Increased Gene Expression Levels Research Articles

Optimizing Transfection Efficiency in CAR-T Cell Manufacturing through Multiple Administrations of Lipid-Based Nanoparticles.

The existing manufacturing protocols for CAR-T cell therapies pose notable challenges, particularly in attaining a transient transfection that endures for a significant duration. To address this gap, this study aims to formulate a transfection protocol utilizing multiple lipid-based nanoparticles (LNPs) administrations to enhance transfection efficiency (TE) to clinically relevant levels. By systematically fine-tuning and optimizing our transfection protocol through a series of iterative refinements, we have accomplished a remarkable one-order-of-magnitude augmentation in TE within the immortalized T-lymphocyte Jurkat cell line. This enhancement has been consistently observed over 2 weeks, and importantly, it has been achieved without any detrimental impact on cell viability. In the subsequent phase of our study, we aimed to optimize the gene delivery system by evaluating three lipid-based formulations tailored for DNA encapsulation using our refined protocol. These formulations encompassed two LNPs constructed from ionizable lipids and featuring systematic variations in lipid composition (iLNPs) and a cationic lipoplex (cLNP). Our findings showcased a notable standout among the three formulations, with cLNP emerging as a frontrunner for further refinement and integration into the production pipeline of CAR-T therapies. Consequently, cLNP was scrutinized for its potential to deliver CAR-encoding plasmid DNA to the HEK-293 cell line. Confocal microscopy experiments demonstrated its efficiency, revealing substantial internalization compared to iLNPs. By employing a recently developed confocal image analysis method, we substantiated that cellular entry of cLNP predominantly occurs through macropinocytosis. This mechanism leads to heightened intracellular endosomal escape and mitigates lysosomal accumulation. The successful expression of anti-CD19-CD28-CD3z, a CAR engineered to target CD19, a protein often expressed on the surface of B cells, was confirmed using a fluorescence-based assay. Overall, our results indicated the effectiveness of cLNP in gene delivery and suggested the potential of multiple administration transfection as a practical approach for refining T-cell engineering protocols in CAR therapies. Future investigations may focus on refining outcomes by adjusting transfection parameters like nucleic acid concentration, lipid-to-DNA ratio, and incubation time to achieve improved TE and increased gene expression levels.

Carotenoid biosynthesis genes LcLCYB, LcLCYE, and LcBCH from wolfberry confer increased carotenoid content and improved salt tolerance in tobacco

Carotenoids play essential roles in plant growth and development and provide plants with a tolerance to a series of abiotic stresses. In this study, the function and biological significance of lycopene β-cyclase, lycopene ε-cyclase, and β-carotene hydroxylase, which are responsible for the modification of the tetraterpene skeleton procedure, were isolated from Lycium chinense and analyzed. The overexpression of lycopene β-cyclase, lycopene ε-cyclase, and β-carotene hydroxylase promoted the accumulation of total carotenoids and photosynthesis enhancement, reactive oxygen species scavenging activity, and proline content of tobacco seedlings after exposure to the salt stress. Furthermore, the expression of the carotenoid biosynthesis genes and stress-related genes (ascorbate peroxidase, catalase, peroxidase, superoxide dismutase, and pyrroline-5-carboxylate reductase) were detected and showed increased gene expression level, which were strongly associated with the carotenoid content and reactive oxygen species scavenging activity. After exposure to salt stress, the endogenous abscisic acid content was significantly increased and much higher than those in control plants. This research contributes to the development of new breeding aimed at obtaining stronger salt tolerance plants with increased total carotenoids and vitamin A content.

Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice.

Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. However, the impact of the material properties of biomolecular condensates on important processes, such as the control of gene expression, remains largely elusive. Here, the material properties of optogenetically induced transcription factor condensates are systematically tuned, and probed for their impact on the activation of target promoters. It is demonstrated that transcription factors in rather liquid condensates correlate with increased gene expression levels, whereas stiffer transcription factor condensates correlate with the opposite effect, reduced activation of gene expression. The broad nature of these findings is demonstrated in mammalian cells and mice, as well as by using different synthetic and natural transcription factors. These effects are observed for both transgenic and cell-endogenous promoters. The findings provide a novel materials-based layer in the control of gene expression, which opens novel opportunities in optogenetic engineering and synthetic biology.

Growth, Physiological, and Transcriptome Analyses Reveal Mongolian Oak Seedling Responses to Shading

Mongolian oak (Quercus mongolica) is a common building material and landscaping tree species in northern China, with significant economic and ecological value. Its seedling growth is inhibited by high light intensity, but the mechanism by which light stress affects the growth and development of its seedlings remains unclear. In this study, we investigated the phenotypes, physiological processes, and molecular responses of 3-year-old Mongolian oak seedlings under different light treatments: full light (Sck), light shading (S1; 40% light), moderate shading (S2; 20% light), and severe shading (S3; 3% light). Compared to Sck, the S1 and S2 treatments resulted in higher leaf area, photosynthetic pigment content, photosynthesis rates, soluble sugar contents, and soluble protein contents in Mongolian oak seedlings. The S1 and S2 treatments also promoted seedling height and diameter growth and resulted in lower degrees of membrane lipid peroxidation, cell membrane permeability, and antioxidant enzyme activity. In contrast, severe shading (S3) significantly inhibited seedling height and diameter growth due to the lower net photosynthetic rate, and exhibiting higher degrees of membrane lipid peroxidation and cell membrane permeability. Shading treatments (S1 and S2) alleviated the negative effects of strong light on the growth and development of Mongolian oak seedlings, with the S2 treatment having the greatest effect. However, severe shading (S3) inhibited growth and development. A total of 3726 differentially expressed genes (DEGs) were detected in leaves under different shading treatments in RNA sequencing analysis. Among these, 1691, 3150, and 824 DEGs were detected in the Sck-S1, Sck-S2, and S1-S2 comparison groups, respectively. The different shading treatments determined common expression regulation pathways, including carotenoid biosynthesis, photosynthetic antenna proteins, and mitogen activated protein kinase (MAPK) signal transduction. Shading induced increases in gene expression levels in light harvesting complexes, which are related to changes in gene expression in the photosynthetic system, leading to changes in photosynthetic physiology. The expression levels of genes related to reactive oxygen species signal perception and activation enzymes were upregulated in Sck. Together, these findings revealed the response mechanisms of Mongolian oak seedlings to different shading levels at the physiological and molecular levels, providing a scientific basis and technical support for the cultivation and large-scale production of Mongolian oak seedlings.

Enhancing precision medicine: Bispecific antibody-mediated targeted delivery of lipid nanoparticles for potential cancer therapy

The precise delivery of therapeutic agents to specific cell populations, including cancer cells, remains a target in modern medicine, to enhance treatment efficacy, while minimizing unintended side effects. This study presents a strategy utilizing bispecific antibodies for the targeted delivery of nucleic acid drugs to the surface of glucose-regulated protein 78 (GRP78)-overexpressing cancer cells. Strong binding affinity of the bispecific antibodies to GRP78-overexpressing cancer cells, including HEPG2 cells, confirmed the tumor-targeting potential of this platform. Functional analyses demonstrated the role of the bispecific antibodies in enhancing lipid nanoparticle (LNP) uptake, causing increased gene expression levels of nucleic acid drugs loaded within LNPs. In vivo imaging confirmed the potency of the bispecific-antibody-modified LNPs in delivering nucleic acid drugs to tumors and sustaining therapeutic expression levels. In vivo therapy results indicated that the bispecific antibodies improved the antitumor activity of PE38-loaded LNPs in tumors overexpressing surface GRP78. This study pioneered a bispecific-antibody-centered platform for the targeted delivery of nucleic acid drugs. The robust antigen–antibody binding affinity, tumor-selective interactions, enhanced cellular uptake, and proficient gene expression promise to advance precision therapeutics in oncology. Continued refinement and translation of this drug delivery strategy are important to unlock its full clinical potential.

Enhanced production of withaferin A from the hairy root culture of Withania somnifera via synergistic effect of Methyl jasmonate and β-cyclodextrin

Due to low amounts of withanolides produced in some plants and high demand for various applications, their biotechnological production is widely researched. The effects of two explant types (i.e., leaf and stem from the in vitro seedlings of three genotypes of Withania somnifera) and four Rhizobium strains (i.e., LBA 9402, A4, ATCC 15834, and C58C1) to improve hairy root formation efficiency was studied. Furthermore, the combined effects of β-cyclodextrin (β-CD) and methyl jasmonate (MeJA) on withaferin A production after 48 h exposure time was examined. Four hairy roots having the maximum percentage of induced roots and mean number of induced roots to analyze their growth kinetics and identified G3/ATCC/LEAF culture having the maximum specific growth rate (μ = 0.036 day−1) and growth index (GI = 9.18), and the shortest doubling time (Td = 18.82 day) were selected. After 48 h exposure of G3/ATCC/LEAF culture to different elicitation conditions, maximum amounts of withaferin A were produced in samples co-treated with 0.5 mM β-CD + 100 μM MeJA (9.57 mg/g DW) and 5.0 mM β-CD + 100 μM MeJA (17.45 mg/g DW). These outcomes represented a 6.8-fold and 12.5-fold increase, respectively, compared to the control. Similarly, combined β-CD/MeJA elicitation increased gene expression levels of HMGR, SQS, SMT-1, and SDS/CYP710A involved in withanolides biosynthetic pathway, of which just SMT-1 had significant correlation with withaferin A production. These results demonstrated the superiority of G1-leaf explant and ATCC 15834 for hairy root induction, and revealed synergistic effect of MeJA and β-CD on withaferin A production.

Effects of Cinnamon (Cinnamomum zeylanicum) Extract on Adipocyte Differentiation in 3T3-L1 Cells and Lipid Accumulation in Mice Fed a High-Fat Diet.

Flavonoids and phenolic acid are two of the rich polyphenols found in cinnamon (Cinnamomum zeylanicum). The effects of cinnamon extract on the inhibition of adipocyte differentiation in 3T3-L1 fibroblast cells and prohibitory lipid accumulation in male mice fed a high-fat diet were examined. Upon treating 3T3-L1 cells with cinnamon for 3 days, the cinnamon inhibited lipid accumulation and increased gene expression levels, such as those of adiponectin and leptin. In in vivo experiments, mice were randomized into four groups after a one-week acclimation period, as follows: normal diet, normal diet + 1% cinnamon extract, high-fat diet, and high-fat diet + 1% cinnamon extract. After 14 weeks of supplementation, we found that cinnamon extract increased the expression of lipolysis-related proteins, such as AMPK, p-ACC, and CPT-1, and reduced the expression of lipid-synthesis-related proteins, such as SREBP-1c and FAS, in liver tissue. Our results show that cinnamon extract may exhibit anti-obesity effects via the inhibition of lipid synthesis and adipogenesis and the induction of lipolysis in both 3T3-L1 fibroblast cells and mice fed a high-fat diet. Accordingly, cinnamon extract may have potential anti-obesity effects.

New synthetic derivatives of isoindoline-dione: synthesis, neuroprotection assay and impact on the expression level of oxidative stress-related genes in neuronal-like cell line

Purpose Oxidative stress can damage cells and cause age-related illnesses such as Alzheimer’s, Parkinson’s, and Huntington’s. This study looked at newly synthesized isoindole derivatives and their effects on SH-SY5Y as a neuroblastoma cell under oxidative stress through the NRF2 signaling pathway. NRF2 transcription factor plays a vital role in the oxidative stress response and cellular homeostasis. Method Three isoindoline-dione derivatives were synthesized by reacting phthalic anhydrides with 4-(2-aminoethyl)-1-benzyl piperidine. Their structures were confirmed through FT-IR, NMR, and Mass spectroscopy. The derivatives were then tested on human SH-SY5Y cells under an oxidative stress model induced by hydrogen peroxide (H2O2). The cell viability, ROS levels, protein carbonyl content, and gene expression of NRF2 and phase II antioxidative enzymes were measured after 24 h. Results Three isoindoline derivatives (3a–3c) were observed to increase the viability of SH-SY5Y cells by protective against oxidative stress, reducing intracellular reactive oxygen species and carbonylated proteins, and increasing gene expression levels of NRF2 and associated genes such as NQO-1, and GSTK1. Conclusion Isoindoline derivatives demonstrated a neuroprotective effect on SH-SY5Y cells through various neuroprotective mechanisms, although more studies are needed.

Abstract P2033: Western Diet Can Cause Adverse Cardiac Remodeling During Pregnancy By Inducing Foxo1 Expression

Introduction: Pregnancy induces physiological cardiac hypertrophy in healthy women. Our recent findings suggest that obesity can disturb this process and induce pathological cardiac hypertrophy during pregnancy both in human patients and Western Diet (WD) fed mice. Animal studies determined the pathological cardiac hypertrophy is concomitant with increased cardiomyocyte cross-sectional area (CSA), fetal gene activation and fibrosis, however, the underlying mechanisms remain unclear. The present study asks if FoxO1, as a transcriptional factor, may play a role in the adverse cardiac response to pregnancy in WD mice. Methods: The expression levels of FoxO1 and its downstream targeting genes were tested in Ctrl Diet (CD) and WD fed non-pregnant and postpartum animals. To further investigate the role of FoxO1 in pathological cardiac hypertrophy in WD animals during pregnancy, FoxO1 was then silenced by AAV9-shFoxO1 virus in WD mice before breeding. AAV9-scramble RNA served as control. Cardiac phenotype in AAV9 treated WD mice were characterized at post-partum day 1. Results: WD feeding led to increased gene expression levels of FoxO1 and its downstream targeting genes, such as CD36 and PDK4, compared with CD mice. While the gene expression levels of FoxO1 were not different between non-pregnant and pregnant WD mice, FoxO1 protein activation was significantly increased in WD mice after pregnancy determined by a decrease of pFoxO1/tFoxO1 ratio, compared with non-pregnant WD mice. Silencing FoxO1 inhibited the expression levels of FoxO1 and its downstream genes CD36 and PDK4. FoxO1 inhibition in WD fed animals prevented WD induced pathological hypertrophy during pregnancy, with decreased heart weight, cardiomyocyte CSA, attenuated fetal gene activation and fibrosis accumulation. FoxO1 silencing also led to less accumulation of lipid peroxidation product in the myocardium. Conclusions: FoxO1 activation in WD mice with metabolic disturbances during pregnancy can induce pathological cardiac hypertrophy observed during pregnancy.

Evaluation of the effect of boron derivatives on cardiac differentiation of mouse pluripotent stem cells

BackgroundThe heart is one of the first organs to form during embryonic development and has a very important place. So much that the formation of a functional heart is completed on the 55th day of human development and the 15th day of mouse development. Myocardial, endocardial and epicardial cells, which are derived from the mesoderm layer, are the cells that form the basis of the heart. Cardiac development, like other embryonic developments, is tightly controlled and regulated by various signaling pathways. The WNT signaling pathway is the most studied of these signaling pathways and the one with the clearest relationship with heart development. It is known that boron compounds and the Wnt/β-catenin pathway are highly correlated. Therefore, this study aimed to investigate the role of boron compounds in heart development as well as its effect on pluripotency of mouse embryonic stem cells for the first time in the literature. MethodsToxicity of boron compounds was evaluated by using MTS analysis and obtained results were supported by morphological pictures, Trypan Blue staining and Annexin V staining. Additionally, the possible boron-related change in pluripotency of embryonic stem cells were analyzed with alkaline phosphatase activity and immunocytochemical staining of Oct4 protein as well as gene expression levels of pluripotency related OCT4, SOX2 and KLF4 genes. The alterations in the embryonic body formation capacity of mouse embryonic stem cells due to the application boron derivatives were also evaluated. Three linage differentiation was conducted to clarify the real impact of boron compounds on embryonic development. Lastly, cardiac differentiation of mESCs was investigated by using morphological pictures, cytosolic calcium measurement, gene expression and immunocytochemical analysis of cardiac differentiation related genes and in the presence of boron compounds. ResultsObtained results show that boron treatment maintains the pluripotency of embryonic stem cells at non-toxic concentrations. Additionally, endodermal, and mesodermal fate was found to be triggered after boron treatment. Also, initiation of cardiomyocyte differentiation by boron derivative treatments caused an increased gene expression levels of cardiac differentiation related TNNT2, Nkx2.5 and ISL-1 gene expression levels. ConclusionThis study indicates that boron application, which is responsible for maintaining pluripotency of mESCs, can be used for increased cardiomyocyte differentiation of mESCs.

Neuroprotection and NRF2 signaling cascade analysis of new synthetic cinnamic acid-Eugenol hybrids

Oxidative stress can damage cells and cause age-related illnesses such as Alzheimer's, Parkinson's, and Huntington's. NRF2 is a protein that regulates the expression of genes involved in antioxidant defense, detoxification, and other cellular processes that protect against oxidative damage and cellular homeostasis. This study looked at newly synthesized Cinnamic Acid-Eugenol hybrid derivatives and their effect on SH-SY5Y neurons under oxidative stress through the NRF2 signaling pathway. Derivatives were synthesized and confirmed through FT-IR, NMR, and Mass spectroscopy. Derivatives of Cinnamic Acid-Eugenol hybrid were then tested on human SH-SY5Y cells under an oxidative stress model induced by hydrogen peroxide (H2O2). Effects; on cell viability, ROS levels, protein carbonyl content, and gene expression of NRF2 and phase II antioxidative enzymes measured after 24 h. Derivatives (A, B) were observed to enhance the viability of SH-SY5Y cells by defending against oxidative stress, reducing intracellular reactive oxygen species and carbonylated proteins, and increasing gene expression levels of NRF2 and associated genes such as; NQO-1 and GSTK1.These study highlights that these derivatives demonstrated a neuroprotective action on SH-SY5Y cells through various neuroprotective mechanisms.

MicroRNAs; their therapeutic and biomarker properties

MicroRNAs (miRNAs) are, small (roughly 19–25 nucleotides in length), conserved, non-coding, single-stranded, and functional RNA molecules with the properties of gene expression regulation through mRNA degradation, translation repression, mRNA deadenylation as well as gene silencing via histone methylation. They even have the ability to increase gene expression levels. The biogenesis of miRNAs is divided into two canonical and non-canonical pathways. The second pathway has a divergent mechanism for the biogenesis of miRNAs. miRNAs can be transcribed from specific genes or introns of protein-coding genes. A single miRNA species can control the expression of hundreds of genes, and also one gene can be the target of different miRNAs. These molecules have been identified in eukaryotic organisms such as mammals and plants and even in viruses. miRNAs play an inevitable role in the life cycle of eukaryotic cells. They are involved in any biological processes such as the regulation of cell proliferation and differentiation, apoptosis, signaling, and defense responses through their spatio-temporal expression manner. Aberrant expression of miRNAs is involved in a large number of biological disorders, which illustrates their great potential to be applied in the diagnosis and treatment of various diseases. miRNA inhibitors (anti-miRs) and artificial miRNAs (miRNA mimics) are two general approaches to balance the dysregulated miRNA levels that make it possible to treat various biological disorders. In this study, in general, the biogenesis and the role of miRNAs, the origin of miRNAs, viral miRNAs, miRNA detection procedures, in silico miRNA analysis tools, miRNA-based therapies and their obstacles, and miRNAs as potential non-invasive biomarkers are discussed. Finally, it is stated the importance of dietary miRNAs.

Development of a method of passaging and freezing human iPS cell-derived hepatocytes to improve their functions.

Human induced pluripotent stem (iPS) cell-derived hepatocyte-like cells (HLCs) are expected to replace primary human hepatocytes as a new source of functional hepatocytes in various medical applications. However, the hepatic functions of HLCs are still low and it takes a long time to differentiate them from human iPS cells. Furthermore, HLCs have very low proliferative capacity and are difficult to be passaged due to loss of hepatic functions after reseeding. To overcome these problems, we attempted to develop a technology to dissociate, cryopreserve, and reseed HLCs in this study. By adding epithelial-mesenchymal transition inhibitors and optimizing the cell dissociation time, we have developed a method for passaging HLCs without loss of their functions. After passage, HLCs showed a hepatocyte-like polygonal cell morphology and expressed major hepatocyte marker proteins such as albumin and cytochrome P450 3A4 (CYP3A4). In addition, the HLCs had low-density lipoprotein uptake and glycogen storage capacity. The HLCs also showed higher CYP3A4 activity and increased gene expression levels of major hepatocyte markers after passage compared to before passage. Finally, they maintained their functions even after their cryopreservation and re-culture. By applying this technology, it will be possible to provide ready-to-use availability of cryopreserved HLCs for drug discovery research.

Investigation of gene expression levels in thyroid tissues of rats treated with Wi-Fi electromagnetic wave (2.4–3 GHz Wi-Fi RF-EMF)

In this study, it was aimed to examine the effects of wireless waves applied to rats in the thyroid tissue by evaluating gene expression levels on 12 determined gene regions. 20 healthy 16-week-old Wistar albino female rats weighting 200–220 g were used. In the experiments, two groups, control and experimental groups, were formed, and ten female rats were used in each group. While WI-FI electromagnetic field was applied to the experimental group of these rats, nothing was applied to the control group. Many different gene regions, including beta catenin, beta-actin, GAPDH, L3B, HIF 1-Alpha, GSk-3B, TCF, WNT7a, WNT10a, WNT2, Beclin 1 and Beclin 2, ATG5 and ATG12, were investigated. ACTB and GAPDH gene primers were used as a house keeping gene. The fold change values were calculated statistically from the data obtained from the gene expression results. Compared to the control group, it was observed that the experimental group had significant increases in gene expression levels of many gene regions investigated in the study (P<0.05). Among the study groups, 12 different genes such as beta catenin, beta-actin, GAPDH, L3B, HIF 1-Alpha, GSk-3B, TCF, WNT7a, WNT10a, WNT2, Beclin 1 and Beclin 2, ATG5 and ATG12, which we have determined according to the literature, are known to be related to autophagy and oxidative stress. When the expression levels were investigated, it was determined that the expression coefficients of all the genes studied in the wnt/ß catenin pathway in the experimental group of rats exposed to the Wi-Fi EM field, except for ATG5 and ATG12, were quite high, and there was significant differences between the groups.

Multi-omics analysis of hepatopancreas of red seabream (Pagrus major) fed a soybean meal-based diet

Dietary intake of a large amount of soybean meal (SBM) adversely affects the physiological condition and growth of fish, while SBM is a commonly used substitute for fish meal (FM) in aquaculture feed. In the present study, we investigated the effects of feeding an SBM-based diet (SBMD) for 8 weeks on hepatopancreatic metabolic condition in red seabream Pagrus major, using comprehensive analyses of the transcriptome and metabolome. Compared with fish fed an FM-based control diet (FMD), fish fed the SBMD showed delayed growth, decreases in hepatopancreatic somatic index and serum cholesterol concentration, and hepatopancreatic tissue degeneration. Transcriptome sequencing analysis identified 454, 353, and 566 differentially expressed genes at 2, 4, and 8 weeks, respectively. Analysis of the hepatopancreas metabolome using capillary electrophoresis-time-of-flight mass spectrometry identified 301 quantifiable metabolites in the FMD and SBMD groups. Transcriptome analysis showed increases in gene expression levels in the terpenoid and steroid biosynthesis pathways, suggesting that hepatic cholesterol biosynthesis was up-regulated in the SBMD group. In addition, the results of transcriptome and metabolome analyses suggested that the SBMD affects glutathione and glycine metabolism. These findings provide valuable information that enhances our understanding of the effects of dietary SBM intake on red seabream metabolism.

Structure-driven protein engineering for production of valuable natural products.

Proteins are the most frequently used biocatalysts, and their structures determine their functions. Modifying the functions of proteins on the basis of their structures lies at the heart of protein engineering, opening a new horizon for metabolic engineering by efficiently generating stable enzymes. Many attempts at classical metabolic engineering have focused on improving specific metabolic fluxes and producing more valuable natural products by increasing gene expression levels and enzyme concentrations. However, most naturally occurring enzymes show limitations, and such limitations have hindered practical applications. Here we review recent advances in protein engineering in synthetic biology, chemoenzymatic synthesis, and plant metabolic engineering and describe opportunities for designing and constructing novel enzymes or proteins with desirable properties to obtain more active natural products.

Transcriptome analysis reveals important regulatory genes and pathways for tuber color variation in Pinellia ternata (Thunb.) Breit.

During the growth of Pinellia ternata (Thunb.) Breit. (P. ternata), the violet-red skin was occasionally produced spontaneously under natural cultivation. However, the specific mechanism leading to the color change is still unclear. This study performed transcriptomes in violet-red and pale-yellow skin and their peeled tubers of P. ternata, and the total flavonoids and anthocyanin contents were also determined. The results showed that the majority of genes involved in anthocyanin production were considerably increased in the violet-red skin of P. ternata tuber compared to the pale-yellow skin. Especially, phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) showed a remarkable increase in gene expression levels. Notably, shikimate O-hydroxycinnamoyltransferase (HCT), naringenin 3-dioxygenase (F3H), flavanone 4-reductase (DFR), and anthocyanidin synthase (ANS) were explicitly expressed in violet-red skin of P. ternata tuber, while undetectable in pale-yellow skin. The upregulation of these genes may explain the accumulation of anthocyanins, which forms the violet-red skin of P. ternata tuber. The transcription factors, including C2H2, bZIP, ERF, GATA, bHLH, C3H, NAC, MYB-related, and MYB families, might trigger the skin color change in P. ternata. The entire anthocyanin content in the violet-red skin of P. ternata tuber was 71.10μg/g, and pale-yellow skin was 7.74μg/g. According to phenotypic and transcriptome results, the elevated expression levels of genes linked to the synthesis of anthocyanins considerably contributed to the violet-red skin alterations in P. ternata tuber. This study provides a new understanding of the formation of the violet-red skin, lays a theoretical foundation for the cultivation of unique varieties of P. ternata, and provides transcriptome data for further study of the differences between different colors of P. ternata.

Assessment of ACC and P450 Genes Expression in Wild Oat (Avena ludoviciana) in Different Tissues Under Herbicide Application.

Target-site resistance (TSR) and non-target-site resistance (NTSR) to herbicides in arable weeds are increasing rapidly all over the world and threatening universal food safety. Resistance to herbicides that inhibit ACCase activity has been identified in wild oat. In this study, expression of ACC1, ACC2, CYP71R4 and CYP81B1 genes under herbicide stress conditions were studied in two TSR (resistant in the residue Ile1781-Leu and Ile2041-Asn of ACCase) biotypes, two NTSR biotypes and one susceptible biotype of A. ludoviciana for the first time. Treated and untreated biotypes with ACCase-inhibitor clodinafop propargyl herbicide were sampled from the stem and leaf tissues at 24h after treatment. Our results showed an increase in gene expression levels in different tissues of both types of resistance biotypes that occurred under herbicide treatment compared with non-herbicide treatment. In all samples, the expression levels of leaf tissue in all studied genes were higher than in stem tissue. The results of ACC gene expression showed that the expression level of ACC1 was significantly higher than that of ACC2. Also, expression levels of TSR biotypes were higher than NTSR biotypes for the ACC1 gene. For both CYP71R4 and CYP81B1 genes, the expression ratio increased significantly in TSR and NTSR biotypes in different tissues after herbicide treatment. In contrast, the expression levels of CYP genes in NTSR biotypes were higher than in TSR biotypes. Our results support the hypothesis that the reaction of plants to herbicide is carried out through a different regulation of genes, which can be the result of the interaction of resistance type in the target or non-target-site.

Activation/Inhibition of Gene Expression Caused by Alcohols: Relationship with the Viscoelastic Property of a DNA Molecule

Alcohols are used in the life sciences because they can condense and precipitate DNA. Alcohol consumption has been linked to many diseases and can alter genetic activity. In the present report, we carried out experiments to make clear how alcohols affect the efficiency of transcription-translation (TX-TL) and translation (TL) by adapting cell-free gene expression systems with plasmid DNA and RNA templates, respectively. In addition, we quantitatively analyzed intrachain fluctuations of single giant DNA molecules based on the fluctuation-dissipation theorem to gain insight into how alcohols affect the dynamical property of a DNA molecule. Ethanol (2-3%) increased gene expression levels four to five times higher than the control in the TX-TL reaction. A similar level of enhancement was observed with 2-propanol, in contrast to the inhibitory effect of 1-propanol. Similar alcohol effects were observed for the TL reaction. Intrachain fluctuation analysis through single DNA observation showed that 1-propanol markedly increased both the spring and damping constants of single DNA in contrast to the weak effects observed with ethanol, whereas 2-propanol exhibits an intermediate effect. This study indicates that the activation/inhibition effects of alcohol isomers on gene expression correlate with the changes in the viscoelastic mechanical properties of DNA molecules.

Genome-Wide Pleiotropy Study Identifies Association of PDGFB with Age-Related Macular Degeneration and COVID-19 Infection Outcomes

Age-related macular degeneration (AMD) has been implicated as a risk factor for severe consequences from COVID-19. We evaluated the genetic architecture shared between AMD and COVID-19 (critical illness, hospitalization, and infections) using analyses of genetic correlations and pleiotropy (i.e., cross-phenotype meta-analysis) of AMD (n = 33,976) and COVID-19 (n ≥ 1,388,342) and subsequent analyses including expression quantitative trait locus (eQTL), differential gene expression, and Mendelian randomization (MR). We observed a significant genetic correlation between AMD and COVID-19 infection (rG = 0.10, p = 0.02) and identified novel genome-wide significant associations near PDGFB (best SNP: rs130651; p = 2.4 × 10-8) in the pleiotropy analysis of the two diseases. The disease-risk allele of rs130651 was significantly associated with increased gene expression levels of PDGFB in multiple tissues (best eQTL p = 1.8 × 10-11 in whole blood) and immune cells (best eQTL p = 7.1 × 10-20 in T-cells). PDGFB expression was observed to be higher in AMD cases than AMD controls {fold change (FC) = 1.02; p = 0.067}, as well as in the peak COVID-19 symptom stage (11-20 days after the symptom onset) compared to early/progressive stage (0-10 days) among COVID-19 patients over age 40 (FC = 2.17; p = 0.03) and age 50 (FC = 2.15; p = 0.04). Our MR analysis found that the liability of AMD risk derived from complement system dysfunction {OR (95% CI); hospitalization = 1.02 (1.01-1.03), infection = 1.02 (1.01-1.03) and increased levels of serum cytokine PDGF-BB {β (95% CI); critical illness = 0.07 (0.02-0.11)} are significantly associated with COVID-19 outcomes. Our study demonstrated that the liability of AMD is associated with an increased risk of COVID-19, and PDGFB may be responsible for the severe COVID-19 outcomes among AMD patients.