Development of Methylorubrum extorquens AM1 as a promising platform strain for enhanced violacein production from co-utilization of methanol and acetate.

Violacein, a blue-violet compound with a wide range of beneficial bioactivities, is an attractive product for microbial production. Currently, violacein production has been demonstrated in several sugar heterotrophs through metabolic engineering; however, the cost of production remains an obstacle for business ventures. To address this issue, the development of host strains that can utilize inexpensive alternative substrates to reduce production costs would enable the commercialization of violacein. In this study, we engineered a facultative methylotroph, Methylorubrum extorquens AM1, to develop a methanol-based platform for violacein production. By optimizing expression vectors as well as inducer concentrations, 11.7 mg/L violacein production was first demonstrated using methanol as the sole substrate. Considering that unidentified bottlenecks for violacein biosynthesis in the shikimate pathway of M. extorquens AM1 would be difficult to address using generic metabolic engineering approaches, random mutagenesis and site-directed mutagenesis were implemented, and a 2-fold improvement in violacein production was achieved. Finally, by co-utilization of methanol and acetate, a remarkable enhancement of violacein production to 118 mg/L was achieved. Our results establish a platform strain for violacein production from non-sugar feedstocks, which may contribute to the development of an economically efficient large-scale fermentation system for violacein production.

Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics.

Riboswitches and toehold switches are considered to have potential for implementation in various fields, i.e., biosensing, metabolic engineering, and molecular diagnostics. The specific binding, programmability, and manipulability of these RNA-based molecules enable their intensive deployments in molecular detection as biosensors for regulating gene expressions, tracking metabolites, or detecting RNA sequences of pathogenic microorganisms. In this review, we will focus on the development of riboswitches and toehold switches in biosensing and molecular diagnostics. This review introduces the operating principles and the notable design features of riboswitches as well as toehold switches. Moreover, we will describe the advances and future directions of riboswitches and toehold switches in biosensing and molecular diagnostics.

Water-soluble chitosan-derived sustainable materials: towards filaments, aerogels, microspheres, and plastics.

Bioinspired materials have aroused great interest as their inherent biocompatible and structural characteristics have given rise to sustainable applications. In this work, we have reported the phase and morphology transformation of chitosan from crystalline nanofibrils into amorphous sheets for fabricating sustainable materials. Acetylation-induced aqueous dissolution of native chitosan nanofibrils affords water-soluble chitosan as a biopolymeric liquid. Water-soluble chitosan macromolecules self-aggregate into amorphous sheets on solidification, presenting an interesting way to inspire new structures of chitosan assemblies. Through control over gelation, lyophilization, and self-assembled confinement of water-soluble chitosan, we have fabricated novel chitosan materials including filaments, aerogels, microspheres, and plastics that are promising for sustainable use.

Regulatory effect of hydroquinone-tetraethylene glycol conjugates on zebrafish pigmentation.

We synthesized two hydroquinone-tetraethylene glycol conjugates (HQ-TGs) and investigated their logP, photophysical stability, and redox chemical stability. HQ-TGs are a little more hydrophilic than hydroquinone (HQ) and show an enhanced photophysical and redox chemical stability compared with HQ. In addition we studied the effect of HQ-TGs on cell viability and on zebrafish pigmentation. MTT assay in HF-16 cells showed HQ-TGs are less cytotoxic than HQ. The phenotype-based image analysis of zebrafish larvae suggests that HQ-TGs suppress the pigmentation of zebrafish in a dose-dependent manner. The comparative experiments on stability, cytotoxicity, and zebrafish pigmentation between HQ and HQ-TGs suggest that mono tetraethylene glycol-functionalization of HQ is an alternative solution to overcome the adverse effect of HQ.

Small polyanion recognition of a triazolium cyclodextrin click cluster in water.

In order to detect small polyanions (sPAs), which play important roles in many biological systems, a triazolium cyclodextrin click cluster (5, hexakis{6-(3-methyl-4-hydroxymethyl-1H-1,2,3-triazolium-1-yl)-6-deoxy}-α-cyclodextrin iodide) was synthesized and characterized. The competition binding to 5 occupied by 5-carboxyfluorescein of inositol-1,4,5-trisphosphate (IP3), phytic acid, adenosine triphosphate (ATP), ethylenediaminetetraacetic acid (EDTA), glucose, and glucose-6-phosphate was evaluated by UV/vis titration in HEPES (10 mM, pH 7.4) : methanol (1 : 1, v/v). We obtained the binding constants of IP3 and phytic acid to 5 (1.4 × 10(6) and 1.9 × 10(6) M(-1), respectively); however, the binding constants of ATP and EDTA were significantly lower (2.1 × 10(5) and 4.5 × 10(4) M(-1), respectively). Moreover, glucose and glucose-6-phosphate did not show any detectable binding. In addition, the sPA recognition of the triazolium cyclodextrin click cluster in water was confirmed by fluorescence titration.

Enrichment and MALDI-TOF MS Analysis of Phosphoinositides in Brain Tissue.

Triazolium cyclodextrin click cluster (+CCC) is an ideal scaffold to specifically bind phosphoinositides (PIPs) via multivalent electrostatic interaction. A new enrichment material, triazolium cyclodextrin click cluster-magnetic agarose bead conjugate (+CCC-MAB), was synthesized and applied to the PIP enrichment of brain tissue. The enriched sample was analyzed using MALDI-TOF MS in negative ion mode without any derivatization. The PIP extract of brain tissue is known to contain abundant lipid interferences. By employing magnetic pull-down separation using +CCC-MAB, we effectively removed the weak-binding interferences in the PIP extract, thereby improving the signal-to-noise ratio (S/N) of the PIPs. Our +CCC-MAB-based PIP enrichment enabled us to analyze 16 PIP species in brain tissue. Six species with high S/N were assigned by MS/MS, while the remaining 10 species with low S/N were characterized by an empirical selection guide based on the biological relevance of PIPs. We conclude that +CCC-MAB-based PIP enrichment is a promising MALDI sample preparation method for specific PIP analysis in brain tissue.

Targeting protein for xenopus kinesin-like protein 2 (TPX2) regulates γ-histone 2AX (γ-H2AX) levels upon ionizing radiation.

The microtubule-associated protein targeting protein for Xenopus kinesin-like protein 2 (TPX2) plays a key role in spindle assembly and is required for mitosis in human cells. In interphase, TPX2 is actively imported into the nucleus to prevent its premature activity in microtubule organization. To date, no function has been assigned to nuclear TPX2. We now report that TPX2 plays a role in the cellular response to DNA double strand breaks induced by ionizing radiation. Loss of TPX2 leads to inordinately strong and transient accumulation of ionizing radiation-dependent Ser-139-phosphorylated Histone 2AX (γ-H2AX) at G(0) and G(1) phases of the cell cycle. This is accompanied by the formation of increased numbers of high intensity γ-H2AX ionizing radiation-induced foci. Conversely, cells overexpressing TPX2 have reduced levels of γ-H2AX after ionizing radiation. Consistent with a role for TPX2 in the DNA damage response, we found that the protein accumulates at DNA double strand breaks and associates with the mediator of DNA damage checkpoint 1 (MDC1) and the ataxia telangiectasia mutated (ATM) kinase, both key regulators of γ-H2AX amplification. Pharmacologic inhibition or depletion of ATM or MDC1, but not of DNA-dependent protein kinase (DNA-PK), antagonizes the γ-H2AX phenotype caused by TPX2 depletion. Importantly, the regulation of γ-H2AX signals by TPX2 is not associated with apoptosis or the mitotic functions of TPX2. In sum, our study identifies a novel and the first nuclear function for TPX2 in the cellular responses to DNA damage.

Antibody functionalization with a dual reactive hydrazide/click crosslinker.

A water-soluble, dual reactive hydrazide/click crosslinker (ethynyl hydrazide, EH) was synthesized and characterized. A model antibody, human immunoglobulin G (hIgG), was ethynylated by conventional oxidation/hydrazide reactions with the hydrazide moiety of EH. The terminal alkyne conjugated to the glycan of hIgG was easily functionalized by quantitative and bioorthogonal Cu(I)-catalyzed azide-alkyne cycloaddition. The potential of the hydrazide/click crosslinker as a reagent to functionalize antibodies was demonstrated with fluorophore labeling and antibody immobilization.

Experimental promoter identification of a foodborne pathogen Salmonella enterica subsp. enterica serovar Typhimurium with near single base-pair resolution.

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common foodborne pathogen which is frequently used as the reference strain for Salmonella. Investigating the sigma factor network and protomers is crucial to understand the genomic and transcriptomic properties of the bacterium. Its promoters were identified using various methods such as dRNA-seq, ChIP-chip, or ChIP-Seq. However, validation using ChIP-exo, which exhibits higher-resolution performance compared to conventional ChIP, has not been conducted to date. In this study, using the representative strain S. Typhimurium LT2 (LT2), the ChIP-exo experiment was conducted to accurately determine the binding sites of catalytic RNA polymerase subunit RpoB and major sigma factors (RpoD, RpoN, RpoS, and RpoE) during exponential phase. Integrated with the results of RNA-Seq, promoters and sigmulons for the sigma factors and their association with RpoB have been discovered. Notably, the overlapping regions among binding sites of each alternative sigma factor were found. Furthermore, comparative analysis with Escherichia coli str. K-12 substr. MG1655 (MG1655) revealed conserved binding sites of RpoD and RpoN across different species. In the case of small RNAs (sRNAs), 50 sRNAs observed their expression during the exponential growth of LT2. Collectively, the integration of ChIP-exo and RNA-Seq enables genome-scale promoter mapping with high resolution and facilitates the characterization of binding events of alternative sigma factors, enabling a comprehensive understanding of the bacterial sigma factor network and condition-specific active promoters.

Small molecular weight PEGylation of diosgenin in an in vivo animal study for diabetic auditory impairment treatment.

Diosgenin was modified to control its in vivo bioavailability by conjugating a hydrophilic unit, tetraethylene glycol. The diosgenin-tetraethylene glycol conjugate (TE) was orally administered in streptozotocin induced diabetic mice for this auditory protection study. The bioactivity improvement of TE for in vivo diabetic auditory impairment treatment was clearly observed in three different auditory tests and compared with that of diosgenin. The improvement in in vivo efficacy suggests that the small molecular weight PEGylation of diosgenin is a synthetically robust and systematically applicable strategy to reform the poor pharmacokinetics of a hydrophobic aglycone.

Insights into C1 and C3 assimilation pathways in type I methanotrophic bacterium from co-production of 1,2-propanediol and lactate.

Methanotrophic bacteria are attractive hosts for mining metabolic pathways of C1 assimilation to produce value-added products. Herein, the type I methanotroph Methylotuvimicrobium alcaliphilum 20Z was employed to explore the carbon flux from methane and methanol via the EMP pathway to produce 1,2-propanediol (1,2-PDO). The production of 1,2-PDO on methane was found to be mainly restricted by the lower carbon flux toward the EMP pathway. The co-utilization of C1 substrates and glycerol (C3) could contribute to enhance 1,2-PDO. Lactate was co-produced in much higher amounts than 1,2-PDO. This unexpected product was probably derived from lactaldehyde by inherent aldehyde dehydrogenases. The 1,2-PDO production without increased accumulation of lactate was observed via establishing the acetol-based pathway by propane utilization with the overexpression of pmoD. This is the first study to provide experimental insights into the operation of metabolic routes for 1,2-PDO and lactate co-production from C1 and C3 compounds in methanotrophs.

The effects of the COVID-19 lockdown on patients with chronic cardiovascular disease in Vietnam.

INTRODUCTION: We evaluated the impact of the lockdown policy during the COVID-19 pandemic on cardiovascular outpatients of a cardiology clinic in Vietnam from April to June 2020. We estimated the occurrence of different cardiovascular problems in general and the stability of blood pressure. METHODOLOGY: During the Covid-19 outbreak in Vietnam, we conducted a cross-sectional study to evaluate its impact on blood pressure stability of hypertensive patients treated as outpatients at the clinic of the University Medical Center (UMC), Ho Chi Minh City. RESULTS: The mean age of the recruited 493 patients was 62.2 ± 10.2 years. The stable blood pressure group consisted of 87% patients, while the unstable blood pressure group consisted of 13% patients. We found that 68% of the study population attended their follow-up appointments as scheduled: 87% with stable blood pressure versus only 13% with unstable blood pressure. Significant differences were noticed in body weight changes and cardiovascular problems between the two groups: body weight increase (22.6% vs. 10.2%), body weight decrease (3.2% vs. 6.7%), worsening of cardiovascular problems (35.5% vs. 17.9%) in the unstable and stable blood pressure groups, respectively. Multivariable regression analysis reflected the impact of the increase in body weight and occurrence of cardiovascular problems on the patients with unstable blood pressure. CONCLUSIONS: Our study provided concrete proof of the impact of the lockdown on chronic patients, which should warrant further surveys, and evaluation of the lockdown policy.

Sustainable biosynthesis of chemicals from methane and glycerol via reconstruction of multi-carbon utilizing pathway in obligate methanotrophic bacteria.

Obligate methanotrophic bacteria can utilize methane, an inexpensive carbon feedstock, as a sole energy and carbon substrate, thus are considered as the only nature-provided biocatalyst for sustainable biomanufacturing of fuels and chemicals from methane. To address the limitation of native C1 metabolism of obligate type I methanotrophs, we proposed a novel platform strain that can utilize methane and multi-carbon substrates, such as glycerol, simultaneously to boost growth rates and chemical production in Methylotuvimicrobium alcaliphilum 20Z. To demonstrate the uses of this concept, we reconstructed a 2,3-butanediol biosynthetic pathway and achieved a fourfold higher titer of 2,3-butanediol production by co-utilizing methane and glycerol compared with that of methanotrophic growth. In addition, we reported the creation of a methanotrophic biocatalyst for one-step bioconversion of methane to methanol in which glycerol was used for cell growth, and methane was mainly used for methanol production. After the deletion of genes encoding methanol dehydrogenase (MDH), 11.6 mM methanol was obtained after 72 h using living cells in the absence of any chemical inhibitors of MDH and exogenous NADH source. A further improvement of this bioconversion was attained by using resting cells with a significantly increased titre of 76 mM methanol after 3.5 h with the supply of 40 mM formate. The work presented here provides a novel framework for a variety of approaches in methane-based biomanufacturing.

Chemistry of the carboxylic acid of dihydrofluorescein in oxidation and its application to fluorogenic ROS sensing.

The conjugation site of dihydrofluorescein (H2F) is important for the rational design of H2F-based reactive oxygen species (ROS) sensors. Despite the prevalence of H2F analogs detecting cellular ROS, the role of the carboxylic acid of H2F in oxidation is still unclear. To get insight into the conjugation site of H2F, we synthesized H2F diacetate (2) and its amide derivative (3). The absorption and emission spectra of deacetylated 2 and 3 in the presence of H2O2/hematin showed that the carboxylic acid of H2F plays a crucial role in the oxidation of H2F. NMR and HPLC analysis of the oxidation product of deacetylated 3 showed a quantitative and fast generation of non-fluorescent spirolactam (F-Lactam). As regards these observations, we untouched the carboxylic acid at the 3rd position and designed an H2F-based ROS sensor (7) that conjugated the lipophilic chain at the 5th position instead. A series of confocal microscopic experiments of 7 demonstrated that 7 prefers the ER location and that ROS are elevated in the cells by ER stress inducers.

Molecular Identification and Characterization of Probiotic Bacillus Species with the Ability to Control Vibrio spp. in Wild Fish Intestines and Sponges from the Vietnam Sea.

Vibriosis in farmed animals is a serious threat to aquaculture worldwide. Using probiotics and anti-Vibrio antimicrobial substances in aquaculture systems can be a means of preventing Vibrio infections. Therefore, we aimed to characterize and compare 16 potential anti-Vibrio probiotics (Vi+) isolated from marine sponges and fish intestines collected from the Vietnam Sea, as well as an anti-Vibrio bacteriocin to fully explore their application potentials. 16S rRNA sequencing confirmed all Vi+ to be Bacillus species with different strain variants across two sample types. An obvious antimicrobial spectrum toward Gram-negative bacteria was observed from intestinal Vi+ compared to sponge-associated Vi+. The reason was the higher gene frequency of two antimicrobial compounds, non-ribosomal peptides (NRPS) and polyketide type-I (PKS-I) from intestinal Vi+ (66.7%) than sponge-associated Vi+ (14.3% and 0%, respectively). Additionally, a three-step procedure was performed to purify an anti-Vibrio bacteriocin produced by B. methylotrophicus NTBD1, including (i) solvent extraction of bacteriocin from cells, (ii) hydrophobic interaction chromatography, and (iii) reverse-phase HPLC. The bacteriocin had a molecular weight of ~2-5 kDa, was sensitive to proteolysis and thermally stable, and showed a broad antimicrobial spectrum, all of which are essential properties for promising feed additives. This study provides necessary information of the potential of probiotic Bacillus species with anti-Vibrio antimicrobial properties to study their further use in sustainable aquaculture.

PTP alpha regulates integrin-stimulated FAK autophosphorylation and cytoskeletal rearrangement in cell spreading and migration.

We investigated the molecular and cellular actions of receptor protein tyrosine phosphatase (PTP) alpha in integrin signaling using immortalized fibroblasts derived from wild-type and PTP alpha-deficient mouse embryos. Defects in PTP alpha-/- migration in a wound healing assay were associated with altered cell shape and focal adhesion kinase (FAK) phosphorylation. The reduced haptotaxis to fibronectin (FN) of PTP alpha-/- cells was increased by expression of active (but not inactive) PTP alpha. Integrin-mediated formation of src-FAK and fyn-FAK complexes was reduced or abolished in PTP alpha-/- cells on FN, concomitant with markedly reduced phosphorylation of FAK at Tyr397. Reintroduction of active (but not inactive) PTP alpha restored FAK Tyr-397 phosphorylation. FN-induced cytoskeletal rearrangement was retarded in PTP alpha-/- cells, with delayed filamentous actin stress fiber assembly and focal adhesion formation. This mimicked the effects of treating wild-type fibroblasts with the src family protein tyrosine kinase (Src-PTK) inhibitor PP2. These results, together with the reduced src/fyn tyrosine kinase activity in PTP alpha-/- fibroblasts (Ponniah et al., 1999; Su et al., 1999), suggest that PTP alpha functions in integrin signaling and cell migration as an Src-PTK activator. Our paper establishes that PTP alpha is required for early integrin-proximal events, acting upstream of FAK to affect the timely and efficient phosphorylation of FAK Tyr-397.

Combination of Microwave-Assisted Girard Derivatization with Ionic Liquid Matrix for Sensitive MALDI-TOF MS Analysis of Human Serum N-Glycans.

We developed a new method for MALDI-TOF MS detection of N-glycans derived from human serum. The synergistic combination of microwave-assisted Girard T derivatization, solid-phase extraction desalting, and an ionic liquid matrix (2, 5-dihydroxybenzoic acid/aniline) (GT-SPE-DHB/An) allowed of more sensitive N-glycans detection than a conventional ionic liquid matrix in MALDI-TOF MS. The superior sensitivity of our method was confirmed by the number of assigned N-glycans in 900-2,000 m/z range. Using our GT-SPE-DHB/An method, we were successfully able to assign 31 glycans. However, with the established method, i.e., DHB/An method, only 15 glycans were assigned. To the best of our knowledge, this GT-SPE-DHB/An method is the first to combine cationic derivatization of N-glycan and ionic liquid matrix for N-glycan analysis in MALDI-TOF MS.

Modulating the GSH/Trx selectivity of a fluorogenic disulfide-based thiol sensor to reveal diminished GSH levels under ER stress.

We synthesized a fluorogenic disulfide-based naphthalimide thiol probe (ER-Naph) with a hydrophilic endoplasmic reticulum (ER)-guiding glibenclamide unit. Its ER targeting ability and high selectivity to GSH over thioredoxin, a potent competitor, were clearly demonstrated, both in solution and in vitro. Finally, a confocal microscopic investigation revealed that GSH levels in the ER were dramatically decreased under thapsigargin, brefeldin A, and tunicamycin-induced ER stress models.

Comparison of genetic variation between northern and southern populations of Lilium cernuum (Liliaceae): Implications for Pleistocene refugia.

The so-called "Baekdudaegan" (BDDG), a mountain range that stretches along the Korean Peninsula, has been recently proposed as a major "southern" glacial refugium for boreal or temperate plant species based on palaeoecological and, especially, genetic data. Genetic studies comparing genetic variation between population occurring on the BDDG and more northern ones (i.e. in NE China and/or in Russian Far East) are, however, still too few to draw firm conclusions on the role of the BDDG as a refugium and a source for possible northward post-glacial recolonizations. In order to fill this gap, we selected a boreal/temperate herb, Lilium cernuum, and compared levels of allozyme-based genetic diversity of five populations from NE China with five populations from South Korea (home of its hypothesized refuge areas). As a complementary tool, we used the maximum entropy algorithm implemented in MaxEnt to infer the species' potential distribution for the present time, which was projected to different past climate scenarios for the Last Glacial Maximum (LGM). Permutation tests revealed that Korean populations harbored significantly higher levels of within-population genetic variation than those from NE China (expected heterozygosity = 0.173 vs. 0.095, respectively). Our results suggest that the lowered levels of genetic diversity in NE Chinese populations might be due to founder effects associated with post-glacial migration from southern regions. Congruent with genetic data, past distribution models showed higher probability of occurrence in southern ranges than in northern ones during the LGM. In addition, a positive correlation was detected between the expected heterozygosity and environmental LGM suitability. From a conservation perspective, our results further suggest that the southern populations in South Korea may be particularly worthy of protection.