Exploring the Potential of a Genome-Reduced Escherichia coli Strain for Plasmid DNA Production

The global demand for nucleic acid-based vaccines, including plasmid DNA (pDNA) and mRNA vaccines, needs efficient production platforms. However, conventional hosts for plasmid production have encountered challenges related to sequence integrity due to the presence of insertion sequences (ISs). In this study, we explored the potential of a genome-reduced Escherichia coli as a host for pDNA production. This strain had been constructed by removing approximately 23% of the genome which were unessential genes, including the genomic unstable elements. Moreover, the strain exhibits an elevated level of NADPH, a coenzyme known to increase plasmid production according to a mathematical model. We hypothesized that the combination of genome reduction and the abundance of NADPH would significantly enhance pDNA production capabilities. Remarkably, our results confirmed a three-fold increase in pDNA production compared to the widely employed DH5α strain. Furthermore, the genome-reduced strain exhibited heightened sensitivity to various antibiotics, bolstering its potential for large scale industrial pDNA production. These findings suggest the genome-reduced E. coli as an exciting candidate for revolutionizing the pDNA industry, offering unprecedented efficiency and productivity.

Soil Mineral Composition and Salinity Are the Main Factors Regulating the Bacterial Community Associated with the Roots of Coastal Sand Dune Halophytes

Soil salinity and mineral deficiency are major problems in agriculture. Many studies have reported that plant-associated microbiota, particularly rhizosphere and root microbiota, play a crucial role in tolerance against salinity and mineral deficiency. Nevertheless, there are still many unknown parts of plant–microbe interaction, especially regarding their role in halophyte adaptation to coastal ecosystems. Here, we report the bacterial community associated with the roots of coastal sand dune halophytes Spinifex littoreus and Calotropis gigantea, and the soil properties that affect their composition. Strong correlations were observed between root bacterial diversity and soil mineral composition, especially with soil Calcium (Ca), Titanium (Ti), Cuprum (Cu), and Zinc (Zn) content. Soil Ti and Zn content showed a positive correlation with bacterial diversity, while soil Ca and Cu had a negative effect on bacterial diversity. A strong correlation was also found between the abundance of several bacterial species with soil salinity and mineral content, suggesting that some bacteria are responsive to changes in soil salinity and mineral content. Some of the identified bacteria, such as Bacillus idriensis and Kibdelosporangium aridum, are known to have growth-promoting effects on plants. Together, the findings of this work provided valuable information regarding bacterial communities associated with the roots of sand dune halophytes and their interactions with soil properties. Furthermore, we also identified several bacterial species that might be involved in tolerance against stresses. Further work will be focused on isolation and transplantation of these potential microbes, to validate their role in plant tolerance against stresses, not only in their native hosts but also in crops.

Recent findings and applications of biomedical engineering for COVID-19 diagnosis: a critical review

COVID-19 is one of the most severe global health crises that humanity has ever faced. Researchers have restlessly focused on developing solutions for monitoring and tracing the viral culprit, SARS-CoV-2, as vital steps to break the chain of infection. Even though biomedical engineering (BME) is considered a rising field of medical sciences, it has demonstrated its pivotal role in nurturing the maturation of COVID-19 diagnostic technologies. Within a very short period of time, BME research applied to COVID-19 diagnosis has advanced with ever-increasing knowledge and inventions, especially in adapting available virus detection technologies into clinical practice and exploiting the power of interdisciplinary research to design novel diagnostic tools or improve the detection efficiency. To assist the development of BME in COVID-19 diagnosis, this review highlights the most recent diagnostic approaches and evaluates the potential of each research direction in the context of the pandemic.

Synthetic Scaffold Systems for Increasing the Efficiency of Metabolic Pathways in Microorganisms

Microbes have been the preferred hosts for producing high-value chemicals from cheap raw materials. However, metabolic flux imbalance, the presence of competing pathways, and toxic intermediates often lead to low production efficiency. The spatial organization of the substrates, intermediates, and enzymes is critical to ensuring efficient metabolic activity by microorganisms. One of the most common approaches for bringing the key components of biosynthetic pathways together is through molecular scaffolds, which involves the clustering of pathway enzymes on engineered molecules via different interacting mechanisms. In particular, synthetic scaffold systems have been applied to improve the efficiency of various heterologous and synthetic pathways in Escherichia coli and Saccharomyces cerevisiae, with varying degrees of success. Herein, we review the recent developments and applications of protein-based and nucleic acid-based scaffold systems and discuss current challenges and future directions in the use of such approaches.

Direct colorimetric LAMP assay for rapid detection of African swine fever virus: A validation study during an outbreak in Vietnam

African swine fever (ASF) is a highly infectious viral disease with high mortality. The most recent ASF outbreak in Vietnam began in 2019, posing a threat to spread to the neighbouring Asian countries. Without a commercial vaccine or efficient chemotherapeutics, rapid diagnosis and necessary biosecurity procedures are required to control the disease. While the diagnostic method of ASF recommended by the World Organization of Animal Health is real-time PCR, the ideal diagnosis procedure including master mix setup, template extraction and a high-cost qPCR equipment for many samples being tested simultaneously is not portable. In this study, a colorimetric loop-mediated isothermal amplification (LAMP) assay was modified and evaluated for ASF virus detection using crude serum samples collected from domestic pigs in Vietnam during the 2019 outbreak. The LAMP results can be readily visualized to the naked eye within 30 min without the requirement of DNA extraction and sophisticated equipment. The sensitivity, specificity and limit of detection of direct colorimetric LAMP assay were comparable to a commercial diagnostic real-time PCR kit. Results strongly indicate that the adapted colorimetric LAMP assay has a remarkable potential for the in-field diagnosis of ASF.

Expression and characterization of a new serine protease inhibitory protein in Escherichia coli

Introduction: Proteases are enzymes that catalyze the hydrolysis of peptide bonds and play an important role in almost all biological processes. However, excessive protein proteolysis can be implicated in several diseases, such as cancer, as well as cardiovascular, inflammatory, neurodegenerative, bacterial, viral and parasitic diseases. In these cases, protease inhibitors can be used as one of versatile tools for regulating proteolytic activity of target proteases as well as therapeutic applications. In this study, we expressed and characterized a new serine protease inhibitory protein (PI-QT) from the metagenome of sponge-associated microorganisms in Escherichia coli. Methods: The gene PI-QT encoding for a new serine protease inhibitory protein was expressed in E. coli BL21(DE3). In addition, the expressed protein was purified and characterized. Results: Optimization of expression of the recombinant protein PI-QT in E. coli showed that suitable conditions for expression of the protein were pre-induction cell density (OD600) of 0.6 - 0.7, IPTG concentration of 1 mM and temperature of 25oC. The protease inhibitory protein was also purified and identified by mass spectrometry LC-MS/MS. The recombinant protein showed inhibitory activity against trypsin anda-chymotrypsin with activity values of 97526 U/mg and 41714 U/mg, respectively. Maximum activity of the protease inhibitory protein was obtained at pH 7 and temperature 20-35oC. The inhibitor was stable over pH 4-9 and up to temperature 50oC. Addition of Zn2+, Mg2+ and Ca2+ enhanced inhibitory activity, whereas other metal ions, surfactants and oxidants reduced inhibitory activity of the protease inhibitor. Conclusion: The recombinant protein PI-QT is a potential protease inhibitor for therapeutic applications.

mRNA Engineering for the Efficient Chaperone-Mediated Co-Translational Folding of Recombinant Proteins in Escherichia coli

The production of soluble, functional recombinant proteins by engineered bacterial hosts is challenging. Natural molecular chaperone systems have been used to solubilize various recombinant proteins with limited success. Here, we attempted to facilitate chaperone-mediated folding by directing the molecular chaperones to their protein substrates before the co-translational folding process completed. To achieve this, we either anchored the bacterial chaperone DnaJ to the 3ʹ untranslated region of a target mRNA by fusing with an RNA-binding domain in the chaperone-recruiting mRNA scaffold (CRAS) system, or coupled the expression of DnaJ and a target recombinant protein using the overlapping stop-start codons 5ʹ-TAATG-3ʹ between the two genes in a chaperone-substrate co-localized expression (CLEX) system. By engineering the untranslated and intergenic sequences of the mRNA transcript, bacterial molecular chaperones are spatially constrained to the location of protein translation, expressing selected aggregation-prone proteins in their functionally active, soluble form. Our mRNA engineering methods surpassed the in-vivo solubilization efficiency of the simple DnaJ chaperone co-overexpression method, thus providing more effective tools for producing soluble therapeutic proteins and enzymes.

Origanum majorana L. Essential Oil-Associated Polymeric Nano Dendrimer for Antifungal Activity against Phytophthora infestans

In this study, the introduction of Origanum majorana L. essential oil into a polyamidoamine (PAMAM) G4.0 dendrimer was performed for creation of a potential nanocide against Phytophthora infestans. The characteristics of marjoram oil and PAMAM G4.0 was analyzed using transmission electron spectroscopy (TEM), nuclear magnetic resonance spectroscopy (¹H-NMR) and gas chromatography mass spectrometry (GC-MS). The success of combining marjoram oil with PAMAM G4.0 was evaluated by FT-IR, TGA analysis, and the antifungal activity of this system was also investigated. The results showed that the antifungal activity of oil/PAMAM G4.0 was high and significantly higher than only PAMAM G4.0 or marjoram essential oil. These results indicated that the nanocide oil/PAMAM G4.0 helped strengthen and prolong the antifungal properties of the oil.

Fatty Acid, Lipid Classes and Phospholipid Molecular Species Composition of the Marine Clam Meretrix lyrata (Sowerby 1851) from Cua Lo Beach, Nghe An Province, Vietnam

This study aims to analyze compositions of fatty acids and phospholipid molecular species in the hard clams Meretrix lyrata (Sowerby, 1851) harvested from Cua Lo beach, Nghe An province, Viet Nam. Total lipid of hard clams Meretrix lyrata occupied 1.7 ± 0.2% of wet weight and contained six classes: hydrocarbon and wax (HW), triacylglycerol (TAG), free fatty acids (FFA), sterol (ST), polar lipid (PoL), and monoalkyl diacylglycerol (MADAG). Among the constituents, the proportion of PoL accounted was highest, at 45.7%. In contrast, the figures for MADAG were lowest, at 1.3%. Twenty-six fatty acids were identified with the ratios of USAFA/SAFA was 2. The percentage of n-3 PUFA (ω-3) and n-6 PUFA (ω-6) was high, occupying 38.4% of total FA. Among PUFAs, arachidonic acid (AA, 20:4n-6), eicosapentaenoic acid (EPA, 20:5n-3), docosapentaenoic acid (DPA, 22:5n-3), and docosahexaenoic acid (DHA, 22:6n-3) accounted for 3.8%, 7.8%, 2.2% and 12.0% of total lipid of the clam respectively. Phospholipid molecular species were identified in polar lipids of the clams consisting six types: phosphatidylethalnolamine (PE, with 28 molecular species), phosphatidylcholine (PC, with 26 molecular species), phosphatidylserine (PS, with 18 molecular species), phosphatidylinositol (PI, with 10 molecular species), phosphatidylglycerol (PG, with only one molecular species), and ceramide aminoethylphosphonate (CAEP, with 15 molecular species). This is the first time that the molecular species of sphingophospholipid were determined, in Meretrix lyrata in particular, and for clams in general. Phospholipid formula species of PE and PS were revealed to comprise two kinds: Alkenyl acyl glycerophosphoethanolamine and Alkenyl acyl glycerophosphoserine occupy 80.3% and 81.0% of total PE and PS species, respectively. In contrast, the percentage of diacyl glycero phosphatidylcholine was twice as high as that of PakCho in total PC, at 69.3, in comparison with 30.7%. In addition, phospholipid formula species of PI and PG comprised only diacyl glycoro phospholipids. PE 36:1 (p18:0/18:1), PC 38:6 (16:0/22:6), PS 38:1 (p18:0/20:1), PI 40:5 (20:1/20:4), PG 32:0 (16:0/16:0) and CAEP 34:2 (16:2/d18:0) were the major molecular species.

Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method

The binding between two biomolecules is one of the most critical factors controlling many bioprocesses. Therefore, it is of great interest to derive a reliable method to calculate the free binding energy between two biomolecules. In this work, we have demonstrated that the binding affinity of ligands to proteins can be determined through biased sampling simulations. The umbrella sampling (US) method was applied on 20 protein-ligand complexes, including the cathepsin K (CTSK), type II dehydroquinase (DHQase), heat shock protein 90 (HSP90), and factor Xa (FXa) systems. The ligand-binding affinity was evaluated as the difference between the largest and smallest values of the free-energy curve, which was obtained via a potential of mean force analysis. The calculated affinities differ sizably from the previously reported experimental values, with an average difference of ∼3.14 kcal/mol. However, the calculated results are in good correlation with the experimental data, with correlation coefficients of 0.76, 0.87, 0.96, and 0.97 for CTSK, DHQase, HSP90, and FXa, respectively. Thus, the binding free energy of a new ligand can be reliably estimated using our US approach. Furthermore, the root-mean-square errors (RMSEs) of binding affinity of these systems are 1.13, 0.90, 0.37, and 0.25 kcal/mol, for CTSK, DHQase, HSP90, and FXa, respectively. The small RMSE values indicate the good precision of the biased sampling method that can distinguish the ligands exhibiting similar binding affinities.

Interaction of carbohydrate binding module 20 with starch substrates

CBM20s are starch-binding domains found in many amylolytic enzymes, including glucoamylase, alpha-amylase, beta-amylases, and a new family of starch-active polysaccharide monooxygenases (AA13 PMOs). Previous studies of CBM20–substrate interaction only concerned relatively small or soluble amylose molecules, while amylolytic enzymes often work on extended chains of insoluble starch molecules. In this study, we utilized molecular simulation techniques to gain further insights into the interaction of CBM20 with substrates of various sizes via its two separate binding sites, termed as BdS1 and BdS2. Results show that substrate binding at BdS1 involving two conserved tryptophan residues is about 2–4 kcal mol⁻¹ stronger than that at BdS2. CBM20 exhibits about two-fold higher affinity for helical substrates than for the amylose random coils. The affinity for amylose individual double helices does not depend on the helices' length. At least three parallel double helices are required for optimal binding. The binding affinity for a substrate containing 3 or more double helices is ∼−15 kcal mol⁻¹, which is 2–3 kcal mol⁻¹ larger than that for individual double helices. 100 ns molecular dynamics simulations were carried out for the binding of CBM20 to an extended substrate containing 3 layers of 9 60-unit double helices (A3L). A stable conformation of CBM20–A3L was found at BdS1. However, when CBM20 binds A3L viaBdS2, it moves across the surface of the substrate and does not form a stable complex. MD simulations show that small amylose helices are quickly disrupted upon binding to CBM20. Our results provide some important molecular insights into the interactions of CBM20 with starch substrates, which will serve as the basis for further studies of CBM20-containing enzymes, including AA13 PMOs.

CBM20 quickly disrupts small helical amylose substrates and exhibits optimal binding affinity when the substrate has three or more parallel double helices.

Influence of green lipped mussels (Perna canaliculus) in alleviating signs of arthritis in dogs

This study evaluated the efficacy of green lipped mussel (GLM), added to a complete dry diet, for alleviating clinical signs of arthritis in dogs. A double-blind longitudinal study design was used with 31 mixed-breed dogs exhibiting varying degrees of arthritis. Each dog was evaluated by a veterinarian and joints were individually scored for degree of pain, swelling, crepitus, and reduction in range of movement. Summation of all scores for an individual dog comprised its total arthritis score. At baseline, dogs were randomly allocated to control and test groups. Both groups were fed the same base dry diet, to which 0.3% GLM powder was added for dogs in the test group. The change in total arthritis score by the end of 6 weeks showed there was significant improvement (P < .05) in the test group versus the control group. Significant improvements were also observed in joint pain and swelling scores in the test group. Changes in joint crepitus and range of joint movement were not significantly different between the test and control groups. These findings provide strong evidence that GLM incorporated into a complete dry diet can help alleviate arthritis symptoms in dogs.

Altered zinc metabolism contributes to the developmental toxicity of 2-ethylhexanoic acid, 2-ethylhexanol and valproic acid

It has been hypothesized that the developmental toxicity of certain compounds is, in part, due to maternal toxicity resulting in alterations in zinc (Zn) metabolism that affects the developing conceptus. In the present work the effects of developmentally toxic doses of 2-ethylhexanoic acid (EHXA), 2-ethylhexanol (EHXO), and valproic acid (VPA) on Zn metabolism were investigated in the pregnant rat. In experiment 1, dams were intubated with EHXA (3.13, 6.25, 9.38 or 12.5 mmol/kg), EHXO (6.25, 9.38 or 12.5 mmol/kg), VPA (1.56, 3.13, 6.25 or 9.38 mmol/kg), or corn oil (control; 1.0 ml/kg) at 14:00 h on gestation day (GD) 11.5, intubated with 32 microCi 65Zn at 22:00 h, and then killed at 08:00 h on GD 12.5. At the higher dose levels of EHXA and EHXO, and at all dosages of VPA, the percentage of 65Zn retained in maternal liver was higher, while that in the embryos was lower, than in controls. Chemical-associated changes in 65Zn distribution were associated with increased maternal liver metallothionein (MT) concentrations. In experiment 2, dams were fed diets containing 1, 25 or 97 microg Zn/g from GD 0-16 and intubated with 3.5 mmol EHXA or 1.0 ml corn oil/kg/d from GD 8-15. Dams were killed on GD 16 or 19. High incidences of encephalocele and tail defects were noted in the GD 16 fetuses of EHXA-treated dams fed either the low or adequate Zn diet, the highest incidences being in the low Zn group. On GD 19 the incidence of tail defects tended to be higher in the EHXA groups than in oil-treated controls, the highest incidence occurring in the low Zn EHXA group. Encephalocele was only observed in the low Zn EHXA-treated group. Fetal weight and crown-rump lengths were decreased by EHXA treatment and low dietary Zn. The incidence of rib anomalies was higher in the EHXA-exposed groups than in their respective oil controls. In experiment 3, GD 10.5 embryos collected from control dams were cultured for 48 h in serum from control or EHXA-treated male rats fed 4.5 or 25.0 microg Zn/g diets. Embryos cultured in either EHXA or low Zn sera exhibited delayed development; the addition of Zn to these sera eliminated their developmental toxicity. These results support the hypothesis that certain chemicals which induce maternal toxicity act, in part, to influence embryonic Zn metabolism and trigger abnormal development. Importantly, the teratogenic effects of these chemicals can be modulated by dietary Zn intake.

Drinking water source and reproductive outcomes in Sprague-Dawley rats

As part of our work on the influence of water source on reproductive outcome, Sprague-Dawley rats were randomized to tap water, bottled water, or deionized water treatment groups, utilizing 160 animals per treatment; animals received the water prior to and during pregnancy. Rats were shipped in four batches (A-D). Batch effects were seen for several reproductive parameters. Because the tap water supply was interrupted by an earthquake resulting in an unbalanced design, primary analyses utilized only batches C and D, which included most of the tap water-treated rats. A treatment effect with respect to resorption frequency was seen that was marginally significant using a fixed-effects analysis of variance (P = 0.053), but not when batch was entered as a random effect (P = 0.36). The data were modeled by logistic regression, controlling for batch, litter size, and batch-treatment interaction. The odds ratio comparing tap to bottled water was 1.8 (95% CI 1.0 to 3.3, P = 0.05), which was similar to the epidemiologic result that prompted this study. The magnitude of this association varied by batch, and the difference in resorption frequency was within the range of variation seen for control animals. Although these findings do not justify public health action at this time, further investigation is warranted.

Comparative effects of 6-week nicotine treatment on blood pressure and components of the antioxidant system in male spontaneously hypertensive (SHR) and normotensive Wistar Kyoto (WKY) rats

Hypertension, cigarette smoking, and nicotine augment the clinical significance of other risk factors associated with cardiovascular diseases by mechanisms which are poorly understood. Since altered trace element metabolism and antioxidant status have also been implicated in these diseases, the present study investigated the interaction of nicotine treatment and hypertension on tissue trace element concentrations and select indices of antioxidant status. Spontaneously hypertensive (SHR) and normotensive Wistar Kyoto (WKY) rats were treated with nicotine, via a time release tablet at an average rate of 75 micrograms/h for 6 weeks. Systolic blood pressure in nicotine-treated SHRs was significantly higher at weeks 3 and 6 of treatment than in the SHR-controls. Blood pressure in WKY rats was not affected by nicotine. Plasma and liver iron concentrations in the nicotine-treated SHR were higher than the SHR-controls and the WKY groups. Nicotine treatment did not affect plasma and liver zinc and copper concentrations or liver manganese (Mn) concentrations. Plasma ceruloplasmin activity was increased by nicotine treatment in the SHRs. Liver Mn superoxide dismutase (MnSOD) activities and glutathione concentrations, and liver and heart glutathione reductase activities, were higher in both groups of SHRs than in the WKY groups. Red cell SOD activity in the nicotine-treated SHR was lower than in the SHR-controls. In summary, blood pressure increased more rapidly in the nicotine-treated SHRs compared to the controls. The marked effects on antioxidant status observed were attributable more to hypertension than to the nicotine treatment.

Influence of 12-week nicotine treatment and dietary copper on blood pressure and indices of the antioxidant system in male spontaneous hypertensive rats

Nicotine treatment and copper (Cu) deficiency have been associated with an increased production of reactive oxygen species that may contribute to the development and/or progression of cardiovascular diseases (CVD). The present study investigated the influence of dietary Cu intake on the response to chronic nicotine treatment in spontaneous hypertensive rats (SHR) with respect to tissue trace mineral levels, several components of the oxidant defense system, and lipid peroxidation rates. SHR weighing 100-110 g were fed a Cu deficient diet (-Cu) (0.5 microgram Cu/g) for 14 d prior to nicotine treatment. SHR were inserted with tablets that released nicotine at a rate of 75 micrograms/h or placebo (control). Following tablet insertion, rats were fed a control diet (+Cu) (12.0 micrograms Cu/g) or the -Cu diet. Nicotine treatment lasted for 12 wk. Blood pressure (BP) was higher in nicotine-treated SHR than in control SHR at wk 3; BP was unaffected by diet. BP was higher in +Cu nicotine-treated SHR at wk 6 compared to -Cu nicotine and control rats. BP was not affected by nicotine or diet at wk 2. Liver, heart, and brain Cu levels and liver, heart, and red cell CuZn superoxide dismutase and plasma ceruloplasmin oxidase activities were lower in the -Cu SHR than in the +Cu SHR. Liver Fe levels were higher and plasma Fe levels were lower in the -Cu rats than in the +Cu rats. Liver selenium-dependent-glutathione peroxidase (Se-GSH-Px) activity was lower in the -Cu rats than in the +Cu rats; heart and thoracic aorta Se-GSH-Px activity was unaffected by -Cu diet. Thoracic aorta, liver, and heart GSH-reductase activities were unaffected by treatments. Plasma thiobarbituric acid reactive substances (TBARS) were higher in the -Cu than in the +Cu SHR. Liver and heart TBARS production was similar among the groups. These data show that nicotine can exacerbate the development of high BP in susceptible individuals; Cu deficiency did not exacerbate the effects of nicotine.

Zinc status and interleukin-1 beta-induced alterations in mineral metabolism in rats

Changes in zinc (Zn) metabolism and interleukin-1 beta (IL-1 beta) release occur as part of the physiological response to tissue injury and trauma. In the present study, the influence of Zn status on the response to continuous low-dose IL-1 beta administration was evaluated. Rats were fed 50 micrograms Zn/g (adequate zinc; AZn) or 5 micrograms Zn/g (marginal zinc; MZn) diets for 14 days. On day 15, rats were infused via osmotic minipumps, with IL-1 beta (2.3 ng/hr) or saline (control, C) and euthanized 1, 3, or 7 days later. In the AZn rats, IL-1 beta infusion resulted in increased plasma copper (Cu) concentrations and ceruloplasmin (Cp) activity, and decreased iron (Fe) concentrations throughout the 7d period. These effects were most pronounced on d1 and d3. A similar trend was observed in the MZn rats, but IL-1 beta-induced increases in plasma Cu and Cp activity were less than in the AZn fed rats. In MZn and AZn IL-1 beta infused rats, plasma Zn was decreased on Day 1, and Day 3, respectively, compared with their respective controls. AZn IL-1 beta-infused rats were characterized by high liver Fe, Zn, and metallothionein (MT) concentrations on Day 1; by Day 7, only MT concentrations remained elevated. Liver MnSOD activity was 13%-29% higher in both the AZn- and MZn-IL-1 beta-infused rats than their respective controls on Day 3 and Day 7, with most significant increase observed on Day 7. These data show that Zn status can influence the response to low-dose IL-1 beta; this influence of Zn should be considered when IL-1 beta is given therapeutically.