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T cells are attractive targets for the development of immunotherapy to treat cancer due to their biological features, capacity of cytotoxicity, and antigen-specific binding of receptors. Novel strategies that can modulate T cell functions or receptor reactivity provide effective therapies, including checkpoint inhibitor, bispecific antibody, and adoptive transfer of T cells transduced with tumor antigen-specific receptors. T cell-based therapies have presented successful pre-clinical/clinical outcomes despite their common immune-related adverse effects. Ongoing studies will allow us to advance current T cell therapies and develop innovative personalized T cell therapies. This review summarizes immunotherapeutic approaches with a focus on T cells. Anti-cancer T cell therapies are also discussed regarding their biological perspectives, efficacy, toxicity, challenges, and opportunities.

Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation and to enhance the stability within the cells, the study on methyltransferases in newly isolated bacteria is essential for genetic engineering. Here, we introduce the mechanism of the RM system, specifically the methyltransferases and their biotechnological applications. These biotechnological strategies could facilitate plasmid DNA-based genetic engineering in bacteria strains that strongly defend against foreign DNA.

Ischemia-reperfusion injury (IRI) is a process in which damage is induced in hypoxic tissue when oxygen supply is resumed after ischemia. During IRI, restoration of reduced nitric oxide (NO) levels may alleviate reperfusion injury in ischemic organs. The protective mechanism of NO is due to anti-inflammatory effects, antioxidant effects, and the regulation of cell signaling pathways. On the other hand, it is generally known that S-nitrosylation (SNO) mediates the detrimental or protective effect of NO depending on the action of the nitrosylated target protein, and this is also applied in the IRI process. In this review, the effect of each change of NO and SNO during the IRI process was investigated.

Interactions among colloidal particles govern the hierarchical microstructure and its physical properties. Here, optical laser tweezers and Monte Carlo simulations are used to evaluate the effects of azimuthal rotation of Janus particles at the oil-water interface on interparticle interactions. We find that the capillary-induced attractive force between two Janus particles at the interface can be relaxed by azimuthal rotation around the critical separation region, at which the capillary force is ∼0.053 pN. Force relaxation leads to a decrease in capillary force around the critical separation region, resulting in a slight increase in the scaling exponent, compared to the theoretical prediction.

Escherichia coli is a widely used platform for metabolic engineering due to its fast growth and well-established engineering techniques. However, there has been a demand for faster-growing E. coli for higher production of desired substances. Here, to increase the growth of E. coli cells, we optimized the expression level of Hfq protein, which plays an essential role in stress responses. Six variants of the hfq gene with a different ribosome binding site sequence and thereby a different expression level were constructed. When the Hfq expression level was optimized in DH5α, its growth rate was increased by 12.1% and its cell density was also increased by 4.5%. RNA-seq and network analyses revealed the upregulation of stress response genes and metabolic genes, which increases the tolerance against pH changes. When the same strategy was applied to five other E. coli strains (BL21 (DE3), JM109, TOP10, W3110, and MG1655), all their growth rates were increased by 18–94% but not all their densities were increased (− 12 − + 32%). In conclusion, the Hfq expression optimization can increase cell growth rate and probably their cell densities as well. Since the hfq gene is highly conserved across bacterial species, the same strategy could be applied to other bacterial species to construct faster-growing strains.

We evaluated and classified forty five onion cultivars according to bulb initiation, bulb and scale characteristics, minerals and organic compounds contents, and storage quality in South Korea during 2016/2017 and 2017/2018 growing seasons. Field experiment was conducted in randomized block design with three replications. Bulb initiation ranged from 153 days after transplanting (DAT, April 2) to 177 DAT (April 26). Fresh bulb weight (FBW) and bulb index (BI) were 285.5 ± 18.5 g/individual, 0.93 ± 0.05, respectively. Number of scales (NS), number of center (NC), and scale thickness (ST) were 7.6 ± 0.2, 2.3 ± 0.2, and 5.5 ± 0.2 mm/scale, respectively. Chroma and Lightness of bulb skin were 27.1 ± 1.9, 61.2 ± 2.3, respectively. Storage loss (SL) on December 12 was 19.4 ± 5.9%. Nitrogen (N), Carbon (C) and sulfur (S) contents were 1.36 ± 0.14, 37.9 ± 3.2 and 0.40 ± 0.06 mg kg−1 on a fresh weight basis. Total soluble solids (TSS) and total phenolics content (TPC) were 8.6 ± 0.6 °Bx, 164.8 ± 15.6 mg GE kg−1 on a fresh weight basis. Days from transplanting to bulb initiation was significantly positively correlated with bulb height, NC, dry matter, N, C, S, TSS, TPC, total flavonoids content (TFC) etc., while it was negatively correlated with rot loss and SL. Dry matter content was significantly positively correlated with N, C, S, TSS, TPC, TFC etc., while it was negatively correlated with SL. Storage loss was negatively correlated with N, S, Potassium and TSS. Dendrogram of agglomerative hierarchical clustering for the forty five cultivars based on bulb initiation, bulb and scale characteristics, and bulb minerals and organic compounds contents classified five cultivar groups. Cluster 1 featured the earliest bulb initiation and the greatest SL. Cluster 2 featured the fewest NS and NR, and the thickest ST. Cluster 3 featured the greatest FBW, and the most NS and NC. Cluster 4 featured the greatest BI and the thinnest ST. Cluster 5 featured the lowest SL, and the highest minerals and antioxidant compounds contents. This information should be helpful for onion growers to decide onion cultivar and for onion breeders to promote new cultivars depending on their purpose.

Deubiquitinase cylindromatosis (CYLD) inhibits MAPK and NF-κB activation pathways by deubiquitinating upstream regulatory factors. Although CYLD has been identified and actively studied in mammals, nothing is known about its putative function in fish. In this study, we identified the gene encoding CYLD (OmCYLD) from rainbow trout, Oncorhynchus mykiss, and examined its role during pathogenic infections. The deduced amino acid sequence of OmCYLD contains conserved CAP-Gly and USP domains. In RTH-149 cells, the expression of OmCYLD was increased by stimulation with Edwardsiella tarda and Streptococcus iniae. Gain-of-function and loss-of-function experiments showed that OmCYLD down-regulates the activation of MAPK and NF-κB and the expression of pro-inflammatory cytokines in E. tarda-stimulated RTH-149 cells. These findings suggest that OmCYLD might function like those of mammals to negatively regulate bacteria-triggered signaling pathway in fish.

The uptake of exogenous DNA materials through the cell membrane by bacteria, known as transformation, is essential for the genetic manipulation of bacteria and, thus, plays key roles in biotechnological and biological research. The efficiency of natural transformation is very low; therefore, various artificial transformation methods have been developed for simple and efficient bacterial transformation. The basic bacterial transformation method is based on chemical, physical, and electrical processes and other means to permeabilize the bacterial cell membrane to allow plasmid DNA uptake. With the introduction of novel chemicals, materials, and devices and the optimization of protocols, new transformation methods have become simpler, cheaper, and more reproducible for use in diverse bacterial species compared with conventional methods. In this review, artificial transformation methods have been classified according to the membrane-permeabilizing mechanisms employed by them. Their influential factors, transformation efficiency, advantages, disadvantages, and practical applications are briefly illustrated. Finally, physicochemical transformation as a new bacterial transformation technique has also been described.

Synthetic biology builds programmed biological systems for a wide range of purposes such as improving human health, remedying the environment, and boosting the production of valuable chemical substances. In recent years, the rapid development of synthetic biology has enabled synthetic bacterium-based diagnoses and therapeutics superior to traditional methodologies by engaging bacterial sensing of and response to environmental signals inherent in these complex biological systems. Biosynthetic systems have opened a new avenue of disease diagnosis and treatment. In this review, we introduce designed synthetic bacterial systems acting as living therapeutics in the diagnosis and treatment of several diseases. We also discuss the safety and robustness of genetically modified synthetic bacteria inside the human body.

In bacterial biotechnology, instead of producing functional proteins from plasmids, it is often necessary to deliver functional proteins directly into live cells for genetic manipulation or physiological modification. We constructed a library of cell-penetrating peptides (CPPs) capable of delivering protein cargo into bacteria and developed an efficient delivery method for CPP-conjugated proteins. We screened the library for highly efficient CPPs with no significant cytotoxicity in Escherichia coli and developed a model for predicting the penetration efficiency of a query peptide, enabling the design of new and efficient CPPs. As a proof-of-concept, we used the CPPs for plasmid curing in E. coli and marker gene excision in Methylomonas sp. DH-1. In summary, we demonstrated the utility of CPPs in bacterial engineering. The use of CPPs would facilitate bacterial biotechnology such as genetic engineering, synthetic biology, metabolic engineering, and physiology studies., Lee et al. construct a cell-penetrating peptides (CPP) library and identify CPPs that can penetrate bacterial cells with minimum or no impact on cell viability. For the identified top CPP candidates, their abilities to deliver macromolecules such as I-SceI and Cre recombinase proteins to bacteria are evaluated as proof-of-concept studies for potential applications.

Background Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipulation of plasmids remains difficult because of the restriction-modification (RM) system present in the bacteria. Therefore, the RM system in Methylomonas sp. DH-1 must be identified to improve the genetic engineering prospects of this microorganism. Results We identified a DNA methylation site, TGGCCA, and its corresponding cytosine methyltransferase for the first time in Methylomonas sp. DH-1 through whole-genome bisulfite sequencing. The methyltransferase was confirmed to methylate the fourth nucleotide of TGGCCA. In general, methylated plasmids exhibited better transformation efficiency under the protection of the RM system than non-methylated plasmids did. As expected, when we transformed Methylomonas sp. DH-1 with plasmid DNA harboring the psy gene, the metabolic flux towards carotenoid increased. The methyltransferase-treated plasmid exhibited an increase in transformation efficiency of 2.5 × 103 CFU/μg (124%). The introduced gene increased the production of carotenoid by 26%. In addition, the methyltransferase-treated plasmid harboring anti-psy sRNA gene exhibited an increase in transformation efficiency by 70% as well. The production of carotenoid was decreased by 40% when the psy gene was translationally repressed by anti-psy sRNA. Conclusions Plasmid DNA methylated by the discovered cytosine methyltransferase from Methylomonas sp. DH-1 had a higher transformation efficiency than non-treated plasmid DNA. The RM system identified in this study may facilitate the plasmid-based genetic manipulation of methanotrophs.

Mulberry (Morus alba) has been used in traditional oriental medicine since ages. Recently, it has been reported that mulberry produces hypotensive effects through the eNOS signaling pathway. However, the mechanism underlying the hypotensive effects of mulberry is not entirely clear. Moreover, the effects of mulberry on vascular remodeling events such as hyperplasia, an important etiology in the pathogenesis of hypertension and arteriosclerosis, are also ambiguous. Here, we hypothesized that an ethanolic extract of mulberry fruit (EMF) has beneficial effects on vascular remodeling and produces hypotensive effects. The effects of a 6-week oral administration of EMF were examined in spontaneously hypertensive rats (SHRs). The animals were divided into four groups: normotensive control (Wistar Kyoto rats), non-treated SHR, low-dose (100 mg/kg) EMF-treated SHR, and high-dose (300 mg/kg) EMF-treated SHR. Our results showed that the EMF-diet normalizes hypertension in SHRs in a dose-dependent manner, by preventing smooth muscle proliferation, thickening of the tunica media, and vascular hyper-reactivity. The endothelial functions were not substantially affected by the EMF diet in our experimental setting. In conclusion, we suggest that the mulberry fruit could act as a food supplement for reducing blood pressure in hypertensive subjects through its effects on smooth muscle proliferation and vascular contractility.

We report fabrication of low-density polymeric microparticles (micropolymofoam particles [μPFPs]) using the piezoelectric inkjet method. After ejecting a polymer solution prepared by dissolving polymers in a volatile organic solvent, microdroplets are periodically generated through an inkjet nozzle in the air. Rapid evaporation of the solvent as it falls through the air leads to a highly porous surface and internal morphology. Optical microscope observation confirms that the inside of the μPFPs is filled with air. Notably, the use of more than two different polymers results in kinetically stable particles, in which the heterogeneous polymer chains are randomly entangled. Shape transformation of the kinetically stable μPFPs occurs upon adding a swelling solvent, spontaneously changing their geometry from porous and rugged-shaped to a Janus-like structure with a clear phase boundary. This transformation is directly monitored using an optical microscope. The surface free energy calculation reveals that particles are transformed to adopt a thermodynamically stable structure; this is achieved by imparting fluidity to the randomly entangled polymer chains, which is energetically unfavorable. In addition, porosity control can be possible by selectively removing one polymer phase of kinetically stable particles comprising two different polymers. Furthermore, the developed inkjet method can be applied for producing composite particles encapsulated with functional nanoparticles and coating or patterning them directly onto a substrate.

Microbial bioremediation has gained attention as a cheap, efficient, and sustainable technology to manage the increasing environmental pollution. Since microorganisms in nature are not evolved to degrade pollutants, there is an increasing demand for developing safer and more efficient pollutant-scavengers for enhanced bioremediation. In this review, we introduce the strategies and technologies developed in the field of synthetic biology and their applications to the construction of microbial scavengers with improved efficiency of biodegradation while minimizing the impact of genetically engineered microbial scavengers on ecosystems. In addition, we discuss recent achievements in the biodegradation of fastidious pollutants, greenhouse gases, and microplastics using engineered microbial scavengers. Using synthetic microbial scavengers and multidisciplinary technologies, toxic pollutants could be more easily eliminated, and the environment could be more efficiently recovered.

Glutathione (GSH)-deprived Dictyostelium discoideum accumulates methylglyoxal (MG) and reactive oxygen species (ROS) during vegetative growth. However, the reciprocal effects of the production and regulation of these metabolites on differentiation and cell motility are unclear. Based on the inhibitory effects of γ-glutamylcysteine synthetase ( gcsA ) disruption and GSH reductase ( gsr ) overexpression on aggregation and culmination, respectively, we overexpressed GSH-related genes encoding superoxide dismutase (Sod2), catalase (CatA), and Gcs, in D. discoideum . Wild-type KAx3 and gcsA -overexpressing ( gcsA OE ) slugs maintained GSH levels at levels of approximately 2.1-fold less than the reference GSH synthetase-overexpressing mutant; their GSH levels did not correlate with slug migration ability. Through prolonged KAx3 migration by treatment with MG and H 2 O 2 , we found that MG increased after the mound stage in this strain, with a 2.6-fold increase compared to early developmental stages; in contrast, ROS were maintained at high levels throughout development. While the migration-defective sod2 - and catA -overexpressing mutant slugs ( sod2 OE and catA OE ) decreased ROS levels by 50% and 53%, respectively, these slugs showed moderately decreased MG levels (36.2 ± 5.8 and 40.7 ± 1.6 nmol g −1 cells wet weight, P 0.05) compared to the parental strain (54.2 ± 3.5 nmol g −1 ). Importantly, defects in the migration of gcsA OE slugs decreased MG considerably (13.8 ± 4.2 nmol g −1 , P 0.01) along with a slight decrease in ROS. In contrast to the increase observed in migrating sod2 OE and catA OE slugs by treatment with MG and H 2 O 2 , the migration of gcsA OE slugs appeared unaffected. This behavior was caused by MG-triggered Gsr and NADPH-linked aldolase reductase activity, suggesting that GSH biosynthesis in gcsA OE slugs is specifically used for MG-scavenging activity. This is the first report showing that MG upregulates slug migration via MG-scavenging-mediated differentiation.

Drug candidates often cause an unwanted blockage of the potassium ion channel of the human ether-a-go-go-related gene (hERG). The blockage leads to long QT syndrome (LQTS), which is a severe life-threatening cardiac side effect. Therefore, a virtual screening method to predict drug-induced hERG-related cardiotoxicity could facilitate drug discovery by filtering out toxic drug candidates. In this study, we generated a reliable hERG-related cardiotoxicity dataset composed of 2130 compounds, which were carried out under constant conditions. Based on our dataset, we developed a computational hERG-related cardiotoxicity prediction model. The neural network model achieved an area under the receiver operating characteristic curve (AUC) of 0.764, with an accuracy of 90.1%, a Matthews correlation coefficient (MCC) of 0.368, a sensitivity of 0.321, and a specificity of 0.967, when ten-fold cross-validation was performed. The model was further evaluated using ten drug compounds tested on guinea pigs and showed an accuracy of 80.0%, an MCC of 0.655, a sensitivity of 0.600, and a specificity of 1.000, which were better than the performances of existing hERG-toxicity prediction models. The neural network model can predict hERG-related cardiotoxicity of chemical compounds with a high accuracy. Therefore, the model can be applied to virtual high-throughput screening for drug candidates that do not cause cardiotoxicity. The prediction tool is available as a web-tool at http://ssbio.cau.ac.kr/CardPred .

Sertraline, a selective serotonin reuptake inhibitor (SSRI), has been reported to lead to cardiac toxicity even at therapeutic doses including sudden cardiac death and ventricular arrhythmia. And in a SSRI-independent manner, sertraline has been known to inhibit various voltage-dependent channels, which play an important role in regulation of cardiovascular system. In the present study, we investigated the action of sertraline on Kv1.5, which is one of cardiac ion channels. The eff ect of sertraline on the cloned neuronal rat Kv1.5 channels stably expressed in Chinese hamster ovary cells was investigated using the whole-cell patch-clamp technique. Sertraline reduced Kv1.5 whole-cell currents in a reversible concentration-dependent manner, with an IC 50 value and a Hill coefficient of 0.71 µM and 1.29, respectively. Sertraline accelerated the decay rate of inactivation of Kv1.5 currents without modifying the kinetics of current activation. The inhibition increased steeply between -20 and 0 mV, which corresponded with the voltage range for channel opening. In the voltage range positive to +10 mV, inhibition displayed a weak voltage dependence, consistent with an electrical distance δ of 0.16. Sertraline slowed the deactivation time course, resulting in a tail crossover phenomenon when the tail currents, recorded in the presence and absence of sertraline, were superimposed. Inhibition of Kv1.5 by sertraline was use-dependent. The present results suggest that sertraline acts on Kv1.5 currents as an open-channel blocker.

Despite the resounding clinical success in cancer treatment of antibodies that block the interaction of PD1 with its ligand PDL11, the mechanisms involved remain unknown. A major limitation to understanding the origin and fate of T cells in tumour immunity is the lack of quantitative information on the distribution of individual clonotypes of T cells in patients with cancer. Here, by performing deep single-cell sequencing of RNA and T cell receptors in patients with different types of cancer, we survey the profiles of various populations of T cells and T cell receptors in tumours, normal adjacent tissue, and peripheral blood. We find clear evidence of clonotypic expansion of effector-like T cells not only within the tumour but also in normal adjacent tissue. Patients with gene signatures of such clonotypic expansion respond best to anti-PDL1 therapy. Notably, expanded clonotypes found in the tumour and normal adjacent tissue can also typically be detected in peripheral blood, which suggests a convenient approach to patient identification. Analyses of our data together with several external datasets suggest that intratumoural T cells, especially in responsive patients, are replenished with fresh, non-exhausted replacement cells from sites outside the tumour, suggesting continued activity of the cancer immunity cycle in these patients, the acceleration of which may be associated with clinical response. Large-scale single-cell sequencing of RNA and T cell receptors in samples from patients with cancer shows clonotypic expansion of effector-like T cells not only in tumour tissue but also in normal adjacent tissues and peripheral blood, which associates with clinical response to cancer immunotherapy.

Reciprocal interactions between B and follicular T helper (Tfh) cells orchestrate the germinal center (GC) reaction, a hallmark of humoral immunity. Abnormal GC responses could lead to the production of pathogenic autoantibodies and the development of autoimmunity. Here we show that miR-146a controls GC responses by targeting multiple CD40 signaling pathway components in B cells; by contrast, loss of miR-146a in T cells does not alter humoral responses. However, specific deletion of both miR-146a and its paralog, miR-146b, in T cells increases Tfh cell numbers and enhanced GC reactions. Thus, our data reveal differential cell-intrinsic regulations of GC B and Tfh cells by miR-146a and miR-146b. Together, members of the miR-146 family serve as crucial molecular brakes to coordinately control GC reactions to generate protective humoral responses without eliciting unwanted autoimmunity., In the germinal center (GC), B and T cells interact to induce the production of protective antibodies against threats. Here the authors show that microRNA miR-146a modulates CD40 signaling in GC B cells, while both miR-146a and miR-146b synergize to control GC T cell responses, thereby implicating intricate controls of GC response by miR-146.

Background Administered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. However, there are more than thousands of different cellular enzymes that potentially convert administered drug into other forms. Result We developed an in silico model to predict which of human enzymes including metabolic enzymes as well as CYP450 family can catalyze a given chemical compound. The prediction is based on the chemical and physical similarity between known enzyme substrates and a query chemical compound. Our in silico model was developed using multiple linear regression and the model showed high performance (AUC = 0.896) despite of the large number of enzymes. When evaluated on a test dataset, it also showed significantly high performance (AUC = 0.746). Interestingly, evaluation with literature data showed that our model can be used to predict not only enzymatic reactions but also drug conversion and enzyme inhibition. Conclusion Our model was able to predict enzymatic reactions of a query molecule with a high accuracy. This may foster to discover new metabolic routes and to accelerate the computational development of drug candidates by enabling the prediction of the potential conversion of administered drugs into active or inactive forms.