarity to members of the genus Enhydrobacter (90.0 %, n =1) followed by Hypericibacter (89.4-90.0 %, n =2), Reyranella (88.8-89.8 %, n =5) and Nitrospirillum (89.2-89.4 %, n =2), and formed a distinct phyletic lineage distantly associated with the clade that predominately accommodated Reynerella species. The DNA G+C composition of the genome (2.1 Mb) was 67.9 mol%. Genes involved in the reduction of nitrate to nitrite, nitric oxide and nitrous oxide were found. In addition, genes encoding dissimilatory nitrate reduction to ammonia, ammonium transport and ammonium assimilation were also detected. Average nucleotide identity values were 73.3 % ( n =1), 74.0-74.6 % ( n =2), 67.5-68.3 % ( n =2) when compared within the type strains of the genera Enhydrobacter , Reyranella and Niveispirillum , respectively. The dominant cellular fatty acids (>5 %) included C 16 : 0 , iso-C 17 : 1  ω 10 c , C 19 : 0 cyclo ω 8 c , C 18 : 1 2-OH and C 18 : 1  ω 7 c /C 18 : 1  ω 6 c . The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids, three unidentified phospholipids and an unidentified aminophospholipid. The major respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequencing, digital DNA-DNA hybridization, average nucleotide identity and phylogenomic placement, strain CC-CFT640 T is considered to represent a novel genus and species of the family Rhodospirillaceae , for which the name Vineibacter terrae gen. nov., sp. nov. is proposed. The type strain is CC-CFT640 T (=BCRC 81219 T =JCM 33507 T ).

Two pairs of novel pentacyclic spermidine alkaloid enantiomers, (±)-orychoviolines A and B ((±)-1 and (±)-2), were isolated from the seeds of Orychophragmus violaceus and represented the first example of a 2-piperidinone-fused hydrodibenzofuran skeleton, constructed from a 6/5/6/6 tetracyclic system and an 18 atomic ring. The most unexpected novelty was the formation of one more piperidinone ring by a connection between C-6 and N-7. Their structures and absolute configurations were determined by spectroscopic analyses, X-ray crystallography, and ECD analysis. Compared to Ex-RAD (sodium salt of 4-carboxystyryl-4-chlorobenzylsulfone), (-)-1 exhibited a significant radioprotective effect on cell survival and DNA damage. (-)-1 also exhibited remarkable anti-inflammatory activity by inhibiting the production of NO in RAW 264.7 cells activated by lipopolysaccharide with an IC 50 value of 20.3 ± 1.58 μM, which was equivalent to that of dexamethasone.

Chromatin fibers must fold or coil in the process of chromosome condensation. Patterns of coiling have been demonstrated for reconstituted chromatin, but the actual trajectories of fibers in condensed states of chromosomes could not be visualized because of the high density of the material. We have exploited partial decondensation of mitotic chromosomes to reveal their internal structure at sub-nucleosomal resolution by cryo-electron tomography, without the use of stains, fixatives, milling, or sectioning. DNA gyres around nucleosomes were visible, allowing the nucleosomes to be identified and their orientations to be determined. Linker DNA regions were traced, revealing the trajectories of the chromatin fibers. The trajectories were irregular, with almost no evidence of coiling and no short- or long-range order of the chromosomal material. The 146-bp core particle, long known as a product of nuclease digestion, is identified as the native state of the nucleosome, with no regular spacing along the chromatin fibers., Competing Interests: Declaration of interests The authors declare no competing financial interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Recently, the hydrogel-forming polysaccharide gellan gum (GG) has gained popularity as a versatile biomaterial for tissue engineering purposes. Here, we examine the modification strategies suitable for GG to overcome processing-related limitations. We emphasize the thorough assessment of the viscoelastic and mechanical properties of both precursor solutions and final hydrogels. The investigated modification strategies include purification, oxidation, reductive chain scission, and blending. We correlate polymer flow and hydrogel forming capabilities to viscosity-dependent methods including casting, injection and printing. Native GG and purified NaGG are shear thinning and feasible for printing, being similar in gelation and compression behavior. Oxidized GGox possesses reduced viscosity, higher toughness, and aldehydes as functional groups, while scissored GGsciss has markedly lower molecular weight. To exemplify extrudability, select modification products are printed using an extrusion-based bioprinter utilizing a crosslinker bath. Our robust modification strategies have widened the processing capabilities of GG without affecting its ability to form hydrogels., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

A novel isolated yellow-pigmented bacterial designated strain UDD2 T was isolated from a maize field soil sample collected in Ilsan, Republic of Korea. Cells of strain UDD2 T were Gram-stain-negative, non-sporulating, long rod-shaped and exhibited flagellar motility. Cells could grow at 15-42 °C and pH 5.5-11.0. Strain UDD2 T was sensitive to NaCl and barely tolerated up to 1 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain UDD2 T formed a separate clade with the members of genus Sphingosinicella within the family Sphingomonadaceae . Strain UDD2 T showed the highest 16S rRNA gene sequence similarity to Sphingosinicella vermicomposti KCTC 224446 T (98.5 %) and Sphingosinicella humi KCTC 62519 T (96.7 %), followed by members of the genus Sphingomonas (96.4-94.5 %) and Sphingobium (96.1-94.9 %), but they were located in other phylogenetic clusters. Average nucleotide identity and digital DNA-DNA hybridization values between strain UDD2 T and S. vermicomposti KCTC 224446 T and S. humi KCTC 62519 T were 80.2/24.2 and 75.6/20.4 %, respectively. The total size of the genome was 2 421 697 bp and composed of one circular chromosome, with a G+C content of 63.7 mol%. Strain UDD2 T produced indole acetic acid (IAA) in the presence of l-tryptophan. Bacterial IAA is a crucial phytohormone in plant growth and development. Gene clusters for indole-3-glycerol phosphate synthase and tryptophan synthase were found in the genome of strain UDD2 T . To the best of our knowledge, no member of the genus Sphingosinicella has been reported to produce IAA to date. The major cellular fatty acids (>10 %) were found to be C 16 : 0 , C 14 : 0 2OH and summed feature 3 (comprising C 16  : 1 ω 7 c and/or iso-C 15  :  0 2-OH). Strain UDD2 T had ubiquinone Q-10 as the major respiratory quinone and homospermidine as the major polyamine. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, three unidentified phosphoglycolipids, one unidentified phospholipid, one unidentified aminoglycophospholipid, one unidentified glycolipid and one unidentified polar lipid. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic data, strain UDD2 T represents a novel species of the genus Sphingosinicella , for which the name Sphingosinicella flava is proposed. The type strain is UDD2 T (=KCTC 82357 T =NBRC 114507 T ).

DNA origami nanostructures (DONs) are promising substrates for the single-molecule investigation of biomolecular reactions and dynamics by in situ atomic force microscopy (AFM). For this, they are typically immobilized on mica substrates by adding millimolar concentrations of Mg 2+ ions to the sample solution, which enable the adsorption of the negatively charged DONs at the like-charged mica surface. These non-physiological Mg 2+ concentrations, however, present a serious limitation in such experiments as they may interfere with the reactions and processes under investigation. Therefore, we here evaluate three approaches to efficiently immobilize DONs at mica surfaces under essentially Mg 2+ -free conditions. These approaches rely on the pre-adsorption of different multivalent cations, i.e., Ni 2+ , poly-l-lysine (PLL), and spermidine (Spdn). DON adsorption is studied in phosphate-buffered saline (PBS) and pure water. In general, Ni 2+ shows the worst performance with heavily deformed DONs. For 2D DON triangles, adsorption at PLL- and in particular Spdn-modified mica may outperform even Mg 2+ -mediated adsorption in terms of surface coverage, depending on the employed solution. For 3D six-helix bundles, less pronounced differences between the individual strategies are observed. Our results provide some general guidance for the immobilization of DONs at mica surfaces under Mg 2+ -free conditions and may aid future in situ AFM studies.

Low molecular weight thiols including trypanothione and glutathione play an important function in the cellular growth, maintenance and reduction of oxidative stress in Leishmania species. In particular, parasite specific trypanothione has been established as a prime target for new anti-leishmania drugs. Previous studies into the interaction of the front-line Sb(V) based anti-leishmanial drug meglumine antimoniate with glutathione, have demonstrated that a reduction pathway may be responsible for its effective and selective nature. The new suite of organometallic complexes, of general formula [MAr 3 (O 2 CR) 2 ] (M = Sb or Bi) have been shown to have potential as new selective drug candidates. However, their behaviour towards the critical thiols glutathione and trypanothione is still largely unknown. Using NMR spectroscopy and mass spectrometry we have examined the interaction of the analogous Sb(V) and Bi(V) organometallic complexes, [SbPh 3 (O 2 CCH 2 (C 6 H 4 CH 3 )) 2 ] S1 and [BiPh 3 (O 2 CCH 2 (C 6 H 4 CH 3 )) 2 ] B1, with the trifluoroacetate (TFA) salt of trypanothione and L-glutathione. In the presence of trypanothione or glutathione at the clinically relevant pH of 4-5 for Leishmania amastigotes, both complexes undergo facile and rapid reduction, with no discernible difference. However, at a higher pH (6-7), the complexes behave quite differently towards glutathione. The Bi(V) complex is again reduced rapidly but the Sb(V) complex undergoes slow reduction over 8 h (t 1/2  = 54 min.) These results give the first insights into why the highly oxidising Bi(V) complexes display low selectivity in their cytotoxicity towards leishmanial and mammalian cells, while the Sb(V) complexes show good selectivity., (Crown Copyright © 2021. Published by Elsevier Inc. All rights reserved.)

Members of the genus Novosphingobium are well known for their metabolically versatile and great application potential in pollution elimination. The three novel bacterial strains, designated 4Y4 T , 4Y9, and 1Y9A T , were isolated from aquaculture water and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequences phylogenetic analysis revealed that the three strains belonged to the genus Novosphingobium. The phylogenomic analysis indicated that the three strains formed two independent and robust branches distinct from all reference strains. The analyses of dDDH values and ANIs between the three strains and their relatives further demonstrated that the three strains represented two different novel genospecies. Comparative genomic analysis of the three isolates and 32 type strains of the genus Novosphingobium showed that the most important central metabolic pathways of these strains appeared to be similar, while specific and specialized metabolic pathways were flexible and variable among these strains. Chemotaxonomic characterization exhibited that the predominant cellular fatty acids were summed feature 8, summed feature 3, and C 14:0 2OH; the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, and sphingoglycolipid; the major respiratory quinone and polyamine were Q-10 and spermidine. The DNA G + C contents were 67.6 and 64.7 %. Based on the genotypic and phenotypic characteristics, strains 4Y4 T and 1Y9A T are concluded to represent two novel species of the genus Novosphingobium, for which the names Novosphingobium aerophilum sp. nov. (type strain 4Y4 T  = GDMCC 1.1828  T  = KACC 21946  T ) and Novosphingobium jiangmenense sp. nov. (type strain 1Y9A T  = GDMCC 1.1936  T  = KACC 22085  T ) are proposed., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021. Published by Elsevier GmbH.)

Histone deacetylase 10 (HDAC10) is a zinc-dependent polyamine deacetylase enriched in the cytosol of eukaryotic cells. The active site of HDAC10 contains catalytic residues conserved in other HDAC isozymes that function as lysine deacetylases: Y307 assists the zinc ion in polarizing the substrate carbonyl for nucleophilic attack, and the H136-H137 dyad serves general base-general acid functions. As an inducer of autophagy, HDAC10 is an attractive target for the design of selective inhibitors that may be useful in cancer chemotherapy. Because detailed structural information regarding the catalytic mechanism of HDAC10 may inform new approaches to inhibitor design, we now report X-ray crystal structures of HDAC10 in which reaction intermediates with substrates N 8 -acetylspermidine and N -acetylputrescine are trapped in the active site. The Y307F substitution prevents activation of the substrate carbonyl for nucleophilic attack by the zinc-bound water molecule, thereby enabling crystallographic isolation of intact enzyme-substrate complexes. The H137A substitution removes the catalytically obligatory general acid, thereby enabling crystallographic isolation of oxyanionic tetrahedral intermediates. Finally, the acetate complex with the wild-type enzyme represents a product complex after dissociation of the polyamine coproduct. Taken together, these structures provide snapshots of the reaction coordinate of acetylpolyamine hydrolysis and are consistent with a mechanism in which tandem histidine residues H136 and H137 serve as general base and general acid catalysts, respectively. The function of the histidine dyad in the HDAC10 mechanism appears to be similar to that in HDAC6, but not HDAC8 in which both functions are served by the second histidine of the tandem pair.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT486 T , isolated from soil sampled in a maize field in Taiwan. Cells of strain CC-CFT486 T were short rods, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT486 T associated with Aeromicrobium panacisoli (97.0 % sequence identity), Aeromicrobium lacus (97.0 %), Aeromicrobium erythreum (96.8 %) and Aeromicrobium alkaliterrae (96.8 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 70.6-77.8 % ( n =11) compared within the type strains of the genus Aeromicrobium . Strain CC-CFT486 T contained C 16 : 0 , C 17 : 0 , C 17 : 1  ω 8c and C 18 : 1  ω 9c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified aminophospholipids and three unknown phospholipids. The cell wall peptidoglycan of strains CC-CFT486 T contained ll-diaminopimelic acid (ll-DAP) and the major polyamine was spermidine. The DNA G+C content was 70.6 mol% and the predominant quinone was menaquinone 9 (MK-9). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-CFT486 T is proposed to represent a novel Aeromicrobium species, for which the name Aeromicrobium terrae sp. nov. (type strain CC-CFT486 T =BCRC 81217 T =JCM 33499 T ).

Adsorption processes are central to ionic transport in industrial and biological membrane systems. Multivalent cations modulate the conductive properties of nanofluidic devices through interactions with charged surfaces that depend principally on the ion charge number. Considering that ion channels are specialized valves that demand a sharp specificity in ion discrimination, we investigate the adsorption dynamics of trace amounts of different salts of trivalent cations in biological nanopores. We consider here OmpF from Escherichia coli, an archetypical protein nanopore, to probe the specificity of biological nanopores to multivalent cations. We systematically compare the effect of three trivalent electrolytes on OmpF current-voltage relationships and characterize the degree of rectification induced by each ion. We also analyze the open channel current noise to determine the existence of equilibrium/non-equilibrium mechanisms of ion adsorption and evaluate the extent of charge inversion through selectivity measurements. We show that the interaction of trivalent electrolytes with biological nanopores occurs via ion-specific adsorption yielding differential modulation of ion conduction and selectivity inversion. We also demonstrate the existence of non-equilibrium fluctuations likely related to ion-dependent trapping-detrapping processes. Our study provides fundamental information relevant to different biological and electrochemical systems where transport phenomena involve ion adsorption in charged surfaces under nanoscale confinement.

Methods for rapid and high-throughput screening of transcription in vitro to examine reaction conditions, enzyme mutants, promoter variants, and small molecule modulators can be extremely valuable tools. However, these techniques may be difficult to establish or inaccessible to many researchers. To develop a straightforward and cost-effective platform for assessing transcription in vitro, we used the "Broccoli" RNA aptamer as a direct, real-time fluorescent transcript readout. To demonstrate the utility of our approach, we screened the effect of common reaction conditions and components on bacteriophage T7 RNA polymerase (RNAP) activity using a common quantitative PCR instrument for fluorescence detection. Several essential conditions for in vitro transcription by T7 RNAP were confirmed with this assay, including the importance of enzyme and substrate concentrations, covariation of magnesium and nucleoside triphosphates, and the effects of several typical additives. When we used this method to assess all possible point mutants of a canonical T7 RNAP promoter, our results coincided well with previous reports. This approach should translate well to a broad variety of bacteriophage in vitro transcription systems and provides a platform for developing fluorescence-based readouts of more complex transcription systems in vitro., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest with the contents of this article., (Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.)

A Gram-staining-negative non endospore-forming strain, T13(2019) T was isolated from water samples from Atlantic salmon ( Salmo salar ) fry culture in Chile and studied in detail for its taxonomic position. The isolate shared highest 16S rRNA gene sequence similarities with the type strains of Flavobacterium chungangense (98.44 %) followed by Flavobacterium tructae and Flavobacterium spartansii (both 98.22 %). Menaquinone MK-6 was the predominant respiratory quinone in T13(2019) T . Major polar lipids were phosphatidylethanolamine, an ornithine lipid and the unidentified polar lipids L1, L3 and L4 lacking a functional group. The major polyamine was sym -homospermidine. The fatty acid profile contained major amounts of iso-C 15 : 0 , iso-C 15 : 0 3-OH, iso-C 17 : 0 3-OH, C 15 : 0 , summed feature 3 (C 16 : 1  ω7 c and/or iso-C 15 : 0 2-OH) and various hydroxylated fatty acids in smaller amounts, among them iso-C 16 : 0 3-OH, and C 15 : 0 3-OH, which supported the grouping of the isolate into the genus Flavobacterium . Physiological/biochemical characterisation and ANI calculations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation. In addition it became obvious, that the type strains of F. tructae and F. spartansii showed 100 % 16S rRNA gene sequence similarities and ANI values of 97.21%/ 97.59 % and DDH values of 80.40 % [77.5 and 83%]. These data indicate that F. tructae and F. spartansii belong to the same species and it is proposed that F. spartansii is a later heterotypic synonym of F. tructae . For strain T13(2019) T (=CIP 111411 T =LMG 30298 T =CCM 8798 T ) a new species with the name Flavobacterium salmonis sp. nov. is proposed.

The novel bacterial strain C33 T was isolated from a freshwater sample collected from the Hapcheon-Changnyeong barrage. The Gram-negative, motile, yellow-pigmented strain C33 T was characterized as a rod-shaped and strictly aerobic bacterium. A 16S-rRNA phylogenetic analysis revealed that this strain was most closely related to Sphingomonas changbaiensis V2M44 T , Sphingomonas tabacisoli X1-8 T , and Sphingomonas flavalba ZLT-5 T with 97.1, 97.0, and 95.0 % 16S-rRNA sequence similarities, respectively. The genomic DNA GC content of strain C33 T was estimated at 65.0 mol%. The average nucleotide identity of strain C33 T relative to S. changbaiensis V2M44 T and S. flavalba ZLT-5 T was found to be 77.0 and 75.6%, with average amino-acid identities of 69.9, and 66.7%, and the digital DNA-DNA hybridization values of 21.3 and 17.7 %, respectively. The cells grew at 19-37 °C and pH 6-9 with 0-0.5 % (w/v) NaCl (optimum: 28 °C, pH 6.5, and 0 % NaCl). The major component identified in the polyamine pattern was sym -homospermidine, and the main ubiquinone was Q-10. The predominant polar lipids characterized were diphophatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, and sphingoglycolipid. Iso-C 15 : 0 , C 15 : 0 anteiso, and summed feature 3 (C 16 : 1 ω 6 c and/or C 16 : 1 ω 7 c ) were found to be the primary cellular fatty acids in strain C33 T . Based on these genotypic and phenotypic characteristics, strain C33 T was classified as a novel species of the genus Sphingomonas ; and the name Sphingomonas changnyeongensis sp. nov. is proposed (=KACC 21511 T =JCM 33880 T ).

A pair of new macrocyclic spermidine alkaloids, (+)-( S )-scocycamide and (-)-( R )-scocycamide, were isolated from the roots of Scopolia tangutica . Their structures were established by extensive spectroscopic data, electronic circular dichroism analyses, and chemical synthesis. They featured a unique 6/18 fused bicyclic framework with spermidine and catechol units, representing a new subtype of natural spermidine alkaloids. A plausible biosynthetic pathway was also proposed. They inhibited butyrylcholinesterase and exhibited antioxidant capacity, suggesting beneficial constituents against Alzheimer's disease and oxidation.

A novel bacterial strain, designated CSW-10 T , isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed yellow-coloured colonies. Optimal growth occurred at 30 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CSW-10 T formed a phylogenetic lineage in the genus Sphingomonas . The 16S rRNA gene sequence similarity indicated that strain CSW-10 T was most closely related to Sphingomonas fonticola TNR-2 T (97.6%). Strain CSW-10 T showed 69.8-70.7% average nucleotide identity and 19.0-23.0% digital DNA-DNA hybridization identity with the strains of other related Sphingomonas species. The major fatty acids of strain CSW-10 T were summed feature 8 (C 18:1 ω 7 c and/or C 18:1 ω 6 c ) and C 17:1 ω 6 c . The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized sphingoglycolipid, five uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamines were homospermidine and spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-10 T was 62.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CSW-10 T should represent a novel species of the genus Sphingomonas , for which the name Sphingomonas lacunae sp. nov. is proposed. The type strain is CSW-10 T (=BCRC 81190 T =LMG 31340 T ).

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480 T , isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480 T were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480 T associated with Cerasibacillus quisquiliarum (97.2 % sequence identity), Virgibacillus soli (95.7 %), Virgibacillus carmonensis (95.4 %) and Virgibacillus byunsanensis (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-CFT480 T and C. quisquiliarum were 74.2 and 20.1 %, respectively. Strain CC-CFT480 T contained iso-C 15:0 , C 16:1 ω7 c alcohol and iso-C 17:1 ω 10 c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480 T is proposed to represent a novel Cerasibacillus species, for which the name Cerasibacillus terrae sp. nov. (type strain CC-CFT480 T =BCRC 81216 T =JCM 33498 T ).

Biofilm-impaired tissue is a significant factor in chronic wounds such as diabetic foot ulcers. Most, if not all, anti-biotics in clinical use have been optimized against planktonic phenotypes. In this study, an in vitro assessment was performed to determine the potential efficacy of a first-in-class series of antibiofilm antibiotics and compare outcomes to current clinical standards of care. The agent, CZ-01179, was formulated into a hydrogel and tested against mature biofilms of a clinical isolate of methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa ATCC 27853 using two separate methods. In the first method, biofilms were grown on cellulose discs on an agar surface. Topical agents were spread on gauze and placed over the biofilms for 24 h. Biofilms were quantified and imaged with confocal and scanning electron microscopy. In the second method, biofilms were grown on bioabsorbable collagen coupons in a modified CDC biofilm reactor. Coupons were immersed in treatment for 24 h. The first method was limited in its ability to assess efficacy. Efficacy profiles against biofilms grown on collagen were more definitive, with CZ-01179 gel eradicating well-established biofilms to a greater degree compared to clinical standards. In conclusion, CZ-01179 may be a promising topical agent that targets the biofilm phenotype. Pre-clinical work is currently being performed to determine the translatable potential of CZ-01179 gel., Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: There are multiple patents secured by Curza Global on which multiple authors (DLW, REL, PRS, TJH, HRKR) are listed as inventors. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

We developed a new procedure for the comprehensive analysis of metabolites and enzymes involved in polyamine metabolism pathways. The procedure utilizes stable isotope-labeled polyamines and directly and precisely determines labeled products from enzymatic reactions by ESI-Q-TOF-MS. The activity of different enzymes could be determined in essentially the same manner by suitably adjusting the reaction conditions for each individual enzyme. We applied the procedure to extracts of regenerating rat liver and analyzed the changes in polyamine-metabolizing enzymes and polyamine contents during recovery from partial hepatectomy. A general outline of polyamine metabolism and information of polyamine dynamics were obtained. This kind of comprehensive information would be valuable in unifying detailed but fragmentary information obtained through conventional analyses focusing on one or a few enzymes and on a limited aspect of polyamine metabolic pathway., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The effectiveness of several functionalized silica materials (cation-exchange materials) for the removal of biogenic amines from wines, and the effects on other wine components and organoleptic characteristics were evaluated. Results have shown that mesoporous silica material bi-functionalized with phosphonic and sulfonic acids allowed the removal of histamine, putrescine, cadaverine, spermine and spermidine from wines, although the dose must be adapted for each wine according to the removal requirements and wine characteristics. A plus of the adsorbent developed is that it can be recovered and re-used for at least 3 treatments. Immediately following the treatments, a decrease in the levels of linear ethyl esters (ethyl hexanoate, ethyl octanoate and ethyl decanoate) was observed, although these levels were re-equilibrated after several days reducing this undesired side effect. A slight, but perceptible, effect on wine color was observed, probably due to the slight decrease in the pH of the wine produced by the treatments. On the basis of the sensory analysis that focused only on the aroma of the wines, the proposed technique would be more adequate for wines aged in barrels than for young wines.

A bacterial strain, designated FSY-8 T , was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8 T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20-40 °C (optimum, 30-37 °C) and pH 5-7 (optimum, pH 6) and in the presence of 0-0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8 T were summed feature 8 (C 18 : 1  ω 7 c and/or C 18 : 1  ω 6 c ) and summed feature 3 (C 16 : 1  ω 7 c and/or C 16 : 1  ω 6 c ). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8 T formed a phylogenetic lineage in the genus Novosphingobium . Strain FSY-8 T showed 71.6-77.2 % average nucleotide identity and 19.9-22.8 % digital DNA-DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8 T should be classified in a novel species of the genus Novosphingobium , for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8 T (=BCRC 81051 T =LMG 30053 T =KCTC 52812 T ).